Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE63525

GEO first seen 2015

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

Organism
Homo sapiens; Mus musculus
Samples
200
Type
Other
Submitted
2014-11-20

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. We identify ~10,000 loops. These loops frequently link promoters and enhancers, correlate with gene...

Provenance — who produced it, who reused it

Linked to 226 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.

Deposited / produced by
Suhas RaoMiriam HuntleyErez Lieberman Aiden
Reused by

10 further papers cite this accession but reuse could not be confirmed.

Deep data QC

metadata only · no data-level QC for this type

Standardized, field-standard QC computed by touching the data — every metric states how it was obtained

No quantitative QC rubric exists for this data type yet, so it is deliberately left unscored — this is an honest "not applicable", not a poor rating.

QC cost 4 s compute

measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0 · provisional — verify independently

Scientific quality

Based on hands-on reproduction of the papers that use this dataset. A reproducible paper that stands on this data is positive evidence; a flagged one is a prompt to look closer — never a verdict on the dataset itself without the evidence.

2 studies use it 2 reproduced mean score 88