Comment[ArrayExpressAccession]	E-GEOD-45280
MAGE-TAB Version	1.1						
Public Release Date	2013-04-11
Investigation Title	Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [expression]						
Comment[Submitted Name]	Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [expression]
Experiment Description	Long noncoding RNAs (lncRNAs) have been described in cell lines and various whole tissues, but lncRNA analysis of development in vivo is limited. Here, we comprehensively analyze lncRNA expression for the adult mouse subventricular zone neural stem cell lineage. We utilize complementary genome-wide techniques including RNA-seq, RNA CaptureSeq, and ChIP-seq to associate specific lncRNAs with neural cell types, developmental processes, and human disease states. By integrating data from chromatin state maps, custom microarrays, and FACS purification of the subventricular zone lineage, we stringently identify lncRNAs with potential roles in adult neurogenesis. shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells. Our data and workflow thus provide a uniquely coherent in vivo lncRNA analysis and form the foundation of a user-friendly online resource for the study of lncRNAs in development and disease. SVZ monolayer cultures were differentiated in vitro for 1, 2, 4 days, and gene expression changes were measured. SVZ lineage was isolated by FACS using established protocols to separate transit amplifying (TA), neuroblast (NB), activated stem cells (NSCs), and niche astrocytes (astros), and gene expression of each cell type was measured. All arrays are Nimblegen Mouse Gene Expression 12x135K 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	Nellore	Ramos	Nellore				
Person First Name	Abhinav	Alexander	Abhinav				
Person Email	abhinav.nellore@ucsf.edu						
Person Affiliation	UCSF						
Person Phone	4439101925						
Person Address	UCSF, 513 Parnassus Avenue, San Francisco, CA, USA						
Person Roles	submitter						
Protocol Name	P-GSE45280-1	P-GSE45280-5	P-GSE45280-6	P-GSE45280-2	P-GSE45280-3	P-GSE45280-4	P-GSE45280-7
Protocol Description	The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249) as implemented in the DEVA package, version 1.2.1 Sample data table contains RMA-normalized, averaged gene-level signal intensity (i.e. values in the 'PM_AVG' conlumn in processed data .calls file) ID_REF =  VALUE = RMA-normalized, averaged gene-level signal intensity (PM_AVG)	Labeling was performed according to standard Nimblegen Protocols	Hybridization was perfomed on a Maui Hybridization System	For FACS isolated cells, total SVZ was dissected and subjected to the FACS protocol detailed in Pastrana, et al 2009	SVZ cells were grown in monolayer in proliferation media. At passage 5-7, cells were switched to media without growth factors for indicated timepoints (1,2,4 days)	Total RNA was isolated with trizol reagent and amplified with Whole Transcriptome Amplification Kit (Thermo).	Scanning was done on a GenePix 4000B scanner according to standard Nimblegen protocols
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	CELL TYPE						
Experimental Factor Type	cell type						
Comment[SecondaryAccession]	GSE45280						
Comment[GEOReleaseDate]	2013-04-11						
Comment[ArrayExpressSubmissionDate]	2013-03-19						
Comment[GEOLastUpdateDate]	2013-04-13						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-45280.sdrf.txt