Corpus 1,273 assessed · 1,174 scored · 643 reproduced ≥75 · 169 flagged ·∅ 74.1/100
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GSE28866

GEO first seen 2012

Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers

Organism
Homo sapiens
Samples
99
Type
Non-coding RNA profiling by...
Submitted
2011-04-26

Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs (lncRNAs), as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type specific biomarkers. However, despite the potential importance of lncRNAs to the cancer field, no comprehensive survey of lncRNA expression across various cancers has been repor...

Provenance — who produced it, who reused it

Linked to 3 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
Alayne L BrunnerAndrew H BeckBadreddin EdrisRobert T SweeneyShirley X ZhuRui LiKelli MontgomerySushama VarmaThea GilksXiangqian GuoJoseph W FoleyDaniela M WittenCraig P GiacominiRyan A FlynnJonathan R PollackRobert TibshiraniHoward Y ChangMatt van de RijnRobert B West
Reused by

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

Deep data QC

metadata only · no data-level QC for this type

Standardized, field-standard QC computed by touching the data — every metric states how it was obtained

Data type / assay
bulk-RNA-seq
Organism
Homo sapiens
Instrument
Illumina Genome Analyzer IIx
Platform
ILLUMINA
Read type
short-read
Files available
FASTQ (raw reads)
N numbers (samples, groups)
114 / 99 runs
Completeness
100%
Metrics (value · how obtained)
checksum ok yes reported
total bases 75862349592 reported
total reads 2028544633 reported
supplementary file types BED, TXT reported
QC cost 7 s compute

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