Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE104782

GEO first seen 2018

Single-cell RNA-seq analysis reveals the progression of human osteoarthritis

Organism
Homo sapiens
Samples
34
Type
Expression profiling by high...
Submitted
2017-10-10

Understanding the molecular mechanisms underlying human cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). Here, we report the molecular programmes and lineage progression patterns controlling human OA pathogenesis using single-cell RNA sequencing (scRNA-seq). We performed unbiased transcriptome-wide scRNA-seq analysis, computational analysis and histological assays on 1464 chondrocytes from 10 patients with OA undergoing kne...

Provenance — who produced it, who reused it

Linked to 5 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
Quanbo JiYuxuan ZhengGuoqiang ZhangYuqiong HuXiaoying FanYu HouLu WenLi LiYameng XuYan WangFuchou Tang
Reused by

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

Deep data QC

69/100 · D

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 4000
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
34 / 34 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 1162467070200 reported
total reads 3874890234 reported
n content pct 0.002 measured
pct q20 bases 89.4 measured
pct q30 bases 79.2 measured
gc content pct 42.7 measured
mean read length 150 measured
mean base quality 34.6 measured
adapter content pct 4.4 measured
duplication rate pct 46.46 measured
supplementary file types TXT, XLSX reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 69/100

The D 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 79.2 measured ×1 46%
mean base quality 34.6 measured ×0.6 100%
adapter content pct 4.4 measured ×0.4 87%
duplication rate pct 46.46 measured ×0.4 63%
QC cost 13 s compute

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