|
| Status |
Public on Apr 11, 2013 |
| Title |
SVZ Capture |
| Sample type |
SRA |
| |
|
| Source name |
Mouse subventricular zone
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: male
genotype/variation: WT
molecule subtype: Capture-enriched cDNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol, and cleaned and DNAse-treated on an Rneasy column.
RNA CaptureSeq was performed according to standard Roche/Nimblegen protocols and as described in Mercer et al, Nature Biotechnology 2011
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX Titanium |
| |
|
| Description |
RNA extracted from SVZ for capture-seq
|
| Data processing |
library strategy: RNA CaptureSeq
Reads aligned using BLAT
Newbler 2.6 used for de novo assembly of transcriptome
FPKM values calculated using RSEM included in the Trinity package
Genome_build: mm9
Supplementary_files_format_and_content: Transcript structure and abundance calls for CaptureSeq-derived transcripts
|
| |
|
| 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 |
GPL16815 |
| Series (2) |
| GSE45277 |
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo [RNA CaptureSeq] |
| GSE45282 |
Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo |
|
| Relations |
| SRA |
SRX252176 |
| BioSample |
SAMN01984489 |
