Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE114564

GEO first seen 2021

Identification of novel serum biomarkers in early-stage HCC patients.

Organism
Homo sapiens
Samples
118
Type
Expression profiling by high...
Submitted
2018-05-17

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and is the one of the few cancers in which a continued increase in incidence has been observed over several years. HCC associated with chronic liver disease evolves from precancerous lesion and early HCC to overt cancer, and identifying key molecules contributing to early stage HCC is an urgent need. α-Fetoprotein (AFP) is the best serum biomarker for diagnosis of HCC, but sensitivity is low, particularly in detecti...

Provenance — who produced it, who reused it

Linked to 10 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
JungWoo EunSukWoo NamKeunhong SonHyungseok Kim
Reused by

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

Deep data QC

93/100 · A

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)
N numbers (samples, groups)
118 / 118 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 761917347514 reported
total reads 3771868057 reported
n content pct 0.008 measured
pct q20 bases 96.6 measured
pct q30 bases 91.4 measured
gc content pct 50.4 measured
mean read length 101 measured
mean base quality 35.7 measured
adapter content pct 0.17 measured
duplication rate pct 48.84 measured
supplementary file types TXT reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 93/100

The A 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 91.4 measured ×1 100%
mean base quality 35.7 measured ×0.6 100%
adapter content pct 0.17 measured ×0.4 100%
duplication rate pct 48.84 measured ×0.4 58%
QC cost 14 s compute

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