CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors
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: 6 conditions, mostly in triplicateGroups 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
- CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factorsCell reports · 2023
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 GSE233946_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 PRJNA978625 and SRA study SRP440754. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM7439551 RNA_ctrl_Rep1 RNA_ctrl
- GSM7439552 RNA_ctrl_Rep2 RNA_ctrl
- GSM7439553 RNA_ctrl_Rep3 RNA_ctrl
- GSM7439554 RNA_siCTCF_Rep1 RNA_siCTCF
- GSM7439555 RNA_siCTCF_Rep2 RNA_siCTCF
- GSM7439556 RNA_siCTCF_Rep3 RNA_siCTCF
- GSM7439557 ATAC_WT_GM_Rep1 ATAC_WT_GM
- GSM7439558 ATAC_WT_GM_Rep2 ATAC_WT_GM
- GSM7439559 ATAC_WT_GM_Rep3 ATAC_WT_GM
- GSM7439560 ATAC_WT_DM_Rep1 ATAC_WT_DM
- GSM7439561 ATAC_WT_DM_Rep2 ATAC_WT_DM
- GSM7439562 ATAC_WT_DM_Rep3 ATAC_WT_DM
- GSM7439563 ATAC_MKO_GM_Rep1 ATAC_MKO_GM
- GSM7439564 ATAC_MKO_GM_Rep2 ATAC_MKO_GM
- GSM7439565 ATAC_MKO_GM_Rep3 ATAC_MKO_GM
- GSM7439566 ATAC_MKO_DM_Rep1 ATAC_MKO_DM
- GSM7439567 ATAC_MKO_DM_Rep2 ATAC_MKO_DM
- GSM7439568 ATAC_MKO_DM_Rep3 ATAC_MKO_DM
- GSE267584 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 22 samples shares transcription, regulatory, factors
- GSE243165 Signal-responsive transcription factors cooperate to establish alveolar macrophage identity 42 samples shares transcription, factors
- GSE290574 Gene Regulatory Networks Orchestrating Oocyte Fate Bifurcation in Primordial Follicles Revealed by Single-Cell Transcriptomics 386 samples shares orchestrating, regulatory
- GSE283382 N6-methyladenosine modulate second cell fate decision by enhancing mRNA stability of pivotal transcription factors during primitive endoderm development [TBLC_RNAseq] 98 samples shares transcription, factors
- GSE282280 DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation. 93 samples shares transcription, factors
- GSE269910 The pioneer transcription factor PBX as a downstream target of MNX1 [ACT] 55 samples shares transcription, pioneer
- GSE281037 Large-scale transcriptomic analyses reveal downstream target genes of ZFY1 and ZFY2 transcription factors in male germ cells 48 samples shares transcription, factors
- GSE283958 Cohesin recruitment to promoters and enhancers by general transcription factors and chromatin regulators 47 samples shares transcription, factors
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.