Corpus 1,277 assessed · 1,178 scored · 644 reproduced ≥75 · 170 flagged ·∅ 74/100
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GSE74377

GEO first seen 2016

Overexpression of PHF8 promotes an EMT-related gene signature in MCF10A cells

Organism
Homo sapiens
Samples
16
Type
Expression profiling by high...
Submitted
2015-10-27

PHF8 exerts distinct functions in different types of cancer. However, the mechanisms underlying its specific functions in each case remain obscure. To establish whether overexpression of PHF8 regulates the TGF-β induced the epithelial-mesenchymal transition (EMT), we treated MCF10A-Mock (control) and MCF10A-PHF8wt (overexpressing wild-type PHF8) cells with TGF-β1 for 0, 24, 48 and 72 hours and performed RNA-seq in biological duplicates. Our data indicated that EMT gene signatures were significan...

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
Peng ShaoHank H Qi
Reused by

1 further paper cites this accession but reuse could not be confirmed.

Deep data QC

96/100 · A

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
Homo sapiens
Instrument
Illumina HiSeq 2500
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
22 / 16 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 25308513300 reported
total reads 253085133 reported
n content pct 0.006 measured
pct q20 bases 99.5 measured
pct q30 bases 98.3 measured
gc content pct 48.6 measured
mean read length 50 measured
mean base quality 38.1 measured
adapter content pct 0.01 measured
duplication rate pct 40.1 measured
supplementary file types XLSX reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 96/100

The A 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 98.3 measured ×1 100%
mean base quality 38.1 measured ×0.6 100%
adapter content pct 0.01 measured ×0.4 100%
duplication rate pct 40.1 measured ×0.4 78%
QC cost 11 s compute

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