Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE121601

GEO first seen 2019

ChIP-seq of H3K27ac and CTCF in primary glioblastoma cultures

Organism
Homo sapiens
Samples
18
Type
Genome binding/occupancy pro...
Submitted
2018-10-22

We characterize H3K27ac and CTCF profiles of three primary glioblastoma cultures, and use them to bolster Hi-C datasets.

Provenance — who produced it, who reused it

Linked to 3 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
Michael J JohnstonAna NikolicMarco Gallo
Reused by

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

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)
19 / 18 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 81368519367 reported
total reads 542119217 reported
n content pct 0.002 measured
pct q20 bases 95.6 measured
pct q30 bases 93.7 measured
gc content pct 41 measured
mean read length 75.4 measured
mean base quality 34.3 measured
adapter content pct 0 measured
duplication rate pct 1.43 measured
supplementary file types BED, BROADPEAK, NARROWPEAK, TDF 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 93.7 measured ×1 100%
QC cost 24 s compute

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