GSE96638

GEO first seen 2018

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

Chromatin Modification and Global Transcriptional Silencing in t... 2018 · 110 cites

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

Mouse bulk RNA-seq with solid base quality (Q30=95.2%, mean=35.8%) but substantial adapter contamination (24.62%, scored 0/100)—a library-prep rather than sequencer artifact. Recoverable with aggressive trimming; reported metadata confirms GEO integrity.

Data type / assay

bulk-RNA-seq

Organism

Mus musculus

Instrument

Illumina HiSeq 2500

Platform

ILLUMINA

Read type

short-read

Files available

FASTQ (raw reads)

N numbers (samples, groups)

50 / 50 runs

Completeness

100%

Metrics (value · how obtained)

checksum ok yes reported

total bases 151164036800 reported

total reads 755820184 reported

n content pct 0.003 measured

pct q20 bases 97.6 measured

pct q30 bases 95.2 measured

gc content pct 49.1 measured

mean read length 100 measured

mean base quality 35.8 measured

adapter content pct 24.62 measured

duplication rate pct 22.52 measured

supplementary file types TXT reported

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 95.2 measured ×1 100%

mean base quality 35.8 measured ×0.6 100%

adapter content pct 24.62 measured ×0.4 0%

duplication rate pct 22.52 measured ×0.4 100%

QC cost 17 s compute

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