|
| Status |
Public on Apr 11, 2013 |
| Title |
SVZ Biological Replicate 1 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Microdissected mouse subventricular zone
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: male
genotype/variation: wild type
age: adult
tissue: microdissected subventricular zone (SVZ)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Brain regions were acutely microdissected from adult animals and snap-frozen. RNA was extracted by Trizol method, cleaned up, and DNAse treated on Rneasy columns (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Mouse SVZ, first bio replicate
|
| Data processing |
Illumina Casava basecalling
Reads aligned with Tophat v1.2.0
Transcripts assembled and quantified with Cufflinks v1.0.0
Genome_build: mm9
Supplementary_files_format_and_content: bed file of assembled lncRNA transcriptome, spreadsheet of coding and noncoding FPKM values from Cufflinks
|
| |
|
| Submission date |
Mar 19, 2013 |
| Last update date |
May 15, 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 |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE45278 |
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA-seq] |
| GSE45282 |
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX252177 |
| BioSample |
SAMN01984490 |
