GSM889256

GEO first seen 2013

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

78/100 · C

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

What this means

claude:haiku

This Arabidopsis thaliana bulk RNA-seq combines exceptional basecalling accuracy (Q20=100%, Q30=100%) with balanced GC content (50.5%), though the 42 bp read length is relatively short for full-transcript assembly—ideal for single-nucleotide resolution expression profiling, splice-variant detection at known loci, and high-sensitivity differential expression analysis in this model plant.

Data type / assay

bulk-RNA-seq

Organism

Arabidopsis thaliana

Metrics (value · how obtained)

n content pct 0.001 measured

pct q20 bases 100 measured

pct q30 bases 100 measured

gc content pct 50.5 measured

mean read length 42 measured

mean base quality 30 measured

adapter content pct 0 measured

duplication rate pct 44.55 measured

How this grade was computed

Weighted mean of 4 scored metric(s) → 78/100

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 44.55 measured ×0.4 68%

QC cost 29 s compute

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