An Interactive Gene Expression Viewer

This module enables interactive visualization of gene expression data from Microarray and RNA-seq experiments from the Gene Expression Omnibus (GEO). The Select a study to compare the expression of single genes across experimental groups as a boxplot, with the conditions on the x-axis and normalized expression levels on the y-axis.

Total Studies
145
Total Samples
3757

GSE Accession ID Title Organism Assay Tissue Disease Num Samples Perturbations Submission Date Study Design PMID Gene Viewer Link
GSE44035 Gene expression from human pancreatic islet Homo sapiens Expression profiling by array Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 8
  • Male
  • Female (all non-diabetics)
 02/04/2013
Islets from cadaver donors were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChip® Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.
Platform: GPL6244
23935095
GSE67543 Novel Observations from Next Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 23
  • adult beta cells
  • beta subtype fetal (12-18 gestational weeks)
  • adult alpha cells
  • alpha subtype fetal (12-18 gestational weeks)
 04/02/2015
RNA-sequencing of highly purified human adult and fetal islet cell subset was performed using our newly developed method. Using this data, we can study and compare the detailed transcriptome or alpha and beta cells during development.
Platform: GPL11154
25931473
GSE73433 Redifferentiation of expanded human islet β cells by inhibition of ARX Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 8
  • Redifferentiation Cocktail + control shRNA
  • Redifferentiation Cocktail + ARX shRNA
  • untreated control
 09/25/2015
Examination of the effect of ARX inhibition on redifferentiation of β-cell-derived (BCD) cells
Platform: GPL16791
26856418
GSE75062 Discovery and validation of a gene expression profile for human islet integrity and transplant functionality Homo sapiens Expression profiling by array Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 58
  • Diabetes Reversal
  • No Diabetes Reversal
 11/16/2015
Microarray profiles of 59 human islet preparations were compared between three data sets using class comparisons, network and biological function analyses. Specific genes were validated by quantitative PCR and immunopathology. Clinical findings were also compared.
Platform: GPL570
28968432
GSE80780 Human islets contain four distinct subtypes of β cells Homo sapiens Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 31
  • beta subtype 3
  • beta subtype 1
  • beta subtype 2
  • beta subtype 4
 04/28/2016
There are 5 biological replicates of 4 different cell types. Each donor yielded all 4 subtypes.
Platform: GPL11154
27399229
GSE86611 Genome-wide RNA-sequencing of human islets 48 hour after transduction with adenoviruses expressing either GFP (control), or histone chaperone ASF1B. Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 19
  • ASF1B
  • GFP
 09/09/2016
Ten different human islet preparations were obtained from 9 individual donors (from IIDP program). Each preparation contained approximately 20,000 islet equivalent units. Each islet preparation was separated into two portions for adenoviral transduction to overexpress GFP (control) or ASF1B genes.
Platform: GPL11154
27753532
GSE86924 Effect of NR4A3 siRNA treatment on gene expression of islet derived hybrid cell of 1.1B4 Homo sapiens Expression profiling by array Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 7
  • NR4A3 siRNA Treated 1 Hour
  • Control cells
  • 100mM H2O2 Treated 2 Hour
  • NR4A3 siRNA Treated 3 Hour
  • NR4A3 siRNA Treated 2 Hour
  • 100mM H2O2 & NR4A3 siRNA 2 Hour
 09/14/2016
We analyzed the comprehensive gene expression changes treated by NR4A3 siRNA in pancreatic beta-cell derived 1.1B4 cells using Agilent microarray.
Platform: GPL13497

N/A
GSE100322 Whole transcriptome sequencing of the human thyroid primary cells with knock-down of the NRG1 gene Homo sapiens Expression profiling by high throughput sequencing Thyroid BTO:0001379 Thyroid Cancer DOID:1540 5
  • control Day 5
  • NRG1 knockdown Day 5
 06/21/2017
Profiling of 3 human thyroid primary cells (generated from 3 different patient samples) transfected with NRG1 siRNA (75pmol) was performed using RNA-seq. Cells were cultured for 24h after transfection and then lysed prior to RNA isolation, DNase treatment, purification and RNA-seq library construction.
Platform: GPL16791
29121253
GSE101207 High-throughput single cell transcriptome analysis and CRISPR screen identify key β cell-specific disease genes Homo sapiens Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 8
  • healthy (dropseq)
  • type II diabetic (dropseq)
 07/11/2017
Single cell sequencing (Drop-seq) for Human Pancreatic islet from 9 individuals respectively. Including 6 Healthy donor and 3 Type II diabetes patient donor. 4 Chipseq for further validation.
Platform: GPL11154
30865899
GSE106148 α Cell Function and Gene Expression Are Compromised in Type 1 Diabetes Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 7
  • Type I diabetes
  • non-diabetic control
 10/25/2017
Total of 8 samples were analyzed, 5 were non-diabetic control donors and 3 were T1D donors. α cells were FACS-sorted and RNA was extracted from each of these samples. RNAseq was performed on all 8 samples
Platform: GPL16791
29514095
GSE107894 Metformin Regulates Metabolic and Non-Metabolic Pathways in Skeletal Muscle and Subcutaneous Adipose Tissues of Older Adults Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Diabetes (Non-specific) DOID:0081062 99
  • Placebo Abdominal subcutaneous adipose
  • Metformin Vastus lateralis muscle
  • Placebo Vastus lateralis muscle
  • Metformin Abdominal subcutaneous adipose
 12/11/2017
This study 'MILES: Metformin in Longevity Study' (ClinicalTrials.gov identifier: NCT02432287) is a randomized, double-blind, placebo controlled, crossover study. 14 men and women aged 60 and older, with impaired glucose tolerance based on 75g Oral Glucose Tolerance Test completed the study. Following a screening visit, the study consisted of two randomly assigned 6-week treatment periods (metformin and placebo). Metformin was introduced at 500 mg twice daily, and increased incrementally to 2000 mg daily at the end of 2 weeks to minimize gastrointestinal side effects. At the end of each 6-week treatment period, skeletal muscle and subcutaneous adipose biopsies were obtained. The samples were immediately homogenized in Trizol, frozen in liquid nitrogen and stored at -80°C for subsequent mRNA extraction. Total RNA was extracted using QIAGEN's RNeasy Mini kit. Samples showing minimal degradation, as measured by RIN > 7 were processed for library preparation and sequenced in two/three technical replicates using multiplexed 100bp paired-end sequencing on Illumina HiSeq2500. Raw sequence reads were preprocessed using WASP 3.0, and FastQC was used for quality control. The raw FASTQ files were trimmed for adapter sequences using Trim Galore! RSEM algorithm (v1.2.25) in conjunction with STAR aligner (v2.4.2a) were used to quantify the raw reads to GRCh38 build of the reference human genome with transcript annotations from GENCODE. The raw counts matrix was exported from RSEM to edgeR, normalized using TMM normalization and used for differential expression analysis.
Platform: GPL16791
29383869
GSE108413 Conventional and neo-antigenic peptides naturally processed and presented by beta cells are targeted by circulating naïve CD8+ T cells in type 1 diabetic and healthy donors Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 9
  • cytokine treatment
  • control
 12/21/2017
5 human islet of Langerhans preparations examined under 2 conditions (control and cytokine treatment)
Platform: GPL11154
30078552
GSE108654 LIN28B is a barrier to the maturation of human embryonic stem cell derived pancreatic β cells Homo sapiens Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 23
  • iCrLin28 hESC-betalike cells +dox
  • human islets rep mRNA
  • iCrLin28 hESC-beta like cells -dox
  • Post Tx hESC-beta like cells mRNA
  • hESC-beta like cells mRNA
 01/02/2018
We performed RNA-seq and small-RNA seq on human ESCs differentiated into β like cells in vitro, same cells transplanted into kidney capsule of mouse recipients, and fresh human islets. We also performed RNA-seq on hESCs genomically modified with dox inducible CRISPR knockout of LIN28 and then differentiated into β like cells plus/mius doxycycline
Platform: GPL11154
31883920
GSE108731 RNA-seq identifies a distinct response in macrophages infected with Mycobacterium tuberculosis for a serial time points. Homo sapiens Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Macrophage BTO:0000801 Tuberculosis DOID:399 15
  • 1h
  • 48h
  • 12h
  • 4h
  • 24h
  • 0h
 01/04/2018
NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to Mycobacterium tuberculosis H37Rv and H37Ra.
Platform: GPL21290

N/A
GSE108796 Analysis of gene expression in co-culture of PBMCs with Hepatocellular carcinoma by High-Throughput Sequencing Homo sapiens Expression profiling by high throughput sequencing PBMC BTO:0001025 Liver Cancer DOID:0070322 8
  • -
  • Huh7
  • HepG2
 01/05/2018
Transcription profiles of PBMC (control) and PBMC co-cultured with cancer (treatment) were generated by deep sequencing, using Illumina HiSeq 4000.
Platform: GPL20301

N/A
GSE108971 Novel Atherogenic Pathways from the Differential Transcriptiome Analysis of Diabetic Epicardial Adipose Tissue Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Diabetes (Non-specific) DOID:0081062 15
  • Diabetic
  • Nondiabetic
 01/09/2018
Examination of transcriptome in human fat samples
Platform: GPL11154
28739185
GSE110935 The role of CFTR in islet function Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 9
  • healthy
  • cystic fibrosis
 02/21/2018
Human samples 3351-ACP-005, -0017, -0020, -0027, -0036 are isolated islets from normal healthy individuals. 3362-ACP-0011, -0012,-0013,-0014,-0015 are isolated from individuals with cystic fibrosis. 12 samples from mouse.
Platform: GPL16791
29669939
GSE113764 Transcriptome of human white and brown adipose tissue biopsies Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: No Specific Disease Mention 29
  • BAT positive
  • BAT negative
 04/27/2018
Paired white and brown fat biopsies from 15 human probands, 9 brown fat positive and 6 brown fat negative judged by 18FDG-PET-CT.
Platform: GPL16791
29909972
GSE114192 Immune dysfunction in intermediate hyperglycaemia and diabetes patients in tuberculosis Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 248
  • DM_only
  • TB_DM
  • IH
  • Healthy_Control
  • TB_IH
  • TB_only
 05/08/2018
Whole blood was collected from patients with TB-only, TB-DM, TB-IH, DM-only and healthy controls in four field sites; South Africa, Peru, Romania and Indonesia. Total 249 patient samples
Platform: GPL18573
32533832
GSE115421 Patient adipose stem cell-derived adipocytes reveal genetic variation that predicts anti-diabetic drug response Homo sapiens Homo sapiens Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Adipose Tissue BTO:0001487 Type 2 Diabetes DOID:9352 41
  • Scramble DMSO
  • shNF1 DMSO
  • Rosi
  • Scramble Rosi
  • shNF1 Rosi
  • DMSO
 06/06/2018
hACSs derived from obstity patient were differentiated into adipocytes; then treated with rosiglitazone
Platform: GPL11154
30639037
GSE116801 The effects of exercise on gene expression in abdominal subcutaneous adipose tissue Homo sapiens Expression profiling by array Adipose Tissue BTO:0001487 Healthy: No Specific Disease Mention 19
  • 12 weeks excercise (60-80 minutes cycling/day, 5 days/week)
  • Sedentary
 07/09/2018
Biopsies of abdominal abdominal subcutaneous adipose tissue (scWAT) were taken from healthy young male subjects before and after 12 weeks of exercise training. The exercise training protocol consisted of 60-80 minutes cycling/day, 5 days/week.
Platform: GPL570

N/A
GSE117454 Diabetes Remission Using Glucose-Responsive Insulin-Producing Human α-Cells Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 38
  • sorted β-cells
  • αGFP singlets
  • αPM
  • βGFP
  • α singlets
  • sorted α-cells
  • αPM singlets
  • αPM grafted
  • αGFP
 07/20/2018
Transcriptomic profiles of human pancreatic α-cells that convert into insulin-producing cells were generated by deep sequencing using Illumina Hi-seq 4000
Platform: GPL20301
30760930
GSE120299 Human Pancreatic Islets Expressing HNF1A Variant Have Defective β cell Transcriptional Regulatory Networks Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 11
  • Control beta cells
  • Control alpha cells
  • HNF1A
 09/21/2018
Total of 12 samples were analyzed, 10 were non-diabetic control donors and 2 were HNF1A donors. GEO accession number for non-diabetic controls are GSE116559(β cell controls) and GSE106148 (α cell controls). α cells and β cells were FACS-sorted and RNA was extracted from each of these samples. RNAseq was performed on all 12 samples
Platform: GPL16791
30507613
GSE120683 Expression data from human kidney tubule epithelial cells Homo sapiens Expression profiling by array Kidney BTO:0000671 Methylmalonic acidemia DOID:14749 5
  • Methylmalonic acidemia (MMA)
  • Healthy
 10/01/2018
Kidney cells were isolated from urine of either healthy controls or patients with MMA who harbor inactivating mutations in MUT. Confluent cells were sub–cultivated until 3rd passage and, subsequently, immortalized using pRSVneo vector containing SV40 DNA (pRNS1). Afterwards, immortalized kidney tubule epithelial cells were characterized for protein expression and enzyme activity. Total RNA was extracted from control and MMA cells to assess changes in gene expression with microarrays.
Platform: GPL570
32080200
GSE120774 Expression Data from epicardial (EAT) and subcutaneous adipose tissue (SAT) in patients with coronary artery disease Homo sapiens Expression profiling by array Adipose Tissue BTO:0001487 Coronary Artery Disease DOID:3393 18
  • Coronary Artery Disease (CAD)
  • control
 10/03/2018
Case control study
Platform: GPL6244
31513547
GSE120904 Specific targeting of the common gamma chain blocks cooperative reprogramming of human tissue-resident cytotoxic T lymphocytes by IL-15 and IL-21 Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 86
  • IL15 + IL21 + BNZ
  • IL21
  • IL15 + IL21
  • UN
  • IL21 + BNZ
  • IL15 + CP
  • IL15
  • IL15 + IL21 + CP
  • IL15 + BNZ
  • IL21 + CP
 10/05/2018
Gene expression profiles of human tissue-resident IE-CTLs (both in vitro and ex vivo), before and after simulation with IL-15 and IL-21 (individually and in combination).
Platform: GPL20301
31622625
GSE121632 Gene expression analysis of a panel of human fibroblasts that generate an aligned (anisotropic) vs non-aligned extracellular matrix Homo sapiens Expression profiling by high throughput sequencing Fibroblast BTO:0000452 Breast Cancer and Vulval Cancer DOID:1612 15
  • VCAF2B
  • MAF2
  • VCAF8
  • 1901T
  • CerCAF
  • OCAF1
 10/22/2018
Human fibroblasts were isolated from a patient tissues of vulval (VCAF8, VCAF2B) cervical (CerCAF), oral (OCAF), breast (1901T) carcinoma and metastatic melanoma (MAF2) and immortalised with lentiviral HTERT as described in Gaggioli, C., et al. Fibroblast derived matrix assays were performed as described in Franco-Barraza, J., et al and RNA extracted after 6 days in culture.
Platform: GPL16791
31659294
GSE122151 Transcriptomic Analysis on Lipid Loaded HepaRG Model for Steatosis Reveal the Influence on the Regulation of Drug Metabolizing Enzymes and Transporters Homo sapiens Expression profiling by high throughput sequencing Liver BTO:0000759 Liver Steatosis 5
  • control
  • Treatment
 11/05/2018
Examination of drug metabolizing enzymes dyregulation in the presence of Oleate and Palmitate (2:1) enriched media in HepaRG cells
Platform: GPL18573

N/A
GSE123658 Transimmunom whole blood RNA-seq data from type 1 diabetic patients and healthy volunteers Homo sapiens Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Type 1 Diabetes DOID:0110743 81
  • healthy
  • type 1 diabetes
 12/11/2018
Starting with a protocol for recruitment of participants followed by sample acquisition (Lorenzon et al., 2018)⁠, whole blood RNA from 43 healthy donors and 39 T1D patients were sequenced and the corresponding gene expressions were estimated. Gene expression estimation was preformed by normalizing read counts using Sex and Batch as covariates.
Platform: GPL18573

N/A
GSE124226 Gene Expression Data of Adipose Stem Cells from Normal-Weight Polycystic Ovary Syndrome Women vs. Controls Homo sapiens Expression profiling by array Adipose Tissue BTO:0001487 Polycystic Ovary Syndrome DOID:11612 7
  • Polycystic Ovary Syndrome (PCOS)
  • control
 12/20/2018
ASCs were isolated from SC adipose tissue following SC abdominal biopsy in 4 PCOS women and 4 age and BMI matched controls for gene expression comparison. First generation of stem cells were cultured until cells reached confluency and isolated for RNA extraction and hybridization on Affymetrix microarrays.
Platform: GPL570
30649347
GSE125012 Expression data from human adipose-derived stem cells (ADSCs) Homo sapiens Expression profiling by array Adipose Tissue BTO:0001487 Healthy: No Specific Disease Mention 7
  • CD271-negative
  • CD271-positive
 01/13/2019
Human adipose-derived stem cells were obtained from subcutaneous adipose tissue of 4 patients. Total RNA was isolated from sorted CD271+ and CD271- ADSCs.
Platform: GPL570

N/A
GSE125856 UCP1-expression associated gene signatures of human epicardial adipose tissue. Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Coronary Artery Disease DOID:3393 29
  • Low UCP1-eAT Non-CAD Lean
  • Low UCP1-eAT Non-CAD Obese
  • High UCP1 -eAT CAD Lean
  • Low UCP1-eAT CAD Obese
  • Low UCP1-eAT CAD Lean
  • High UCP1 -eAT CAD Obese
  • High UCP1 -eAT Non-CAD Obese
  • High UCP1 -eAT Non-CAD Lean
 01/29/2019
Paired biopsies of eAT, mAT and sAT obtained from cardiac surgery patients (n=10), with specific criteria of high- and low- expression of UCP1 in eAT, were subjected to RNA sequencing. While the primary objective was to compare high- vs. low UCP1 expression in eAT, our study design further allowed us to investigate depot- and disease specific transcriptomic shifts in these patients. Specifically, 10 patients provided 30 samples (n = 10 each for eAT, mAT and sAT) that could be compared based on depot specificity (n = 10), obesity (n = 5 lean, n = 5 obese) and coronary artery disease (CAD) (n = 6 CAD, 4 = Non-CAD).
Platform: GPL16791
30996144
GSE126296 Sprint exercise shares gene signatures with other exercise modes and hormone exposure and induces stronger upregulation of immediate early genes Homo sapiens Expression profiling by array Adipose Tissue BTO:0001487 Healthy: No Specific Disease Mention 27
  • 240 minutes post-sprint exercise
  • Control
 02/08/2019
Skeletal muscle gene expression at rest and after acute sprint interval exercise (3x30-s all-out cycle sprints). The first biopsy sample was obtained randomly in either right or left leg before the first sprint. The second sample was obtained 2 h and 20 min after the third sprint from the opposite leg. Fourteen human subjects (Seven males and seven females) volunteered for the present study.
Platform: GPL6244
31647849
GSE128331 HNF1A deficiency impairs β-cell fate, granule maturation and function Homo sapiens Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 11
  • HNF1A R200Q homozygous
  • HNF1A WT
  • HNF1A KO
  • HNF1A Het
 03/14/2019
Human embryonic stem cells with different HNF1A genotypes (WT, KO1, KO2, R200Q homozygous) were differentiated into islet-like clusters of endocrine cells for 27-28 days in vitro. First set of 6 samples, clusters of islet-like cells were dissociated into single cells and analyzed by single cell RNA sequencing. There are two WT, two KO and two R200Q samples.
Platform: GPL11154
35918471
GSE131320 Human Islet Response to Selected Type 1 Diabetes Associated Bacteria Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 39
  • Ruminococcus gnavus (RG) 24h
  • Bacteroides dorei (BD) 24h
  • Escherichia coli (EC) 6h
  • IL-1B 24h
  • Escherichia coli (EC) 24h
  • Bacteroides dorei (BD) 6h
  • Ruminococcus gnavus (RG) 6h
  • Serum-Free Control 24h
  • IL-1B 6h
 05/16/2019
In the present study, we experimentally tested the hypothesis that intestinal dysbiosis and leakage of bacteria into the human pancreas could trigger an islet anti-bacterial immune response. This response could lead to subsequent recruitment of immune cells to islets, initiating autoimmunity. To achieve that aim, isolated human islets were exposed to Bacteroides dorei and Ruminococcus gnavus, two bacteria overrepresented in the gut just before/at incidence of autoimmunity and Escherichia coli, a ubiquitous bacterium associated with accelerated maturation of the gut microbiome for 6h or 24h. Islets exposed to the potent cytokine IL-1β for the same time periods were used as positive controls. Islets exposed to serum-free medium were additionally used as negative controls.
Platform: GPL16791
31781116
GSE133903 Transcriptome analyses of human pancreatic islets and pseudoislets Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 8
  • isolated islets
  • pseudoislets (reaggregated single-islet cells)
 07/06/2019
human islets preparations and pseudoislets from 4 different human donors
Platform: GPL18573
31311971
GSE134068 Human islets of varying quality: the good, the (not so) bad and the ugly Homo sapiens Non-coding RNA profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 17
  • Group 1 (high quality)
  • Group 3 (poor quality)
  • Group 2 (intermediate quality)
 07/10/2019
Randomly selected islet preparations based on their post-isolation quality.
Platform: GPL20795
31361602
GSE134431 Deregulated immune signature orchestrated by FOXM1 impairs human diabetic wound healing Homo sapiens Expression profiling by high throughput sequencing Skin BTO:0001253 Diabetes (Non-specific) DOID:0081062 20
  • Ulcer - Nonhealer
  • Ulcer - Healer
  • Skin
 07/17/2019
Transcriptome profiles from patients with diabetic foot ulcers generated by deep sequencing using Illumina NextSeq500.
Platform: GPL18573
32938916
GSE134870 RNA-Seq of human adipose tissue (siNT vs siRND3 KD) Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 11
  • siRND3
  • siNT
 07/25/2019
Individual samples were treated with either a control/vehicle RNA treament (siNT) or a targetted siRND3 KD treatment
Platform: GPL20301

N/A
GSE135445 RNA-sequencing of epicardial adipose tissue of patients with atrial fibrillation Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Atrial Fibrillation DOID:0050650 11
  • persistent non-valvular atrial fibrillation (AF)
  • sinus rhythm (control)
 08/06/2019
Epicardial adipose samples collected from patients with persistent non-valvular AF (n=6) and sinus rhythm (n=6) were profiled using RNA-sequencing on the Illimina HiSeq 4000.
Platform: GPL20301

N/A
GSE135448 High- and low-protein diet: effects on human hepatic fat content, autophagy, mitochondrial function and fat metabolism Homo sapiens Expression profiling by high throughput sequencing Liver BTO:0000759 Non-alcoholic fatty liver disease (NALFD) DOID:0080208 18
  • High protein
  • Low protein
 08/06/2019
19 morbidly obese subjects undergoing bariatric surgery were randomized into two hypocaloric (1500 kcal/day) diet groups, a low protein (LP: 10 E% protein, n=10) and a high protein (HP: 30 E% protein, n=9), for three weeks prior to surgery. RNA-seq analyses were performed on liver samples collected during surgery.
Platform: GPL20301
32652799
GSE135917 Subcutaneous fat transcriptome in obstructive sleep apnea and after treatment with CPAP Homo sapiens Expression profiling by array Adipose Tissue BTO:0001487 Obstructive sleep apnea DOID:0050848 65
  • Obstructive Sleep Apnea (OSA)
  • After CPAP Intervention
  • control
  • Before
 08/16/2019
Total RNA was isolated from subcutaneous fat in two Study Group designs: 1) 10 subjects with OSA vs. 8 controls; 2) 24 subjects with OSA at baseline vs. after effective CPAP therapy. Each sample was hybridized to an GeneChip Human Gene 1.0 ST Affymetrix microarray for a total of 66 experiments.
Platform: GPL6244
31872261
GSE136134 The effect of insulin on mRNA transcription of human pluripotent stem cells Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Healthy: No Specific Disease Mention 11
  • Without insulin 72hrs
  • Without insulin 24hrs
  • With insulin 72hrs
  • With insulin 24hrs
 08/21/2019
3 hiPSCs lines were each cultured with or without insulin for 1 or 3 days (24 hours and 72 hours, respectively). RNA was extracted and used for RNA Sequencing
Platform: GPL11154
31358052
GSE137136 The impact of pro-inflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 9
  • pro-inflammatory cytokine exposure
  • control
 09/09/2019
Five independent preparations of EndoC-βH1 cells examined under 2 conditions (control and pro-inflammatory cytokine exposure)
Platform: GPL11154
33281748
GSE137631 Effects of exercise training on skeletal muscle insulin sensitivity in obesity patients undergoing RYGB surgery: a randomized controlled trial Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Obesity DOID:9970 29
  • RYGB POST SURGERY
  • RYGB + exercise training PRE SURGERY
  • lean control
  • RYGB + exercise training POST SURGERY
  • RYGB PRE SURGERY
 09/18/2019
Women patients with morbid obesity were undergone to RYGB and randomized to exercise training or not. Muscle biopsies were assessed before the RYGB surgery (PRE) and 9-month after RYGB surgery in both groups (RYGB and RYGB + exercise training). At baseline (PRE), muscle samples from lean control women were obtained as well.
Platform: GPL18573
32409493
GSE138252 Differential transcriptional responses in human cardiomyocytes Homo sapiens Expression profiling by high throughput sequencing Heart BTO:0000562 Atrial Fibrillation DOID:0050650 47
  • left ventricle No Atrial Fibrillation
  • control left atrium
  • left atrium No Atrial Fibrillation
  • right atrium Atrial Fibrillation
  • right ventricle No Atrial Fibrillation
  • left atrium Atrial Fibrillation
  • right atrium No Atrial Fibrillation
  • control right atrium
 10/01/2019
Cardiomyocyte nuclear mRNA profiles of human heart tissue samples (RA, LA, RV, LV).
Platform: GPL16791
32841220
GSE138900 Gene expression profile of HMT3522 S1 cells grown on 2D and in 3D matrix in response to the death ligand TRAIL Homo sapiens Expression profiling by array Skin BTO:0001253 Healthy: No Specific Disease Mention 11
  • Death Ligand TRAIL
  • Control
 10/15/2019
Three replicated cultures were established for each of the 4 experiment groups, including S1 cells grown as 2D monolayers (S1-2D CA, S1-2D CB, S1-2D CC), S1 cells grown as 2D monolayers and treated with TRAIL (S1-2D TA, S1-2D TB, S1-2D TC), S1 cells embedded in 3D rBM (S1-3D CA, S1-3D CB, S1-3D CC), S1 cells embedded in 3D rBM and treated with TRAIL (S1-3D TA, S1-3D TB, S1-3D TC). Cells were embeded in rBM for 12 days and then treated with TRAIL (1 μg/mL) or vehicle for 8 hours before the collection of RNA samples.
Platform: GPL96

N/A
GSE139929 Combined use of astragalus polysaccharide and berberine attenuates insulin resistance in IR-HepG2 cells via regulation of the gluconeogenesis signaling pathway Homo sapiens Expression profiling by high throughput sequencing Liver BTO:0000759 Type 2 Diabetes DOID:9352 8
  • none
  • Insulin induction and APBBR treatment
  • Insulin induction
 11/05/2019
HepG2 cells (Cell Bank of the Chinese Academy of Sciences, Shanghai, China) were cultured in 1640 medium (Hyclone, Beijing, China) containing 10% fetal bovine serum (FBS, Hyclone, Beijing, China) and 1 × streptomycin in a 37 ℃ 5% CO2 saturated humidity incubator. The normally cultured HepG2 cell lines in log phase were centrifuged at 100grpm for 5 min, and 20000 cells/well were placed in a 96-well plate and incubated at 37°C.The experiment was performed in 24-h control group, 24-h model group, 36-h control group, 36-h model group, 48-h control group, 48-h model group, 72-h control group and 72-h model group. Insulin (Gibco, NY, USA) was diluted to a final concentration of 10-6 mol/L in complete medium. 200µl insulin preparation was added into each well for the model group and an equal amount of complete medium was added into each well for the control group. Culture was performed in a 37 ℃ 5% CO2 and saturated humidity incubator. The supernatant of the corresponding medium was collected according to the time point by centrifugation at 3000 r/min for 5 min and stored at-80 ℃ for use. RNA isolation, purification and quantification: Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample were quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.cDNA Library Construction: Poly(A) RNA was purified from total RNA (5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Then, the poly(A) RNA was fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA, which was subsequently used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP. An A-base was then added to the blunt ends of each strand, which were prepared for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified by PCR under the following conditions: initial denaturation at 95℃ for 3 min, 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, extension at 72℃ for 30 sec, and then final extension at 72℃ for 5 min. The mean insert size for the final cDNA library was 300 bp (±50 bp). Finally, 150bp paired-end sequencing was performed on an Illumina Hiseq 4000 (LC Bio, China) following the vendor's recommended protocol.Pathway enrichment analysis: Using the DAVID database and mouse genome as background control, the differentially expressed genes were analyzed by gene ontology under "FunctionalAnnotation Chart" functional module. The differentially expressed genes were divided into three categories according to their functions: the biological process, the cell component and the molecular function. Pathway analysis was carried out by KEGG analysis function.
Platform: GPL20301

N/A
GSE139932 Profiling of RNAs from human islet-derived exosomes in a model of type 1 diabetes Homo sapiens Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 9
  • Untreated
  • Cytokines IL-1β and IFN-γ
 11/05/2019
Identification of differentially expressed mRNA and lncRNA from cytokine treated vs. untreated human pancreatic islets.
Platform: GPL20301
31775218
GSE140230 Tacrolimus- and sirolimus-induced human b cell dysfunction is reversible and preventable Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 12
  • TAC for 4 weeks
  • PBS for 4 weeks
  • SIR for 4 weeks
 11/12/2019
Human islets were tranplanted under kidney capsule of NSG mouse. After two weeks engraftment period, the mice were treated with tacrolimus, sirolimus, or PBS-control for 4 weeks. The grafts were then removed for analysis.
Platform: GPL16791
31941840
GSE141309 In vivo hyperglycemia exposure elicits distinct period-dependent effects on human pancreatic progenitor differentiation, conveyed by oxidative stress Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 13
  • Pancreatic progenitor Reprogrammed fibroblast
  • Pancreas
  • beta-like cells Reprogrammed fibroblast
 12/02/2019
hiPSCs were differantiated towards S5 pancreatic progenitor cells and S7 beta-like cells following the protocol by Rezania 2014
Platform: GPL18573
31942009
GSE141891 Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 7
  • Encapsulated in alginate
  • Growth on Matrigel
 12/12/2019
human induced pluriopotent stem cells were differentiated towards S7 beta like cells either in 2D the entire protocol (CTRL), or in 3D by encapsulation in alginate (3D). We have 4 replicates.
Platform: GPL18573
31942009
GSE142025 Comparison of Kidney Transcriptomic Profiles of Early and Advanced Diabetic Nephropathy Reveals Potential New Mechanisms for Disease Progression Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 35
  • Early_DN
  • Control
  • Advanced_DN
 12/13/2019
A total of 28 patients with biopsy-proven DN hospitalized from January 2015 to December 2016 in Shanghai Jiao Tong University Affiliated Sixth People's Hospital were enrolled in the study. Nine control human kidney samples were obtained from the unaffected portion of tumor nephrectomies. RNA-seq was performed on 28 DN and 9 control samples.
Platform: GPL20301
31578193
GSE142209 RNA-seq of human and mouse brain microvessels isolated by laser capture microdissection and matched whole brain samples Homo sapiens Expression profiling by high throughput sequencing Brain BTO:0000142 Healthy: No Specific Disease Mention 5
  • Brain Microvessels
  • Whole Brain
 12/17/2019
A total of 12 samples were analyzed: 6 mouse samples and 6 human samples. For each species, there are 3 biological replicates of brain microvessels isolated by laser capture microdissection, and 3 matched whole brain controls.
Platform: GPL11154
32704093
GSE143223 Whole transcriptome data of human liver organoids cultured in Matrigel and polyisocyanopeptides-based hydrogel Homo sapiens Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: No Specific Disease Mention 17
  • PIC 5k
  • PIC 1k
  • Matrigel
 01/07/2020
Whole transcriptome data of human liver organoids cultured in Matrigel or a novel hybrid hydrogel based on polyisocyanopeptides (PIC) and laminin-111. Hydrogel stiffness varied by using PIC different molecular weights, namely 1 kDa PIC (1k PIC) and 5 kDa PIC (5k PIC). The proliferative capacity of organoids in hydrogel was tested by culturing in organoid expansion medium (EM). By culturing liver organoids in differentiation medium (DM) these organoids are capable to differentiate towards hepatocyte-like cells. RNA Seq data is produced on Illumina NextSeq500 using a single-end 75 bp configuration.
Platform: GPL18573
34658689
GSE143319 Inhibition of Grb14, a negative modulator of insulin signaling, improves glucose homeostasis without causing cardiac dysfunction Homo sapiens Expression profiling by high throughput sequencing Liver BTO:0000759 Type 2 Diabetes DOID:9352 49
  • Post
  • MUO
  • Pre
  • MHO
 01/08/2020
We compared 1) Metabolically healthy obese (MHO, n=15) vs metabolically unhealthy obese (MUO, n=15) people, and 2) before vs. after weight loss (n=10).
Platform: GPL20301
32099031
GSE143482 Comparison of the LIGHT and TGF-B1 induced transcriptomes in esophageal FBL Homo sapiens Expression profiling by high throughput sequencing Esophagus BTO:0000959 Healthy: No Specific Disease Mention 11
  • LIGHT 50 ng/ml
  • Vehicle
  • TGF 5 ng/ml
 01/12/2020
Esophageal FBL isolated from esophagus specimens from 4 different human donors were treated with vehicle or 5ng/ml TGF-B1 or 50ng/ml LIGHT for 24 hours. RNA was extracted and analyzed.
Platform: GPL16791
32712105
GSE143735 RNA-sequencing analysis of forearm skin in diabetic patients with or without foot ulcerations Homo sapiens Expression profiling by high throughput sequencing Skin BTO:0001253 Diabetes (Non-specific) DOID:0081062 12
  • Diabetes - Ulcer - Healer
  • Diabetes - Ulcer - Non Healer
  • Diabetes - No Ulcer
 01/15/2020
mRNA profiles from skin isolated from the volar aspect of the forearm from 13 diabetic patients; 5 who healed their ulcers, 4 who didn't heal and 4 who had no ulcers.
Platform: GPL11154
32763913
GSE144274 RNA sequencing of healthy and diseased (idiopathic pulmonary hypertension) human pulmonary artery smooth muscle cells Homo sapiens Expression profiling by high throughput sequencing Muscle BTO:0000887 Idiopathic Pulmonary Hypertension DOID:6432 7
  • IPAH PASMC
  • healthy
 01/27/2020
Four biological replicates each in two groups a) Healthy subjects b) IPAH patients
Platform: GPL20301
32337710
GSE144441 Genome Wide Analysis of Gene Expression Changes in Skin from Patients with Type 2 Diabetes Homo sapiens Expression profiling by high throughput sequencing Skin BTO:0001253 Type 2 Diabetes DOID:9352 26
  • Non-Diabetic
  • Type 2 diabetic
 01/29/2020
mRNA profiles of the skin of type 2 diabetic and non-diabetic patients were generated by Illumina Hi Seq 4000.
Platform: GPL20301

N/A
GSE146108 VEGF-B Signaling Impairs Endothelial Glucose Transcytosis via an LDLR-dependent Decrease in Membrane Cholesterol Loading [HBMEC] Homo sapiens Expression profiling by array Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 14
  • VEGF-B186
  • VEGF-B167
  • control
  • VEGF-A165
  • PlGF
 02/28/2020
15 samples; n = 3 per treatment group, 5 treatments
Platform: GPL6244
32449307
GSE148519 Expression data of CD107aLow and CD107aHigh cells isolated from human adipose tissue Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 5
  • CD107aHigh
  • CD107aLow
 04/12/2020
6 Total samples were analyzed: 3 CD107aHigh biological replicates and three CD107aLow controls as determined by FACS.
Platform: GPL18573
33044169
GSE148697 Identification of Lead Drug Candidates for COVID-19 based on Drug Screening Using Human Pluripotent Stem Cell-Derived Cells/Organoids Homo sapiens Expression profiling by high throughput sequencing Lung BTO:0000763 Covid 19 DOID:0080600 5
  • Mock
  • sars-Cov2
 04/15/2020
Transcriptomic analysis of stem cell derived lung organoids
Platform: GPL24676
32511403
GSE149294 RNA-seq of in vitro differentiated human abdominal and gluteal adipocyte cell lines following doxycycline induced RSPO3-knockdown Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 23
  • dox (0.05 ug/ml)
  • vehicle
 04/24/2020
Abdominal and gluteal DFAT preadipocyte cells stably transduced with the tet-pLKO-puro-shRSPO3 (tet-shRSPO3) or tet-pLKO-puro-shCON (tet-shCON) lentiviral vectors were differentiated in standard adipogenic media. On day 13 of differentiation, cells were treated with doxycycline (final concentration of 0.05 µg ml-1), or vehicle, in hormone-free basal media for ~48 hours. On day 15, cells were harvested for RNA. Total RNA purification and on-column DNase I-treatment were performed using the RNeasy Mini kit (Qiagen). RNA-seq was performed on samples from three independent experiments. In addition to tet-shCON cells, vehicle-treated cells were used as controls.
Platform: GPL20301
32493999
GSE151505 Gene expression profile of bladder cancer cell lines treated with Mitomycin C Homo sapiens Expression profiling by high throughput sequencing Bladder BTO:0000123 Healthy: Treatment Focus 23
  • MCC
  • NT
 05/30/2020
mRNA profiles of T24, 5637, TCC-SUP and CLS-439 bladder cancer cell lines treated or not with Mitomicyn C (3 biological replicates for each condition)
Platform: GPL18573
33408185
GSE151588 Identification of an Anti-diabetic, Orally Available Small Molecule that Regulates TXNIP Expression and Glucagon Action Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • Control
  • SRI-37330 Treated
 06/01/2020
High-throughput screening of 300,000 compounds and extensive medicinal chemistry optimization.
Platform: GPL16791
32726606
GSE151839 Obesity and Race Alter Gene Expression in Skin Homo sapiens Expression profiling by array Skin BTO:0001253 Obesity DOID:9970 19
  • Normal Weight
  • Overweight
 06/04/2020
Skin and fat biopsies were collected from 20 subjects (10 obese, 10 normal wight). Biopsies were evaluated by immunohistochemical staining, and gene expression profiling with Affymetrix U133 2.0Plus arrays and RT-PCR.
Platform: GPL570
32826922
GSE154198 Genetic profiling of fetal human hepatocytes immortalized with hTERT Homo sapiens Expression profiling by array Liver BTO:0000759 Healthy: Treatment Focus 17
  • Passage 113
  • control
  • Passage 8
  • Passage 58
  • Passage 22
  • Passage 1
 07/10/2020
Cells were examined with Affimetrix microarrays for gene expression over prolonged passaging after immortalization. The major goal was to demonstrate genetic stability.
Platform: GPL571

N/A
GSE154649 Next generation sequencing to reveal the transcriptome of a DUX4 inducible FSHD model Homo sapiens Expression profiling by high throughput sequencing Muscle BTO:0000887 Healthy: No Specific Disease Mention 19
  • intact 8.5h doxycline induction
  • intact no treatment
  • intact 4.5h doxycline induction
  • knocked-out 8.5h doxycline induction
  • knocked-out no treattment
 07/17/2020
The transcriptomes of induced DIE cells were compared to uninduced or DIE cells, to identify differentially expressed genes or pathways that change upon DUX4 induction. Induced and uninduced DIE cells in which the DUX4 transgene was knocked-out (DIE_KO) served as controls. Samples were sequenced using Illumina Nextseq 500, 2x75 kit, high output. Four technical replicates per samples were send for sequencing.
Platform: GPL18573

N/A
GSE154964 Transcriptome map of cancerous and para-cancerous tissues in patients with liver hepatocellular carcinoma Homo sapiens Expression profiling by high throughput sequencing Liver BTO:0000759 Liver Hepatocellular Carcinoma 9
  • Liver Para-cancerous
  • Liver Cancerous
 07/23/2020
Examination of differences in transcriptome expression levels between cancerous and para-cancerous tissues of liver hepatocellular carcinoma patients
Platform: GPL16791
33344233
GSE155271 Expression data from human skeletal muscle in endurance-trained athletes Homo sapiens Expression profiling by array Skeletal Muscle BTO:0001103 Healthy: No Specific Disease Mention 12
  • Endurance-Trained
  • Control
 07/28/2020
Human skeletal muscle sample selected from Vastus lateralis for RNA extraction and hybridization on Affymetrix microarrays.
Platform: GPL570
33291227
GSE155482 Regulated expression and function of the GABAB receptor in human pancreatic beta cell line and islets Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • ECN90 Cells
  • EndoC-BetaH1 Cells
 07/31/2020
mRNA profiles of ECN90 and EndoC-βH1 cells
Platform: GPL18573
32778664
GSE156067 RNA-seq Data of Newly-Formed Adipocytes from Adipose Stem Cells of Normal-Weight Polycystic Ovary Syndrome Women vs. Controls Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Polycystic Ovary Syndrome DOID:11612 17
  • PCOS
  • control
 08/11/2020
ASCs were isolated from SC adipose tissue following SC abdominal biopsy in 3 PCOS women and 3 age and BMI matched controls for RNA-sequencing. Second generation of stem cells were cultured until cells reached confluency and expanded for two additional generations until fourth generation. Fourth generation ASCs were then cultured in adipogenic differentiation medium for 3-12 days and isolated for RNA extraction at days 3, 7, and 12. Extracted RNA were processed using Roche KAPA HyperPrep mRNA kit according to manufacturer's instructions and subjected to sequencing on a HiSeq4000 single-end 50 nt.
Platform: GPL20301
33228780
GSE156124 Common and private vitamin D target genes of human primary immune cells: a personalized approach Homo sapiens Expression profiling by high throughput sequencing PBMC BTO:0001025 Healthy: Treatment Focus 29
  • 0.1percent ethanol 24 h
  • 10 nM 1,25(OH)2D3 24 h
 08/12/2020
RNA-seq of PBMCs of 5 individuals (#5, 9,12,13,14) treated in 3 biologial repeats with the biologically active form of vitamin D, 1,25(OH)2D3 (1,25D) or solvent (0.1% Ethanol (EtOH))
Platform: GPL18573
33273683
GSE156903 Differential effects of voclosporin and tacrolimus on insulin secretion from human islets Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 20
  • TAC
  • VCS
  • DMSO
 08/26/2020
There are 3 conditions. Groups of 200 islets from 7 independent donors were treated for 48 hours with vehicle (DMSO), TAC (30 ng/ml) or VCS (60 ng/ml) then immediately flash-frozen in liquid nitrogen and stored at -80°C until RNA isolation and sequencing was performed.
Platform: GPL18573
32894758
GSE156993 Transcriptomic analysis of peripheral blood mononuclear cells (PBMC) of patients with type 2 Diabetes Melittus(T2DM), Dyslipidemia (DL) and Periodontitis (P) Homo sapiens Expression profiling by array PBMC BTO:0001025 Type 2 Diabetes DOID:9352 29
  • Periodontitis + Dyslipidemia
  • control
  • Periodontitis + Dyslipidemia + Type 2 Diabetes (Poorly Controlled)
  • Periodontitis + Dyslipidemia + Type 2 Diabetes (Well Controlled)
  • Periodontitis
 08/27/2020
PBMC were collected from 150 patients divided into 5 groups, the RNA was extracted using the Trizol® and purified by RNeasy Protection Mini Kit. It was used the GeneChip IVT Labeling Kit protocol and hybridized to U133 Plus 2.0 (Affymetrix)
Platform: GPL570

N/A
GSE157585 Metformin Alters Skeletal Muscle Transcriptome Adaptations to Resistance Training in Older Adults Homo sapiens Expression profiling by high throughput sequencing Skeletal Muscle BTO:0001103 Healthy: Treatment Focus 135
  • metPRT
  • Young
  • plaPRT
 09/07/2020
The Metformin to Augment Strength Training Effective Response in Seniors (MASTERS) Trial (ClinicalTrials.gov identifier: NCT02308228) is a randomized, controlled, double blind trial comparing the effects of metformin versus placebo during a 14-week progressive resistance training (PRT) intervention in healthy men and women ≥ 65 years of age. Participants were recruited at University of Kentucky and University of Alabama at Birmingham, UAB. The detailed study design and participant characteristics have been published previously (PMID: 28441958 and PMID: 31557380). Total RNA was isolated from baseline muscle biopsies in 37 plaPRT and 28 metPRT participants and from 16-week post-training muscle biopsies from 26 plaPRT and 24 metPRT participants. Of these, 24 plaPRT and 23 metPRT participants had biopsies at both timepoints. Additionally, total RNA was isolated from muscle biopsies in 21 young healthy donors. RNA content, integrity and purity were determined with a Nanodrop 2000 spectrophotometer and the 2100 Bioanalyzer. A minimum RNA Integrity Number (RIN) of 6.5 was set for all samples.
Platform: GPL20301
33071237
GSE158230 Secretory Leukocyte Peptidase Inhibitor (SLPI) is a Novel Predictor of Tubulointerstitial Injury and Renal Outcome in Patients with Diabetic Nephropathy Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 5
  • empty vetor
  • SLPI overexpression
 09/18/2020
We examined the effect of SLPI overexpression by gene expression profiling in HK-2 cells.
Platform: GPL16791
35910382
GSE158407 Ketogenic Diet dependent Immunometabolic Reprogramming of human T cells Homo sapiens Expression profiling by high throughput sequencing T cells BTO:0000782 Healthy: Diet Focus 55
  • pre ketogenic diet
  • post ketogenic diet
 09/23/2020
RNAseq analysis of human CD4+/CD8+ T cells prior and post 21 days of ketogenic diet
Platform: GPL20301
34151532
GSE158578 RNA-seq of human induced pluripotent stem cell differentiation into cardiomyocytes using Wnt inhibition Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Healthy: No Specific Disease Mention 11
  • iPSC derived mesoderm
  • iPSC derived cardiomyocyte
  • iPSC
 09/25/2020
RNA-seq of iPSC, iPSC derived mesoderm and iPSC derived cardiomyocyte
Platform: GPL18573

N/A
GSE158834 RNA sequencing of ADIPOR2 knockout HEK293 cells undergone various treatments with palmitic acid Homo sapiens Expression profiling by high throughput sequencing Umbilical vein endothelial cells BTO:0004296 Healthy: Gene KO Focus 41
  • 1% BSA + 200µM Palmitic acid
  • 1% BSA
  • Full medium
 09/30/2020
Triplicate samples of knockout (KO) and wildtype (WT) cells treated with BSA (control) or Palmitic acid (PA) for 0, 3, 9 and 24h
Platform: GPL18573
33444759
GSE159220 Search for a novel diagnostic marker for liver cancer. Homo sapiens Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Liver BTO:0000759 Liver Cancer DOID:0070322 5
  • Hepatocellular carcinoma tissue
  • martched normal liver tissue
 10/08/2020
Tumor and non-tumor parts are extracted from obtained HCC tissues.
Platform: GPL11154
35068348
GSE159612 Obesity in cardiac surgery patients Homo sapiens Expression profiling by high throughput sequencing Heart BTO:0000562 Obesity DOID:9970 52
  • BMI<25
  • BMI>32
  • 25<=BMI<=32
 10/19/2020
Patients attending surgery were recruited as part of a clinical trial. Total RNA was obtained from myocardial tissue (specifically atrial biopsies), sequenced and analyzed. Comparison of gene expression was made among obese, normal-weight and overweight groups as well as comorbidity and other patient characteristics
Platform: GPL20301
35082386
GSE160145 Myocardial adaptations in advanced kidney disease Homo sapiens Expression profiling by high throughput sequencing Heart BTO:0000562 Chronic Kidney Disease DOID:784 67
  • atrial cardio myofibroblast + high phosphate and calcium
  • Human Peritoneal dialysis
  • Ventricule cardio-myofibroblast + high calcium
  • atrial cardio myofibroblast + vehicle
  • Ventricule cardio-myofibroblast + vehicle
  • Ventricule cardio-myofibroblast + high phosphate
  • Human healthy control
  • Human Hemodialysis
  • atrial cardio myofibroblast + high phosphate
  • Ventricule cardio-myofibroblast + high phosphate and calcium
  • Human Hypertension
 10/26/2020
We conducted a 3-arm observational cross-sectional controlled cohort study of explanted human heart tissues. 109 donor hearts were collected, 50 met eligibility criteria for inclusion from hemodialysis-dependent patients (HD), hypertension (HTN) with relatively preserved GFR and healthy controls. Left ventricular tissues were subjected to pathologic examination and RNA-sequencing.
Platform: GPL18573
35179046
GSE161355 Type 2 Diabetes Mellitus is Associated with Transcriptome Alterations in Cortical Neurones and Associated Neurovascular Unit Cells in the Ageing Brain Homo sapiens Expression profiling by array Brain BTO:0000142 Type 2 Diabetes DOID:9352 10
  • Type 2 Diabetes
  • Control
 11/12/2020
Neurone, astrocyte, and endothelial cell-enriched RNA, obtained by immuno-laser capture microdissection of temporal cortex (Brodmann area 21/22) from 6 cases with self-reported T2D in the Cognitive Function and Ageing Study neuropathology cohort, and 5 age and sex-matched controls, was hybridised onto Affymetrix GeneChip® HG-U133 Plus 2.0 arrays.
Platform: GPL570
33407907
GSE161357 RNA-seq on human muscle progenitor cells cultured with (1000 uM) or without serine and glycine Homo sapiens Genome variation profiling by high throughput sequencing Expression profiling by high throughput sequencing Muscle BTO:0000887 Healthy: Treatment Focus 9
  • minus serine/glycine
  • plus serine/glycine
 11/12/2020
RNA was harvested from human muscle progenitor cells (n = 5 separate donors) after 5 days of culture with or without 1000uM serine/glycine
Platform: GPL18573
33122122
GSE161643 Skeletal muscle gene expression changes one year following Roux-en-Y gastric bypass (RYGB) surgery Homo sapiens Expression profiling by array Skeletal Muscle BTO:0001103 Healthy: No Specific Disease Mention 23
  • Control
  • 1 year post-RYGB surgery
 11/17/2020
Vastus Lateralis samples were taken prior to and one year follow RYGB surgery. We sought to explore skeletal muscle gene expression profiles following surgical weightloss.
Platform: GPL570

N/A
GSE162265 RNA sequencing of human primary myotubes from lean and obese subjects Homo sapiens Expression profiling by high throughput sequencing Muscle BTO:0000887 Obesity DOID:9970 5
  • obese
  • lean
 11/27/2020
Total RNA from three samples per group was isolated by Qiagen RNeasy kit and quality was assessed on a bioanalyzer (RIN>8 for each sample). Poly-A selected cDNA libraries were constructed and sequenced on an Illumina HiSeq2000 by Otogenetics Corp (Norcross, GA) producing at least 20 million 2X101 paired end reads per sample. Reads were aligned to the NCBI GRCh37 USCS hg 19 reference genome with TopHat. RefSeq annotations were used as the gene model and differential expression was assessed with Cufflinks, correcting for multiple comparisons. Gene enrichment and pathway analysis were conducted with the Database for Annotation, Visualization and Integrated Discovery (DAVID).
Platform: GPL11154
25970801
GSE164081 Alternative transcription start sites contribute to acute-stress–induced transcriptome response in human skeletal muscle Homo sapiens Homo sapiens Homo sapiens Expression profiling by high throughput sequencing Skeletal Muscle BTO:0001103 Healthy: No Specific Disease Mention 49
  • + 2 min after exercise
  • + 6 h after exrecuse
  • prior
  • + 1 h after exrecuse
  • + 3 h after exrecuse
 12/30/2020
Ten amateur endurance-trained athletes (long distance runners, cyclists and cross country skiers, median age 32 years [interquartile range, 30–36 years]; weight 75 kg [71–78 kg]; V'O2max/kg [maximal pulmonary O2 consumption rate] 58 ml/min/kg [54–60 ml/min/kg of body mass]) were involved in our study. Each subject carried out an intermittent exercise (60 min, [3 min at intensity 50% of lactate threshold [LT4 , power at blood lactate 4 mmol/l] + 2 min, 100% LT4] x 12) on a cycle ergometer 2 h after a standardized breakfast (3582 kJ; 22 g protein, 154 g carbohydrates and 16 g fat). Subjects ate a standardized lunch (3714 kJ; 45 g protein, 183 g carbohydrates and 27 g fat) 1 h 15 min after an intermittent exercise. Biopsy samples were taken under local anesthesia (2 mL 2% lidocaine) using a Bergstrome needle with aspiration from the m. vastus lateralis prior to, 2 min, 1 h, 3 h, and 6 h after an intermittent exercise (1st, 2d, and 3d from the one leg, 4st and 5st from another leg).
Platform: GPL11154
35869513
GSE164266 Gene expression profiles of liver sinusoidal Vγ9+Vδ2+ T cells from healthy donors and patients with hepatitis B virus-related chronic liver disease Homo sapiens Expression profiling by high throughput sequencing T cells BTO:0000782 Chronic Liver Disease DOID:409 9
  • hepatitis B virus-related chronic liver disease
  • healthy donor
 01/05/2021
Examination of gene expression profiles in liver sinusoidal Vγ9+Vδ2+ T cells from 5 healthy donors and 5 patients with hepatitis B virus-related chronic liver disease.
Platform: GPL18573
33472894
GSE166785 Unravelling the Biological Functions of Type 1 Diabetes Associated Noncoding Single-Nucleotide Polymorphism in Human Pancreatic β Cells Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 5
  • PTPN2-/-
  • WT
 02/15/2021
WT or PTPN2-/- hESC derived beta cells were purified based on INS-GFP expression.
Platform: GPL24676

N/A
GSE176216 RNA-sequencing of IRF5+ and IRF5- circulating monocytes from patients with Type-2 Diabetes Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 47
  • IRF5-_1
  • IRF5+_6
  • IRF5-_3
  • IRF5+_5
  • IRF5+_2
  • IRF5+_4
  • IRF5-_4
  • IRF5+_3
  • IRF5-_2
  • IRF5-_5
  • IRF5+_1
  • IRF5-_6
 06/05/2021
mRNA-sequencing of FACS sorted cells
Platform: GPL18573
36042203
GSE201908 Development of a physiological insulin resistance model in human stem cell-derived adipocytes Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Type 2 Diabetes DOID:9352 20
  • WT hESC-adipocyte differentiation
  • WT hESC-adipocyte differentiation, then 5 days low-glucose DMEM+3nM insulin
  • WT Primary cell isolation
  • WT hESC-adipocyte differentiation, then 5 days low-glucose DMEM+100pM insulin
 04/29/2022
Development of a physiological insulin resistance model in human stem cell-derived adipocytes
Platform: GPL24676
35714187
GSE202295 Distinctive exercise-induced inflammatory response and exerkine induction in skeletal muscle of people with type 2 diabetes Homo sapiens Expression profiling by high throughput sequencing Muscle BTO:0000887 Type 2 Diabetes DOID:9352 110
  • NGT Basal
  • T2D Post
  • NGT Post
  • NGT Recovery
  • T2D Basal
  • T2D Recovery
 05/05/2022
Skeletal muscle biopsies were collected from normal glucose tolerant (NGT) and type 2 diabetic (T2D) middle age men, before (rest), just after (post) and 3-hours after (recovery) a 30-minute bout of cycling, at an intensity of 85% of measured maximal heart rate.
Platform: GPL16791
36070371
GSE102371 Functional Genomics Analysis of Islets from Recent and Longstanding T1D Reveals the Need for Distinct Approaches to Therapy Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 5
  • short duration type 1
  • normo-glycemic
  • long duration type 1 diabetes
 08/08/2017
5 human islets of Langerrhans preparations. 3 in normo-glycemic individual, one individual with a long duration type 1 diabetes and one individual with short duration type 1 diabetes
Platform: GPL21290
29569324
GSE102485 Induced Expression of VEGFC, ANGPT, and EFNB2 and Their Receptors Characterizes Neovascularization in Proliferative Diabetic Retinopathy Homo sapiens Expression profiling by high throughput sequencing Retina BTO:0001175 Diabetes (Non-specific) DOID:0081062 30
  • branch retinal vein occlusion
  • abbreviations of type I diabetes
  • abbreviations of type II diabetes
  • Normal retina
  • retinal periphlebitis
 08/10/2017
Total 30 transcriptome profile of neovascular proliferative membrane specimens from patients with PDR and normal samples.
Platform: GPL18573
31574534
GSE109163 Derivation and Characterization of a UCP1 Reporter Human ES Cell Line Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Diabetes (Non-specific) DOID:0081062 4
  • mCherry +
  • mCherry -
 01/12/2018
RNA-seq was performed on isolated mCherry positive and negative cells in duplicate.
Platform: GPL20301
29777802
GSE111876 GABA regulates release of inflammatory cytokines from peripheral blood mononuclear cells and CD4+ T cells and is immunosuppressive in type 1 diabetes Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Type 1 Diabetes DOID:0110743 49
  • Nondiabetic
  • Type 1 diabetes
 03/15/2018
Total RNA was extracted from CD3+ T cells of 18 nondiabetic individuals and 31patients with type 1 diabetes and subjected to deep sequencing using Illumina HiSeq 2500.
Platform: GPL16791
29627388
GSE112594 Elevated T cell levels in peripheral blood predict poor clinical response following rituximab treatment in new-onset type 1 diabetes Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Type 1 Diabetes DOID:0110743 195
  • Placebo
  • Active
 04/02/2018
The rituximab trial was a randomized, double-blind study of patients (N = 87) with newly diagnosed T1D assigned to receive infusions of rituximab or placebo on days 1, 8, 15, and 22 of the study. The primary outcome was the geometric mean area under the curve (AUC) for the serum C-peptide level during the first 2 hours of a mixed-meal tolerance test assessed after 1 year. We obtained RNA-seq data from a subset of subjects in the original trial (N = 56 subjects originally), sampled at different visits (0, 26, 52, 78 and 104 weeks) for a total of 205 samples (mean ~4 samples per patient). Of 205 initial samples, 195 yielded high-quality RNA-seq data consistent with subject annotation, and were used in downstream analyses.
Platform: GPL16791
29925930
GSE129666 RNA sequence data in whole cell extracts of differentiated human podocytes Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 6
  • SMPDL3b OE
  • control
 04/11/2019
RNA sequence data in whole cell extracts of differentiated human podocytes
Platform: GPL21290
31217420
GSE136053 Comparative Analysis of the Transcriptome of Latent Autoimmune Diabetes (LADA) Patients from Eastern China Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 9
  • healthy control
  • Latent Autoimmune Diabetes (LADA)
 08/20/2019
RNA-seq analyses were conducted on peripheral blood mononuclear cells of LADA patients and healthy controls
Platform: GPL16791
31950067
GSE140308 Genomewide transcriptional analysis of growth hormone-treated human podocytes Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 4
  • none
  • human growth hormone for 30 min
 11/13/2019
Human podocytes in duplicates were treated with (500 ng/ml) or without growth hormone for 30 min and total RNA was isolated. Both by running on an agarose gel and using the bioanalyzer confirmed the quality of RNA. High-quality RNA libraries were constructed using mRNA templates, random hexamers, oligo-dT primers, and Illumina second strand synthesis buffer. RNA sequencing was performed on Illumina 2500 Hi-Seq devise by pair-end reads at Nucleome Informatics Facility, Hyderabad, India.
Platform: GPL16791

N/A
GSE140627 Urinary sediment transcriptomic and longitudinal data to investigate renal function decline in type 1 diabetes Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Type 1 Diabetes DOID:0110743 10
  • healthy control
  • type 1 diabetes
 11/18/2019
mRNA profiles of urine sediment cells from healthy volunteers and from type 1 diabetes patients with different rates of kidney funcion decline were used to select genes with the potential do predict renal function decline
Platform: GPL16791
32425885
GSE143143 Neutrophil extracellular trap induced dendritic cell activation leads to Th1 polarization in type 1 diabetes Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Type 1 Diabetes DOID:0110743 30
  • healthy
  • type 1 diabetes
 01/06/2020
T1D moDCs were cultivated with healthy NETs, autologous T1D NETs or left untreated. Simularly, healthy moDCs were treated with own healthy NETs, T1D NETs or left untreated
Platform: GPL20301
32346380
GSE143979 Skeletal muscle regeneration is compromised in advanced diabetic peripheral neuropathy Homo sapiens Expression profiling by high throughput sequencing Muscle BTO:0000887 Diabetes (Non-specific) DOID:0081062 15
  • DPN
  • MNC
  • DPN (sev)
 01/21/2020
Biopsies were acquired from two muscles in individuals with and without diabetic neuropathy undergoing below knee amputation surgery. Biopsies were subdivided for histological analysis, transcriptional profiling and satellite cell isolation and culture.
Platform: GPL21290
32059624
GSE144169 Angiogenin derived from ABCB5+ mesenchymal stem cells improves diabetic wound via enhancing angiogenesis Homo sapiens Expression profiling by high throughput sequencing Skin BTO:0001253 Diabetes (Non-specific) DOID:0081062 2
  • 250 uM of sodium palmitate for 24 hrs
  • PBS control
 01/23/2020
Transcriptome profiling of HUVEC
Platform: GPL18573

N/A
GSE150586 Next generation sequencing identifies differentially expressed genes between breast cancer with diabetes and breast cancer without diabetes Homo sapiens Expression profiling by high throughput sequencing Breast BTO:0000149 Diabetes (Non-specific) DOID:0081062 13
  • Breast cancer patient without diabetes
  • Breast cancer patient with diabetes
 05/14/2020
Comparison of mRNA expression profiles between breast cancer with diabetes and breast cancer without diabetes
Platform: GPL24676

N/A
GSE150621 Gestational diabetes and human amniocytes Homo sapiens Expression profiling by high throughput sequencing Uterus BTO:0001424 Diabetes (Non-specific) DOID:0081062 14
  • GDM
  • control
 05/14/2020
A nested case-control study was performed in second trimeseter amniocytes matched for offspring sex, maternal race/ethnicity, maternal age, gestational age at amniocentesis, gestational age at birth and gestational diabetes status. Sex-specific RNA-sequencing was completed and gene expression changes were identified.
Platform: GPL16791

N/A
GSE152615 RNAseq from human islets treated with brefeldin A as a model of Golgi stress Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 8
  • control
  • Brefeldin A treated
 06/16/2020
Identification of differentially expressed mRNA from Brefeldin A treated vs. control human pancreatic islets.
Platform: GPL24676
32820009
GSE155713 Modeling human T-cell mediated beta cell destruction Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 11
  • Not sorted
  • Sorted based on tdT expression
  • Sorted based on CD19 expression.
  • Sorted based on expression of HPi2 positive and absence of HPx1.
 08/04/2020
Examination of gene expression differences in primary human islets and human pluripostent stem cells differentiated beta-like cells under control or T cell conditioned medium condition.
Platform: GPL16791
33205073
GSE159717 SARS-CoV-2 infection of human pancreatic islets Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 6
  • Uninfected
  • SARS-CoV-2 infection
  • SARS-CoV-2 infection and Remdesivir
 10/20/2020
Islet preparations of two different donors were infected with SARS-CoV-2 and treated with Remdesivir for 5 days. Uninfected pancreatic islets served as control.
Platform: GPL20301
33536639
GSE161914 Gene cascade analysis in human granulosa tumor cells (KGN) following exposure to high levels of free fatty acids and insulin Homo sapiens Expression profiling by high throughput sequencing Ovary BTO:0000975 Diabetes (Non-specific) DOID:0081062 4
  • -
  • 100 ng/mL insulin
  • PA 75 microM + SA 25 microM + OA 100 microM
  • PA 75 microM + SA 25 microM + OA 100 microM +100 ng/mL insulin
 11/20/2020
Cells treated with differents concentations of free fatty acids and insulin alone or in combination. 3 reps per treatment were pooled for RNAseq analysis.
Platform: GPL20301
34930403
GSE166640 VPA-treatment of Panc-1-cells to study epigenetic impact mediated by histone acetylation on epithelial-mesenchymal transmission Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 6
  • VPA-1mM
  • VPA-6mM
  • control
 02/11/2021
Panc-1-cells were incubated with VPA at 1 or 6 mM for 5 days with 2 replicates for each conditions. Treatment without VPA was employed as control.
Platform: GPL18573
35451037
GSE168705 Ten-hour time-restricted eating improves glycaemic control and alters transcriptomic profile in adipose tissue in men at increased risk of type 2 diabetes Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Type 2 Diabetes DOID:9352 96
  • Baseline 6PM
  • Time restricted eating 6AM
  • Time restricted eating 6PM
  • Baseline 12PM
  • Time restricted eating 12PM
  • Time restricted eating 12AM
  • Baseline 12AM
  • Baseline 6AM
 03/11/2021
In a single-arm, within-subject trial, 15 men (aged 62.9 ± 4 years, waist circumference 113 ± 4 cm) with no history of diabetes were enrolled and instructed to eat their regular diets within a contiguous 10-hour time frame each day for 8 weeks. The timing of food intake was tracked via a photograph-based application. After 2-weeks of baseline monitoring period and 8-weeks of TRE, participants were provided with a 3-day lead-in diet before they underwent a 35-hour metabolic ward stay, during which all food intake was strictly controlled within 14-hours (pre) or 10-hours (post). Identical standardized meal tolerance tests were performed at breakfast and dinner (52% carbohydrate, 33% fat, 15% protein). Transcriptional profiles in subcutaneous adipose tissue were measured in by RNA-sequencing (n=11).This study was designed to examine the effects of eight weeks of TRE (10-hours per day) on the glucose area under the curve (AUC) and appetite regulation at breakfast and dinner, and gene expression in adipose tissue in men with obesity.
Platform: GPL16791
35912794
GSE169514 Transcriptome analysis of human pancreatic preadipocytes and in vitro differentiated adipocytes Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 24
  • In vitro differentiated adipocytes
  • Isolated preadipocytes
 03/24/2021
Isolated preadipocytes and respective in vitro differentiated adipocytes from 12 different human donors stratified between non-diabetic, prediabetic and type 2 diabetic metabolic status.
Platform: GPL18573
33788629
GSE172148 RNA sequencing of control and PTPN2 knocked down transcriptomes in EndoC-𝛽H1 cells with or without the treatment of pro-inflammatory cytokines Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 18
  • PTPN2 silencingInterferon-gamma
  • ControlInterferon-alpha
  • PTPN2 silencingControl
  • ControlControl
  • ControlInterferon-gamma
  • PTPN2 silencingInterferon-alpha
 04/15/2021
mRNA profiles of control and PTPN2 knocked down 𝛽-cells with or without treatment of human interferon-𝛾 or interferon-α
Platform: GPL24676
35044456
GSE174502 RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of adipose stem cells from diabetic, old and young patients Homo sapiens Homo sapiens Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Adipose Tissue BTO:0001487 Diabetes (Non-specific) DOID:0081062 18
  • Normal
  • Diabetes mellitus
 05/16/2021
MRNAs, lncRNAs, circRNAs and miRNAs profiles of adipose stem cells from diabetic, old and young patients were generated by RNA sequencing.
Platform: GPL20795

N/A
GSE179143 Areca catechu-(Betel-nut)-induced whole transcriptome changes in a human monocyte cell line that may have relevance to diabetes and obesity; a pilot study Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Type 2 Diabetes DOID:9352 6
  • MNPA
  • Arecoline
 06/29/2021
3 THP1 samples treated with Arecoline and 3 samples treated with MNPA
Platform: GPL18573
34391409
GSE179568 In-depth molecular characterization of neovascular membranes suggests a role for hyalocytes-to-myofibroblasts transdifferentiation in proliferative diabetic retinopathy Homo sapiens Expression profiling by high throughput sequencing Retina BTO:0001175 Diabetes (Non-specific) DOID:0081062 24
  • Macular hole
  • Macular pucker
  • RNV
 07/06/2021
RNA sequencing of 7 human RNV membranes, 10 macular pucker and 7 macular hole samples
Platform: GPL15433
34795670
GSE180504 Impaired bone fracture healing in type 2 diabetes is caused by defective functions of skeletal progenitor cells Homo sapiens Expression profiling by high throughput sequencing Bone BTO:0000140 Type 2 Diabetes DOID:9352 6
  • 10 days osteogenic differentiation + serum from lean subjects
  • 10 days osteogenic differentiation + serum from obese subjects
  • 10 days osteogenic differentiation + serum from type 2 diabetes subject
 07/20/2021
mRNA profiles of primary bone marrow derived stromal cells that were differentiated to osteoblasts in vitro in the presence of serum from lean, obese or typ 2 diabtes subjects.
Platform: GPL11154
35257177
GSE181328 Exploratory study reveals far reaching systemic and cellular effects of verapamil treatment in subjects with type 1 diabetes Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 6
  • incubated with 25mM glucose for 24h
  • incubated with 25mM glucose + 100uM Verapamil for 24h
 08/02/2021
Treatment of islet cells with compond (verapamil) followed by transcriptomics.
Platform: GPL16791
35241690
GSE181674 Islet Sympathetic Innervation and Islet Neuropathology in Patients with Type 1 Diabetes Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 18
  • control non-diabetic
  • diabetic
  • non-diabetic islet autoantibody-positive individuals
 08/09/2021
Laser microdissected islets from pancreas organ donors were analyzed by RNA-sequencing and bioinformatics to determine differentially regulated genes.
Platform: GPL21290
33753784
GSE182138 Transcriptome analysis and weighted gene co-expression network reveal candidate genes and pathways responses to lactate dehydrogenase inhibition (oxamate) in hyperglycemic human renal proximal epithelial tubular cells Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 5
  • Case group
  • Control group
 08/15/2021
Six replicates of HK-2 cells were firstly exposed to HG treatments for seven days, then three replicates of them were exposed 40 mM oxamate (case group), while the other three replicates were still under the same HG condition but 40 mM oxamate expose (control group). Unfortunately, one replicate of case group failed in RNA sample preparation, so five replicates of cells were finally chosen for RNA sequencing in this study.
Platform: GPL20795
35370938
GSE182923 Altered Human Alveolar Bone Gene Expression in Type 2 Diabetes Homo sapiens Expression profiling by high throughput sequencing Bone BTO:0000140 Type 2 Diabetes DOID:9352 18
  • healthy control
  • diabetic
 08/27/2021
Cross-sectional, no replicates, 10 healthy, 8 diabetic
Platform: GPL20301

N/A
GSE184050 Novel diabetes gene discovery through comprehensive characterization and integrative analysis of longitudinal gene expression changes Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Type 2 Diabetes DOID:9352 116
  • control
  • T2D case
 09/13/2021
Longitudinal whole blood transcriptome profile of T2D progression
Platform: GPL11154
35157052
GSE184831 Persistent Coxsackievirus B1 infection results in extensive changes in the transcriptome of a pancreatic cell line Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 9
  • persistent carrier state infection CVB1 ATCC strain
  • non-infected control
  • persistent carrier state infection CVB1 10796 strain
 09/27/2021
Carrier-state persistent infection in human pancreatic ductal-like cell line PANC-1 cells using two distinct CVB1 strains (ATCC and 10796, 3 replicates in each) was established and compared to non-infected controls (3 replicates) for infection-induced changes in cellular transcriptome.
Platform: GPL21290
35024587
GSE185011 The expression of mRNA and lncRNA in peripheral blood mononuclear cells (PBMCs) of diabetes mellitus, diabetic retinopathy (DR), diabetic peripheral neuropathy (DPN) and diabetic nephropathy (DN) patients Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Type 2 Diabetes DOID:9352 25
  • Peripheral blood mononuclear cells
 09/29/2021
mRNA and lncRNA transcriptional spectrums of peripheral blood mononuclear cells in health control, T2DM, DR, DPN and DN patients were obtained through high-throughput sequencingene technology.
Platform: GPL24676
35989592
GSE185598 Lnc-SLC15A1-1 Up-regulates CXCL10/CXCL8 Expression in Endothelial Cells by Sponging MicroRNAs (RNA-Seq) Homo sapiens Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 6
  • primary human cells were purchased from Lonza Walkersville, Inc
 10/09/2021
HUVECs were purchased from Lonza Walkersville, Inc. Cells from the fifth passage were incubated in 30 mM D-glucose (high glucose, HG) or 30 mM D-glucose treated with 0.1 mM IS (HG+IS) for 96 h.Total RNAs was extractied form the HUVECS with HG and HUVECs.Total RNA was extracted from cultured cells in these two conditions then RNA-seq was performed.
Platform: GPL18573
34941711
GSE188827 Spatial Environment Affects HNF4A Mutation-Specific Proteome Signatures and Cellular Morphology in hiPSC-Derived β-Like Cells Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 28
  • HNF4A+/corrected
  • HNF4A+/c811dupA
 11/15/2021
Examination of the transcription profile effects by HNF4A mutation in hiPSC-derived β-Like cells
Platform: GPL18573
35043148
GSE193510 A miR-125 / Sirtuin-7 pathway drives pro-calcific potential of myeloid cells in diabetic vascular disease Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 8
  • 5mM
  • 20mM
 01/12/2022
mRNA profile on osteo-THP-1 cultured in high (20mM) glucose and normal (5 mM) glucose
Platform: GPL21697
35708762
GSE193979 Transcriptional profiles predict treatment outcome in patients with tuberculosis and diabetes at diagnosis and at two weeks after initiation of anti-tuberculosis treatment Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 231
  • TB-only
  • TB-DM
  • TB-preDM
  • TB-IH
 01/19/2022
Whole blood was collected from patients with TB-only, TB-DM throughout anti tuberculosis treatment at four time points: Diagnosis, Week 2, Month 2 and Month 6 from two field sites; South Africa and Indonesia. Treatment outcome data were collected at Month 12
Platform: GPL18573
35841871
GSE197850 Glucagon-like Peptide-1 (GLP-1) Rescue Diabetic Cardiac Dysfuntions in Human iPSC-Derived Cardiomyocytes Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 16
  • diabetic cardiomyocytes modeling+GLP-17-36 treatment
  • diabetic cardiomyocytes modeling
  • untreated
  • diabetic cardiomyocytes modeling+GLP-19-36 treatment
 03/03/2022
CM control group ( iPSC-CMs,n=4 ), DCM model group (diabetic cardiomyocytes,n=4), GLP-17-36 treatment group (diabetic cardiomyocytes treated with GLP-17-36,n=4), GLP-19-36 treatment group (diabetic cardiomyocytes treated with GLP-19-36,n=4)
Platform: GPL11154

N/A
GSE199838 RNAs sequencing revealing the gene expression profiling in kidney tissues between diabetic kidney disease and control Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 6
  • non-diabetic renal cancer patients undergoing surgical resection
  • diabetic kidney disease
 03/31/2022
kidney tissues from renal biopsies of 3 DKD patients and normal tissues from 3 non-diabetic renal cancer patients undergoing surgical resection
Platform: GPL21290
36792603
GSE200477 Polysome profiling quantified by RNA sequencing in PANC1 cells treated with MNK2 inhibitors or DMSO Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 24
  • CID661578 (40 uM), 6hrs
  • DMSO, 6hrs
  • cercosporamide (5 uM), 6hrs
 04/08/2022
Four replicated of polysome profiling were performed on PANC1 cells treated with MNK2 inhibitors (CID661578 [40uM], and cercosporamide [5uM]) or DMSO for 6 hours. Total cytosolic RNA, and polysome-associated mRNA (mRNA associated with > 3 ribosomes) were quantified using RNA sequencing.
Platform: GPL24676
35697798
GSE205674 Transcriptomic signatures responding to PKM2 activator TEPP-46 in the hyperglycemic human renal proximal epithelial tubular cells Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 6
  • Case group (TEPP-46)
  • Control group
 06/08/2022
The obtained HK-2 cells were exposed to 25-mM HG medium as the hyperglycemic condition for 7 days. Thereafter, three replicates of cells exposed to HG were treated with (case group) or without (control group) 10-μM TEPP-46 for 1 day, separately. We extracted 2 μg RNA per cell replicate sample for RNA sample preparation, generated the sequencing libraries using NEBNext Library Prep Kit (NEB, USA) following the manufacturer's recommendations and sequenced on the Illumina Hiseq X ten platform to generate the 150 bp paired-end reads step by step.
Platform: GPL20795
36120453
GSE205891 Worksite-based intensive lifestyle therapy has profound cardiometabolic benefits in people with obesity and type 2 diabetes Homo sapiens Expression profiling by high throughput sequencing Skeletal Muscle BTO:0001103 Type 2 Diabetes DOID:9352 62
  • SC
  • ILT
 06/10/2022
In this study, we evaluated the effects of standard care (SC) and intensive lifestyle therapy (ILT) treatments on gene expression profiling in skeletal muscle and subcutaneous adipose tissue obtained from people with obesity and type 2 diabetes.
Platform: GPL24676
36084645
GSE226888 The effect of DFMO on the gene expression in pro-inflammatory cytokine-treated human islets Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 20
  • Treated with IL-1β and IFN-γ for 24 hours
  • Unstimulated control
  • Treated with DFMO for 24 hours
  • Treated with DFMO and IL-1β and IFN-γ for 24 hours
 03/07/2023
Comparative gene expression profiling analysis of RNA-seq data for human islets treated with DFMO in presence or absence of proinflammatory cytokines
Platform: GPL24676

N/A
GSE77108 HDAC inhibitor SAHA reverses inflammatory gene expression in diabetic endothelial cells Homo sapiens Expression profiling by high throughput sequencing Heart BTO:0000562 Diabetes (Non-specific) DOID:0081062 30
  • Diabetic endothelial cells_NT_siRNA
  • Diabetic endothelial cells_DMSO
  • Healthy endothelial cells_EP300_siRNA
  • Diabetic endothelial cells_SAHA
  • Healthy endothelial cells_SAHA
  • Diabetic endothelial cells_C646
  • Healthy endothelial cells_C646
  • Healthy endothelial cells_NT_siRNA
  • Diabetic endothelial cells_EP300_siRNA
  • Healthy endothelial cells_DMSO
 01/21/2016
Human aortic endothelial cells from a diabetic and non-diabetic individual were stimulated with DMSO (control), SAHA (2 μM, HDAC inhibitor) or C646 (10 μM, EP300 inhibitor) for 12 hours, or EP300 siRNA or non-target siRNA (control) for 4 hours, followed by 48 hours in fresh media. Study performed in triplicate.
Platform: GPL16791
28886276
GSE89475 Endothelial cells derived from iPSC in response to diabetic medium Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 4
  • control
  • diabetic
 11/02/2016
Vascular organoids were differentiated from human iPS cells and treated for 3 weeks with a diabetic media containing 75mM Glucose, 1ng/mL TNF-α, 1ng/mL IL6 (DI) or left untreated in 17mM Glucose (NG). Endothelial cells were FACS sorted for CD31 directly into Trizol and stored at -80°C before RNA preparation. The 2 NG and 2 DI are pools of sorted endothelial cells from multiple vascular organoids (>100) from 2 independent differentiations/treatments.
Platform: GPL20301
30651639
GSE92724 Dermal endothelial cells of type 2 diabetic patients Homo sapiens Expression profiling by high throughput sequencing Skin BTO:0001253 Type 2 Diabetes DOID:9352 10
  • Healthy control
  • Diabetic Patient
 12/22/2016
Surgical samples of human skin were taken from Type 2 diabetic patients and non-diabetic patients. The study was approved by the local ethics committee and all included patients gave their informed consent (no. 449/2001; 81/2008). Endothelial cells (CD31+, CD45-, Podoplanin-) from 4 diabetic patients (Pat) and 6 controls (Ctrl) were FACS sorted and processed for RNA Seq.
Platform: GPL20301
30651639
GSE94019 Transcriptomic Analysis of Endothelial Cells from Fibrovascular Membranes in Proliferative Diabetic Retinopathy Homo sapiens Expression profiling by high throughput sequencing Retina BTO:0001175 Diabetes (Non-specific) DOID:0081062 13
  • non-Diabetic
  • Diabetes Mellitus/proliferative diabetic retinopathy
 01/24/2017
CD31+ retinal mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.
Platform: GPL11154
28400392
GSE97647 Glucose impairs tamoxifen sensitivity modulating CTGF in breast cancer cells Homo sapiens Expression profiling by high throughput sequencing Breast BTO:0000149 Type 2 Diabetes DOID:9352 2
  • grown in high glucose
  • grown in high glucose and then shifted in low glucose
 04/11/2017
The gene expression profile of MCF7 cells grown in high glucose and then shifted in low glucose (HG→LG; n=1) were compared to MCF7 cells grown in high glucose (HG; n=1).
Platform: GPL11154

N/A
GSE98485 A SRp55-regulated alternative splicing network controls pancreatic beta cell survival and function Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 10
  • SRpP55 KD (siSR#2)
  • control siRNA
 05/02/2017
Five independent preparations of EndoC-βH1 cells exposed to control (siCTL) or SRp55 (siSR#2) siRNAs
Platform: GPL11154
29246973
GSE134901 Nutrient regulation of the islet epigenome controls adaptive insulin secretion Homo sapiens Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 10
  • tranylcypromine
  • vehicle
 07/25/2019
Human or mouse pancreatic islets were assessed for genomewide enrichment of H3K27ac under different conditions or for binding by the histone demethylase Lsd1 using ChIP-seq. mRNA-seq was used to assess transcriptional changes in islets under different nutrient states or following inactivation of the histone demethylase Lsd1.
Platform: GPL20301
36821378
GSE205853 Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines Homo sapiens Homo sapiens Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Other Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 16
  • 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose)24h
  • no treatment24h
  • 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose)24h
  • 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β (low dose)24h
  • 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β, 0.02 ng/mL TNF-α (low dose)24h
 06/10/2022
Primary human islets from 12 donors were cultured in vitro with pro-inflammatory cytokines (IL-1b, IFNg, and TNFa) at multiple doses and durations. ATAC-seq, snATAC-Seq (10x Genomics) and RNA-seq were performed in treated and untreated matched samples to map islet and beta cells regulatory programs in response to cytokine stimulation. The cell line EndoC-βH1, a model for human beta cells, was profiled with HiChIP in untreated and cytokine-treated conditions, to identify long range chromatin interaction, and was used to perform a CRIPSR-KO screen to identify genes affecting cytokine-induced beta cell loss. SELEX-Seq was used to determine the in-vitro binding of hundreds of transcription factors at genetic variants located within islet regulatory elements.
Platform: GPL20301
36778047
GSE7196 Differential gene expression between WT and ERRa-null hearts Mus musculus Expression profiling by array Heart BTO:0000562 Healthy: Gene KO Focus 5
  • ERRa Knockout
  • Wildtype
 03/05/2007
3 hearts from WT and 3 hearts from ERRa-null mice were used in the study. The expression of genes in the ERRa KO hearts were compared to the reference WT hearts.
Platform: GPL1261
17488637
GSE10849 Caveolin-1 Knockout Hearts Mus musculus Expression profiling by array Heart BTO:0000562 Healthy: Gene KO Focus 5
  • Wildtype
  • Caveolin-1 Knockout
 03/14/2008
3 wild types, 3 knockouts
Platform: GPL1261
18719368
GSE12337 Transcriptomic analysis of PPARalpha-dependent alterations during cardiac hypertrophy Mus musculus Expression profiling by array Heart BTO:0000562 Healthy: Gene KO Focus 7
  • TAC Intervention PPARalpha-/-
  • Sham WT
  • TAC Intervention WT
  • Sham PPARalpha-/-
 08/05/2008
Wild-type and PPARalpha-/- mice were sham-operated or subjected to TAC for 28 days. Left ventricular gene expression profile was determined using Affymetrix 430 2.0 arrays containing over 45,000 probe sets (covering over 34,000 mouse genes) to detect PPARalpha-related differences in cardiac gene expression under basal conditions and after imposition of a sustained hemodynamic stress.
Platform: GPL1261
18812456
GSE13432 Adipose tissue exposed to cold Mus musculus Expression profiling by array Adipose Tissue BTO:0001487 Healthy: Treatment Focus 5
  • 5 weeks 30C
  • 1 week 30C
  • 5 weeks 4C
  • 1 week 4C
 11/01/2008
Mice were exposed to cold and white addipose tissue was collected at different time points
Platform: GPL1261
19117550
GSE13583 Expression data from liver of the KRAP deficient mice Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Gene KO Focus 5
  • KRAP Knockout
  • Wildtype
 11/13/2008
Total RNA was extracted from livers of three pairs of littermates (KO1 vs. WT1, KO2 vs. WT2 and KO3 vs. WT3) fed normal chow.
Platform: GPL1261
19156225
GSE16048 Expression profiling of pancreatic beta-cells harboring a pancreatic-specific deletion of PPAR-beta Mus musculus Expression profiling by array Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • Pdx1Cre;PPARbetafl/fl Knockout
  • control
 05/11/2009
Pancreas-specific knock-out animals were generated by breeding mice harbouring a floxed Ppar-beta (PPARbetafl/fl) to mice expressing the Cre transgene under the control of the Pdx1 promoter (Pdx1Cre). Islets from 3 different animals from the knock-out group Pdx1Cre;PPARbetafl/fl and the control littermates group PPARbetafl/fl were compared.
Platform: GPL1261
23093780
GSE20165 Expression data from white and brown adipose tissue (WAT and BAT) of per2-/- and control mice Mus musculus Expression profiling by array Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 5
  • BAT per2+/+
  • WAT per2-/-
  • BAT per2-/-
  • WAT per2+/+
 02/02/2010
Per2-/- and per2+/+ male mice (Bae et al., 2001) were housed under 12 hr light/12 hr dark (LD) cycles. Mice 20 weeks old were sacrificed at the same time and adipose tissue (WAT and BAT) was collected for RNA extraction. 3 biological replicates per mouse/tissue.
Platform: GPL6246
21035761
GSE24031 Adipose tissue dysfunction signals progression of hepatic steatosis towards nonalcoholic steatohepatitis in C57Bl/6 mice Mus musculus Expression profiling by array Liver BTO:0000759 Diabetes (Non-specific) DOID:0081062 17
  • Pre-NASH
  • Normal Liver Morphology
  • Benign Hepatic Steatosis
  • Overt NASH
 09/08/2010
Male wildtype C57Bl/6 mice were fed LFD or HFD for 21 weeks. Mice were divided into 4 groups based on liver histology.
Platform: GPL1261
20858684
GSE26978 Expression data from pancreatic islets from Men1flf RIP-Cre mice, Rbp2flf RIP-Cre mice, Men1flf Rbp2flf RIP-Cre mice and matched control. Mus musculus Expression profiling by array Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 16
  • Genotype RIP-Cre
  • control
  • Genotype Men1flf , Rbp2flf RIP-Cre
  • Genotype Men1flf RIP-Cre
  • Genotype Rbp2flfRIP-Cre
 01/31/2011
Pancreatic islets were isolated from Men1flf RIP-Cre mice, Rbp2flf RIP-Cre mice, Men1flf Rbp2flf RIP-Cre mice and two month old matched control mice. Total mRNA was extracted from islets and expression profiled on microarrays.
Platform: GPL6246
21788502
GSE27547 Gene expression differences in mouse islets after isolation at different time points (0-48hr) Mus musculus Expression profiling by array Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 16
  • 24 hrs
  • 48 hrs
  • control
 02/27/2011
Six independent batches of islets were isolated. For each batch, islets from 4 C57BL/6 mice were pooled, and were divided into 3 groups, which were harvested at 0 h, 24 h and 48 h after culture. Total RNA was extracted from the islets with QIAGEN RNeasy Micro Kits. After reverse transcription, cDNA served as a template for PCR-based cRNA amplification. It was then reverse-transcribed to produce second-generation cDNA, which was employed to generate biotin-labelled cRNA probes. The probes were hybridized on GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA), which contains 39,000 transcripts. DNA microarray analysis was performed at the McGill University Genome Quebec Innovation Centre.
Platform: GPL1261
21471441
GSE29048 Expression Profiling Identifies Novel Gene Targets and Functions for Pdx1 in the Duodenum of Mature Mice Mus musculus Expression profiling by array Small Intestine BTO:0000651 Diabetes (Non-specific) DOID:0081062 7
  • Control
  • Intestinal epithelium-specific Pdx1 inactivation
 05/04/2011
Pdx1 was conditionally inactivated in the intestinal epithelium of Pdx1flox/flox;VilCre mice, by crossing mutant mice homozygous for loxP site-flanked Pdx1 alleles with transgenic mice expressing Cre recombinase under the control of the mouse villin 1 gene promoter. Total RNA was isolated from the first five centimeters of the small intestine from adult Pdx1flox/flox;VilCre and littermate control mice. Microarray analysis was performed to investigate genome-wide transcriptional profiles in the proximal small intestine.
Platform: GPL1261
22135308
GSE32095 GPR120 mediates high-fat diet induced obesity Mus musculus Expression profiling by array Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 11
  • WT Normal Diet
  • GPR120 KO High Fat Diet
  • WT High Fat Diet
  • GPR120 KO Normal Diet
 09/13/2011
GPR120 KO mice and the corresponding wild-type with normal diet(ND) or high fat diet(HFD), were subjected to Affymetrix Mus musculus microarrays. Epididymal adipose tissue and liver were analyzed in triplicates.
Platform: GPL1261
22343897
GSE37248 Farnesoid X Receptor alters adipose tissue architecture in mice and limits its storage capacity leading to metabolic derangements Mus musculus Expression profiling by array Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 7
  • hFXR WAT: Adipose-Specific Human FXR Overexpression
  • hFXR BAT: Adipose-Specific Human FXR Overexpression
  • WT BAT
  • WT WAT
 04/13/2012
Total RNA optained from 10 BAT and 8 WAT samples, where compaired in 2 by 2 different groups, consisting of biological replicates n=4,5
Platform: GPL6246
31253637
GSE38067 Hepatic gene expression in streptozotocin-induced diabetic mice fed a quercetin diet Mus musculus Expression profiling by array Liver BTO:0000759 Diabetes (Non-specific) DOID:0081062 23
  • Streptozotocin (STZ) treatment
  • control
  • [Streptozotocin (STZ) treatment + 0.5 Percent Quercetin Diet]
  • [Streptozotocin (STZ) treatment + 0.1 Percent Quercetin Diet]
 05/21/2012
Six-week-old male mice were divided into 4 groups of 6 mice each, housed in groups of 3 per cage. After 1 week mice were intraperitoneally injected with STZ. Mice (n=6) in the untreated control group did not receive any treatment. After 1 week, 18 mice showing non-fasting blood glucose levels of 230-400 mg/dL were divided into 3 groups: one group was fed with AIN93G only (control group), the others with an AIN93G diet containing 0.1% or 0.5% quercetin (Funakoshi, Tokyo, Japan) for 2 weeks.
Platform: GPL1261
19496084
GSE38138 Hepatic gene expression in streptozotocin-induced diabetic mice fed a phloridzin diet Mus musculus Expression profiling by array Liver BTO:0000759 Diabetes (Non-specific) DOID:0081062 19
  • Streptozotocin (STZ) treatment
  • [Streptozotocin (STZ) treatment + 0.5 Percent Phloridzin Diet]
  • control
  • [Streptozotocin (STZ) treatment + 0.1 Percent Phloridzin Diet]
 05/22/2012
Six-week-old male mice were divided into 4 groups of 6 mice each, housed in groups of 3 per cage. After 1 week mice were intraperitoneally injected with STZ. Mice (n=6) in the untreated control group did not receive any treatment. After 1 week, 18 mice showing non-fasting blood glucose levels of 330-590 mg/dL were divided into 3 groups: one group was fed with AIN93G only (control group), the others with an AIN93G diet containing 0.1% or 0.5% phloridzin (Funakoshi, Tokyo, Japan) for 2 weeks.
Platform: GPL1261
19413312
GSE39752 Liver adapts mitochondrial function to insulin-resistant and diabetic states in mice Mus musculus Expression profiling by array Liver BTO:0000759 Diabetes (Non-specific) DOID:0081062 12
  • Streptozotocin (STZ)
  • Control
 07/30/2012
We performed gene expression microarray analysis on liver tissue derived from mice treated with STZ or standard diet (control).
Platform: GPL6246
24291365
GSE40439 Gene expression analysis of Ncor1 muscle-specific knockout and PGC-1alpha muscle-specific transgenic skeletal muscle Mus musculus Expression profiling by array Skeletal Muscle BTO:0001103 Healthy: Gene KO Focus 19
  • PGC-1alpha-mTg
  • NCoR1-MKO
  • wild type
  • control
 08/28/2012
Gene expression of a total of 20 gastrocnemius samples from control (CON, n = 5), NCoR1 muscle-specific knockout (NCoR1 MKO, n = 5), wild type (WT, n = 5) and PGC-1alpha muscle-specific transgenic (PGC-1alpha mTg, n = 5) adult male mice was analyzed using GeneChip® Gene 1.0 ST Array System (Affymetrix). NCoR1 MKO and PGC-1alpha mTg samples were compared to CON and WT samples, respectively.
Platform: GPL6246
23028049
GSE41203 Transcriptional analysis of type 1 diabetes reveals an interferon signature that precedes T cell activation Mus musculus Expression profiling by array Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 80
  • NOD 6 weeks
  • NOD 4 weeks
  • NODRAG 2 weeks
  • NOD 2 weeks
  • B6g7 6 weeks
  • NOD 8 weeks
  • NOD DBX
  • C57BL6 6 weeks
  • NODRAG 6 weeks
 09/27/2012
57 RNA samples isolated from the pancreatic islets of langerhans of experimental mice: 2-18 wk old non-obese diabetic (NOD) and newly diabetic NOD were compared to controls: NOD.RAG-/-, B6.g7 and C57BL/6. There were 3 or 6 biological replicates per condition. All mice were female. All data was normalized using RMA in Arraystar. Data table includes normalized probe intensity for every probe.
Platform: GPL6246
23555752
GSE43106 Phenotypic comparison of common mouse strains developing high-fat diet-induced hepatosteatosis Mus musculus Expression profiling by array Liver BTO:0000759 Type 2 Diabetes DOID:9352 71
  • Control
  • 21-day High-Fat Diet
 12/21/2012
We performed gene expression microarray analysis on liver from C3HeB/FeJ (C3H), C57BL/6NTac, C57BL/6J, and 129P2/OlaHsd (129) males during 21 days HFD challenge.
Platform: GPL6246
24327959
GSE46515 Expression data from mouse model using targeted deletion of hepatic RICTOR (Albumin-Cre Rictor LoxP/LoxP) Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Gene KO Focus 7
  • Wildtype
  • Rictor Floxed
 04/30/2013
Rictor floxed (RKO) and control mice (n=4 per group) were fasted overnight, refed for 3 hr, then sacrificed. Livers were removed, rinsed in PBS, and flash frozen in liquid nitrogen. RNA was extracted and hybridized to Affymetrix Genechip Mouse Gene 1.0 ST arrays
Platform: GPL6246
24072782
GSE47504 Gene expresssion changes in pancreatic islets of 11 weeks old IKK2-CApdx-1 mice compared to control and Pdx-1+/- mice Mus musculus Expression profiling by array Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 13
  • IKK2-CApdx-1 genotype
  • control
  • Pdx-1+/- genotype
 05/30/2013
Pancreatic islets were isolated from 11 weeks old control (n=5), Pdx-1+/- (n=4) and IKK2-CApdx-1 (n=5) mice, total RNA was extracted with RNeasy mini kit (QIAGEN). Microarray analyses were performed using 200 ng total RNA as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA). The total RNAs were amplified and labeled following the Whole Transcript (WT) Sense Target Labeling Assay (http://www.affymetrix.com). Labeled ssDNA was hybridized to Mouse Gene 1.0 ST Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA). The chips were scanned with a Affymetrix GeneChip Scanner 3000 and subsequent images analyzed using Affymetrix® Expression Console Software (Affymetrix). Probe level data were obtained using the robust multichip average (RMA) normalization algorithm.
Platform: GPL6246
24296718
GSE48009 Gene expression in IRfl/fl Cre- and IRfl/fl Cre+ mice Mus musculus Expression profiling by array Breast BTO:0000149 Healthy: Gene KO Focus 5
  • Insulin Receptor Diminished
  • Control
 06/17/2013
Mouse strains containing a floxed insulin receptor (IRfl/fl) were crossed with a mouse expressing Cre recombinase from a BLG promoter
Platform: GPL6246
23982156
GSE51108 Gene expression in liver tissue from Ghrh-KO and normal (wild-type) mice Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Gene KO Focus 5
  • Ghrh-KO
  • Wildtype
 09/23/2013
Hepatic tissue was obtained from 3 Ghrh-KO mice and 3 control (wild-type) mice (males). Expression in each sample was profiled using Affymetrix Mouse Genome 430 2.0 arrays.
Platform: GPL1261
24175087
GSE55746 Transcriptional profiling of liver from wild type and PXR-null mice treated with PCN Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Gene KO Focus 15
  • Pregnenolone 16alpha-carbinonitrile (PCN)
  • Control
 03/10/2014
The animal studies were carried out at the University of Kansas Medical Center (Kansas City, KS) under federal guidelines for the use and care of laboratory animals and was approved by the KUMC Institutional Animal Care and Use Committee. Eight-week-old adult C57BL/6 mice were purchased from Jackson Laboratories (Bar Harbor, ME). Generation of the PXR-null mice was previously described (Staudinger et al., (2001), Proc Natl Acad Sci USA 98:3369–3374). PXR-null breeder pairs were engineered and backcrossed into the C57BL/6 background. Adult male wild-type mice and PXR-null mice were maintained on standard laboratory chow and were allowed food and water ad libitum. All mice were treated once a day i.p. with either vehicle (corn oil) or PCN at 400 mg/kg/day for 4 days. Livers were removed 24-hrs after the last dose. Portions of the livers were rapidly snap-frozen in liquid nitrogen and stored at -70°C until analysis. Liver gene expression analysis was performed according to the Affymetrix recommended protocol using Affymetrix Mouse Genome 430 2.0 GeneChips®. Total RNA (5 μg per sample) was labelled using the Affymetrix® One-Cycle cDNA Synthesis protocol and hybridized to arrays as described by the manufacturer (Affymetrix®, Santa Clara, CA). Microarray hybridizations were conducted overnight at 45°C while rotating in an Affymetrix hybridization oven. After 16 hours of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip® fluidics station 450 according to the Affymetrix-recommended protocol. Arrays were scanned on an Affymetrix GeneChip® scanner. Four mice per group were examined.
Platform: GPL1261
26215100
GSE58025 Aldehyde dehydrogenase activity is necessary for beta cell development and functionality in mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 11
  • null_P1
  • WT_P1
  • mutant_week8
  • WT_week8
 05/28/2014
Islets were isolated from postnatal day one and 8 week old Aldh1b1 null and wt mice. For each P1 samples islets from three mice were combined. Each week 8 sample came from a single mouse. Three samples were analysed per genotype and time point
Platform: GPL17021
26518685
GSE59141 Expression data from islets of non-pregnant and pregnant PRLR+/+ and PRLR-/- mice Mus musculus Expression profiling by array Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • PRLR-/- Day 9.5 of Pregnancy
  • PRLR+/+ Day 9.5 of Pregnancy
  • PRLR-/- Non-Pregnant
  • PRLR+/+ Non-Pregnant
 07/07/2014
Islets were isolated from non-prengant (NP) and pregnant (day 9.5) PRLR+/+ and PRLR-/- mice for RNA extraction and hybridization on Affymetrix microarrays. For every condition 3 biological replicates were used.
Platform: GPL6246
25816302
GSE59143 Expression data from normal and transplanted islets in non-pregnant and pregnant condition Mus musculus Expression profiling by array Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 12
  • Non-Pregnant + Female Islet Graft
  • Day 12.5 of Pregnancy + Male Islet Graft
  • Day 12.5 of Pregnancy
  • Day 12.5 of Pregnancy + Female Islet Graft
  • non-pregnant female mouse islets
  • Non-Pregnant + Male Islet Graft
 07/07/2014
Islets and islet grafts were isolated from non-prengant and pregnant mice for RNA extraction and hybridization on Affymetrix microarrays. For every condition, at least 3 biological replicates were used.
Platform: GPL6246
25816302
GSE65098 Adiponectin-cre FTO flox/flox and FTO flox/flox mouse white fat tissues Mus musculus Expression profiling by array Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 5
  • Adiponectin-cre FTO flox/flox
  • FTO flox/flox
 01/20/2015
FTO flox/flox and Adiponectin-cre FTO flox/flox (AFO) mice were fed with chow diet. White fat tissues from epididymal adipose pad were harvested under ad lib condition for RNA isolation. Three independent pools of FTO flox/flox and AFO mouse white fat RNA were included in the study.
Platform: GPL1261
26671148
GSE66766 Effect of Mut heterozygosity in skeletal muscle gene expression Mus musculus Expression profiling by array Muscle BTO:0000887 Type 2 Diabetes DOID:9352 9
  • Mut+/-
  • Wildtype (Mut+/+)
 03/10/2015
5-week-old Mut+/+ and Mut+/- male mice were fed a high-fat diet with 45% kcal from fat for 4 months. Mice were fasted overnight prior to sacrifice and quadriceps muscle was flash frozen in liquid nitrogen.
Platform: GPL1261
27689005
GSE67991 RNA seq of pancreatic islets isolated from free fatty acid receptor 3 knockout (Ffar3 KO) and wildtype (Ffar3 WT) male mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • Ffar3 Wildtype
  • Ffar3 KO
 04/17/2015
Analysis of total RNA from 3 biological replicates of pancreatic islets isolated from free fatty acid receptor 3 knockout (Ffar3 KO) and wildtype (Ffar3 WT) male mice
Platform: GPL13112
26091414
GSE70213 The effect of Nebulin-Deficiency on Skeletal Muscle Mus musculus Expression profiling by array Skeletal Muscle BTO:0001103 Healthy: Gene KO Focus 11
  • Quad Control
  • Soleus Conditional Nebulin KO
  • Quad Conditional Nebulin KO
  • Soleus Control
 06/24/2015
Two skeletal muscle groups were studied: Quadriceps (which is markedly smaller in the Neb cKO mice relative to control) and Soleus (which is not significantly smaller in the Neb cKO relative to control). Six biological replicates for each muscle group were selected; all are age-matched males.
Platform: GPL6246
26123491
GSE70681 Deletion of Pten leads to liver steatosis and tumor formation Mus musculus Expression profiling by array Liver BTO:0000759 Liver Steatosis 17
  • Wildtype
  • Pten deletion: Pten loxP/loxP; Alb-Cre+
 07/09/2015
Pten is deleted specifically in the liver (Pten loxP/loxP; Alb-Cre+). Liver tissues were analyzed at 3 months (steatosis stage) and 15 months (tumor stage)
Platform: GPL6246

N/A
GSE73036 Insulin resistance in high fat diet mouse Mus musculus Expression profiling by array Skeletal Muscle BTO:0001103 Type 2 Diabetes DOID:9352 11
  • High-Fat Diet: Day 5
  • High-Fat Diet: Day 42
  • control
 09/15/2015
Comparison of gene expression in muscle tissue during High Fat Diet (HFD) time course (day 5 and day 42). Chow diet will serve as control for HFD. 4 samples per group serve as experimental replicates.
Platform: GPL1261
28725461
GSE73131 Sphingosine-1-phosphate Phosphatase 2 Regulates Pancreatic Islet β-cell Endoplasmic Reticulum Stress and Proliferation Mus musculus Expression profiling by array Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 11
  • Normal Diet
  • High-Fat Diet
 09/17/2015
Three replications of Mouse (WT vs KO) that were treated with with Normal and HFD foods.
Platform: GPL1261
27059959
GSE73436 Chronic Activation of γ2 AMPK Induces Obesity and Reduces Beta Cell Function Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Diabetes (Non-specific) DOID:0081062 9
  • Homozygote AMPK R299Q Knock-in
  • control
  • Homozygous AMPK R299Q Knock-in
 09/25/2015
Transcriptomic profiling of the hypothalamic arcuate nucleus from AMPK γ2 R299Q knock-in mice
Platform: GPL17021
27133129
GSE74113 Reduced insulin production relieves endoplasmic reticulum stress and induces beta-cell proliferation Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Healthy: Gene KO Focus 15
  • Cre+T
  • Cre-T
 10/16/2015
Examination of the transcriptome of adult pancreatic islets from mice with acute Ins2 gene knockout out on an Ins1 null background
Platform: GPL17021
26626461
GSE78183 Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers Elovl2 as a novel regulator of glucose-induced insulin secretion Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 337
  • Regular Chow (RC) D02
  • Regular Chow (RC) D90
  • High Fat, High Sugar (HFHS) D90
  • Regular Chow (RC) D10
  • Regular Chow (RC) D30
  • High Fat, High Sugar (HFHS) D02
  • High Fat, High Sugar (HFHS) D30
  • High Fat, High Sugar (HFHS) D10
 02/22/2016
6 mouse strains, 4 time points, 2 diets
Platform: GPL13112
28377873
GSE79164 The Nuclear Receptor Rev-erb alpha Regulates Adipose Tissue-Specific FGF21 Signaling (Microarray) Mus musculus Expression profiling by array Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 7
  • Wildtype
  • Rev-erb alpha KO
 03/14/2016
Examination of the transcriptome in epididymal white adipose tissue of Rev-erb alpha kockout mice compared to wildtype mice.
Platform: GPL6246
27002153
GSE81648 The effect of antibiotic mediated gut microbiome perturbation on ileal gene expression in NOD mice. Mus musculus Expression profiling by array Small Intestine BTO:0000651 Type 1 Diabetes DOID:0110743 16
  • Control (male mice)
  • Sub-Therapeutic Antibiotic Treatment (male mice)
  • Sub-Therapeutic Antibiotic Treatment (female mice)
  • Pulsed Therapeutic Antibiotic Treatment (female mice)
  • Control (female mice)
  • Pulsed Therapeutic Antibiotic Treatment (male mice)
 05/19/2016
Microarray experiment was performed on RNA extracted from the terminal ileum of control; STAT; and PAT mice. (Female n=3/group; Male n=5/group except STAT n=3).
Platform: GPL1261
27782139
GSE84759 LIM-Domain-Binding 1 maintains the terminally-differentiated state of pancreatic β-cells Mus musculus Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 17
  • Isl1 KO
  • Ldb1 KO
  • control
 07/24/2016
The total RNA profiles for FACS-enriched populations of WT, Ldb1-negative, and Isl1-negative β-cells isolated from tamoxifen-induced male mice at post-natal day (P) 56, P56, and P49, respectively, were generated by RNA-seq. The LDB1 and ISL1 whole pancreatic islet cistromes from 8-10-week-old male CD1 mice were generated by ChIP-seq.
Platform: GPL17021
27941246
GSE86949 RNAseq data from mouse beta-cells expressing mutant (GCK Y214C) versus wild-type Glucokinase Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Healthy: Gene KO Focus 5
  • Wildtype
  • mutGCK(Y214C)
 09/14/2016
RNA profiles of pancreatic islets from 5-6 week old transgenic mice expressing mutant GCK ( Y214C) (Pdx1Cre-ER; Rosa-LSL-Y214C-GCK) and from their control littermates (Rosa-LSL-Y214C-GCK) were generated by deep sequencing
Platform: GPL13112
27882918
GSE87354 RNAseq analysis of Rpl13a-snoless and wild type islets Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 7
  • Rpl13a-snoless
  • Wildtype
 09/26/2016
Examination of murine pancreatic islet mRNA differential expression between wild type mice and mice with loss-of-function of U32a, U33, U34, and U35a snoRNAs.
Platform: GPL17021
27820699
GSE87854 Insulin resistance in high fat diet mouse (adipose) Mus musculus Expression profiling by array Adipose Tissue BTO:0001487 Healthy: Diet Focus 11
  • High-Fat Diet (Day 14)
  • control
  • High-Fat Diet (Day 5)
 10/11/2016
Comparison of gene expression in adipose tissue during HFD time course (day 5, day 14). Chow diet will serve as control for HFD. 4 samples per group serve as experimental replicates.
Platform: GPL1261

N/A
GSE88779 Mouse Pancreatic Islet Maturation Time Series Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 12
  • control
  • E18
  • P21
  • P14
  • P7
 10/14/2016
Breeders homozygous for Ins1-H2b-mCherry (Jax #028589) were crossed to wild type C57bl6 mates to ensure offspring were uniformly hemizygous for the mCherry reporter. Islets from single litters (a mix of male and female is expected) were pooled for each sample to obtain sufficient material. Pooled islets were dissociated, sorted and collect in Trizol for RNA isolation and library construction.
Platform: GPL13112
28380380
GSE89035 Interruption of Hepatic Glucagon Signaling Reveals a Hepatic-α-Islet Cell Axis Where L-Glutamine Stimulates α-Cell Proliferation Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Diabetes (Non-specific) DOID:0081062 8
  • Gcgr-mAb Treatment; Both Gcgr+/+ genotype
  • Gcgr-/-
  • control
 10/21/2016
Ten days of GCGR mAb treatment increased the percentage of proliferating α-cell approximately 14-fold while Gcgr-/- mice also have increased α-cell proliferation (Dean et al., unpublished; Longuet et al., 2013). Therefore, we used these two models for liver transcriptomics. Mice were fasted for 6 hours prior to tissue collection. For RNA isolation, approximately 100mg punches of liver tissue were stored in RNAlater (Ambion) according to the manufacturer's instructions until isolation using RNeasy Mini kit with DNase I (Qiagen Hilden, DE) digestion. RNA purity and quantity were determined by Bioanalyzer. Transcriptome expression was determined as described previously (Reinert et al, 2014; Brissova et al., 2014).
Platform: GPL17021

N/A
GSE90531 Deletion of Histone Deacetylase 3 in Adult Beta Cells Improves Glucose Tolerance via Increased Insulin Secretion Mus musculus Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 15
  • HDAC3f/f;Tam
  • HDAC3f/f;Cre;Veh
  • HDAC3betaKO
  • HDAC3betaKO (those lacking histone deacetylase 3)
 11/25/2016
Genomic occupancy profiled by high throughput sequencing (ChIP-seq) from mouse islets for HDAC3 (3 control and 3 KO, and corresponding inputs); and transcriptome profiling through RNA-seq of control mouse islets and those lacking histone deacetylase 3 (two separate experiments, n=3 an n=5)
Platform: GPL13112
28123935
GSE95029 The developmental and metabolic roles of the diabetes candidate gene TCF7L2 in adipose tissue Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Type 2 Diabetes DOID:9352 19
  • shRNA - Tcf7l2 4 d
  • shRNA - Scrambled 0 d
  • shRNA - Scrambled 8 d
  • shRNA - Tcf7l2 6 d
  • shRNA - Scrambled 2 d
  • shRNA - Tcf7l2 0 d
  • shRNA - Scrambled 4 d
  • shRNA - Tcf7l2 2 d
  • shRNA - Tcf7l2 8 d
  • shRNA - Scrambled 6 d
 02/17/2017
For the identification of genes regulated during adipogenesis by Tcf7l2, Tcf7l2 was silenced in murine 3T3-L1 preadipocyte cells using lentivirally delivered stable silencing of Tcf7l2 with a scrambled shRNA as control. Sampling times were at 0, 2, 4, 6, and 8 days of differentiation. RNA-seq timecourse was performed in duplicate.
Platform: GPL13112
29317436
GSE95283 Estrogen signaling and fatty liver disease Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Gene KO Focus 11
  • aERKO (Esr1-/-)
  • Wildtype
 02/23/2017
The liver tissue was collected from high-fat diet fed and regular diet fed WT and aERKO females for RNA extraction and hybridization on Affymetrix microarrays.
Platform: GPL1261
28220039
GSE95595 Successful transplantation of islets into inguinal subcutaneous white adipose tissue Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 11
  • Transplanted islet day 120
  • Transplanted islet day 60
  • Isolated islet
 03/01/2017
Gene expression of was observed before and after islet translplantation
Platform: GPL18480

N/A
GSE100067 The islet resident macrophage is in an inflammatory state and senses microbial products in blood Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 18
  • Lung macrophages
  • control
  • Pancreatic LN Dendritic Cells
  • NOD.Rag1-/- (NOD.129S7(B6)-Rag1tm1)
  • B6.g7 B6.NOD-(D17Mit21-D17M)
 06/15/2017
We examined the transcriptional profiles of macrophages that reside in the islets of Langerhans of NOD, NOD.Rag1-/-, and B6.g7 mice at three weeks of age. Lung macrophages and pancreatic LN dendritic cells of NOD mice were also examined.
Platform: GPL17021
28630088
GSE101537 Neurog3-Cre p300/CBP mouse islets RNA-seq Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 14
  • Triallelic
  • CBP KO
  • control
  • p300 KO
 07/17/2017
Six WT, three p300IsletKO, three CBPIsletKO and three CBPHet; p300KO samples were sequenced in two batches at UBC Biomedical Research Centre Sequencing Core. Each library was sequenced to a depth of at least 20 million paired end reads on a NextSeq 500 (Illumina, CA, USA).
Platform: GPL19057
29217654
GSE101657 Gene expression changes in ketogenic and high-fat diets Mus musculus Expression profiling by high throughput sequencing Not Specified Healthy: Diet Focus 17
  • Kindey High-Fat Diet
  • Liver High-Fat Diet
  • Liver Control Diet
  • Liver Ketogenic Diet
  • Kindey Control Diet
  • Kindey Ketogenic Diet
 07/19/2017
Control diet N=5, high-fat diet N=6, ketogenic diet N=7. Pairwise comparisons between all three conditions. These gene expression studies were carried out on 12 month-old male C56BL/6 mice from the NIA Aged Rodent Colony, habituated to AIN-93M control diet and then either maintained on this diet or switched for one week to a 75% kcal fat non-ketogenic high-fat diet or a 90% kcal fat ketogenic diet (all diets with 10% kcal from carbohydrates). Tissues were harvested in the middle of the nighttime feeding period (MN-3am).
Platform: GPL13112

N/A
GSE101722 Inhibition of 12/15-Lipoxygenase Protects Against β Cell Oxidative Stress and Glycemic Deterioration in Mouse Models of Type 1 Diabetes Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 11
  • ML351
  • ML351 + Proinflammatory cytokine cocktail
  • control
  • Proinflammatory cytokine cocktail
 07/20/2017
RNA-seq of Mouse islets treated with vehicle, Proinflammatory cytokine cocktail, and/or ML351 for 24 hours
Platform: GPL21103
28842399
GSE102137 FOXO in mouse brain Mus musculus Expression profiling by array Brain BTO:0000142 Healthy: Gene KO Focus 16
  • FOXO 1/3/4 Knockout
  • Wildtype
 08/01/2017
Total RNA was isolated and analyzed
Platform: GPL1261
29178390
GSE106295 Transcriptome of cardiac tissue from WT mice, cardiac macrophages depleted mice, and mice deficient for Mertk and LxR Mus musculus Expression profiling by high throughput sequencing Heart BTO:0000562 Healthy: Gene KO Focus 10
  • LxRαβ DKO
  • Mertk-KO
  • control
  • cTMs Depleted
 10/27/2017
Standard RNA extraction procedures were performed in whole cardiac tissue from those mice.
Platform: GPL17021

N/A
GSE108609 RNA Sequencing Analysis of Control and Blnc1 liver specific knockout mice (LKO) Liver Transcriptomes after 24 weeks NASH diet feeding Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Nonalcoholic Steatohepatitis (NASH) 5
  • Ctrl
  • Blnc1 liver-specific knockout
 12/28/2017
Liver mRNA profiles of control and Blnc1 liver specific knockout mice after 24 weeks NASH diet feeding were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.
Platform: GPL17021
30061575
GSE109285 Pancreatic Islet-Autonomous Signals Modulate Identity Changes of Glucagon+ α-Cells Mus musculus Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 22
  • alpha Cells Ectopically Expressing PDX1
  • alpha Cells Expressing PDX1
  • alpha Cells 30 Days after DT
  • control
 01/17/2018
RNA-Seq analyses on five purified cells namely, mature α-cells, mature β-cells, α-cells 30 days after DT, α-cells ectopically expressing PDX1 and α-cells expressing PDX1
Platform: GPL13112

N/A
GSE110528 Effect of LXR agonist T0901317 on the intestinal transcriptome in mice. Mus musculus Expression profiling by high throughput sequencing Small Intestine BTO:0000651 Healthy: Treatment Focus 6
  • control
  • Synthetic LXR ligand T0901317
 02/13/2018
7 male mice (C57BL/6J): 4 vehicle and 3 T09 treated, RNAseq analysis of the duodenum
Platform: GPL17021

N/A
GSE110569 Hepatic phosphorylation of transcription factor SREBP-1a interferes with gene regulation and peroxisomal function Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Gene KO Focus 23
  • alb-SREBP-1a
  • control
  • alb-SREBP-1a∆P
 02/13/2018
C57Bl6 (C57Bl6), C57Bl6-TgN alb-HA-hSREBP-1a-NT (alb-SREBP-1a) and C57Bl6-TgN alb-HA-hSREBP-1a∆P-NT (alb-SREBP-1a∆P) [Kotzka et al. PLoS One. 2012;7(2):e32609. doi: 10.1371/journal.pone.0032609] mice were bred and maintained under standard conditions to until alb-SREBP-1a mice develop fatty liver and adipositas phenotype (24 weeks of age).
Platform: GPL6246
29587401
GSE112213 Next Generation Sequencing of LdlrKO LXRα-phosphorylation disrupted macrophage transcriptomes Mus musculus Expression profiling by high throughput sequencing Bone BTO:0000140 Healthy: Gene KO Focus 5
  • WT no ligand
  • Ldlr KO + ligand
  • WT + ligand
  • Ldlr KO control
  • Ldlr KO no ligand
 03/22/2018
BMDM mRNA profiles of either LdlrKO or M-LXRα-S196A-LdlrKO male mice after being fed a Western diet for 12 weeks. 12 samples, 4 groups, in triplicate: (1) LdlrKO basal, (2) LdlrKO+ ligand, (3) M-LXRα-S196A-LdlrKO basal, (4) M-LXRα-S196A-LdlrKO+ligand
Platform: GPL19057
29950315
GSE120429 AMPK activation protects against diet induced obesity through Ucp1-independent thermogenesis in subcutaneous white adipose Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 23
  • D316A Transgenic Genotype
  • Wildtype
 09/25/2018
Whole subcutaneous white adipose tissue mRNA profiles were generated from mice fed either chow or 45% high-fat diet.
Platform: GPL19057
30887000
GSE122348 Glucagon receptor blocked liver gene signature Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Obesity DOID:9970 22
  • Glucagon Receptor Blocking Antibody REGN1193
  • Isotype Control Antibody
 11/08/2018
C57BL/6J male mice that had been on regular chow or high fat diet for 4 months were administered with glucagon receptor blocking antibody REGN1193 or isotype control antibody at 10 mg/kg for 3 weeks.
Platform: GPL17021
30582457
GSE124621 PGRMC2 is an Intracellular Heme Chaperone Critical for Adipocyte Function Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 7
  • control
  • PGRMC2 Adipose Tissue Knockout
 01/03/2019
PolyA+ RNAseq profilling of Brown Adipose Tissue (BAT) isolated from wild-type and PGRMC2 adipose tissue knockout mice housed at 30°C
Platform: GPL17021
31748741
GSE124774 RNA-seq of diabetic or non-diabetic murine bone marrow derived macrophages (BMDM) Mus musculus Expression profiling by high throughput sequencing Blood BTO:0000089 Diabetes (Non-specific) DOID:0081062 23
  • control
  • LPS + IFNy
 01/07/2019
6 diabetic mice samples and 6 non-diabetic control mice samples were used. Each sample was split in half, one half submitted as a baseline, unstimulated control and the other was stimulated with LPS + IFNy.
Platform: GPL21103

N/A
GSE124944 A Glis3-CD133-Wnt signaling axis regulating the self-renewal of adult murine pancreatic progenitor-like cells in colonies/organoids Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • Glis3 knockdown
  • control
  • CD133 knockdown
 01/10/2019
Total RNAs were extracted from 3-week-old colonies (grown in Matrigel- and RSPO1-containing culture) treated with lenti-shRNAs against Glis3, CD133 or control. RNAseq analysis was conducted subseuqently.
Platform: GPL17021

N/A
GSE125637 Gene Expression in wild type and Atp7b-/- mice Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Gene KO Focus 11
  • Atp7b -/-
  • control
  • [Atp7b -/- with ZN]
 01/25/2019
Livers from 3-month old and wild type C57Bl/6 mice were isolated and processed for gene expression with four replicates.
Platform: GPL1261
31924743
GSE125682 Postprandial blood glucose and triglyceride metabolism govern bone marrow stem cell transcriptional regulation, premature aging and rejuvenation. Mus musculus Expression profiling by high throughput sequencing Blood BTO:0000089 Type 2 Diabetes DOID:9352 7
  • glucose+lipid (G+L)
  • glucose (G)
  • PBS control
 01/25/2019
We obtained LSK cells from G injected mice (G-LSK cells), GL injected mice (GL-LSK cells) and respective PBS injected control mice (cont-LSK cells), and carried out RNA sequence analysis (n = 2, for each).
Platform: GPL17021
34533398
GSE127056 Expression data from hypothalamic samples of WT mice fed normal diet vs high fat diet Mus musculus Expression profiling by array Brain BTO:0000142 Healthy: Diet Focus 8
  • High-Fat Diet (4 weeks)
  • High-Fat Diet (8 weeks)
  • control
 02/25/2019
Young adult WT mice fed either normal chow or a high fat diet were sacrificed and hypothalamic samples were isolated. RNA extraction and hybridization on Affymetrix microarrays was performed. We sought to compare the effects of the consumption of a high fat diet versus normal chow on the hypothalamus. We decided to compare either a short exposure to high fat diet (4 wks) or long exposure (8 wks) to mice fed a normal chow.
Platform: GPL6246
31076569
GSE127251 Transcriptome differences between white and brown adipose tissue from wildtype and uncoupling protein 1 knockout mice exposed to different diets and ambient temperatures Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 47
  • UCP1 KO BAT
  • UCP1 KO WAT
  • Wildtype WAT
  • Wildtype BAT
 02/27/2019
Male C57BL/6J mice of wildtype or Ucp1-KO genotype were fed a high fat diet (48% energy from fat) or control diet (13% energy from fat) at thermoneutrality (30°C). Control diet was also fed at 20°C, resulting in a total of 6 groups of 8 animals each. After 4 weeks, we prepared interscapular brown adipose tissue and inguinal white adipose tissue, resulting in 96 samples. Of these, we sequenced total RNA and determined transcript abundance.
Platform: GPL17021
31714796
GSE128361 Hepatic transcriptomics reveals that lipogenesis is a key signaling pathway in isocitrate dehydrogenase 2 deficient mice Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: Gene KO Focus 11
  • Wildtype
  • Knockout Idh2-/-
 03/15/2019
Hepatic mRNA profiles of wild type (WT) and Idh2-/- mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.
Platform: GPL17021
31546946
GSE128945 The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 5
  • BetaDKO
  • control
 03/27/2019
Comparison of TdTomato flow-sorted Swi/Snf-deficient islet β cells to those from TdTomato flow-sorted control islet β cells
Platform: GPL24247

N/A
GSE129020 RNA sequencing of wildtype and PHOSPHO1 knockout brown fat Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 5
  • control
  • PHOSPHO1 knockout
 03/29/2019
Examine gene expression of two type of cells (WT and KO). Each sample is from 3 mice and each type of cells has triplicates (WT1-3 and KO1-3).
Platform: GPL17021
32554489
GSE129369 SMRT regulates metabolic homeostasis and adipose tissue macrophage phenotypes in tandem Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 7
  • adSMRT-/- (adipocyte-specific SMRT knockout)
  • Wildtype
 04/04/2019
RNA sequencing on 20-week old high-fat diet-fed mice was conducted on a total of 8 mouse perigonadal whole adipose tissue samples, which were collected from either wildtype or knockout age- and weight-matched mice (4 mice/genotype). Following sample homogenization, RNA was collected using a commercially available kit (E.Z.N.A Total RNA Kit, Omega Bio-Tek, GA) per manufacturer's instructions. Samples were then prepared for RNAseq on the Illumina HiSeq4000 platform, and provided to the University of Chicago's Center for Research Informatics core for sequencing.
Platform: GPL21103

N/A
GSE130979 CCL21 Expression in Beta Cells Induces Antigen-Expressing Stromal Cell Networks in the Pancreas and Prevents Autoimmune Diabetes in Mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 1 Diabetes DOID:0110743 26
  • Ins2-CCL21 NOD
  • NOD/ShiLtJ
 05/09/2019
Examination of lymph node derived Fibroblastic Reticular Cells (FRCs), FRC-like cells from pancreatic islets and islet infiltrating leukocytes in both Ins2-CCL21 transegnic NOD (TG+ samples) and non-transgenic NOD (TG- samples) mice
Platform: GPL21493
31371518
GSE134327 Arctigenin attenuates diabetic kidney disease through the activation of PP2A in podocytes Mus musculus Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 11
  • Control, ATG-treated
  • Streptozotocin, 5% DMSO vehicle-treated
  • Control, ATG treated
  • Streptozotocin, ATG-treated
  • Control, 5% DMSO vehicle-treated
 07/16/2019
To elucidate the underlying mechanism of renoprotection conferred by ATG in DKD, we performed the RNA sequencing of isolated glomeruli from the diabetic and control eNOS-/- mice treated with ATG or vehicle. Diabetes was induced in 8-week old mice with intraperitoneal administration of streptozotocin (STZ, Sigma S0130, dissolved in 0.1 M citrate buffer, PH 4.5) at 50mg/kg after 4-6 hours of food deprivation each day for 5 consecutive days. Citrate buffer-injected mice served as nondiabetic controls. 10 weeks after diabetes induction, mice were given ATG (Cayman Chemicals) dissolved in 5% DMSO by oral gavage at a dose of 40mg/kg body weight/day for 8 weeks. 5% DMSO vehicle-treated mice served as controls.
Platform: GPL17021
31586053
GSE134846 An insulin-stimulated proteolytic mechanism links energy expenditure with glucose uptake Mus musculus Expression profiling by high throughput sequencing Muscle BTO:0000887 Diabetes (Non-specific) DOID:0081062 5
  • mTUGUBX-Cter Genotype
  • Wildtype
 07/25/2019
Examination of gene expression differences between wiltype mice and transgenic mice with constitutive, insulin-independent TUG cleavage in muscle
Platform: GPL17021
33686286
GSE135391 Transcriptome analysis of brown fat in young or old mice in cold exposure Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Treatment Focus 8
  • BAT in Old mouse
  • BAT in Young mouse
 08/05/2019
Five young (3 months) male mice were exposed to cold room (4°c); five young male mice were exposed to room temperature (24°c); four old (24 months) male mice were expposed to cold room (4°c); five old male mice were exposed to room temperature. After 24 hours for exposure, mice were sacrificed and BAT was extracted from between the shoulder blades.
Platform: GPL13112
32795388
GSE136396 RNASeq of cold-sensitive and cold-insensitive neurons from the pre-optic area of hypothalamus of mice Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Healthy: Treatment Focus 5
  • Cold-Insensitive
  • Cold-Sensitive
 08/27/2019
~100-200 individual cold-sensitive or cold-insensitive neurons from the POA of mouse hypothalamus were collected and pooled together for 1 sample. RNA was isolated from samples and high-throughput deep sequencing of the RNA performed. The study included 3 biological replicates of each type, with a total of 6 samples.
Platform: GPL17021
32270761
GSE137060 Hltf-deletion activates an IL33/β cell-CD8+T cell axis that triggers neonatal death Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • beta cell specific Hltf-/-
  • control Hltf +/+
 09/08/2019
We previously used RNA-seq in conjunction with 3SEQ/transcriptome to quantify expression levels in brain (14), heart (15), and placenta (7). RNase levels in pancreas are 181,000-fold higher than brain (https://www.thermofisher.com/us/en/home/references/ambion-tech-support/nuclease-enzymes/tech-notes/rnase-activity-in-mouse-tissue.html). As a result, isolation of total RNA was highly variable. Total RNA (n=47 samples) was isolated, its integrity and purity were assessed (Agilent Bioanalyzer). Ultimately pancreata (n=6 samples; 3 test (Hltf rIPCre fl/fl with low (<15 mg/dL) blood sugar, and 3 Hltf +/+ euglycemic controls) perfused in situ with RNAlater (21) using a 1 CC syringe and a 26g ½ needle, and snap frozen were suitable (Table 2) for rRNA-depletion. cDNA was generated from rRNA-depleted samples and subjected to Illumina library preparation. Libraries were sequenced utilizing Illumina sequencing technology. Paired-end 100 nucleotide reads were aligned to genomic assembly mm10 and analyzed using the platform provided by DNAnexus, Inc. (Mountain View, CA) to generate an unbiased gene expression analysis report of RNA-seq; alternative splicing analysis of Hltf; mutation/RNA-editing analysis and parallel comparison of expression profiles between β cell-specific Hltf-deleted pancreata and control pancreata. The power in detecting alternative splicing was dramatically increased by paired-end sequencing relative to single-end sequencing. FPKM (fragments per kilobase of transcript per million mapped reads) were mapped against mm10 with Tophat (V1.3.3) to obtain .bam mapping files that were input into Cufflinks for transcript assembly. Cuffdiff (V 1.3.0), part of the Cufflinks package, used the alignment reads for rigorous statistical comparison of two conditions (β cell-specific Hltf-deleted and wild type control pancreata) and 3 biological replicates for each condition. The depth of sequencing was a minimum of 20 million sequencing reads per sample [90% Power, 5% significance level: 91+/- 4% of all annotated genes are sequenced at a frequency of 0.1 times/103 bases X 3 x 109 bases/sequencing read x 3 samples = 9 x104 reads/gene]. Data were imported into iPathwayGuide (Advaita Corporation) a next-generation pathway analysis tool. Standard enrichment parameters (log fold change, logFC = 0.6, p<0.05) were used.
Platform: GPL17021

N/A
GSE137149 Adipose tissue NAD+ biosynthesis is required for regulating adaptive thermogenesis and whole-body energy homeostasis in mice Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 7
  • Adipocyte-specific Nampt knockout
  • control
 09/09/2019
We analzyed BAT obtained from 4 control mice and 4 ANKO mice.
Platform: GPL21493
31694884
GSE137187 Klf6 protects β-cells against insulin resistance-induced dedifferentiation Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 27
  • βKlf6KO
  • Ctrl
 09/10/2019
Islet transcriptomic analysis, searching for genes differentially expressed between Ctrl and βKlf6KO mouse islets in saline or S961 treated mice. 12 mice were treated with saline (6 Ctrl and 6 βKlf6KO mice), and 16 with S961 (8 Ctrl and 8 βKlf6KO mice)
Platform: GPL17021
32244185
GSE137678 STAT5 is required for lipid breakdown and beta-adrenergic responsiveness of brown adipose tissue Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 9
  • control
  • Stat5-Adipoq
 09/18/2019
Wildtype and Stat5Adipoq, 5 replicates per condition
Platform: GPL21493
32473405
GSE138782 Gene expression profiles of PGAM5-knockout brown adipose tissue Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 6
  • PGAM5 Knockout
  • control
 10/11/2019
Tissue samples were collected from 10-week-old male mice, and RNA samples derived from 3 (WT) or 4 (PGAM5 KO) individuals were analyzed.
Platform: GPL21103

N/A
GSE140678 Cardiac specific deletion of natriuretic peptide receptor A induces different myocardial expression of circular RNA and mRNA involved with metabolism in mice Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: Gene KO Focus 9
  • NPRA-/-: myocardium-specific deletion of NPRA
  • control
 11/19/2019
The cardiac expressing mRNA profiles in the C57BL/6 mice (NPRA+/+) and C57BL/6 mice with myocardium-specific deletion of NPRA (NPRA-/-) were sequenced by Illumina HiSeq instrument, and differently expressed mRNAs were detected. Then,a high throughout screening for the different expression of circRNAs between the NPRA-deficient mice and the matched littermates.
Platform: GPL21103
33200806
GSE140953 Expression data from brown adipose tissue of DBA/2 Ahsg -/- and WT mice Mus musculus Expression profiling by array Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 11
  • Wiltype
  • Ahsg Knockout
 11/25/2019
Animals were perfused with 20 ml ice-cold PBS to rinse blood from the circulation unless otherwise stated. RNA was extracted from pelvic brown adipose tissue.
Platform: GPL1261

N/A
GSE142209 RNA-seq of human and mouse brain microvessels isolated by laser capture microdissection and matched whole brain samples Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Healthy: Treatment Focus 5
  • Brain Microvessels
  • Whole Brain
 12/17/2019
A total of 12 samples were analyzed: 6 mouse samples and 6 human samples. For each species, there are 3 biological replicates of brain microvessels isolated by laser capture microdissection, and 3 matched whole brain controls.
Platform: GPL11154
32704093
GSE143818 Estrogen receptor alpha signaling establishes a sexually dimorphic regulatory node of energy expenditure Mus musculus Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Healthy: Gene KO Focus 5
  • Female
  • Male
 01/16/2020
Single cell RNA sequencing of cells in the mouse ventromedial hypothalamus. N = 3 male and 3 female mice sacrificed on post-natal day 10, and FACS purified
Platform: GPL16417

N/A
GSE144061 Transcriptomics of FGF6-stimulated mouse brown preadipocytes Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 5
  • control 8hr
  • control 24hr
  • FGF6 24hr
  • FGF6 8hr
  • control 4hr
  • FGF6 4hr
 01/22/2020
Immortalized murine brown preadipocytes were treated with vehicle or FGF6 for 4, 8, and 24 hours. Total RNA was isolated using Direct-zol™ RNA miniprep Kits (Zymo Research, Irvine, CA). High-throughput sequencing was performed using a HiSeq 4000 instrument (Illumina) at BGI Americas.
Platform: GPL21103
32184391
GSE144953 Retinoic acid signaling within pancreatic endocrine progenitors regulates mouse and human pancreatic islet cell specification Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • Neurog3:cre;RARdnfl/fl
  • Neurog3:cre alone
 02/07/2020
e16.5 pancreas RNA-seq from Neurog3:cre alone (n=3) and Neurog3:cre;RARdnfl/fl (n=3)
Platform: GPL24247
32467243
GSE145070 RNA-seq analysis of Control and BSCL2-deleted mature brown adipose tissue in mice Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 5
  • Bscl2f/f Ucp1Cre (BKO)
  • Bscl2f/f
 02/10/2020
Brown fat mRNA profiles of 10 week old 10 week old male Bscl2f/f (Ctrl) and Bscl2f/f Ucp1Cre (BKO) were generated by deep sequencing, in triplicate, using Illumina 2000.
Platform: GPL13112
32246911
GSE145202 Deletion of brain-specific isoforms of adapter protein SH2B1 protects mice from obesity in a non-leptin-mediated manner Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Healthy: Gene KO Focus 20
  • SH2B1adKO
  • control
 02/12/2020
Hypothalamus mRNA was sequenced from control (WT, n = 9) and mutant mice lacking alpha/delta isoforms of Sh2b1 (SH2B1adKO, n = 12) to identify genes differentially expressed in mutant animals.
Platform: GPL24247
33214137
GSE146543 Estrogen receptor-α expressing neurons in the ventrolateral VMH regulate glucose balance Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Healthy: Gene KO Focus 7
  • Glucose-Excited (GE-ERαvlVMH) Neurons
  • Glucose-Inhibited (GI-ERαvlVMH)
 03/06/2020
Genetically identified single ERα neurons in the vlVMH were first tested for glucoses-sensing features, and then subjected to RNA-seq analyses. Differentially expressed genes were validated through multiple functional assays.
Platform: GPL17021

N/A
GSE148997 Alleviating FGF19's tumorigenic risk by suppressing its FGF Receptor dimerization ability Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Type 2 Diabetes DOID:9352 8
  • FGF19ΔKLB
  • FGF19WT
  • control
 04/21/2020
Lver tissues of db/db mice treated with PBS, FGF19WT, or FGF19ΔKLB for 12 weeks were collected. Total RNA was extracted using the TRIzol reagent (Invitrogen) and analyzed using a Bio-analyzer 2100 and an RNA 6000 Nano Lab Chip Kit
Platform: GPL21103
33144503
GSE149468 Multi-organ transcriptomic profiling of short-term fasted mice Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Diet Focus 17
  • perigonadal white adipose tissue 12h
  • brainstem 0h
  • olfactory bulb 0h
  • perigonadal white adipose tissue 0h
  • liver 22h
  • posterior-subcutaneous white adipose tissue 18h
  • brain 2h
  • olfactory bulb 12h
  • cerebellum 2h
  • brainstem 12h
  • interscapular brown adipose tissue 8h
  • brain 8h
  • cerebellum 8h
  • brainstem 18h
  • stomach 8h
  • posterior-subcutaneous white adipose tissue 0h
  • interscapular brown adipose tissue 2h
  • stomach 18h
  • perigonadal white adipose tissue 18h
  • interscapular brown adipose tissue 12h
  • liver 8h
  • brainstem 2h
  • brainstem 8h
  • liver 2h
  • liver 18h
  • posterior-subcutaneous white adipose tissue 22h
  • brain 18h
  • brain 12h
  • stomach 22h
  • brainstem 22h
  • liver 0h
  • olfactory bulb 18h
  • brain 22h
  • posterior-subcutaneous white adipose tissue 2h
  • cerebellum 18h
  • olfactory bulb 8h
  • cerebellum 22h
  • interscapular brown adipose tissue 18h
  • cerebellum 12h
  • olfactory bulb 22h
  • stomach 12h
  • stomach 2h
  • perigonadal white adipose tissue 8h
  • olfactory bulb 2h
  • liver 12h
  • interscapular brown adipose tissue 22h
  • perigonadal white adipose tissue 2h
  • cerebellum 0h
  • stomach 0h
  • posterior-subcutaneous white adipose tissue 8h
  • posterior-subcutaneous white adipose tissue 12h
  • interscapular brown adipose tissue 0h
  • perigonadal white adipose tissue 22h
  • brain 0h
 04/27/2020
mRNA profiling of nine organs obtained from wild type (WT) mice subjected to six different short term fasting duration
Platform: GPL21103
32526449
GSE149662 Muscle Specific Insulin Receptor Overexpression Protects Mice from Diet-Induced Glucose Intolerance but Leads to Post-Receptor Insulin Resistance Mus musculus Expression profiling by high throughput sequencing Skeletal Muscle BTO:0001103 Type 2 Diabetes DOID:9352 11
  • Control
  • IRMOE
 04/30/2020
Male mice were used for studies unless indicated. Mice transgenic for loxP-stop-loxP insulin receptor (LSL-IR) were generated through pronuclear injection of a linearized cassette carrying mouse IR isoform A cDNA driven by CAG promoter and interrupted by a floxed beta-gal cDNA and a stop codon. IRMOE mice were then generated by crossing the LSL-IR mice with mice carrying a Cre transgene driven by the human skeletal muscle actin (HSA) promoter. Muscle RNA of Control or IRMOE mice was extracted by homogenizing tissues in TRIzol, treating with chloroform, and precipitating in 70% ethanol. cDNA was made using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, catalog 4368813). RNA-seq libraries were made and sequencing was performed on an Illumina NextSeq 500.
Platform: GPL19057
32868340
GSE150679 RNA-seq analysis of gestationally Cd-exposed hepatic transcriptome Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: Gene KO Focus 15
  • Post natal day 1 Control
  • Post natal day 21 CdCl2 Exposure
  • Post natal day 21 Control
  • Post natal day 42 Control
  • Post natal day 42 CdCl2 Exposure
  • Post natal day 1 CdCl2 Exposure
 05/15/2020
Examination of three different timepoints and one exposure group
Platform: GPL17021
33259630
GSE151030 Gene expression effects of PPAR-gamma serine 273 to alanine knock-in mutation in epididymal white adipose tissue Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 7
  • S273A Genotype
  • Wildtype
 05/21/2020
Overnutrition and obesity promote adipose tissue dysfunction, often leading to systemic insulin resistance. The thiazolidinediones (TZDs) are a potent class of insulin-sensitizing drugs and ligands of PPAR-gamma that improve insulin sensitivity, but their use is limited due to significant side effects. Recently, we demonstrated a mechanism by which TZDs improve insulin sensitivity distinct from receptor agonism and adipogenesis: reversal of obesity-linked phosphorylation of PPAR-gamma at Serine 273. However, the role of this modification has not been tested genetically. Here we demonstrate that mice encoding an allele of PPAR-gamma which cannot be phosphorylated at S273 are protected from insulin resistance, without exhibiting differences in body weight or TZD-associated side effects. Indeed, hyperinsulinemic-euglycemic clamp experiments confirm improved insulin sensitivity, as evidenced by increased whole-body glucose uptake. RNA-seq experiments reveal PPAR-gamma S273 phosphorylation specifically enhances transcription of Gdf3, a BMP family member. Ectopic expression of Gdf3 is sufficient to induce insulin resistance in lean, healthy mice. We find that Gdf3 can impact metabolism by inhibition of BMP signaling. Together, these results highlight the diabetogenic role of PPAR-gamma S273 phosphorylation and focuses attention on a putative target, Gdf3.
Platform: GPL19057
32941798
GSE152576 Sexually dimorphic roles for the type 2 diabetes-associated C2cd4b gene in murine glucose homeostasis Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 8
  • control
  • C2CD4B KO
 06/16/2020
C2cd4b-null mice (C2cd4bem2Wtsi) were generated at the International Mouse Phenotyping Consortium (IMPC), using CRISPR/Cas9. RNA from pacreatic islets was isolated and
Platform: GPL21103
33492421
GSE153222 Temporal Transcriptomic Landscape of Interorgan Crosstalk between Islets and Liver in High-fat Diet Model Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 7
  • Chow Diet 24 weeks
  • Chow Diet 12 weeks
  • Chow Diet 4 weeks
  • Chow Diet 20 weeks
  • High Fat Diet 20 weeks
  • High Fat Diet 24 weeks
  • High Fat Diet 16 weeks
  • High Fat Diet 4 weeks
  • High Fat Diet 12 weeks
  • Chow Diet 8 weeks
  • High Fat Diet 8 weeks
  • Chow Diet 16 weeks
 06/25/2020
Islet and liver mRNA profiles of C57BL/6N mice fed a 60% HFD or CD for 24 weeks (including 48 islets samples and 48 liver samples, quadruplicates for each group and each time point)
Platform: GPL23479
33817571
GSE155064 Gene expression profiling of Control and Low BCAA fed aged mouse muscle Mus musculus Expression profiling by high throughput sequencing Muscle BTO:0000887 Healthy: Diet Focus 23
  • Low-BCAA Diet
  • Control Diet
 07/24/2020
RNA-Seq experiments were conducted on total RNA isolated from quadriceps muscle of aged mice of both sexes fed a Control or Low BCAA diet until 16 months of age
Platform: GPL24247

N/A
GSE155612 The effects of METTL3 on islet β-cell function Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 5
  • Mettl3flox/flox
  • β-Mettl3-KO
 08/03/2020
mRNA profiles in pancreatic islets of Mettl3flox/flox and β-Mettl3-KO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).
Platform: GPL24247
33417895
GSE155973 Macrophage-derived thrombospondin1 promotes obesity-associated non-alcoholic fatty liver disease Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Non-alcoholic fatty liver disease (NALFD) DOID:0080208 11
  • WildtypeTSP1flox-1
  • Macrophage-Specific TSP1 Knockout
 08/10/2020
TSP1 floxed mice and macrophage specific TSP1 knockout mice were fed with LF or HF diet for 8 months. Then mie were sacrficed and livers were harvested for further analysis.
Platform: GPL23479
33294831
GSE156774 Regulation of islet function and gene expression by prolactin during pregnancy Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 6
  • pancreatic beta cells knockout
  • Whole-body knockout (all tissues)
 08/24/2020
A total of 7 samples were included. Heterozygous whole body knock-out mice (N=3) obtained from Jackson Laboratory were used as a reference to compare to conditional Plr deletion in beta pancreatic cells (n=4). (Pdx1CreERTM:PrlR-/- ). Breifly, the confitional ready lines (Tm1a) were obtained from EUCOMM (The European Conditional Mouse Mutagenesis Program) and generated by breeding with FLPeR mice (The Jackson Laboratories) (Tm1c) and then Pdx1CreERTM mouse (from Mutant Mouse Resource & Research Centers supported by NIH, Stock No.:000350-UCD) (Tm1d). At 3-4 months of age, heterozygous whole-body and homozyous conditionally deleted Plr knock-out mice were bred to wild-type males and islets were isolated at gestational day 15.
Platform: GPL21626
33990661
GSE158359 Intestinal FGF15/19 physiologically represses hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: Gene KO Focus 5
  • Vehicle
  • FGF19
 09/22/2020
Deep sequencing generated liver mRNA profiles in C57BL/6 mouse liver which was treated by vehicle or FGF19 for 6 hr after fasting overnight.
Platform: GPL13112
33235221
GSE160802 Therapeutic PYY/GLP-1 receptor co-agonism in obese-diabetic mice Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Diabetes (Non-specific) DOID:0081062 58
  • IP118/PY115
  • Vehicle
 11/04/2020
Gene expression profiles of brain regions in mice four hours following IP injection of a single acute systemic administration of IP118/PY115 or vehicle
Platform: GPL19057
34781035
GSE161693 Notch2 deficiency prevents muscle atrophy induced by mechanical unloading and diabetes. Mus musculus Expression profiling by high throughput sequencing Muscle BTO:0000887 Diabetes (Non-specific) DOID:0081062 23
  • 14 days after STZ injection
  • 7-days hindlimb suspension
  • Control
 11/18/2020
mRNA profiles of gastrocnemius muscle tissues obtained from WT and Notch2-mKO mice under unloading, diabetic, or control condition.
Platform: GPL24247
35228746
GSE162037 RNA Sequencing Analysis of wild type (WT) and Mrp4 knock out (Mrp4-/-) mice adipose tissue Transcriptomes Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Healthy: Gene KO Focus 7
  • Mrp4 Knockout (Mrp4-/-)
  • Wildtype
 11/23/2020
We have analysed white adipose tissue mRNA profiles of 16 week old wild type (WT) and Mrp4 knock out (Mrp4-/-) mice. In this experiment we have n=4 samples per genotype
Platform: GPL23479
33417247
GSE162493 Cardiac transcriptome in iron-deficiency anemia Mus musculus Expression profiling by high throughput sequencing Heart BTO:0000562 Anemia DOID:2355 19
  • Iron-Deficient Diet
  • Control Diet
 12/02/2020
Cardiac mRNA from control and iron-deficient anemic mice (males)
Platform: GPL21103
33553263
GSE178726 MYCL-mediated in vivo reprogramming expands pancreatic insulin-producing cells to reverse diabetes - RNA-Seq Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Diabetes (Non-specific) DOID:0081062 8
  • R26-M2-rtTA; Col-TetOP-c-Myc-ires-mCherry
  • R26-M2-rtTA; Col-TetOP-Mycl-ires-mCherry
 06/23/2021
For RNAseq in mouse liver, we transduced c-Myc or Mycl in 4-week-old adult mice for 48 hrs by intraperitoneal injection of Dox (0.2 ml; 2.0mg/mL). For the control, liver were harvested from no treatment Mycl inducible mice at 4wks(WT).
Platform: GPL21626

N/A
GSE111125 Therapeutic effects of Rosuvastatin in hypercholesterolemic prediabetic mice in the absence of low density lipoprotein receptor Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Diabetes (Non-specific) DOID:0081062 21
  • Rosuvastatin Western Diet
  • Rosuvastatin Chow diet
  • Placebo Chow diet
  • Placebo Western Diet
 02/26/2018
Gene expression profiling of mouse liver tissue from Rosuvastatin and placebo fed mice overexpressing IGF-II with a knock-out of LDL-receptor and expressing only ApoB100.
Platform: GPL13112
30508567
GSE121539 Acceleration of beta cell aging plays a key role in diabetes and senolysis improves metabolic, functional and cellular outcomes Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 14
  • positive
  • negative
 10/19/2018
Cells from dispersed islets of 7 month old male C57BL/6J mice were FACS sorted based on acidic beta-galactosidase activity and RNA was extracted using PicoPure Arcturus kit. Gene expression profiling was performed using HiSeq v4 SE50 250 mil reads by Hudson Alpha Institute for Biotechnology (Huntsville, AL). Reads were aligned to the mouse genome (GRCm38) using Subread and counted with featureCounts.
Platform: GPL17021
31155496
GSE124394 Role of p110a subunit of PI3-kinase in skeletal muscle mitochondria Mus musculus Expression profiling by high throughput sequencing Skeletal Muscle BTO:0001103 Type 2 Diabetes DOID:9352 29
  • Fed
  • Fast
 12/26/2018
All studies were performed in male mice on C57BL/6J background. Muscle-specific p110alpha or p11beta knockout mice were generated by crossing mice carrying the Cre recombinase gene driven by the human alpha-skeletal actin (HSA) promoter (Jackson Laboratories Stock Number: 006149) with mice carrying either floxed p110alpha or p110beta alleles in which exon 1 of p110alpha or exon 2 of p110bet was flanked with loxP sites. Skeletal muscle from 2-3-month-old male mice was harvested and RNA was extracted using Trizol. Gene expression profiling was performed using NEBNext mRNA Sample Prep Master Mix kit (NEB) by BioPolymers Facility at Harvard Medical School. Reads were aligned to the mouse genome (GRCm38) using STAR aligner and counted with Subread featureCounts.
Platform: GPL17021
31363081
GSE125387 Gut microbiota mediates intermittent-fasting alleviation of diabetes-induced cognitive impairment Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Diabetes (Non-specific) DOID:0081062 31
  • db/db
  • db/m
 01/21/2019
11 db/m mice,10 db/db mice,10 db/db-IF mice
Platform: GPL23479
32071312
GSE157798 Removal of visceral adipose tissue prevents obesity-induced multi-organ insulin resistance, dyslipidemia, and NAFLD in mice Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Type 2 Diabetes DOID:9352 20
  • VAT-R
  • Sham
 09/10/2020
We evaluated the effects of epididymal visceral adipose tissue (VAT) removal on liver and subcutaneous adipose tissue (SAT) gene expression profiling under a high-fat diet condition (n=5 per group).
Platform: GPL24247
33869980
GSE159882 Targeting methylglyoxal in diabetic kidney disease using the novel mitochondria-targeted compound MitoGamide Mus musculus Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 40
  • non-diabetic ethanol vehicle
  • diabetic water vehicle
  • non-diabetic MitoQ (water vehicle)
  • diabetic ethanol vehicle
  • diabetic MitoGamide (ethanol vehicle)
  • diabetic MitoQ (water vehicle)
  • non-diabetic MitoGamide (ethanol vehicle)
  • non-diabetic water vehicle
 10/22/2020
Heterozygous Ins2-Akita mice (C57BL/6J-Ins2Akita) and their wild type littermates underwent treatment with mitoGamide or mitoQ or their respective vehicle controls at 6 weeks of age via oral gavage. The treatment was continued until mice were 22 weeks of age, at which time the kidneys were harvested and renal cortex tissue underwent RNA extraction and sequencing. Only male mice were used.
Platform: GPL17021
33922959
GSE186971 Dietary curcumin ameliorates perturbed insulin homeostasis in the diet-induced obese aged mice Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Type 2 Diabetes DOID:9352 12
  • NCD Supplemented with Curcumin (NCD_Cur)
  • HFHSD Supplemented with Curcumin (HFHSD_Cur)
  • Normal Control Diet (NCD)
  • High Fat High Sugar Diet (HFHSD)
 11/02/2021
Hepatic mRNA profiles of 83-91 weeks old NCD, NCD+CUR, HFHSD, HFHSD+CUR supplemented mice
Platform: GPL24247
35017319
GSE202418 Retinol Dehydrogenase 10 Reduction Mediated Retinol Metabolism Disorder Promotes Diabetic Cardiomyopathy Mus musculus Expression profiling by high throughput sequencing Heart BTO:0000562 Type 2 Diabetes DOID:9352 8
  • db/db
  • db/+
 05/06/2022
Comparative gene expression profiling analysis of RNA-seq data for db/m and db/db miceat 4, 24, and 32 weeks of age.
Platform: GPL17021
36864033
GSE202935 Accumulation of auranofin in white adipose tissues lowers leptin levels and exerts anti-diabetic effects Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Type 2 Diabetes DOID:9352 32
  • auranofin
  • vehicle
 05/13/2022
Comparative gene expression profiling analysis of RNA-seq data for liver, epididymal and inguinal white adipose tissue, and intrascapular brown adipose tissue from C57Bl/6 mice. Mice were ffed 60% HFD diet for 12 weeks before receiving vehicle or auranofin (1 mg/kg BW) 3 times per week for 4 weeks.
Platform: GPL24247
36243005
GSE210401 Effect of deletion of von-Hippel-Lindau (VHL) in the proximal tubule in diabetic kidney disease Mus musculus Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 9
  • VHL knockout
  • WT
 08/03/2022
We then performed gene expression profiling analysis using data obtained from RNA-seq of control mice and proximal tubular-specific VHL-deletion mice with and without STZ-treatment (induction of diabetes mellitus).
Platform: GPL24247

N/A
GSE211749 Gene expresssion analysis in liver and white adipose tissues from miR-322-503-351 knock out mice. Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Type 2 Diabetes DOID:9352 12
  • global miR-322-503-351 deleted
  • wild type
 08/22/2022
We then performed gene expression profiling analysis using data obtained from RNA-seq of liver and WAT from 52-week-old WT and KO mice.
Platform: GPL24247

N/A
GSE214089 HBP1 inhibits the development of type 2 diabetes mellitus through transcriptional activation of the IGFBP1 gene Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Type 2 Diabetes DOID:9352 6
  • KO-HBP1
  • WT
 09/23/2022
Comparative gene expression profiling analysis of RNA-seq data for mouse liver tissue and its KD derivatives (KO-HBP1).
Platform: GPL17021

N/A
GSE217145 Gut microbial DNA and immune checkpoint gene Vsig4/CRIg are key antagonistic players in healthy aging and age-associated development of hypertension and diabetes Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Diabetes (Non-specific) DOID:0081062 6
  • WT
  • CgA KO
 11/02/2022
Comparative gene expression profiling of WT and CgA-KO mouse liver tissue by high throughput sequencing.
Platform: GPL24247
36440192
GSE217153 Deficiency of CFB attenuates renal tubulointerstitial damage via inhibiting ceramide synthesis in diabetic kidney disease Mus musculus Expression profiling by high throughput sequencing Kidney BTO:0000671 Diabetes (Non-specific) DOID:0081062 14
  • Healthy control
  • Diabetic kidney disease
 11/03/2022
Comparative gene expression profiling analysis of RNA-seq data for Cfb knockout mice (STZ/HFD induced diabetic Cfb knockout mice and non-diabetic Cfb knockout mice) and its wide type control (diabetic mice and non-diabetic mice).
Platform: GPL17021
36546481
GSE138419 Neutralization of Oxidized Phospholipids Restrains Nonalcoholic Steatohepatitis Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Nonalcoholic Steatohepatitis (NASH) 11
  • AMLN
  • Chow
 10/04/2019
Bulk RNA-Seq of RNA isolated from Ldlr-/- or E06-scFvLdlr-/- mice fed AMLN diet.
Platform: GPL21103
31761566
GSE112002 Expansion of Islet-Resident Macrophages Leads to Inflammation Affecting Beta Cell Proliferation and Function in Obesity Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 9
  • High fat diet
  • Normal chow diet
 03/19/2018
RNA-Seq of F480 Hi and CD11c Hi Islet macrophages in nomal chow diet and high fat diet fed mice
Platform: GPL19057
30595478
GSE131613 The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress [Mus musculus] Mus musculus Expression profiling by high throughput sequencing Embryonic fibroblast BTO:0004725 Healthy: Gene KO Focus 12
  • Dox
  • DMSO
 05/22/2019
Wild-type and CBP/p300 KO MEFs treated with or without Dox
Platform: GPL23479
33718883
GSE173256 Increased cardiac fatty acid oxidation in a mouse model with decreased malonyl-CoA sensitivity of CPT1B Mus musculus Expression profiling by high throughput sequencing Heart BTO:0000562 Healthy: Gene KO Focus 13
  • E3A/E3A
  • WT/E3A
  • WT/WT
 04/25/2021
13 samples from heart (4 WT, 4WT/E3A and 5 E3A/E3A) were analyzed
Platform: GPL17021
29635338
GSE193888 Notch-mediated Ephrin signaling disrupts islet architecture and β cell function Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 8
  • RIP-Cre+, Rosa26-rtTA+, tetO_NICD+
  • RIP-Cre+, Rosa26-rtTA+, tetO_NICD-
 01/18/2022
RNA-seq of pancreatic islets from beta cell NICD-gain of function model
Platform: GPL24247
35167496
GSE194321 Sex- and age-dependent genetics of longevity in a heterogeneous mouse population Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: Age Focus 34
  • Female 6months
  • Male 6months
  • Male 22months
  • Female 22months
 01/25/2022
RNA sequencing of livers of male and female UM-HET3 mice at two ages, 6 months and 22 months.
Platform: GPL23479
36173858
GSE195479 The Slc25a47 locus is a novel determinant of hepatic mitochondrial function implicated in liver fibrosis Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: Gene KO Focus 16
  • Overnight fasting
  • Fed state (Chow diet)
 01/26/2022
Hepatic mRNA profiles of 9 week- old- Slc25a47hep-/- and Slc25a47hep+/+ mice
Platform: GPL17021
35714811
GSE199074 Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of Skeletal Muscle-Specific Akt Knockout Mice Mus musculus Expression profiling by high throughput sequencing Skeletal Muscle BTO:0001103 Healthy: Gene KO Focus 6
  • Akt1/2-floxed
  • Mlc1f-Cre
 03/21/2022
Fast-twitch muscle mRNA profiles of 50-week-old skeletal muscle-specific Akt knockout mice and the control floxed mice
Platform: GPL19057
36198696
GSE199702 Transcriptomics analysis of heart, kidney, and liver tissues from 58 Collaborative Cross strains Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: No Specific Disease Mention 348
  • CC003/Unc
  • CC051/TauUnc
  • CC080/TauUnc
  • CC011/Unc
  • CC042/GeniUnc
  • CC032/GeniUnc
  • CC055/TauUnc
  • CC015/Unc
  • CC026/GeniUnc
  • CC009/Unc
  • CC013/GeniUnc
  • CC030/GeniUnc
  • CC045/GeniUnc
  • CC021/Unc
  • CC016/GeniUnc
  • CC035/Unc
  • CC062/Unc
  • CC071/TauUnc
  • CC075/Unc
  • CC006/TauUnc
  • CC072/TauUnc
  • CC002/Unc
  • CC031/GeniUnc
  • CC082/Unc
  • CC024/GeniUnc
  • CC037/TauUnc
  • CC079/TauUnc
  • CC001/Unc
  • CC005/TauUnc
  • CC023/GeniUnc
  • CC039/Unc
  • CC061/GeniUnc
  • CC081/Unc
  • CC012/GeniUnc
  • CC036/Unc
  • CC038/GeniUnc
  • CC025/GeniUnc
  • CC058/Unc
  • CC027/GeniUnc
  • CC044/Unc
  • CC040/TauUnc
  • CC049/TauUnc
  • CC033/GeniUnc
  • CC060/Unc
  • CC008/GeniUnc
  • CC057/Unc
  • CC059/TauUnc
  • CC029/Unc
  • CC041/TauUnc
  • CC004/TauUnc
  • CC078/TauUnc
  • CC017/Unc
  • CC046/Unc
  • CC010/GeniUnc
  • CC007/Unc
  • CC019/TauUnc
  • CC043/GeniUnc
  • CC053/Unc
 03/29/2022
RNA profiling of heart, kidney, and liver bulk tissues of male/female pairs from 58 Collaborative Cross (CC) mouse strains
Platform: GPL24247

N/A
GSE201819 The genetic background shapes the susceptibility to mitochondrial dysfunction and NASH progression Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Nonalcoholic Steatohepatitis (NASH) 93
  • 129S1/SvImJ
  • WSB/EiJ
  • DBA/2J
  • A/J
  • PWK/PhJ
  • C57BL/6J
  • CAST/EiJ
 04/28/2022
RNA sequencing of male livers of 6-8 domesticated (C57BL/6J, DBA/2J, A/J, 129S1/SvlmJ) or wild-derived (CAST/EiJ, PWK/PhJ, WSB/EiJ) inbred mouse strains housed at Thermoneutrality (30°C) and fed with Western Diet or Chow Diet.
Platform: GPL23479
36787127
GSE213110 Skeletal muscle of aged mice, and aged treated with myriocin Mus musculus Expression profiling by high throughput sequencing Skeletal Muscle BTO:0001103 Healthy: Treatment Focus 11
  • Myriocin
  • DMSO
 09/11/2022
Comparative gene expression profiling analysis of RNA-seq data skeletal muscle of myriocin treatment for 10 weeks of aged C57L/6JRj mice, treatment started at age of 18 months
Platform: GPL23479

N/A
GSE217739 Transcriptional changes of adult liver biliary epithelial cells in vivo upon high-fat diet Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Liver Steatosis 12
  • CD
  • HFD
 11/10/2022
BECs isolated from 5 healthy livers (CD) and 7 steatotic livers (HFD) by FACS were subjected to RNA seq.
Platform: GPL23479
36876915
GSE218047 Genetic and pharmacologic inhibition of ALDH1A3 as a treatment of β-cell failure Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 7
  • db/db
  • db/+
  • CKO
 11/15/2022
Sorted beta cells from db/db, db/+ or Aldh1a3 KO_db/db mice
Platform: GPL24247
36732513
GSE77652 FoxO1 Deacetylation Decreases Fatty Acid Oxidation in beta-cells and Sustains Insulin Secretion in Diabetes Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Type 2 Diabetes DOID:9352 4
  • Fasted for 48 hours, and refed for 6 hours
  • Fasted for 48 hours
 02/08/2016
Examined 2 different feeding state and 2 different genotypes
Platform: GPL13112
26984405
GSE78966 Progenitor Cell Marker Aldehyde Dehydrogenase 1a3 Defines a Subset of Failing Pancreatic Beta Cells in Diabetic Mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Diabetes (Non-specific) DOID:0081062 15
  • Aldh- FoxO Het
  • Aldh+ FoxO Het
  • Aldh+ FoxO tKO
  • Aldh- FoxO tKO
 03/07/2016
RNA-Sequencing analysis of 2 different cell types in 2 different genotype categories.
Platform: GPL13112
27572106
GSE90815 Cell-specific discrimination of desmosterol and desmosterol mimetics confers selective regulation of LXR and SREBP pathways in macrophages Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Hypertriglyceridemia 30
  • Vehicle (DMSO / EtOH)
  • DMHCA 1 uM
  • MePipHCA 1 uM
  • desmosterol 10 uM
  • T0901317 1 uM
  • GW3965 1 uM
 12/02/2016
Primary mouse hepatocytes (in duplicate) and thioglycollate elicited mouse macrophages (in triplicate) were treated in vitro with various ligands for 18-20 hours prior to RNA isolation and RNA-Seq library preparation
Platform: GPL13112
29632203
GSE96093 RNA-sequencing of hepatocyte specific ABCA1 deletion mice Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Healthy: Gene KO Focus 6
  • wildtype
  • ABCA1 deletion
 03/10/2017
mRNA profiles of C57BL/6 mice with hepatocyte specific (Albumin-Cre) ABCA1 deletion and floxed controls were generated by high throughput sequencing using the Illumina HiSeq 2500 platform.
Platform: GPL17021
28591582
GSE182668 Genetic, metabolic, and molecular insights into the diverse outcomes of diet-induced obesity in mice Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Obesity DOID:9970 37
  • CD
  • HFD
 08/24/2021
Design: This RNAseq dataset covers the response to HFD in the mouse liver of 9 mouse strains (PWK/PhJ, CAST/EiJ, WSB/EiJ, NZO/HlLt, JNOD/ShiLtJ, 129S1/SvImJ, A/J, DBA/2J, C57BL/6J). 6 female and 6 male animals from 9 inbred mouse strains were fed with either a chow diet (CD) or high-fat diet (HFD) from the age of 8 to 21 weeks and various metabolic and fitness phenotypes were measured. Eight of these strains are known as the founders of the Collaborative Cross (CC) and Diversity Outbred (DO) populations, with the addition of the DBA/2J strain.
Platform: GPL23479
35677645
GSE60149 Global hepatic transcript data from fasted male BXD strains on chow or high fat diet Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Diet Focus 81
  • High Fat
  • Chow Diet
 08/06/2014
29-week-old male mice were fasted overnight (6pm-9am), anesthetized under isoflurane, and perfused, then livers were snap-frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.
Platform: GPL6246
25215496
GSE60151 Global quadriceps skeletal muscle transcript data from fasted male BXD strains on chow or high fat diet Mus musculus Expression profiling by array Skeletal Muscle BTO:0001103 Healthy: Diet Focus 79
  • High Fat
  • Chow Diet
 08/06/2014
29-week-old male mice were fasted overnight (6pm-9am), anesthetized under isoflurane, and perfused, then quadriceps were snap-frozen in liquid nitrogen for RNA extraction and RNEasy cleanup. Each dietary and strain cohort consisted of ~5 animals which were prepared independently then pooled evenly by µg RNA before the Affymetrix arrays were run.
Platform: GPL6246
25255223
GSE62013 Diabetes and Insulin in Regulation of Brain Cholesterol Metabolism Mus musculus Expression profiling by array Brain BTO:0000142 Diabetes (Non-specific) DOID:0081062 17
  • ob/ob
  • wildtype
 10/02/2014
Hypothalamus was compared between streptozotocin (STZ)-induced diabetic, ob/ob, and control mice, with 5-6 replicates per goup.
Platform: GPL8321
21109190
GSE65624 Hepatic Gene Expression in LIRKO Mice Mus musculus Expression profiling by array Liver BTO:0000759 Healthy: Gene KO Focus 6
  • IR flox/flox albuminCRE -
  • IR flox/flox albuminCRE +
 02/04/2015
Three arrays per group were used.
Platform: GPL81
25849138

This module was developed by the Ma'ayan Laboratory, and it is funded by NIH grants R01DK131525 and RC2DK131995.