PRJNA229096

BioProject first seen 2014

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:haiku

Homo sapiens bulk RNA-seq (HiSeq 2000); grade B—proceed with duplication filtering. Duplication rate of 74.56% is severe and dominates the QC score; this likely reflects overamplification rather than true transcript abundance and will bias transcript quantification below saturation. Strong Q30 (89.6%) and mean quality (35.1) provide a foundation, but deduplication is essential.

Data type / assay

bulk-RNA-seq

Organism

Homo sapiens

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

14 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 80265602348 reported

total reads 542335151 reported

n content pct 0.014 measured

pct q20 bases 94.7 measured

pct q30 bases 89.6 measured

gc content pct 60 measured

mean read length 74 measured

mean base quality 35.1 measured

adapter content pct 0.21 measured

duplication rate pct 74.56 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 89.6 measured ×1 98%

mean base quality 35.1 measured ×0.6 100%

adapter content pct 0.21 measured ×0.4 100%

duplication rate pct 74.56 measured ×0.4 1%

QC cost 17 s compute

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