Comment[ArrayExpressAccession]	E-GEOD-46098
MAGE-TAB Version	1.1				
Public Release Date	2013-12-31
Investigation Title	Directed differentiation of human pluripotent stem cells into cortical interneurons				
Comment[Submitted Name]	Directed differentiation of human pluripotent stem cells into cortical interneurons
Experiment Description	Here we demonstrate the highly efficient derivation of human cortical interneurons in a NKX2.1::GFP hESC reporter line. Manipulating the timing of SHH activation yields three distinct GFP+ populations with specific transcriptional profiles, neurotransmitter phenotypes and migratory behaviors. Total RNA was isolated at day 18 of differentiation from FACS sorted NKX2.1::GFP+ cells from three varying differentiation conditions and a “No SHH” condition (no sonic hedgehog treatment) that did not contain any GFP-expressing cells (Trizol, Sigma). Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.				
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	Maroof	Ganat	Studer	
Person First Name	Jeffrey	Asif	Yosif	Lorenz	
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, NY, USA				
Person Roles	submitter				
Protocol Name	P-GSE46098-1	P-GSE46098-3	P-GSE46098-4	P-GSE46098-2	P-GSE46098-5
Protocol Description	The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done. ID_REF =  VALUE = quantile normalized and background subtracted Avg_NBEADS =  BEAD_STDERR =  Detection Pval = 	Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.	Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.	Trizol extraction of total RNA was performed according to the manufacturer's instructions.	Slides were scanned using Illumina iScanner
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	nucleic acid extraction protocol	array scanning protocol
Comment[SecondaryAccession]	GSE46098				
Comment[GEOReleaseDate]	2013-12-31				
Comment[ArrayExpressSubmissionDate]	2013-04-16				
Comment[GEOLastUpdateDate]	2013-12-31				
Comment[AEExperimentType]	transcription profiling by array				
Comment[AdditionalFile:Data1]	GSE46098_nonorm_nobkgd.txt				
SDRF File	E-GEOD-46098.sdrf.txt