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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 11, 2013 |
| Title |
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [lncRNA Array] |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by array
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| 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.
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| 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 custom lncRNA arrays.
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| Contributor(s) |
Ramos A, Nellore A |
| Citation(s) |
23583100 |
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| Submission date |
Mar 19, 2013 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Abhinav Nellore |
| E-mail(s) |
abhinav.nellore@ucsf.edu
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| Phone |
4439101925
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| Organization name |
UCSF
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| Street address |
513 Parnassus Avenue
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0794 |
| Country |
USA |
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| Platforms (1) |
| GPL16745 |
NimbleGen Mouse lncRNA array [110815_MM9_AR_exp] |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE45282 |
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo |
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| Relations |
| BioProject |
PRJNA193412 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45281_RAW.tar |
37.6 Mb |
(http)(custom) |
TAR (of CALLS, PAIR) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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