In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer

Abu-Jamous, Basel; Buffa, Francesca M.; Harris, Adrian L.; Nandi, Asoke K.

doi:10.1186/s12943-017-0673-0

Molecular Cancer

Table 1 Breast cancer microarray datasets in contexts related to hypoxia

From: In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer

ID	GEO acc.	Year	Platform acc.	Platform	N^b	Cell line(s)	Description	Ref.
D01	GSE3188^a	2005	GPL2507	Sentrix Human-6	7	MCF7	Same samples of the last two datasets in the same order, but a different platform.	[67]
D02	GSE47533	2014	GPL6884	Illumina HumanWG-6 v3.0	4	MCF7	Time-series data through 48 h of exposure to hypoxia (1% O)	[40]
D03	GSE41491	2012	GPL14877	Affymetrix HG-U133+ 2.0	8	MCF7	Time-series data through 24 h of exposure to hypoxia (1% O)	[68]
D04	GSE47009	2014	GPL16686	Affymetrix HuGene 2.0 ST	3	MCF7	Samples at normoxia, hypoxia, and anoxia, respectively	-
D05	GSE18494	2009	GPL9419	Affymetrix HG-U133+ 2.0	4	MDA-MB-231	Time-series data through 12 h of exposure to hypoxia (0.5% O)	[43]
D06	GSE3188^a	2005	GPL96	Affymetrix HG-U133A	3	MCF7	Samples at normoxia, hypoxia, and normoxia exposed to DMOG, respectively	[67]
D07	GSE17188^a	2010	GPL6480	Agilent Whole Human Genome G4112F	3	SCP2 subline of MDA-MB-231	Time-series data through 24 h of exposure to hypoxia.	[69]
D08	GSE17188^a	2010	GPL6480	Agilent Whole Human Genome G4112F	3	LM2 subline of MDA-MB-231	Time-series data through 24 h of exposure to hypoxia.	[69]
D09	GSE15530	2010	GPL6947	Illumina HumanHT-12 V3.0	4	MCF7	Normoxia samples versus hypoxia samples, each is either transfected with non-specific shRNA or with reptin shRNA.	[28]
D10	GSE45362	2013	GPL10558	Illumina HumanHT-12 V4.0	4	MB231RN-LM derived from MDA-MB-231	Non-transfected samples versus transfected with has-miR-18a, each is in either a control medium or treated with Cobalt(II) chloride (CoCl2) hypoxia-mimicking agent.	[70]
D11	GSE29406	2012	GPL571	Affymetrix HG-U133A 2.0	4	MCF7	Normoxia samples versus hypoxia samples, each is either untreated or treated with lactic acid.	[71]
D12	GSE18384	2010	GPL6884	Illumina HumanWG-6 v3.0	4	MCF7	Normoxia samples versus hypoxia samples, each is either non-transfected or transfected with siRNA#1 against JMJD2B	[72]
D13	GSE3188^a	2005	GPL570	Affymetrix HG-U133+ 2.0	4	MCF7	Samples exposed to / transfected with oligogectamine, HIF1α siRNA, HIF2α siRNA, or both siRNAs, respectively. All samples were grown under hypoxia (1% O) for 16 h.	[67]
D14	GSE33438	2011	GPL1708	Agilent Whole Human Genome G4112A	4	MCF7 & ZR-75-1	Samples from each of the two cell lines were exposed to hypoxia for 24 h or 48 h	[73]
D15	GSE49953	2013	GPL570	Affymetrix HG-U133+ 2.0	4	T47D & MDA-MB-231	A control sample and an XBP1-knocked-down sample from each of the two cell lines. All samples are under hypoxia and glucose deprivation.	[74]
D16	GSE30019	2012	GPL6884	Illumina HumanWG-6 v3.0	6	MCF7	Time-series data through 24 h of reoxygenation after having been in hypoxia (0.5% O) for 24 h.	[75]

^aSome accession numbers refer to datasets which include samples that in reality represent more than one dataset, either because they belong to different microarray platforms or to different cell lines
^bThis is either the number of time-points in time-series data or the number of conditions in other types of data

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