Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE79543

GEO first seen 2017

Stress-induced accumulation of DNA N6-Methyladenine in prefrontal cortex

Organism
Mus musculus
Samples
12
Type
Expression profiling by high...
Submitted
2016-03-23

Chemical covalent modifications on the 5-carbon position of cytosine, such as 5- methylcytosine and 5-hydroxymethylcytosine, are a set of well-characterized epigenetic marks that shape transcriptional landscaping. Compiling evidence suggests central roles of cytosine modification dynamics in neuronal functions such as memory formation and stress response. N6-methyladenine (6mA) that previously described in bacteria has been recently found in higher eukaryotes, including worms, flies and mice. Ho...

Provenance — who produced it, who reused it

Linked to 2 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
Bing Yao
Reused by

Deep data QC

72/100 · C

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

Data type / assay
bulk-RNA-seq
Organism
Mus musculus
Metrics (value · how obtained)
n content pct 0.002 measured
pct q20 bases 92.1 measured
pct q30 bases 81.4 measured
gc content pct 55.8 measured
mean read length 101 measured
mean base quality 33.4 measured
adapter content pct 0.48 measured
duplication rate pct 49.54 measured
How this grade was computed
Weighted mean of 4 scored metric(s) → 72/100

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

pct q30 bases 81.4 measured ×1 57%
mean base quality 33.4 measured ×0.6 90%
adapter content pct 0.48 measured ×0.4 100%
duplication rate pct 49.54 measured ×0.4 57%
QC cost 39 s compute

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