HNF1A regulates a β-cell RNA splicing program that is disrupted in type 2 diabetes [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 6 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
- Mus musculus (mouse)
- Samples
- 6 samples: 6 samples, each with a distinct title — no replicated groupsGroups 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
- HNF1A and A1CF coordinate a beta cell transcription-splicing axis that is disrupted in type 2 diabetesCell metabolism · 2025
Read the full summary ↓
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 GSE277552_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 PRJNA1162789 and SRA study SRP533591. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 6 sample titles: 6 distinct titles with little repetition. 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.
- GSM8524423 ChIP-seq MIN6-HNF1A-CS1
- GSM8524424 ChIP-seq mouse_islets H3K4me3
- GSM8524425 ChIP-seq mouse islets H3K27ac
- GSM8524426 ChIP-seq EndoC-BH3-HNF1A-CS
- GSM8524427 ChIP-seq EndoC-BH3 H3K4me3
- GSM8524428 ChIP-seq EndoC-BH3 H3K27ac
- GSE278354 Aberrant splicing in Huntington’s disease accompanies disrupted TDP-43 activity and altered m6A RNA modifications 60 samples shares disrupted, splicing
- GSE303179 SRSF12 is a primate-specific splicing factor that induces a tissue-specific gene expression program 18 samples shares splicing, program
- GSE226003 Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape. 170 samples shares splicing
- GSE86336 m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover 20 samples shares splicing
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.