Comment[ArrayExpressAccession]	E-GEOD-68995
MAGE-TAB Version	1.1				
Public Release Date	2015-05-21
Investigation Title	Gene expression profiles of PTPRZ1-knocking-down human glioblastoma stem cells [PrimeView]				
Comment[Submitted Name]	Gene expression profiles of PTPRZ1-knocking-down human glioblastoma stem cells [PrimeView]
Experiment Description	Glioblastoma stem cells (GSCs), are at the apex of its cellular hierarchy and contribute to glioblastoma progression and tumor recurrence. Gene expression profiling is useful in determining the genome-wide gene expression changes based on the experimental purpose. In order to interrogate the downstream targets of PTPRZ1, we applied gene expression profiling approach to screen the altered genes that are responsible for the functional phenotype changes. The results will provide a cue for mechanical analysis with potential translational values. PTPRZ1-knocking down glioblastoma stem cells (GSCs) and control GSCs were used in this study. RNA were isolated using  Primescript RT Master Mix (Takara). Profiling was established by applying PrimeView Affymetrix Human Gene Expression Array.				
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	Shi	Shi	Ping		
Person First Name	Yu	Yu	Yi-fang		
Person Email	cadet_toutou@126.com				
Person Affiliation	Institute of Pathology and Southwest Cancer Center				
Person Address	Southwest Hospital, Institute of Pathology and Southwest Cancer Center, Gao-tan Yan Street, Chongqing, Chongqing, China				
Person Roles	submitter				
Protocol Name	P-GSE68995-1	P-GSE68995-3	P-GSE68995-4	P-GSE68995-2	P-GSE68995-5
Protocol Description	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method, following the manufacture's protocol. Differentially expressed genes were identified when the gene expression ratio between the control group and KD group was more than 2-fold. ID_REF =  VALUE = MAS 5.0 signal ABS_CALL = 	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20ug total RNA (Cat. AM1792, Ambion).	Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on PrimeView Affymetrix Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.	The PTPRZ1 knocking-down glioblastoma stem cells and control cells were used for RNA isolatation using Primescript RT Master Mix (Takara) according to the manufacture's protocol.	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Comment[SecondaryAccession]	GSE68995				
Comment[GEOReleaseDate]	2015-05-21				
Comment[ArrayExpressSubmissionDate]	2015-05-18				
Comment[GEOLastUpdateDate]	2015-05-21				
Comment[AEExperimentType]	transcription profiling by array				
Comment[AdditionalFile:Data1]	GSE68995_all_expression_signal_PrimeView.txt				
SDRF File	E-GEOD-68995.sdrf.txt