SRP056795

ENA first seen 2016

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

79/100 · C

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

What this means

claude:haiku

Arabidopsis bulk RNA-seq hampered by 14.43% adapter contamination and exceptionally high duplication at 54.32%—both major limitations. Read counts are severely biased; reuse requires aggressive deduplication and validation.

Data type / assay

bulk-RNA-seq

Organism

Arabidopsis thaliana

Instrument

Illumina HiSeq 2000

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

16 runs

Metrics (value · how obtained)

checksum ok yes reported

total bases 118040048600 reported

total reads 2360800972 reported

n content pct 0.005 measured

pct q20 bases 99.3 measured

pct q30 bases 97.9 measured

gc content pct 50 measured

mean read length 50 measured

mean base quality 38.5 measured

adapter content pct 14.43 measured

duplication rate pct 54.32 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 79/100

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 97.9 measured ×1 100%

mean base quality 38.5 measured ×0.6 100%

adapter content pct 14.43 measured ×0.4 31%

duplication rate pct 54.32 measured ×0.4 46%

QC cost 28 s compute

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