GEO series

CTCF binding polarity determines chromatin looping [4C]

GSE72539 Mus musculus (mouse) Other 504 samples Submitted 2015/10/29 Platform GPL19057Platform GPL13112

At a glance

mouse · 504 samples

Organism: Mus musculus (mouse)
Samples: 504 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentally stable and dynamic chromatin loops.

Read the full summary ↓

As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR-Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher order chromatin structure.

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 (GSE72539_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 ↓

Also filed as BioProject PRJNA294301 and SRA study SRP063007. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26527277) ↗

Samples in this study

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GSE274040 Transcriptional and chromatin accessibility landscapes of hematopoiesis in a mouse model of breast cancer 16 samples shares chromatin
GSE281122 INO80/SWR Remodelers Regulate Pol II Transcription through BRD2 and Chromatin Landscape (TT-seq) 16 samples shares chromatin
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