Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 109 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
- 109 samples: 81 distinct titles, 16 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.
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 GSE163012_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 PRJNA684313 and SRA study SRP297583. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 109 sample titles: 81 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
- GSM4970149 D2H3_Fwd_EB_ATAC
- GSM4970150 D3F3_EB_Fwd_ATAC
- GSM4970151 F2D3_Fwd_EB_ATAC
- GSM4970152 D2D6_Rev_EB_ATAC
- GSM4970153 D3H2_EB_Rev_ATAC
- GSM4970154 F2G6_Rev_ATAC_EB
- GSM4970155 EB_ATAC_wt_A
- GSM4970156 EB_ATAC_wt_B
- GSM4970157 EB_ATAC_wt_C
- GSM4970158 5-1_Fwd_FL_ATAC
- GSM4970159 5-4_Fwd_FL_ATAC
- GSM4970160 i-2_Fwd_FL_ATAC
- GSM4970161 f-3_Rev_FL_ATAC
- GSM4970162 g-1_Rev_FL_ATAC
- GSM4970163 g-4_Rev_FL_ATAC
- GSM4970164 5-2_wt_FL_ATAC
- GSM4970165 g7_WT_FL_ATAC
- GSM4970166 f-4_WT_ATAC_FL
- GSM4970167 D2H3_HS3839_Fwd
- GSM4970168 D2H3_HS4448_Fwd
- GSM4970169 D2H3_R1R2_Fwd
- GSM4970170 D3F3_HS3839_Fwd
- GSM4970171 D3F3_HS4448_Fwd
- GSM4970172 D3F3_R1R2_Fwd
- GSM4970173 D3H2_HS3839_Rev
- GSM4970174 D3H2_HS4448_Rev
- GSM4970175 D3H2_R1R2_Rev
- GSM4970176 F2D3_HS3839_Fwd
+ 69 more — browse all 109 samples with per-sample file links →
- GSE163008 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-seq) 26 samples shares enhancer-activated, extrusion, cohesin, plays, early, loop
- GSE163010 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ATAC-seq) 18 samples shares enhancer-activated, extrusion, cohesin, plays, early, loop
- GSE329202 Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-Seq, Rad21 and Stag2) 18 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
- GSE279297 Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption 63 samples shares extrusion, cohesin, loop
- GSE305208 Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption 30 samples shares extrusion, cohesin, loop
- GSE306297 Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer [ATAC-seq] 6 samples shares extrusion, cohesin, loop
- GSE288605 Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery 96 samples shares extrusion, loop
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.