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A three-dimensional map of the human genome at kilobase resolution reveals prinicples of chromatin looping

GSE63525 Homo sapiens (human) Other 200 samples Submitted 2014/12/11 Platform GPL16791Platform GPL15520Platform GPL13112Platform GPL11154Platform GPL17021
At a glance

human · 200 samples

Organism
Homo sapiens (human)
Samples
200 samples: 197 × HICGroups 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.
Summary (written by the submitters)
We use in situ Hi-C to probe the three-dimensional architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1-kilobase resolution. We find that genomes are partitioned into local domains, which are associated with distinct patterns of histone marks and segregate into six subcompartments.
Read the full summary ↓
We identify ~10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs ‘facing’ one another. The inactive X-chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.
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 (GSE63525_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 PRJNA268125 and SRA study SRP050102. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25497547) ↗
Study design
197 × HIC

Supports a between-group comparison across 197 samples.

How we read this: 1 replicated groups read from 200 sample titles; they account for 197 of them. 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.

Samples in this study

+ 160 more — browse all 200 samples with per-sample file links →

Datasets on a similar topic

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