Comment[ArrayExpressAccession]	E-GEOD-51083
MAGE-TAB Version	1.1									
Public Release Date	2013-09-24
Investigation Title	Global gene expression changes in patient-derived CML cell line K562 after short- and long-term BCR-ABL kinase inhibition.									
Comment[Submitted Name]	Global gene expression changes in patient-derived CML cell line K562 after short- and long-term BCR-ABL kinase inhibition.
Experiment Description	K562 cells were treated with the BCR-ABL kinase inhibitor dasatinib over an extended period of time to determine how BCR-ABL inhibition affects BCR-ABL-dependent negative feedback and erythropoietin receptor (EPO-R) signaling.  Specifically, what types of changes (upregulation versus downregulation) occur in both the negative and positive regulators of growth-factor receptor signaling. Total RNA was extracted from K562 cells treated with 0.2% DMSO for 24hrs or 100nM dasatinib for 4hrs, 8hrs, and 24hrs.									
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	Shah	Gajan	Tajon	Lasater	Oses-Prieto	Jun	Taylor	Burlingame	Craik	Shah
Person First Name	Neil	Jennifer	Cheryl	Elisabeth	Juan	Young-wook	Barry	Alma	Charles	Neil
Person Mid Initials				A			S			P
Person Email	geo@ncbi.nlm.nih.gov									
Person Affiliation	UCSF									
Person Address	UCSF, 513 Parnassus, San Francisco, USA									
Person Roles	submitter									
Protocol Name	P-GSE51083-1	P-GSE51083-5	P-GSE51083-6	P-GSE51083-2	P-GSE51083-3	P-GSE51083-4	P-GSE51083-7			
Protocol Description	Data was adjusted and normalized using the lumi pipeline (PMID: 18467348). ID_REF =  VALUE = lumi normalized log signal Detection Pval = 	Biotinylated cRNA was prepared using the Ambion Illumina TotalPrep RNA Amplification kit.	Standard Illumina hybridization protocol	K562 cells were treated with 0.2% DMSO or 100nM dasatinib in RPMI 1640 medium (0.1% FBS) for the indicated amount of time prior to cell lysis and RNA extraction.	K562 cells were propogated in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (FBS, Omega Scientific), L-glutamine (1%) and penicillin/streptomycin (1%) (Invitrogen).	Total cellular RNA was extracted using the Qiagen RNeasy kit with Dnase I treatment. RNA integrity was assessed on a Bioanalyzer using the Agilent RNA 6000 Nano Kit and cRNA was generated using the Ambion Illumina TotalPrep RNA Amplification kit.	Standard Illumina scanning protocol			
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol			
Experimental Factor Name	TREATMENT	TIME								
Experimental Factor Type	treatment	time								
Comment[SecondaryAccession]	GSE51083									
Comment[GEOReleaseDate]	2013-09-24									
Comment[ArrayExpressSubmissionDate]	2013-09-23									
Comment[GEOLastUpdateDate]	2013-09-25									
Comment[AEExperimentType]	transcription profiling by array									
Comment[AdditionalFile:Data1]	GSE51083_non-normalized.txt									
SDRF File	E-GEOD-51083.sdrf.txt