An Interactive Visualization and Analysis Viewer

This module enables interactive visualization and anlysis of gene expression data from Single Cell RNA Sequence experiments from the Gene Expression Omnibus(GEO). Select a study to visualize the PCA, UMAP, and tSNE plots as defined by leiden clusters, followed by gene expression visualization, and differential gene expression analysis.

Total Studies
17
Total Samples
86
Total Single Cells
439937

GSE Title Organism Assay Tissue Cell Type of Interest Disease Num Samples Perturbations Single Cells Submission Date Study Design PMID Analysis Viewer Link
GSE138857 A method for the generation of human stem cell-derived alpha cells Homo sapiens Expression profiling by high throughput sequencing Not Specified Pluripotent Stem Cells Diabetes (Non-specific) DOID:0081062 2
  • Pancreatic alpha progenitor cells
  • Pancreatic alpha cells
 Profile 1: 2131 Profile 2: 1694 Total: 3825 10/15/2019
Single cell mRNA sequencing data generated from stem cell-derived alpha cells and precursor (2 samples total, no replicates)
Platform: GPL20301
32382023
GSE151889 RIPK1 gene variants associate with increased obesity in humans and can be therapeutically silenced to improve metabolic dysfunction in obese mice Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Macrophages Obesity DOID:9970 2
  • CD45+ cells
 Profile 1: 2227 Total: 2227 06/05/2020
Single-cell RNA sequencing (scRNA-seq) profiles of adipose tissues from mice treated with Control or RIPK1-targeting antisense oligonucleotides, and scRNA-seq profiles of human omentum.
Platform: GPL18573
32989316
GSE156341 Stress-induced RNA–chromatin interactions promote endothelial dysfunction (scRNA-seq human vascular) Homo sapiens Expression profiling by high throughput sequencing Blood BTO:0000089 Endothelial Cells Diabetes (Non-specific) DOID:0081062 10
  • healthy donor
  • Endothelial Cells from Type 2 Diabetes
 Profile 1: 8447 Profile 2: 3900 Total: 12347 08/17/2020
Performing single-cell RNA-seq in human mesenteric arterial endothelial cells in two healthy and two Type 2 Diabetes donors.
Platform: GPL20301
33060583
GSE139535 Single Cell Sequencing Analysis for Wolfram Syndrome (WS4) Unedited and Corrected Stem Cell-Derived Beta Cells Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Beta Cells Diabetes (Non-specific) DOID:0081062 2
  • Wolfram Syndrome pathogenic variant
  • corrected by CRISPR/Cas9
 Profile 1: 7215 Profile 2: 3640 Total: 10855 10/29/2019
Single cell RNA sequencing of human Wolfram Syndrome patient stem cell-derived beta cells and other stage 6 cells derived from differentiation protocol. The cells were differentiated from both diseased (unedited) and CRISRP/Cas9-corrected induced pluripotent stem cells.
Platform: GPL16791
32846125
GSE153834 Self-Renewing Tri-Potent Stem/Progenitor-like Cells from Adult Human Pancreas Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 1
  • Pancreas
 Profile 1: 12656 Total: 12656 07/06/2020
Total RNAs were extracted from individual cells obtained following dissociation of freshly obtained human adult islet-depleted pancreas tissue.
Platform: GPL24676

N/A
GSE159556 scRNA-seq analysis of SARS-CoV-2 infected human islets Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Covid 19 DOID:0080600 5
  • infected with SARS-CoV-2 integrated stress response inhibitor treated (ISRIB)
  • mock
  • infected with SARS-CoV-2
 Profile 1: 16523 Profile 2: 18780 Profile 3: 11859 Total: 47162 10/19/2020
Human islets were infected with SARS-CoV-2 and analyzed using scRNA-seq
Platform: GPL24676
34081913
GSE173193 Single cell RNA-sequencing reveals placenta cellular heterogeneity in adverse pregnancy Homo sapiens Expression profiling by high throughput sequencing Placenta BTO:0001078 Placental Cells Diabetes (Non-specific) DOID:0081062 8
  • GDM group
  • elderly group
  • control group
  • PE group
 Profile 1: 12573 Profile 2: 14871 Profile 3: 14427 Profile 4: 16311 Total: 58182 04/23/2021
2 placenta samples from PE, GDM, the elderly group and the control group respectively.
Platform: GPL24676
34025588
GSE190726 TYK2 regulates human pancreatic beta-cell development and its responses to interferon-alpha [tyk2_scRNAseq] Homo sapiens Expression profiling by high throughput sequencing Not Specified Pancreatic Islets Diabetes (Non-specific) DOID:0081062 6
  • TYK2 KO
  • WT
 Profile 1: 15320 Profile 2: 16940 Total: 32260 12/12/2021
We performed single cell RNA-seq in two stages (S5 & S6) of pancreatic differentiation for CRISPR/Cas9 generated TYK2 KO hiPSC lines and non-edited negative control (WT) samples. We also performed scRNA-seq on same samples (in S6) treated with IFNa.
Platform: GPL24676
36289205
GSE212256 Multidimensional analysis and therapeutic development using patient iPSC-derived disease models of Wolfram syndrome Homo sapiens Expression profiling by high throughput sequencing Not Specified Pancreatic Islets Wolfram Syndrome DOID:10632 2
  • WFS1c.1672C>T, c.1672C>T
  • WFS1c.1672C>T, c.2654C>T
 Profile 1: 8021 Profile 2: 12444 Total: 20465 08/29/2022
Single cell RNAseq of SC-islets derived from Wolfram syndrome iPSCs
Platform: GPL24676
36134655
GSE213290 Characterization and reduction of non-endocrine cells accompanying islet-like endocrine cells differentiated from human iPSC Homo sapiens Expression profiling by high throughput sequencing Not Specified Pancreatic Islets Diabetes (Non-specific) DOID:0081062 6
  • induced pluripotent stem cells
  • cadaveric human tissue
 Profile 1: 2959 Profile 2: 17351 Total: 20310 09/13/2022
Single-cell mRNA sequencing of cadaveric human islet, and pluripotent stem cells differentiating in vitro towards pancreatic islet like cells.
Platform: GPL20795
35304548
GSE135356 Stress-induced RNA–chromatin interactions promote endothelial dysfunction (scRNA-seq) Homo sapiens Expression profiling by high throughput sequencing Umbilical Cord BTO:0001415 Endothelial Cells Diabetes (Non-specific) DOID:0081062 6
  • Human umbilical Vein Endothelial Cells treatment combining high glucose (HG, to mimic hyperglycemia) and TNFalpha (to mimic inflammation)
  • Human umbilical Vein Endothelial Cells cultured under osmotic control (25 mM mannitol)
 Profile 1: 27523 Profile 2: 33307 Total: 60830 08/04/2019
Performing single-cell RNA-seq in HUVEC human cell lines in three samples: control (no treatment) and after 3 and 7 days of treatment to mimic endothelial to mesenchymal transition.
Platform: GPL16791
33060583
GSE168071 Modelling HNF1B-associated monogenic diabetes using human iPSCs reveals an early stage impairment of the pancreatic developmental program Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Beta Cells Diabetes (Non-specific) DOID:0081062 2
  • Het
  • WT
 Profile 1: 1615 Profile 2: 1987 Total: 3602 03/02/2021
We generated hIPSC lines carrying loss of function mutation in the HNF1B gene and then differentiated the resulting cells into pancreatic b-like cells in vitro.
Platform: GPL16791
34450036
GSE185036 Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates [human_singlecell] Homo sapiens Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Fibroblasts Diabetes (Non-specific) DOID:0081062 3
  • islets derived from pluripotent stem cellssample collected at Stage 6 Day 2
  • islets derived from donor pancreas
  • islets derived from pluripotent stem cellssample collected at 10 weeks post transplantation (wpt)
 Profile 1: 4676 Profile 2: 9885 Profile 3: 6927 Total: 21488 09/29/2021
Single-cell RNA sequencing analysis on hCiPSC-islets and islets to analyze all pancreatic endocrine cell types.
Platform: GPL20795
35115708
GSE218316 Single-cell transcriptomics of primary human pancreatic islet cells exposed to stress conditions associated with beta-cell failure. Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 5
  • 72h
  • 24h
 Profile 1: 25232 Profile 2: 17660 Total: 42892 11/18/2022
Pancreatic islet cells from non-diabetic donors were treated with stressors (glucose (22 mM) and/or palmitate (0.5 mM), thapsigargin (0.1 μM), IL-1β (1 ng/ml) and/or IFNγ (1000 U/ml), IFNα (2000 U/ml), hydrogen peroxide (H2O2, 50 μM), FGF2 (100 ng/ml), hypoxia) and untreated as control for 24h and 72h
Platform: GPL24676

N/A
GSE163947 MYCL-mediated in vivo reprogramming expands pancreatic insulin-producing cells to reverse diabetes Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 3
  • hMYCL
  • mMycl
  • zsGreen
 Profile 1: 1699 Profile 2: 2455 Profile 3: 1918 Total: 6072 12/28/2020
For scRNAseq in chimeric mouse islets, we transduced Mycl in 8-week-old adult chimeric mice for 8 weeks by drinking Dox-containing water (Dox: 2.0mg/mL). After dissociation of the islets into single cells in TrypLE, we generated chromium single cell 3′ v1 libraries and sequenced them using Illumina Novaseq 6000. We profiled 7,001 cells (ex1: 4,307 cells; ex2: 2,694 cells).For scRNAseq in mouse islets, we transduced Mycl in 8-week-old adult mice for 8 weeks by drinking Dox-containing water (Mycl ON, Dox: 2.0mg/mL) and ceased Mycl expression for 4 weeks (Mycl ON-OFF). For the control, islet cells were harvested from no treatment Mycl inducible mice at 20wks(WT). After dissociation of the islets into single cells, we generated chromium single cell 3′ v1 libraries and sequenced them using Illumina Novaseq 6000. We profiled 6,394 cells (Mycl ON: 3,513 cells; Mycl ON-OFF: 1,560 cells; WT: 1321 cells).
Platform: GPL20301

N/A
GSE215376 Vascularization of pluripotent stem cell-derived islet organoids improves β-cell function Homo sapiens Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Healthy: No Specific Disease Mention 1
  • Day 8
 Profile 1: 1857 Total: 1857 10/13/2022
In this analysis, we used single-cell RNA-seq (scRNA-seq) to profile 1809 vasculature forming cells (endothelial cells and fibroblasts). We annotate cell types based on the known marker genes. Through cell-cell communication network analyses, we predicted heterotypic cell-cell interactions between beta cells, endothelial cells and fibroblasts.
Platform: GPL20301

N/A
GSE220939 SGLT2 inhibitors mitigate kidney tubular metabolic and mTORC1 perturbations in youth onset type 2 diabetes Homo sapiens Expression profiling by high throughput sequencing Kidney BTO:0000671 Renal Cells Diabetes (Non-specific) DOID:0081062 22
  • None Healthy control
  • SGLT2 inhibitor T2D
  • None T2D
 Profile 1: 40710 Profile 2: 23615 Profile 3: 18582 Total: 82907 12/14/2022
Cryostor-preserved kidney biopsies were subjected to single cellular RNA-sequencing.
Platform: GPL11154
36637914
GSE155593 Characterization of immune cells infiltrating islets using scRNA-seq Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 2
  • 7 weeks old
  • 12 weeks old
 Profile 1: 1113 Profile 2: 2809 Total: 3922 08/03/2020
Gene expression profiles of single immune cells infiltrating islets of 7-week old and 12-week old NOD mice prepared using 10x Genomics Chromium platform
34507949
GSE156665 Pancreatic Ppy-expressing gamma-cells display mixed phenotypic traits and adaptive plasticity to engage insulin production Mus musculus Mus musculus Expression profiling by high throughput sequencing Third-party reanalysis Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 4
  • Mix background
 Profile 1: 5982 Total: 5982 08/21/2020
Transcriptomic profile of pancreatic Ppy-expressing cells using single cell and bulk RNA-seq
34294685
GSE171252 Single-cell RNA-seq in pancreatic islets of Tg7 mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 2
  • Wild-type
  • Tg7
 Profile 1: 768 Profile 2: 1024 Total: 1792 03/31/2021
We performed single-cell RNA-Sequencing (RNA-seq) in islets obtained from beta-cell-specific miR-7a2 overexpressing mice (Tg7), a murine model of beta-cell dedifferentiation and diabetes. These analyses were performed with islets isolated from 12-week-old male Tg7 mice and littermate controls.
33989778
GSE155798 Insulin secretory granules release exosomal miR-503 to promote insulin resistance and β-cell senescence. Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Beta Cells Diabetes (Non-specific) DOID:0081062 2
  • Beta cell specific miR-503 transgenic
  • wild type
 Profile 1: 4156 Profile 2: 4539 Total: 8695 08/06/2020
Single-cell RNA-sequencing (scSeq) profiles of 10-week old wild type (WT) and βTG mice islets.

N/A
GSE156175 Single-cell RNA-sequencing of mouse islets exposed to proinflammatory cytokines Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 4
  • Untreated
  • 6 hours IL-1B treatement
  • 6 hours IL-1B and IFNg treatement
  • 6 hours IFNg treatement
 Profile 1: 2484 Profile 2: 2934 Profile 3: 3067 Profile 4: 2280 Total: 10765 08/13/2020
Four samples of murine islets (no cytokine treatment, IL-1B only, IFNg only, IL-1B and IFNg exposure for 6 hours) were prepared using 10x Genomics Chromium platform
33883217
GSE200531 Single-cell RNA-seq uncovers the pathological alterations of pancreatic islets in type 2 diabetes mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 2
  • C57BLKS-Leprwt/wt
  • C57BLKS-Leprdb/db
 Profile 1: 8432 Profile 2: 8504 Total: 16936 04/09/2022
The Lepr knockout mouse model was used. The islets were isolated from three control (BKS_WT; m/m) and three type 2 diabetes (BKS_DB; db/db) mice at ages of 9 weeks. The isolated islets were cultured overnight and enzymatically digested to generate single-cell suspensions for scRNA-seq.
36339258
GSE200608 scRNA-seq and scTCR-seq of autoreactive CD8 T cells from NOD mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 6
  • Islets
  • Spleen
 Profile 1: 20371 Profile 2: 6373 Total: 26744 04/11/2022
scRNA-seq and scTCR-seq of IGRP+ and IGRP- CD8 T cells from islets and IGRP+ CD8 T cells from spleens of NOD mice
35667687
GSE205123 Single-cell RNA-seq uncovers the early alterations of retina in type 2 diabetes mice Mus musculus Expression profiling by high throughput sequencing Retina BTO:0001175 Retinal Cells Diabetes (Non-specific) DOID:0081062 2
  • C57BLKS-Leprwt/wt
  • C57BLKS-Leprdb/db
 Profile 1: 10307 Profile 2: 11076 Total: 21383 05/31/2022
The Lepr knockout mouse model was used. The retinas were isolated from two control (BKS_WT; m/m) and two type 2 diabetes (BKS_DB; db/db) mice at ages of 13 weeks. The isolated retinas were enzymatically digested to generate single-cell suspensions for scRNA-seq.

N/A
GSE213973 Repertoire analysis of the repertoire of insulin-reactive B cells in type 1 diabetes-prone mice Mus musculus Expression profiling by high throughput sequencing Other Spleen BTO:0001281 B cells Diabetes (Non-specific) DOID:0081062 1
  • VH125.NOD
 Profile 1: 6367 Total: 6367 09/22/2022
Splenocytes from VH125.NOD mice were isolated. High affinity insulin-binding cells were enriched by serial incubation with biotinylated insulin, streptavidin-Alexa Fluor 647 and anti-Cy5/anti-Alexa Flour 647 microbeads (Miltenyi) followed by passage through a magnet-mounted LS column (Miltenyi). These cells were then FACS sorted to further enrich insulin binding B cells and these cells were then analyzed via scRNASeq
36275764
GSE117770 Targeted elimination of senescent beta cells prevents Type 1 Diabetes Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Beta Cells Diabetes (Non-specific) DOID:0081062 9
  • 8 weeks
  • 16 weeks
  • 14 weeks
 Profile 1: 9014 Profile 2: 12058 Profile 3: 11161 Total: 32233 07/27/2018
Examination of scRNA-seq in beta cells across three different age groups
30799288
GSE141036 Single-cell RNA sequencing of visceral adipose tissue leukocytes reveals that caloric restriction following obesity promotes the accumulation of a distinct macrophage population with features of phagocytic cells Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Leukocytes Obesity DOID:9970 2
  • obese
  • Life-long caloric restriction
 Profile 1: 5728 Profile 2: 3541 Total: 9269 11/26/2019
Single-cell RNA sequencing of CD45+ VAT cells.
31396408
GSE145228 Targeting OCA-B/Pou2af1 blocks type-1 diabetes and reduces infiltration of activated, islet-reactive T cells Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Leukocytes Diabetes (Non-specific) DOID:0081062 4
  • Ocabfl/fl.CD4-Cre
  • Ocabfl/fl
 Profile 1: 4407 Profile 2: 6901 Profile 3: 3050 Profile 4: 6524 Total: 20882 02/13/2020
Leukocytes were isolated from pancreata or pancreatic lymph nodes pre-diabetic week-old females of Ocabfl/fl (control) and Ocabfl/fl.CD4Cre.
33295943
GSE151889 RIPK1 gene variants associate with increased obesity in humans and can be therapeutically silenced to improve metabolic dysfunction in obese mice Mus musculus Expression profiling by high throughput sequencing Adipose Tissue BTO:0001487 Immune Cells Obesity DOID:9970 3
  • RIPK1-targeting antisense oligonucleotides
  • Control
 Profile 1: 2152 Profile 2: 5451 Total: 7603 06/05/2020
Single-cell RNA sequencing (scRNA-seq) profiles of adipose tissues from mice treated with Control or RIPK1-targeting antisense oligonucleotides, and scRNA-seq profiles of human omentum.
32989316
GSE174194 Vertical sleeve gastrectomy triggers fast β-cell recovery upon overt diabetes Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 7
  • db/db WT WT-Control
  • db/db hom Sham
  • db/db hom PF
  • db/db hom VSG
 Profile 1: 23636 Profile 2: 19091 Profile 3: 20645 Profile 4: 21283 Total: 84655 05/10/2021
7 single-cell RNA sequencing experiments of pancreatic islets isolated from male Lepr-deficient db/db and WT mice, 16-18 weeks of age, were performed using 10X Genomics technology to generate single-cell transcriptomic profiles of healthy and db/db diabetic mice undergoing surgical interventions.
34500108
GSE183010 Single-cell RNA-sequencing of mouse islets exposed to proinflammatory cytokines [18hrs] Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 8
  • 18 hours IL-1B and IFNg treatement
  • 18 hours NMMA treatement
  • Untreated
  • 18 hours IL-1B, IFNg, and NMMA treatement
 Profile 1: 5305 Profile 2: 3157 Profile 3: 3503 Profile 4: 3834 Total: 15799 08/30/2021
Four samples of murine islets (no cytokine treatment, IL-1β and IFNγ only, IL-1β and IFNγ with NMMA, NMMA only exposure for 18 hours) were prepared using 10x Genomics Chromium platform
34927076
GSE188217 Single-cell Transcriptomic Atlas of Gingival Mucosa in Type 2 Diabetes Mus musculus Expression profiling by high throughput sequencing Gingiva BTO:0000519 Stromal Cells Diabetes (Non-specific) DOID:0081062 2
  • db/db
  • WT
 Profile 1: 11919 Profile 2: 6976 Total: 18895 11/04/2021
Gingival single-cell transcriptomic profile of 16-wk-old db/db mice and control mice were generated by sc-RNA sequencing.

N/A
GSE203042 Gene expression profile at single cell level of GFP labeled islet β cells from streptozotocin (STZ) treated Ins/β-lineage-labeled mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Beta Cells Diabetes (Non-specific) DOID:0081062 1
  • Ins1-CreERT; Rosa26-mT/mG
 Profile 1: 2218 Total: 2218 05/14/2022
Ins/β-lineage-labeled (Ins1-CreERT; Rosa26-mT/mG) mice underwent 5-day STZ treatment after 5-day tamoxifen (TAM) treatment and 2-wk washout. At 12wk after STZ treatment, islets were isolated and dispersed into single cells. GFP positive cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

N/A
GSE212009 Heterogeneity of islet-infiltrating interleukin-21+ CD4 T cells in a mouse model of type 1 diabetes Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 T Cells Diabetes (Non-specific) DOID:0081062 2
  • Venus negative
  • Venus positive
 Profile 1: 2583 Profile 2: 3112 Total: 5695 08/25/2022
Islet-infiltrating CD4 T cells from NOD.Il21V/+ mice were isolated by fluorescence-activated cell sorting (FACS) according to the presence of absence of Venus signal and analyzed by scRNA-seq.
36762954
GSE223832 Recruitment of stem-like T cells and resistance to exhaustion support CD4 T cell responses in autoimmunity (scRNA-Seq). Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 T Cells Diabetes (Non-specific) DOID:0081062 4
  • 8wk
  • 16wk
 Profile 1: 3976 Profile 2: 4058 Total: 8034 01/26/2023
We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 16-week-old NOD females to compare their transcriptome profile.

N/A
GSE163947 MYCL-mediated in vivo reprogramming expands pancreatic insulin-producing cells to reverse diabetes Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 5
  • R26-M2-rtTA; Col-TetOP-Mycl-ires-mCherry Dox on 8wks and Dox off 4wks in 8-week-old mice
  • R26-M2-rtTA; Col-TetOP-Mycl-ires-mCherry 20wks
  • R26-M2-rtTA; Col-TetOP-Mycl-ires-mCherry Dox on 8wks in 8-week-old mice
  • R26-M2-rtTA; Col-TetOP-Mycl-ires-mCherry; Gcg-CreERT2; R26-mTmG Dox on 8wks in 8-week-old mice
 Profile 1: 2563 Profile 2: 5034 Profile 3: 3138 Profile 4: 15783 Total: 26518 12/28/2020
For scRNAseq in chimeric mouse islets, we transduced Mycl in 8-week-old adult chimeric mice for 8 weeks by drinking Dox-containing water (Dox: 2.0mg/mL). After dissociation of the islets into single cells in TrypLE, we generated chromium single cell 3′ v1 libraries and sequenced them using Illumina Novaseq 6000. We profiled 7,001 cells (ex1: 4,307 cells; ex2: 2,694 cells).For scRNAseq in mouse islets, we transduced Mycl in 8-week-old adult mice for 8 weeks by drinking Dox-containing water (Mycl ON, Dox: 2.0mg/mL) and ceased Mycl expression for 4 weeks (Mycl ON-OFF). For the control, islet cells were harvested from no treatment Mycl inducible mice at 20wks(WT). After dissociation of the islets into single cells, we generated chromium single cell 3′ v1 libraries and sequenced them using Illumina Novaseq 6000. We profiled 6,394 cells (Mycl ON: 3,513 cells; Mycl ON-OFF: 1,560 cells; WT: 1321 cells).

N/A
GSE165267 A simple strategy effectively improves glucose homeostasis and prevents loss of islet beta cells in diabetic mice Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 4
  • db/db(C57BL/KsJ) post natal day 70d
  • db/db(C57BL/KsJ) post natal day 98d
 Profile 1: 18999 Profile 2: 5666 Total: 24665 01/21/2021
Examination of pancreas islets cells in 4 different groups of mice.

N/A
GSE203151 Gene expression profile at single cell level of pancreatic islets cells from mice fed with regular or high fat diet for 6 weeks after weaning. Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 2
  • Wild type Animals fed with high fat diet
  • Wild type Animals fed with chow diet
 Profile 1: 6509 Profile 2: 4538 Total: 11047 05/17/2022
C57BL/6J wild-type mice were fed a regular chow diet (RD, N=4) or a 60% high fat diet (HFD, N=5) (Research Diets) for 6 weeks after weaning. Mouse pancreatic islets were isolated by perfusion of the pancreases with CIzyme (VitaCyte) through the common hepatic duct and digested at 37°C for 17 minutes. After gradient-based separation using Histopaque-1077 (Sigma), islets were then hand-picked to avoid exocrine contamination. For details of the analyses, see https://github.com/abcwcm/RubioNavarro_Pancreas

N/A
GSE213337 Single cell analysis reveals the heterogeneity of fibroblasts in the diabetic heart Mus musculus Expression profiling by high throughput sequencing Heart BTO:0000562 Fibroblasts Diabetes (Non-specific) DOID:0081062 2
  • wild type untreated control
  • wild type STZ-induced diabetes
 Profile 1: 8614 Profile 2: 8626 Total: 17240 09/14/2022
We lead the single cell RNA sequence. Cells were comprised of endothelial, fibroblast, cardiomyocyte, smooth muscle cells, macrophage and other type cells. Single cell sequence illustrates novel fibroblast sub-clusters and highlights the role of Lox. Real-time quantitative PCR, western blotting, immunofluorescence was used to verify the sequence data.
36706988
GSE217665 Single cell transcriptomic analysis of cortical cell type composition underlying diabetes-associated cognitive decline Mus musculus Expression profiling by high throughput sequencing Brain BTO:0000142 Neurons Diabetes (Non-specific) DOID:0081062 2
  • control
  • diabetic
 Profile 1: 5636 Profile 2: 4136 Total: 9772 11/09/2022
For scRNA-seq, mouse were sacrificed at 16 weeks of age. The cortex was dissected and dissociated using the papain dissociation system (Worthington, Lakewood, NJ) as per the manufacturer's instructions.

N/A
GSE218563 single cell RNA-sequencing of diabetic mouse kidney Mus musculus Expression profiling by high throughput sequencing Kidney BTO:0000671 Renal Cells Diabetes (Non-specific) DOID:0081062 16
  • BTBR ob/ob 6 weeks
  • BTBR +/+ 6 weeks
  • BTBR +/+ 12 weeks
  • BTBR ob/ob 12 weeks
 Profile 1: 30840 Profile 2: 30423 Profile 3: 27343 Profile 4: 25136 Total: 113742 11/22/2022
Glomeruli were enriched by depleting the PT segment from the kidneys using Percoll density gradient centrifugation, then the single-cell RNA sequencing was performed to BTBR ob/ob vs. BTBR +/+ in glomerular cells.
36627643
GSE221936 Osteoblast-intrinsic defect in glucose metabolism impairs bone formation in type II diabetic male mice. Mus musculus Expression profiling by high throughput sequencing Bone BTO:0000140 Stromal Cells Diabetes (Non-specific) DOID:0081062 2
  • T2D
  • CTRL
 Profile 1: 8034 Profile 2: 8091 Total: 16125 12/30/2022
Examination of the metabolic alteration of bone marrow stromal cells (T2D vs CTRL)
37144869
GSE232737 Genetic activation of glycolysis in osteoblasts preserves bone mass in type I diabetes [scRNA-seq] Mus musculus Expression profiling by high throughput sequencing Bone BTO:0000140 Endosteal Cells Diabetes (Non-specific) DOID:0081062 4
  • WT 8 weeks
  • Akita 20 weeks
  • WT 20 weeks
  • Akita 8 weeks
 Profile 1: 7447 Profile 2: 10400 Profile 3: 9440 Profile 4: 11202 Total: 38489 05/17/2023
single-cell RNA-sequencing profiling of endosteal cells from WT and Akita at 8 weeks and 20weeks, n=1 for each genotype

N/A
GSE234741 Multiparity increases the risk of diabetes by impairing proliferative capacity of beta cells II Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Diabetes (Non-specific) DOID:0081062 2
  • Wild type (C57BL/6J )
 Profile 1: 9574 Total: 9574 06/12/2023
Nine weeks aged C57BL/6J female mice underwent 3 consecutive pregnancies to establish multipara mice model. Aged matched virgin mice were used as control.

N/A
GSE128334 Niche-Specific Re-Programming of Epigenetic Landscapes Drives Myeloid Cell Diversity in NASH [scRNA-seq] Mus musculus Expression profiling by high throughput sequencing Liver BTO:0000759 Liver non-parenchymal cells Nonalcoholic Steatohepatitis (NASH) 4
  • C57BL/6Jcontrol
  • C57BL/6Jnash-amln
 Profile 1: 3341 Profile 2: 3571 Total: 6912 03/14/2019
Single-cell RNA-seq of CD45+ CD146- FACS purified liver non-parenchymal cells from control mice or mice on fed the Amylin liver NASH model diet
32362324
GSE201776 Gene expression profile at the single-cell level of Neurog3 derived tomato cells from Neurog3Cre and Neurog3Cre-FoxO1 f/f (NFKO) of the small intestine Mus musculus Expression profiling by high throughput sequencing Small Intestine BTO:0000651 Epithelial Cells Diabetes (Non-specific) DOID:0081062 2
  • Neurog3Cre-FoxO1 f/f; Rosa26tdtomato NFKO 4-6 weeks old
  • Neurog3Cre; Rosa26tdtomato WT 4-6 weeks old
 Profile 1: 3987 Profile 2: 6972 Total: 10959 04/28/2022
Intestinal Neurog3 derived epithelial cells from the Neurog3Cre; Rosa26tdtomato and Neurog3Cre-FoxO1 f/f; Rosa26tdtomato mice were isolated by fluorescence-activated cell sorting (FACS) according to the presence or absence of tomato signal and analyzed using scRNAseq.
36282594
GSE162512 Single-Cell Transcriptional Profiling of Mouse Islets Following Short-Term ObesogenicDietary Intervention Mus musculus Expression profiling by high throughput sequencing Pancreas BTO:0000988 Pancreatic Islets Obesity DOID:9970 7
  • HFD
  • LFD
 Profile 1: 25446 Profile 2: 32856 Total: 58302 12/02/2020
Islet isolation. Male C57BL/6J mouse pancreas were isolated from 8 weeks of age, animals were fed either a LFD (10% kcal from fat; Research Diets D12450B), or HFD (60% kcal from fat; Research Diets D12492) for one week. Islets were isolated from collagenase-perfused pancreata as previously described (Stull, 2017). After isolation, mouse islets were handpicked and digested with Accutase (EMD Millipore Corporation) containing 2U/ml of DNAse during 5min at 37°C sob agitation (1000rpm). Digested cell islets were washed several times with PBS+2%FBS to eliminate DNAse and then filtered using a cell strainer (40mm). Single cells suspension and samples with more than 90% viability were used for scRNAseq.
33353164
GSE171417 Single-nuclear transcriptomics reveals a diversity of proximal tubule cell states in a dynamic response to acute kidney injury. Mus musculus Expression profiling by high throughput sequencing Kidney BTO:0000671 Proximal Tubule Cells Acute Kidney Injury 9
  • 18min IRI 28 days
  • Control
  • 18min IRI 7 days
 Profile 1: 10990 Profile 2: 6839 Profile 3: 6925 Total: 24754 04/02/2021
Krt20 was previously identified as a marker of injured proximal tubule cells (Liu et al., JCI Insight, 2017). We generated a Krt20T2A-CE; INTACTnuGFP/+ mouse line to enable the isolation and tracing of Krt20+ cells in acute kidney injury. A reporter mouse expressing GFP linked to the histone protein H2B in all nephron cells was used as control (Legouis et al., Nature Metabolism, 2020). In total nine samples were processed for snRNA-seq: two Krt20T2A-CE; INTACTnuGFP/+ samples collected on day 7 after IRI, three Krt20T2A-CE; INTACTnuGFP/+ samples collected on day 28 after IRI and four control samples (three sham surgery mice and one non-surgery mouse).
34183416

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