Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 26 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
- 26 samples: 25 distinct titles, 1 of them repeatedGroups 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.
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 GSE163008_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 PRJNA684314 and SRA study SRP297583. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 26 sample titles: 25 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.
- GSM4970137 CTCF_ChIP_FL_Fwd_rep1_i2
- GSM4970138 CTCF_ChIP_FL_Fwd_rep2_5-1
- GSM4970139 CTCF_ChIP_FL_Fwd_rep3_5-4
- GSM4970140 CTCF_ChIP_FL_Rev_rep1_f3
- GSM4970141 CTCF_ChIP_FL_Rev_rep2_g-1
- GSM4970142 CTCF_ChIP_FL_Rev_rep3_g-4
- GSM4970143 CTCF_ChIP_EB_WT_rep1
- GSM4970144 CTCF_ChIP_EB_WT_rep2
- GSM4970145 CTCF_ChIP_EB_Fwd_rep1_D2H3
- GSM4970146 CTCF_ChIP_EB_Fwd_rep2_F2D3
- GSM4970147 CTCF_ChIP_EB_Rev_rep1_D2D6
- GSM4970148 CTCF_ChIP_EB_Rev_rep2_D3H2
- GSM7774304 Spleen, Fwd A, Rad21
- GSM7774305 Spleen, Fwd A rep, Rad21
- GSM7774306 Spleen, Fwd B, Rad21
- GSM7774307 Spleen, Fwd B rep, Rad21
- GSM7774308 Spleen, Fwd C, Rad21
- GSM7774309 Spleen, Rev A, Rad21
- GSM7774310 Spleen, Rev A rep, Rad21
- GSM7774311 Spleen, Rev C, Rad21
- GSM7774312 EB, WT, Rad21
- GSM7774313 EB, D3F3 Fwd, Rad21
- GSM7774314 EB, D3F3 rep Fwd, Rad21
- GSM7774315 EB, F2D3, Fwd, Rad21
- GSM7774316 EB, D3H2, Rev, Rad21
- GSM7774317 EB, WT rep, Rad21
- GSE163012 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation 109 samples shares enhancer-activated, extrusion, cohesin, plays, early, loop
- GSE306301 Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer. 81 samples shares extrusion, cohesin, loop
- GSE243959 The mitotic STAG3–cohesin complex shapes male germline nucleome [ChIP-seq] 92 samples shares chip-seq, cohesin
- GSE274792 CTCF tunes gene expression in a loop-dependent and -independent manner [ChIP-Seq] 30 samples shares chip-seq, loop
- GSE261412 Acute hormonal signaling-induced 3D chromatin loop reorganization controls adipocyte thermogenesis [ChIP-Seq mouse, H3K27ac, H3K4me3, H2AZ] 24 samples shares chip-seq, loop
- GSE267320 Early-life ketone body signaling promotes beige fat biogenesis through changes in histone acetylome and β-hydroxybutyrylome [ChIP-seq] 20 samples shares chip-seq, early
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares extrusion, loop
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares chip-seq, early
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.