Corpus 1,272 assessed · 1,173 scored · 643 reproduced ≥75 · 168 flagged ·∅ 74.1/100
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GSE75367

GEO first seen 2023

HER2 expression identifies dynamic functional states within circulating breast cancer cells

Organism
Homo sapiens
Samples
74
Type
Expression profiling by high...
Submitted
2015-11-24

Circulating tumour cells in women with advanced oestrogen-receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer acquire a HER2-positive subpopulation after multiple courses of therapy. In contrast to HER2-amplified primary breast cancer, which is highly sensitive to HER2-targeted therapy, the clinical significance of acquired HER2 heterogeneity during the evolution of metastatic breast cancer is unknown. Here we analyse circulating tumour cells from 19 wom...

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
Nicole V JordanBen S WittnerAditya BardiaCyril BenesMatteo LigorioYu ZhengMin YuTilak SundaresanRushil DesaiRyan O’KeefeRichard Y EbrightThomas A BarberRavi KapurDennis SgroiDavid T TingSridhar RamaswamyMehmet TonerWilhelm HaasShyamala MaheswaranDaniel A Haber
Reused by

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

Deep data QC

88/100 · 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)
N numbers (samples, groups)
148 / 74 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 29523767020 reported
total reads 261180310 reported
n content pct 0.007 measured
pct q20 bases 95.1 measured
pct q30 bases 90.3 measured
gc content pct 43.2 measured
mean read length 101 measured
mean base quality 35.3 measured
adapter content pct 15.26 measured
duplication rate pct 23.72 measured
supplementary file types TXT reported
How this grade was computed
Weighted mean of 4 scored metric(s) → 88/100

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 90.3 measured ×1 100%
mean base quality 35.3 measured ×0.6 100%
adapter content pct 15.26 measured ×0.4 26%
duplication rate pct 23.72 measured ×0.4 100%
QC cost 23 s compute

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