Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C [ATAC-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 3 × EndoC-BH1 ATAC-Seq vs 3 × SGBS Differentiated ATAC-Seq vs 3 × SGBS Undifferentiated ATAC-Seq vs 3 × HEPG2 ATAC-SeqGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-CDiabetologia · 2024
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE262479_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1091960 and SRA study SRP497910. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8170378 EndoC-BH1 ATAC-Seq replicate 1 EndoC-BH1 ATAC-Seq
- GSM8170379 EndoC-BH1 ATAC-Seq replicate 2 EndoC-BH1 ATAC-Seq
- GSM8170380 EndoC-BH1 ATAC-Seq replicate 3 EndoC-BH1 ATAC-Seq
- GSM8170381 SGBS Differentiated ATAC-Seq replicate 1 SGBS Differentiated ATA…
- GSM8170382 SGBS Differentiated ATAC-Seq replicate 2 SGBS Differentiated ATA…
- GSM8170383 SGBS Differentiated ATAC-Seq replicate 3 SGBS Differentiated ATA…
- GSM8170384 SGBS Undifferentiated ATAC-Seq replicate 1 SGBS Undifferentiated A…
- GSM8170385 SGBS Undifferentiated ATAC-Seq replicate 2 SGBS Undifferentiated A…
- GSM8170386 SGBS Undifferentiated ATAC-Seq replicate 3 SGBS Undifferentiated A…
- GSM8170387 HEPG2 ATAC-Seq replicate 1 HEPG2 ATAC-Seq
- GSM8170388 HEPG2 ATAC-Seq replicate 2 HEPG2 ATAC-Seq
- GSM8170389 HEPG2 ATAC-Seq replicate 3 HEPG2 ATAC-Seq
- GSE262484 Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C 35 samples shares promoter-focused, implicating, capture-c, diabetes, effector, relevant, cellular
- GSE262496 Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C [Capture-C] 11 samples shares promoter-focused, implicating, capture-c, diabetes, effector, relevant, cellular
- GSE262480 Implicating type 2 diabetes effector genes in relevant metabolic cellular models using promoter-focused Capture-C [RNA-Seq] 10 samples shares promoter-focused, implicating, capture-c, diabetes, effector, relevant, cellular
- GSE273598 Single-cell multiome profiling reveals pancreas cell type-specific gene regulatory programs of type 1 diabetes progression [snATAC-seq] 32 samples shares diabetes, atac-seq
- GSE254468 Eicosapentaenoic acid induces an anti-inflammatory transcriptomic landscape in T cells implicating a pathway independent of triglyceride lowering in cardiovascular risk reduction [ATAC-seq] 32 samples shares implicating, atac-seq
- GSE255566 Single-cell RNA sequencing of peripheral blood mononuclear cells reveals complex cellular signalling signatures of type 2 diabetes mellitus 8 samples shares diabetes, cellular
- GSE261281 Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [Capture-C] 3 samples shares capture-c, effector
- GSE261392 CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant [H3K27ac_ChIP-seq] 12 samples shares diabetes
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.