PRJNA399082

BioProject first seen 2020

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

20/100 · F

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

What this means

claude:haiku

NextSeq 500 bulk RNA-Seq of Mus musculus with 5.2 billion short reads and 439 Gb; note high N content (31.1%) and lower Q-scores (65.3% Q20, 63.7% Q30) indicating potential library prep or sequencing issues. Requires aggressive quality filtering or re-sequencing validation before downstream analysis.

Data type / assay

bulk-RNA-seq

Organism

Mus musculus

Instrument

NextSeq 500

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

40 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 439258548158 reported

total reads 5177850613 reported

n content pct 31.102 measured

pct q20 bases 65.3 measured

pct q30 bases 63.7 measured

gc content pct 26.9 measured

mean read length 35 measured

mean base quality 23.9 measured

adapter content pct 0.2 measured

duplication rate pct 67.07 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 20/100

The F 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 63.7 measured ×1 0%

mean base quality 23.9 measured ×0.6 0%

adapter content pct 0.2 measured ×0.4 100%

duplication rate pct 67.07 measured ×0.4 18%

QC cost 24 s compute

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