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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 [RNA CaptureSeq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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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 |
RNA CaptureSeq was perfomed on RNA extracted from adult mouse subventricular zone to better characterize rare lncRNA isoforms. Genomic regions used to design capture array are included in the raw file target_regions.bed.
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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 |
May 15, 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) |
| GPL16815 |
454 GS FLX Titanium (Mus musculus) |
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| Samples (1) |
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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 |
PRJNA193408 |
| SRA |
SRP019779 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE45277_RAW.tar |
2.6 Mb |
(http)(custom) |
TAR (of BED, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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