A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set6.H3K27Ac and H3K4me2 ChIP-Seq cerebellum P18 WT]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 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
- Mus musculus (mouse)
- Samples
- 12 samples: 12 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
- A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesisCell reports · 2024
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 GSE245544_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 PRJNA1028973 and SRA study SRP466795. 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 12 sample titles: 12 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.
- GSM7844773 WT rep1 input (Set6)
- GSM7844774 WT rep1 H3K27AC ChIP (Set6)
- GSM7844775 WT rep1 H3K4me2 ChIP (Set6)
- GSM7844776 WT rep2 input (Set6)
- GSM7844777 WT rep2 H3K27AC ChIP (Set6)
- GSM7844778 WT rep2 H3K4me2 ChIP (Set6)
- GSM7844779 KO rep1 input (Set6)
- GSM7844780 KO rep1 H3K27AC ChIP (Set6)
- GSM7844781 KO rep1 H3K4me2 ChIP (Set6)
- GSM7844782 KO rep2 input (Set6)
- GSM7844783 KO rep2 H3K27AC ChIP (Set6)
- GSM7844784 KO rep2 H3K4me2 ChIP (Set6)
- GSE245547 A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set8.Bulk RNA-Seq P18 Cerebellum WT and Atoh7 remote Enhancer KO] 6 samples shares p18, cis-regulatory, axonogenesis, cerebellum, underlies
- GSE245546 A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set7.Bulk RNA-Seq P18 Cerebellum WT and Atoh7 Large Enhancer KO] 6 samples shares p18, cis-regulatory, axonogenesis, cerebellum, underlies
- GSE313433 CTCF-mediated cis-regulatory chromatin insulation enforces a central B-cell tolerance checkpoint [ChIP-Seq_H3K27ac] 6 samples shares h3k27ac, cis-regulatory
- GSE332794 Epigenomic profiling of H3K27ac in mouse brain regions under morphine and LPS exposure 206 samples shares h3k27ac
- GSE190102 Ageing-Related Changes to H3K4me3, H3K27ac and H3K27me3 in Purified Mouse Neurons 43 samples shares h3k27ac
- GSE245442 Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide [Chipseq_H3K27ac_spikein] 36 samples shares h3k27ac
- GSE317929 Effect of intrauterine growth restriction on the H3K4me3, H3K9ac, H3K27ac and H3k9me3 histione modification of microglia in hippocampus 34 samples shares h3k27ac
- GSE276779 YAP-Driven Malignant Reprogramming of Oral Epithelial Stem Cells, CUT&TAG sequencing for YAP, H3K27ac, and H3K27me3 32 samples shares h3k27ac
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.