Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE125159

GEO first seen 2020

Phosphorylation of the ancestral histone variant H3.3 amplifies stimulation-induced transcription

Organism
Mus musculus
Samples
74
Type
Expression profiling by high...
Submitted
2019-01-16

Complex organisms are able to rapidly induce select genes among thousands in response to diverse environmental cues. This occurs in the context of large genomes condensed with histone proteins into chromatin. The macrophage response to pathogen sensing, for example, rapidly engages highly conserved signaling pathways and transcription factors (TF) for coordination of inflammatory gene induction. Enriched integration of histone H3.3, the ancestral histone H3 variant, is a feature of inflammatory...

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
Anja ArmacheSteven Z Josefowicz
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
Mus musculus
Metrics (value · how obtained)
n content pct 0.014 measured
pct q20 bases 98 measured
pct q30 bases 94 measured
gc content pct 42.6 measured
mean read length 51 measured
mean base quality 38.4 measured
adapter content pct 0.01 measured
duplication rate pct 11.37 measured
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 94 measured ×1 100%
QC cost 28 s compute

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