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Series GSE45280 Query DataSets for GSE45280
Status Public on Apr 11, 2013
Title Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [expression]
Organism Mus musculus
Experiment type Expression profiling by array
Summary 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.
 
Overall design 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.
 
Contributor(s) Ramos A, Nellore A
Citation(s) 23583100
Submission date Mar 19, 2013
Last update date Jan 01, 2019
Contact name Abhinav Nellore
E-mail(s) abhinav.nellore@ucsf.edu
Phone 4439101925
Organization name UCSF
Street address 513 Parnassus Avenue
City San Francisco
State/province CA
ZIP/Postal code 94143-0794
Country USA
 
Platforms (1)
GPL15887 NimbleGen Mouse gene expression array [100718_MM9_EXP] (gene-level version)
Samples (11)
GSM1100711 SVZ_NSCs_1 [gene expression]
GSM1100712 SVZ_NSCs_2 [gene expression]
GSM1100713 TA_1 [gene expression]
This SubSeries is part of SuperSeries:
GSE45282 Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo
Relations
BioProject PRJNA193411

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE45280_RAW.tar 77.4 Mb (http)(custom) TAR (of CALLS, PAIR)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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