Corpus 1,273 assessed · 1,174 scored · 643 reproduced ≥75 · 169 flagged ·∅ 74.1/100
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SRR3540304

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 a mouse small-RNA (miRNA-Seq) library sequenced on a HiSeq 2000, and overall it is a solid, trustworthy dataset (grade B, 83/100) whose score rests almost entirely on directly measured QC metrics. Base quality is excellent — pct_q30_bases of 100% and a mean base quality well above any concern, with zero adapter contamination and negligible N content — so per-base accuracy is not a limiting factor for downstream mapping or miRNA quantification. The one metric that pulled the grade down is the duplication_rate_pct of 96.28%, which scored 0; for most assays this signals a low-complexity library, but in short small-RNA sequencing such high duplication is expected and partly artefactual, since mature miRNAs are short, highly abundant, and identical reads are biologically genuine rather than purely PCR duplicates — so do not naively deduplicate before counting. With evidence_strength at the maximum and the key quality metrics all measured rather than extrapolated, this reading is firm and not provisional; the dataset is reusable for miRNA expression work provided the duplication is interpreted in that small-RNA context.

Data type / assay
bulk-RNA-seq
Organism
Mus musculus
Instrument
Illumina HiSeq 2000
Platform
ILLUMINA
N numbers (samples, groups)
1 runs
Metrics (value · how obtained)
checksum ok yes reported
total bases 703283574 reported
total reads 14352726 reported
n content pct 0.002 measured
pct q20 bases 100 measured
pct q30 bases 100 measured
gc content pct 51.5 measured
mean read length 49 measured
mean base quality 71 measured
adapter content pct 0 measured
duplication rate pct 96.28 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 100 measured ×1 100%
mean base quality 71 measured ×0.6 100%
adapter content pct 0 measured ×0.4 100%
duplication rate pct 96.28 measured ×0.4 0%
QC cost 19 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