Analysis of three-dimensional enhancer network regulated by CTCF in CD4+ T cells [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 33 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
- 33 samples: 16 conditions, mostly in duplicateGroups 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
- 3D enhancer architecture coordinated by CTCF determines immune-related gene expression patterns via RNA polymerase II pause-release in CD4+ T cellsNucleic acids research · 2025
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 GSE243710_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 PRJNA1019670 and SRA study SRP462475. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 32 samples.
How we read this: 16 replicated groups read from 33 sample titles; they account for 32 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.
- GSM7794589 CD4T, Input
- GSM7794590 CD4T, KO CTCF rep1 CD4T, KO CTCF
- GSM7794591 CD4T, KO CTCF rep2 CD4T, KO CTCF
- GSM7794592 CD4T, KO H3K27ac rep1 CD4T, KO H3K27ac
- GSM7794593 CD4T, KO H3K27ac rep2 CD4T, KO H3K27ac
- GSM7794594 CD4T, KO H3K27me3 rep1 CD4T, KO H3K27me3
- GSM7794595 CD4T, KO H3K27me3 rep2 CD4T, KO H3K27me3
- GSM7794596 CD4T, KO H3K4me1 rep1 CD4T, KO H3K4me1
- GSM7794597 CD4T, KO H3K4me1 rep2 CD4T, KO H3K4me1
- GSM7794598 CD4T, KO H3K4me3 rep1 CD4T, KO H3K4me3
- GSM7794599 CD4T, KO H3K4me3 rep2 CD4T, KO H3K4me3
- GSM7794600 CD4T, KO RPB1-S5P rep1 CD4T, KO RPB1-S5P
- GSM7794601 CD4T, KO RPB1-S5P rep2 CD4T, KO RPB1-S5P
- GSM7794602 CD4T, KO SMC1A rep1 CD4T, KO SMC1A
- GSM7794603 CD4T, KO SMC1A rep2 CD4T, KO SMC1A
- GSM7794604 CD4T, KO STAT5 rep1 CD4T, KO STAT5
- GSM7794605 CD4T, KO STAT5 rep2 CD4T, KO STAT5
- GSM7794606 CD4T, WT CTCF rep1 CD4T, WT CTCF
- GSM7794607 CD4T, WT CTCF rep2 CD4T, WT CTCF
- GSM7794608 CD4T, WT H3K27ac rep1 CD4T, WT H3K27ac
- GSM7794609 CD4T, WT H3K27ac rep2 CD4T, WT H3K27ac
- GSM7794610 CD4T, WT H3K27me3 rep1 CD4T, WT H3K27me3
- GSM7794611 CD4T, WT H3K27me3 rep2 CD4T, WT H3K27me3
- GSM7794612 CD4T, WT H3K4me1 rep1 CD4T, WT H3K4me1
- GSM7794613 CD4T, WT H3K4me1 rep2 CD4T, WT H3K4me1
- GSM7794614 CD4T, WT H3K4me3 rep1 CD4T, WT H3K4me3
- GSM7794615 CD4T, WT H3K4me3 rep2 CD4T, WT H3K4me3
- GSM7794616 CD4T, WT RPB1-S5P rep1 CD4T, WT RPB1-S5P
- GSM7794617 CD4T, WT RPB1-S5P rep2 CD4T, WT RPB1-S5P
- GSM7794618 CD4T, WT SMC1A rep1 CD4T, WT SMC1A
- GSM7794619 CD4T, WT SMC1A rep2 CD4T, WT SMC1A
- GSM7794620 CD4T, WT STAT5 rep1 CD4T, WT STAT5
- GSM7794621 CD4T, WT STAT5 rep2 CD4T, WT STAT5
- GSE278338 ChIP-seq to measure binding of NIPBL/MAU2, RAD21, and CTCF in mouse embryonic stem cells and neural progenitor cells 50 samples shares ctcf, chip-seq
- GSE234273 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [ChIP-seq] 32 samples shares ctcf, chip-seq
- GSE245647 The Heme-regulated transcriptional repressor, BACH1 safeguards macrophage enhancer selection, activation andtissue adaptation [ChIP-seq] 62 samples shares enhancer, chip-seq
- GSE329244 Polycomb erasers BAP1 and UTX are dispensable for rapid bivalent gene activation but essential for enhancer establishment [ChIP-seq] 64 samples shares enhancer, chip-seq
- GSE295340 Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq] 42 samples shares enhancer, chip-seq
- GSE163008 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-seq) 26 samples shares enhancer, chip-seq
- GSE339012 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain [ChIP-Seq] 22 samples shares enhancer, chip-seq
- GSE290082 Enhancer-driven gene regulatory networks reveal transcription factors governing T cell adaptation and differentiation in the tumor microenvironment. 25 samples shares enhancer, network
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.