Comment[ArrayExpressAccession]	E-GEOD-28049									
MAGE-TAB Version	1.1									
Public Release Date	2012-08-16									
Investigation Title	Gene expression data from MDA-MB231 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble) or two shRNAs targeting Coco (shco2 and shco4)									
Comment[Submitted Name]	Gene expression data from MDA-MB231 cells stably transduced with lentiviral vectors encoding a control shRNA (shscramble) or two shRNAs targeting Coco (shco2 and shco4)									
Experiment Description	Metastatic relapse of breast cancer and other tumor types usually occurs several years after surgical resection of the primary tumor. Early dissemination of tumor cells followed by an extended period of dormancy is thought to explain this prevalent clinical behavior. By using a gain-of-function retroviral cDNA screen in the mouse, we found that Coco, a secreted antagonist of TGF-beta ligands, induces solitary mammary carcinoma cells that have extravasated in the lung stroma to exit from dormancy. Mechanistic studies demonstrate that Coco awakens dormant metastasis-initiating cells by blocking stroma-derived Bone Morphogenetic Proteins. Inhibition of canonical BMP signaling reverses the commitment to differentiation of these cells and enhances their self-renewal and tumor-initiation capacity. Expression of Coco induces a discrete gene expression signature strongly associated with metastatic relapse to the lung but not to the bone or brain in primary patients’ samples. Accordi ngly, silencing of Coco does not inhibit metastasis to the bone or brain in mouse models. These findings suggest that metastasis-initiating cells require the self-renewal capability typically associated with stem cells in order to exit from dormancy and identify Coco as a master regulator of this process. The Affymetrix HG-U133A and Agilent platforms, which were used to build MSK82 [GSE2603], EMC192 [GSE12276], EMC286 [GSE2034], and NKI295 [van 't Veer et al., 2002; van de Vijver et al.,2002; Fan et al., 2006] datasets, do not contain probes for Coco, preventing a direct analysis of the correlation of the expression of Coco with metastatic relapse. We therefore examined the changes in gene expression caused by silencing of Coco in MDA-MB231 cells in vitro and used the resulting signature as a proxy of Coco expression. Compare the gene expression profile between shscramble with shCoco knockingdown MDA-MB231 cells Coco shRNA #2 corresponds to TRCN0000149666 and Coco shRNA #4 corresponds to TRCN0000148148.									
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	Zhao	Gao	Lee-Lim	Chakraborty	Mo	Decker	Vonica	Shen	Brivanlou	Giancotti
Person First Name	Jeffrey	Hua	Ai	Goutam	Qianxing	Markus	Alin	Ronglai	Ali	Filippo
Person Mid Initials			P						H	G
Person Email	zhaoy@mskcc.org									
Person Affiliation	Memorial Sloan Kettering Cancer Center									
Person Address	Genomics Core, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, RRL417A, USA									
Person Roles	submitter									
Protocol Name	P-GSE28049-1	P-GSE28049-6	P-GSE28049-3	P-GSE28049-8	P-GSE28049-7	P-GSE28049-2	P-GSE28049-4	P-GSE28049-5		
Protocol Description	ID_REF =  VALUE = MAS5.0 signal ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = 	10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.	10% fetal bovine serum with DMEM media, 37 degree 5% CO2 incubator	Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files.	Affymetrix GeneArray scanner 7G	The lentivirus pLKO vector expression Coco shRNAs (TRCN0000149666 and TRCN0000148148) was used to make stable cell line knocking down Coco.	RNA extraction plus kit was used to isolate RNA, and cDNA was made with invitrogen superscriptase.	200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).		
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling		
Experimental Factor Name	RNA interference									
Experimental Factor Type	RNA interference									
Publication Title	The BMP Inhibitor Coco Reactivates Breast Cancer Cells at Lung Metastatic Sites.									
Publication Author List	Gao H, Chakraborty G, Lee-Lim AP, Mo Q, Decker M, Vonica A, Shen R, Brogi E, Brivanlou AH, Giancotti FG									
PubMed ID	22901808									
Publication DOI	10.1016/j.cell.2012.06.035									
Comment[SecondaryAccession]	GSE28049									
Comment[GEOReleaseDate]	2012-08-16									
Comment[ArrayExpressSubmissionDate]	2011-03-21									
Comment[GEOLastUpdateDate]	2012-08-23									
Comment[AEExperimentType]	transcription profiling by array									
SDRF File	E-GEOD-28049.sdrf.txt