SRP043127

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

73/100 · C

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

What this means

claude:haiku

Bulk RNA-seq (*Solanum lycopersicum*), Illumina HiSeq 2000. C-grade (73/100) with mean base quality floor (BQ=30, scoring 33/100) and moderate-high duplication (56.8%), indicating PCR bias or uneven transcript amplification. Short reads (51 bp) compound quality sensitivity; the duplication-QC double-hit makes low-abundance transcripts unreliable. Reuse acceptable for highly abundant genes only.

Data type / assay

bulk-RNA-seq

Organism

Solanum lycopersicum

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

9 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 6422345391 reported

total reads 125928341 reported

n content pct 0.002 measured

pct q20 bases 100 measured

pct q30 bases 100 measured

gc content pct 47.4 measured

mean read length 51 measured

mean base quality 30 measured

adapter content pct 0 measured

duplication rate pct 56.8 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 73/100

The C 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 measured ×0.4 100%

duplication rate pct 56.8 measured ×0.4 40%

QC cost 13 s compute

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