SRP000395

ENA first seen 2012

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

33/100 · F

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

What this means

claude:haiku

Castanea dentata (American chestnut) EST library from a 454 GS 20 platform with 2 million reads at low Q30 (22%), capturing early-era transcriptome data. The dataset has historical value for plant genomics but is limited by platform constraints and quality.

Data type / assay

bulk-RNA-seq

Organism

Castanea dentata

Instrument

454 GS 20

Platform

LS454

Files available

FASTQ (raw reads)

N numbers (samples, groups)

24 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 475338778 reported

total reads 2071283 reported

n content pct 0.142 measured

pct q20 bases 89.2 measured

pct q30 bases 21.9 measured

gc content pct 45.4 measured

mean read length 228.9 measured

mean base quality 25.7 measured

adapter content pct 0 measured

duplication rate pct 13.02 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 33/100

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 21.9 measured ×1 0%

mean base quality 25.7 measured ×0.6 0%

adapter content pct 0 measured ×0.4 100%

duplication rate pct 13.02 measured ×0.4 100%

QC cost 5 s compute

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