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RNA-seq of 50 paired hepatocellular carcinoma
RNA-seq of Illumina sequencing of 50 paired normal and tumor samples
Provenance — who produced it, who reused it
Linked to 31 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
Guojun HouGang LiuLei LiuWeiping Zhou
Reused by
- Systematic evaluation of differential splicing tools for RNA-seq... 2019 · 185 cites
- Long non-coding RNA XIST regulates PTEN expression by sponging m... 2017 · 127 cites
- MiR-126 negatively regulates PLK-4 to impact the development of... 2018 · 86 cites
- Potential diagnostic and prognostic marker dimethylglycine dehyd... 2016 · 83 cites
27 further papers cite this accession but reuse could not be confirmed.
Deep data QC
70/100 · CStandardized, 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 Genome Analyzer
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
100 / 100 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok
yes
reported
total bases
673915299600
reported
total reads
3369576498
reported
n content pct
0.023
measured
pct q20 bases
88.3
measured
pct q30 bases
79.6
measured
gc content pct
49.1
measured
mean read length
100
measured
mean base quality
32
measured
adapter content pct
0.15
measured
duplication rate pct
28.97
measured
supplementary file types
XLSX
reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 70/100
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
79.6
measured
×1
48%
mean base quality
32
measured
×0.6
67%
adapter content pct
0.15
measured
×0.4
100%
duplication rate pct
28.97
measured
×0.4
100%
QC cost
21 s compute
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0