GEO series
Loop extrusion by cohesin plays a role in enhancer-activated gene expression early in differentiation (ChIP-seq)
GSE163008
Mus musculus
Genome binding/occupancy profiling by high throughput sequencing
26 samples
Submitted 2026/04/14
Platform GPL19057
Summary
Enhancers and their target promoters often come into close physical proximity when activated. This may be explained by a variety of mechanisms, including cohesin-mediated chromatin loop extrusion. However, acute depletion of cohesin does not cause widespread changes in gene expression. We have tested the role of cohesin-mediated loop extrusion in gene expression at the mouse alpha-globin locus during erythropoiesis. Acute depletion of cohesin disrupts alpha-globin expression at early but not late stages of differentiation. Furthermore, when single or multiple CTCF sites, known to block cohesin, are placed between the alpha-globin enhancers and promoters, alpha-gene expression is disrupted. Importantly, the CTCF site’s orientation is critical, suggesting that within this activated domain, in definitive erythroid cells cohesin predominantly but not exclusively, translocates from the enhancers to the promoters. We find that loop extrusion does play an important role in establishing enhancer-promoter proximity and consequent expression of inducible genes during differentiation.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE163008_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 26 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA684314 and SRA study SRP297583. Searching any of these in the dataset finder brings you back here.
Study design
25 conditions, each sampled once — no replicated groups
CTCF_ChIP_EB_WT ×2
Read from 26 sample titles: 25 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- 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
Similar datasets
- GSE261221 Scaffolding element rewires genome architecture during differentiation at the Zfp608 locus (ChIP-Seq) 189 samples
- GSE272524 Chromatin-dependent motif syntax defines differentiation trajectories [ChIP-seq] 76 samples
- GSE295340 Polycomb Chromatin Topology Enables Long-Range Enhancer Recruitment during Craniofacial Development [ChIP-seq] 42 samples
- GSE267882 Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for effector Treg cell differentiation [ChIP-Seq] 34 samples
- GSE294851 Utx (Kdm6a) promotes differentiation non-catalytically in somatic self-renewing epithelia [ChIP-seq] 17 samples
- GSE303384 Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq] 92 samples
- GSE294085 SIRT6 Overexpression Counteracts Chromatin Aging [ChIP-Seq] 74 samples
- GSE297574 H3K9 di-methylation dynamics underlies mouse minor zygotic genome activation [spike-in ChIP-seq of mESC] 64 samples
Share this dataset
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.