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E-GEOD-45280 - Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [expression]

Status
Released on 11 April 2013, last updated on 2 June 2014
Organism
Mus musculus
Samples (11)
Array (1)
Protocols (7)
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.
Experiment type
transcription profiling by array 
Contacts
Abhinav Nellore, Alexander Ramos
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-45280.idf.txt
Sample and data relationshipE-GEOD-45280.sdrf.txt
Raw data (1)E-GEOD-45280.raw.1.zip
Processed data (1)E-GEOD-45280.processed.1.zip
Array designA-GEOD-15887.adf.txt
Links