Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE101737

GEO first seen 2017

p53 binding during the DNA double-strand break response

Organism
Homo sapiens
Samples
6
Type
Genome binding/occupancy pro...
Submitted
2017-07-21

We used ChIP-seq to assess where p53 binds in the human genome and how that binding changes during the DNA double-strand break response. In particular, we considered the 1-Mb-wide window centered on the MYC locus. Contrary to previous reports, we found no evidence of p53 binding at the MYC promoter. Rather, we identified three locations downstream of MYC at which p53 was bound; binding at each of these regions increased during the DNA double-strand break response.

Provenance — who produced it, who reused it

Linked to 1 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
Joshua R PorterLaura BaranelloEric Batchelor
Reused by

Deep data QC

insufficient data to score

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

Data type / assay
ChIP-seq
Organism
Homo sapiens
Instrument
NextSeq 500
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
6 / 6 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 15745939236 reported
total reads 207183411 reported
n content pct 0.003 measured
pct q20 bases 97.4 measured
pct q30 bases 96.2 measured
gc content pct 41.2 measured
mean read length 76 measured
mean base quality 34.9 measured
adapter content pct 0.09 measured
duplication rate pct 2.33 measured
supplementary file types BW, TXT reported
How this grade was computed

The insufficient grade is a transparent weighted average. Each metric below scored from 0–100% against the published ChIP-seq thresholds, weighted by its importance; nothing is hidden or subjective.

pct q30 bases 96.2 measured ×1 100%
QC cost 30 s compute

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