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

GSE130970

GEO first seen 2023

Gene expression predicts histological severity and reveals distinct molecular profiles of nonalcoholic fatty liver disease

Organism
Homo sapiens
Samples
78
Type
Expression profiling by high...
Submitted
2019-05-09

Transcriptomic analysis of liver biopsies that cover the spectrum of nonalcoholic fatty liver disease reveals genes that are progressively regulated over the course of the disease. This study demonstrates that progressive changes in expression of these genes can be used to approximate the histological grade of a liver biopsy. Furthermore, the relative progression profiles of these disease-responsive genes are shown to be distinct across patient biopsies. This observation suggests that there may...

Provenance — who produced it, who reused it

Linked to 33 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
Stephen A HoangAbdul OseiniRyan E FeaverBanumathi ColeAmon AsgharpourRobert VincentMohammad SiddiquiMark J LawsonNathan C DayJustin M TaylorBrian R WamhoffFaridoddin MirshahiMelissa J ContosMichael IdowuArun J Sanyal
Reused by

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

Deep data QC

97/100 · 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 2500
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
78 / 78 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 439938287837 reported
total reads 4313371057 reported
n content pct 0.008 measured
pct q20 bases 99 measured
pct q30 bases 97.7 measured
gc content pct 45.6 measured
mean read length 51 measured
mean base quality 38.2 measured
adapter content pct 0 measured
duplication rate pct 39.41 measured
supplementary file types CSV reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 97/100

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 97.7 measured ×1 100%
mean base quality 38.2 measured ×0.6 100%
adapter content pct 0 measured ×0.4 100%
duplication rate pct 39.41 measured ×0.4 79%
QC cost 14 s compute

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