SRP013894

ENA 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

Columba livia (rock pigeon) bulk RNA-seq on HiSeq 2000 spans 5.4B reads with perfect quality (100% ≥Q20/Q30), providing ultradeep transcriptome for urban-ecology and vertebrate-physiology studies. Exceptional read depth enables comprehensive isoform mapping and rare-transcript discovery; pigeon genome less-annotated than chickens but comparative genomics to avian species feasible.

Data type / assay

bulk-RNA-seq

Organism

Columba livia

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

62 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 989728295479 reported

total reads 5466734153 reported

n content pct 0.044 measured

pct q20 bases 100 measured

pct q30 bases 100 measured

gc content pct 43.8 measured

mean read length 100 measured

mean base quality 30 measured

adapter content pct 0.31 measured

duplication rate pct 5.11 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 30 measured ×0.6 33%

adapter content pct 0.31 measured ×0.4 100%

duplication rate pct 5.11 measured ×0.4 100%

QC cost 38 s compute

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