A gene regulatory network of the endothelial-to-hematopoietic transition
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 63 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
- 63 samples: 18 conditions, mostly with about 4 replicates eachGroups 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.
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 GSE233057_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 PRJNA974839 and SRA study SRP438834. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 63 samples.
How we read this: 18 replicated groups read from 63 sample titles; they account for 63 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.
- GSM7400991 ATAC, E10.5 EC, rep 1 ATAC, E10.5 EC,
- GSM7400992 ATAC, E10.5 EC, rep 2 ATAC, E10.5 EC,
- GSM7400993 ATAC, E10.5 EC, rep 3 ATAC, E10.5 EC,
- GSM7400994 ATAC, E10.5 EC, rep 4 ATAC, E10.5 EC,
- GSM7400995 ATAC, E10.5 HE, rep 1 ATAC, E10.5 HE,
- GSM7400996 ATAC, E10.5 HE, rep 2 ATAC, E10.5 HE,
- GSM7400997 ATAC, E10.5 HE, rep 3 ATAC, E10.5 HE,
- GSM7400998 ATAC, E10.5 HE, rep 4 ATAC, E10.5 HE,
- GSM7400999 ATAC, E10.5 pre-HSC I, rep 1 ATAC, E10.5 pre-HSC I,
- GSM7401000 ATAC, E10.5 pre-HSC I, rep 2 ATAC, E10.5 pre-HSC I,
- GSM7401001 ATAC, E10.5 pre-HSC I, rep 3 ATAC, E10.5 pre-HSC I,
- GSM7401002 ATAC, E10.5 pre-HSC I, rep 4 ATAC, E10.5 pre-HSC I,
- GSM7401003 ATAC, E10.5 pre-HSC II, rep 1 ATAC, E10.5 pre-HSC II,
- GSM7401004 ATAC, E10.5 pre-HSC II, rep 2 ATAC, E10.5 pre-HSC II,
- GSM7401005 ATAC, E10.5 pre-HSC II, rep 3 ATAC, E10.5 pre-HSC II,
- GSM7401006 ATAC, E10.5 pre-HSC II, rep 4 ATAC, E10.5 pre-HSC II,
- GSM7401007 ATAC, E8.5 EC, rep 1 ATAC, E8.5 EC,
- GSM7401008 ATAC, E8.5 EC, rep 2 ATAC, E8.5 EC,
- GSM7401009 ATAC, E8.5 EC, rep 3 ATAC, E8.5 EC,
- GSM7401010 ATAC, E8.5 EC, rep 4 ATAC, E8.5 EC,
- GSM7401011 ATAC, E8.5 HE, rep 1 ATAC, E8.5 HE,
- GSM7401012 ATAC, E8.5 HE, rep 2 ATAC, E8.5 HE,
- GSM7401013 ATAC, E8.5 HE, rep 3 ATAC, E8.5 HE,
- GSM7401014 ATAC, E8.5 HE, rep 4 ATAC, E8.5 HE,
- GSM7401015 ATAC, E9.5 EC, rep 1 ATAC, E9.5 EC,
- GSM7401016 ATAC, E9.5 EC, rep 2 ATAC, E9.5 EC,
- GSM7401017 ATAC, E9.5 EC, rep 3 ATAC, E9.5 EC,
- GSM7401018 ATAC, E9.5 EC, rep 4 ATAC, E9.5 EC,
- GSM7401019 ATAC, E9.5 HE, rep 1 ATAC, E9.5 HE,
- GSM7401020 ATAC, E9.5 HE, rep 2 ATAC, E9.5 HE,
- GSM7401021 ATAC, E9.5 HE, rep 3 ATAC, E9.5 HE,
- GSM7401022 ATAC, E9.5 HE, rep 4 ATAC, E9.5 HE,
- GSM7401023 ATAC, E9.5 pro-HSC/HPC, rep 1 ATAC, E9.5 pro-HSC/HPC,
- GSM7401024 ATAC, E9.5 pro-HSC/HPC, rep 2 ATAC, E9.5 pro-HSC/HPC,
- GSM7401025 ATAC, E9.5 pro-HSC/HPC, rep 3 ATAC, E9.5 pro-HSC/HPC,
- GSM7401026 RNA, E10.5 EC, rep 1 RNA, E10.5 EC,
- GSM7401027 RNA, E10.5 EC, rep 2 RNA, E10.5 EC,
- GSM7401028 RNA, E10.5 EC, rep 3 RNA, E10.5 EC,
- GSM7401029 RNA, E10.5 HE, rep 1 RNA, E10.5 HE,
- GSM7401030 RNA, E10.5 HE, rep 2 RNA, E10.5 HE,
+ 23 more — browse all 63 samples with per-sample file links →
- GSE290082 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 25 samples shares regulatory, network
- GSE236450 SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes 24 samples shares regulatory, network
- GSE290574 Gene Regulatory Networks Orchestrating Oocyte Fate Bifurcation in Primordial Follicles Revealed by Single-Cell Transcriptomics 386 samples shares regulatory, network
- GSE260656 A smooth muscle cell gene-regulatory network critical for the development of advanced-stage and symptomatic atherosclerosis 23 samples shares regulatory, network
- GSE267584 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 22 samples shares regulatory, network
- GSE287483 Competing dynamic gene regulatory networks involved in fibroblast reprogramming to haematopoietic progenitor cells [RNA-Seq] 12 samples shares regulatory, network
- GSE200051 Genome-wide analysis of microRNA-mRNA gene regulatory networks reveals widespread involvement of microRNAs in visually guided eye emmetropization and myopia [mRNA retina] 10 samples shares regulatory, network
- GSE223050 The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1–linked chromatin opening 336 samples shares regulatory
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.