Comment[ArrayExpressAccession]	E-GEOD-69125
MAGE-TAB Version	1.1			
Public Release Date	2016-03-02
Investigation Title	The effect of knockdown Abl kinases on breast cancer cells' global transcriptome			
Comment[Submitted Name]	The effect of knockdown Abl kinases on breast cancer cells' global transcriptome
Experiment Description	To gain insight into the signaling pathway(s) required for ABL1/ABL2-dependent bone metastasis, we evaluated the consequences of single or double inactivation of ABL1 and ABL2 on the transcriptome of breast cancer cells. Double ABL1/ABL2 knockdown was required to decrease the levels of p-CrKL by more than 90%, indicative of inactivation of the endogenous ABL kinases. To examine the consequences of depleting the ABL kinases on the transcriptome of metastatic breast cancer cells we employed next generation sequencing (RNAseq) analysis. We found that 180 genes were significantly down-regulated and 40 genes were significantly up-regulated in ABL1/ABL2 knockdown cells. Four samples were analyzed control, Abl single knockdown, Arg single knockdown, Abl/Arg double knockdown. Experiments were performed in triplicate.			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	Wang	Wang	Pendergast	
Person First Name	Jun	Jun	Ann	
Person Mid Initials			M	
Person Email	geo@ncbi.nlm.nih.gov			
Person Affiliation	Duke University			
Person Address	Pharmacology and Cancer Biology, Duke University, 308 Research Drive LSRC C231, Durham, North Carolina, USA			
Person Roles	submitter			
Protocol Name	P-GSE69125-4	P-GSE69125-1	P-GSE69125-3	P-GSE69125-2
Protocol Description	Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using tophat Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff based on the protocol Cole Trapnell et al. Nature Biotechnology 31, 46-53 (2013) Genome_build: hg18 Supplementary_files_format_and_content: diff files include RPKM values for each Sample	1833 cells were incubated 48 h with lentiviral medium containing Scr, or miAbl, or miArg or miAA microRNA in the presence of 8ug/mL Polybrene.	RNA was harvested using Qiagen Rneasy kit RNA libraries were prepared for sequencing using standard Illumina protocols	1833 cells were cultured in DMEM with 10% FBS
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	knockdown			
Experimental Factor Type	knockdown			
Publication Title	ABL kinases promote breast cancer osteolytic metastasis by modulating tumor-bone interactions through TAZ and STAT5 signaling.			
Publication Author List	Wang J, Rouse C, Jasper JS, Pendergast AM			
PubMed ID	26838548			
Publication DOI	10.1126/scisignal.aad3210			
Comment[SecondaryAccession]	GSE69125			
Comment[GEOReleaseDate]	2016-03-02			
Comment[ArrayExpressSubmissionDate]	2015-05-21			
Comment[GEOLastUpdateDate]	2016-03-16			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[AdditionalFile:Data1]	GSE69125_10408_gene_exp.diff			
Comment[SecondaryAccession]	SRP058587			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR2036181-SRR2036196			
SDRF File	E-GEOD-69125.sdrf.txt