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Series GSE45278 Query DataSets for GSE45278
Status Public on Apr 11, 2013
Title Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
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 RNA-seq (both paired end and single) from the adult neurogenic niches- subventricular zone (SVZ), olfactory bulb (OB), dentate gyrus (DG) and control non-neurogenic tissue, striatum (STR). Reads were used to assemble a lncRNA catalogue and determine expression values for both protein-coding and noncoding genes
Contributor(s) Ramos A, Nellore A
Citation(s) 23583100
Submission date Mar 19, 2013
Last update date May 15, 2019
Contact name Abhinav Nellore
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)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (5)
GSM1100703 SVZ Biological Replicate 1 [RNA-seq]
GSM1100704 STR Lane 1 [RNA-seq]
GSM1100705 SVZ Biological Replicate 2 [RNA-seq]
This SubSeries is part of SuperSeries:
GSE45282 Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo
BioProject PRJNA193409
SRA SRP019780

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Supplementary file Size Download File type/resource
GSE45278_expressionmatrix.txt.gz 1.4 Mb (ftp)(http) TXT
GSE45278_lncRNA_annotation.bed.gz 240.2 Kb (ftp)(http) BED
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