Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE71434

GEO first seen 2018

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

Organism
Danio rerio; Mus musculus
Samples
57
Type
Genome binding/occupancy pro...
Submitted
2015-07-28

Histone modifications are considered as fundamental epigenetic regulators that control many crucial cellular processes 1. However, whether these marks can be passed on from gametes to the next generation in mammals is a long-standing question that remains unclear. By developing a highly sensitive approach, STAR ChIP-seq, we provided a panoramic view of the landscape of H3K4me3, a histone hallmark for transcription initiation 2, from developing gametes to postimplantation embryos. Interestingly,...

Provenance — who produced it, who reused it

Linked to 25 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
Bingjie ZhangHui ZhengBo HuangWenzhi LiWei Xie
Reused by

16 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
Mus musculus; Danio rerio
Instrument
Illumina HiSeq 1500
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
72 / 57 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 280151478931 reported
total reads 1379244044 reported
n content pct 0.008 measured
pct q20 bases 90.6 measured
pct q30 bases 86.5 measured
gc content pct 42.8 measured
mean read length 126 measured
mean base quality 34 measured
adapter content pct 5.01 measured
duplication rate pct 3.27 measured
supplementary file types BED, 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 86.5 measured ×1 83%
QC cost 16 s compute

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