A SOX2-VSX2 axis modulates a core cis-regulatory circuitry to safeguard retinal neural competence
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
- 18 samples: 4 × Sox2 RNAseq KO repeat vs 3 × WT RNAseq repeat vs 2 × WT ATACseq repeat vs 2 × Sox2 KO ATACseq repeatGroups 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
- SOX2-driven enhancer landscape defines the transcriptional architecture of retinogenesisDevelopment (Cambridge, England) · 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 GSE281033_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 PRJNA1181861 and SRA study SRP543076. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 4 replicated groups read from 18 sample titles; they account for 11 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.
- GSM8609556 WT ATACseq repeat 1 WT ATACseq repeat
- GSM8609557 WT ATACseq repeat 2 WT ATACseq repeat
- GSM8609558 Sox2 KO ATACseq repeat 1 Sox2 KO ATACseq repeat
- GSM8609559 Sox2 KO ATACseq repeat 2 Sox2 KO ATACseq repeat
- GSM8609560 Sox2 E14.5 CUT&RUN repeat 1 Input
- GSM8609561 Sox2 E14.5 CUT&RUN repeat 1 Treatment
- GSM8609562 Sox2 E14.5 CUT&RUN repeat 2 Input
- GSM8609563 Sox2 E14.5 CUT&RUN repeat 2 Treatment
- GSM8609564 WT RNAseq repeat 1 WT RNAseq repeat
- GSM8609565 WT RNAseq repeat 2 WT RNAseq repeat
- GSM8609566 WT RNAseq repeat 3 WT RNAseq repeat
- GSM8609567 Sox2 RNAseq KO repeat 1 Sox2 RNAseq KO repeat
- GSM8609568 Sox2 RNAseq KO repeat 2 Sox2 RNAseq KO repeat
- GSM8609569 Sox2 RNAseq KO repeat 3 Sox2 RNAseq KO repeat
- GSM8609570 Sox2 RNAseq KO repeat 4 Sox2 RNAseq KO repeat
- GSM9229103 Sox2 E14.5 IgG CUT&RUN
- GSM9229104 Sox2 E14.5 ChIP-seq Input
- GSM9229105 Sox2 E14.5 ChIP-seq
- GSE264172 The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube 184 samples shares cis-regulatory, neural
- GSE245549 A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis 48 samples shares cis-regulatory, retinal
- GSE325932 Disease-associated microRNA, miR-9-2, is required for the timing of retinal progenitor cell competence and the maintenance of Müller glial identity 32 samples shares competence, retinal
- GSE236450 SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes 24 samples shares cis-regulatory, neural
- GSE281091 A distinct vagus-beta cell neural circuit senses glucose and modulates insulin secretion 24 samples shares modulates, neural
- GSE305064 FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [mouse_Tconv_ChIP-seq] 15 samples shares cis-regulatory, circuitry
- GSE236448 SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes [RNA-seq] 11 samples shares cis-regulatory, neural
- GSE297178 Targeting EBF2 condensates modulates adipose thermogenesis 90 samples shares modulates
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.