A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 48 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
- 48 samples: 48 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
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 GSE245549_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 PRJNA1028963 and SRA study SRP466790. 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 48 sample titles: 48 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.
- GSM7844715 ALD216A1 (Set1)
- GSM7844716 ALD216A2 (Set1)
- GSM7844751 WT rep1 (Set2)
- GSM7844752 WT rep2 (Set2)
- GSM7844753 WT rep3 (Set2)
- GSM7844754 WT rep4 (Set2)
- GSM7844755 KO rep1 (Set2)
- GSM7844756 KO rep2 (Set2)
- GSM7844757 KO rep3 (Set2)
- GSM7844758 KO rep4 (Set2)
- GSM7844759 WT rep1 (Set3)
- GSM7844760 WT rep2 (Set3)
- GSM7844761 WT rep3 (Set3)
- GSM7844762 KO rep1 (Set3)
- GSM7844763 KO rep2 (Set3)
- GSM7844764 KO rep3 (Set3)
- GSM7844765 WT rep1 (Set4)
- GSM7844766 WT rep2 (Set4)
- GSM7844767 KO rep1 (Set4)
- GSM7844768 KO rep2 (Set4)
- GSM7844769 WT Input E14.5 Retina ChIP (Set5)
- GSM7844770 WT H3K27me3 E14.5 Retina ChIP (Set5)
- GSM7844771 Atoh7 RE KO Input E14.55 Retina ChIP (Set5)
- GSM7844772 Atoh7 RE KO H3K27me3 E14.5 Retina Chip (Set5)
- 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)
- GSM7844794 WT rep1 (Set7)
- GSM7844795 WT rep2 (Set7)
- GSM7844796 WT rep3 (Set7)
- GSM7844797 KO rep1 (Set7)
+ 8 more — browse all 48 samples with per-sample file links →
- GSE245544 A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis [Set6.H3K27Ac and H3K4me2 ChIP-Seq cerebellum P18 WT] 12 samples shares cis-regulatory, axonogenesis, underlies, ganglion, retinal, genesis, module
- GSE305554 m6A epitranscriptome regulates axonogenesis and reprogramming of retinal ganglion cells [RNA-seq] 12 samples shares axonogenesis, ganglion, retinal, genesis
- GSE281033 A SOX2-VSX2 axis modulates a core cis-regulatory circuitry to safeguard retinal neural competence 18 samples shares cis-regulatory, retinal
- GSE267419 Retinal ganglion cell-derived semaphorin 6A segregates starburst amacrine cell dendritic scaffolds to organize the mouse inner retina 855 samples shares ganglion, retinal
- GSE318351 IL1A enhances TNF-induced retinal ganglion cell death 109 samples shares ganglion, retinal
- GSE233822 Transcriptional profiles of mouse retinal ganglion cells after optic nerve crush [RGC_injury_2019-9205_He] 30 samples shares ganglion, retinal
- GSE304931 Alpha retinal ganglion cell-derived SPP1 instructs microglia to limit neurodegeneration 23 samples shares ganglion, retinal
- GSE252860 Nuclear-localized HDAC4 promotes neuroprotection of retinal ganglion cells after optic nerve injury 12 samples shares ganglion, retinal
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.