Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE89408

GEO first seen 2018

RNAseq study of synovial biopsies

Organism
Homo sapiens
Samples
218
Type
Expression profiling by high...
Submitted
2016-11-01

Total RNA sequencing was performed on samples isolated from joint synovial biopsies from subjects with and without rheumatoid arthritis

Provenance — who produced it, who reused it

Linked to 41 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.

Deposited / produced by
A M WalshY Guo
Reused by

35 further papers cite this accession but reuse could not be confirmed.

Deep data QC

85/100 · B

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

Data type / assay
bulk-RNA-seq
Organism
Homo sapiens
Instrument
Illumina HiSeq 2000
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads), BAM/CRAM (aligned)
N numbers (samples, groups)
218 / 218 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 3737734710007 reported
total reads 18780822907 reported
n content pct 0 measured
pct q20 bases 97.6 measured
pct q30 bases 94.5 measured
gc content pct 52.2 measured
mean read length 100.7 measured
mean base quality 36.5 measured
adapter content pct 1.48 measured
duplication rate pct 69.59 measured
supplementary file types TXT reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 85/100

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 94.5 measured ×1 100%
mean base quality 36.5 measured ×0.6 100%
adapter content pct 1.48 measured ×0.4 100%
duplication rate pct 69.59 measured ×0.4 12%
QC cost 19 s compute

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