Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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ERR409900

ENA first seen 2018

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.

Reused by

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

Deep data QC

83/100 · B

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

What this means
claude:opus

This is bulk human RNA-seq from an Illumina HiSeq 2000, and it earned a solid B (83/100): the per-base quality is excellent, with mean base quality of 37.9 and 96.7% of bases at Q30, alongside zero adapter contamination, so the raw sequence itself is clean and reliable for expression analysis. The single factor dragging the grade down is an 85% duplication rate, which scored 0 on its metric — though for high-depth RNA-seq a large fraction of duplicates is expected from highly expressed transcripts rather than purely a library-complexity defect, so judge it against your application (it matters more if you intend to deduplicate or call variants than for standard differential-expression work). One caveat for reuse is the short 51 bp single-end-length reads, which limit confident multi-mapping resolution and splice-junction detection. Note that the core quality metrics here are genuinely measured rather than extrapolated, so this reading is reasonably firm rather than provisional, though the headline read/base counts are reported rather than independently verified.

Data type / assay
bulk-RNA-seq
Organism
Homo sapiens
Instrument
Illumina HiSeq 2000
Platform
ILLUMINA
N numbers (samples, groups)
1 runs
Metrics (value · how obtained)
checksum ok yes reported
total bases 3060000000 reported
total reads 60000000 reported
n content pct 0.022 measured
pct q20 bases 98.9 measured
pct q30 bases 96.7 measured
gc content pct 51.9 measured
mean read length 51 measured
mean base quality 37.9 measured
adapter content pct 0 measured
duplication rate pct 85 measured
How this grade was computed
Weighted mean of 4 scored metric(s) → 83/100

The B 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 96.7 measured ×1 100%
mean base quality 37.9 measured ×0.6 100%
adapter content pct 0 measured ×0.4 100%
duplication rate pct 85 measured ×0.4 0%
QC cost 15 s compute

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

Scientific quality

Based on hands-on reproduction of the papers that use this dataset. A reproducible paper that stands on this data is positive evidence; a flagged one is a prompt to look closer — never a verdict on the dataset itself without the evidence.

1 studies use it 1 reproduced mean score 89