GEO series

Cohesin mediates transcriptional insulation by CCCTC-binding factor

GSE9613 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 50 samples Submitted 2008/01/30 Platform GPL6137Platform GPL6134Platform GPL6140Platform GPL6143Platform GPL570Platform GPL6129Platform GPL6132Platform GPL6135Platform GPL6138Platform GPL6141Platform GPL6144Platform GPL6136Platform GPL6130Platform GPL6133Platform GPL6139Platform GPL6142Platform GPL6131

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 50 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: Homo sapiens (human)
Samples: 50 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Chromosome segregation in mitosis and meiosis depends on sister chromatid cohesion mediated by cohesin complexes. Mutation of cohesin and other cohesion proteins causes transcriptional and developmental defects in animals and humans, but the molecular cause of these phenotypes is unknown. Here we describe 8811 cohesin binding sites in the human genome and show that the CCCTC-binding factor (CTCF) is associated with 88% of these.

Read the full summary ↓

CTCF is dispensable for loading of cohesin onto DNA but is required for enrichment of cohesin at its binding sites. We provide evidence that cohesin is required for the role of CTCF sites in insulating promoters from distant enhancers. Like CTCF, cohesin is located on the maternal but not on the paternal allele of the H19 imprinting control region (ICR) and is required for imprinting of the H19-Igf2 locus. We find that cohesin is widely expressed in mammalian tissues, consistent with a cohesionindependent role in regulating gene expression. We propose that cohesin functions as a transcriptional insulator and speculate that subtle deficiencies in this function may be the cause of "cohesinopathies" such as Cornelia de Lange and Roberts syndrome. Keywords: ChIP-chip analysis

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE9613_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

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 PRJNA103467. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 18235444) ↗

Samples in this study

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+ 50 more — browse all 50 samples with per-sample file links →

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GSE229150 The transcription factor LHX2 mediates and enhances oncogenic BMP signaling in medulloblastoma 30 samples shares mediates, factor
GSE293071 Pioneer factors orchestrate tissue-specific cohesin-NIPBL chromatin entry and 3D genome organization 14 samples shares cohesin, factor
GSE95520 The cohesin release factor WAPL restricts chromatin loop extension [DamID] 12 samples shares cohesin, factor
GSE268035 STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia 541 samples shares cohesin
GSE260852 Cohesin acts as a transcriptional gatekeeper by restraining pause–release to promote processive elongation [ChIP-seq] 68 samples shares cohesin

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