Gene Expression Data Explorer
Info Gene counts are sourced from ARCHS4, which provides uniform alignment of GEO samples. You can learn more about ARCHS4 and its pipeline here.
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GROUP CONDITION SAMPLES
Pancreatic islets
GSM6234546 GSM6234551 GSM6234556 GSM6234559
GSM6234549 GSM6234554
GSM6234550 GSM6234555 GSM6234558 GSM6234561
GSM6234547 GSM6234552
GSM6234548 GSM6234553 GSM6234557 GSM6234560
Description

Submission Date: Jun 10, 2022

Summary: Beta cells intrinsically contribute to the pathogenesis of type 1 diabetes (T1D), but the genes and molecular processes that mediate beta cell survival in T1D remain largely unknown. We combined high throughput functional genomics and human genetics to identify T1D risk loci regulating genes affecting beta cell survival in response to the proinflammatory cytokines IL-1b, IFNg, and TNFa. We mapped cytokine-responsive candidate cis­­-regulatory elements (cCREs) active in beta cells using ATAC-seq and single nuclear ATAC-seq (snATAC-seq), and linked cytokine-responsive beta cell cCREs to putative target genes using single cell co-accessibility and HiChIP. We performed a genome-wide pooled CRISPR loss-of-function screen in EndoC-βH1 cells, which identified hundreds of genes affecting cytokine-induced beta cell loss. We identified thousands of variants in cytokine-responsive beta cell cCREs altering transcription factor (TF) binding using high-throughput SNP-SELEX. Together our findings reveal processes and genes acting in beta cells during cytokine exposure that intrinsically modulate risk of T1D.

GEO Accession ID: GSE205853

PMID: 36778047

Description

Submission Date: Jun 10, 2022

Summary: Beta cells intrinsically contribute to the pathogenesis of type 1 diabetes (T1D), but the genes and molecular processes that mediate beta cell survival in T1D remain largely unknown. We combined high throughput functional genomics and human genetics to identify T1D risk loci regulating genes affecting beta cell survival in response to the proinflammatory cytokines IL-1b, IFNg, and TNFa. We mapped cytokine-responsive candidate cis­­-regulatory elements (cCREs) active in beta cells using ATAC-seq and single nuclear ATAC-seq (snATAC-seq), and linked cytokine-responsive beta cell cCREs to putative target genes using single cell co-accessibility and HiChIP. We performed a genome-wide pooled CRISPR loss-of-function screen in EndoC-βH1 cells, which identified hundreds of genes affecting cytokine-induced beta cell loss. We identified thousands of variants in cytokine-responsive beta cell cCREs altering transcription factor (TF) binding using high-throughput SNP-SELEX. Together our findings reveal processes and genes acting in beta cells during cytokine exposure that intrinsically modulate risk of T1D.

GEO Accession ID: GSE205853

PMID: 36778047

Visualize Samples

Info Visualizations are precomputed using the Python package scanpy on the top 5000 most variable genes.

Precomputed Differential Gene Expression

Info Differential expression signatures are automatically computed using the limma R package. More options for differential expression are available to compute below.

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Perturbation Condition

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Differential Gene Expression Analysis
Info Differential expression signatures can be computed using DESeq2 or characteristic direction.
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