PRJEB13884

BioProject first seen 2017

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

89/100 · B

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

What this means

claude:haiku

Mus musculus RNA-seq limited primarily by extreme duplication rate (58.8%) suggesting PCR overamplification or transcript complexity collapse, partially offset by strong base quality (Q30 96.4%); usable for coarse expression calls but elevated duplication introduces systematic bias for isoform quantification.

Data type / assay

bulk-RNA-seq

Organism

Mus musculus

Instrument

Illumina HiSeq 2500

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads), BAM/CRAM (aligned)

N numbers (samples, groups)

18 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 64905988200 reported

total reads 649059882 reported

n content pct 0.009 measured

pct q20 bases 99.2 measured

pct q30 bases 96.4 measured

gc content pct 44.7 measured

mean read length 100 measured

mean base quality 37 measured

adapter content pct 1.2 measured

duplication rate pct 58.82 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 89/100

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 96.4 measured ×1 100%

mean base quality 37 measured ×0.6 100%

adapter content pct 1.2 measured ×0.4 100%

duplication rate pct 58.82 measured ×0.4 36%

QC cost 19 s compute

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