|
| Status |
Public on Aug 16, 2012 |
| Title |
WT, biological rep3 |
| Sample type |
SRA |
| |
|
| Source name |
wild-type hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6 and 129 SvlmJ mixed
genotype/variation: WT
age: 2-3 months
gender: female
tissue: hippocampus
|
| Growth protocol |
Hippocampi dissected from MBNL2 ΔE2/ΔE2 mice or WT female mice, 2-3 months of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were genotyped and hippocampii were dissected from 3 mutant and 3 wild-type animals. Total RNA was extracted using Trizol and samples were purified with RNeasy™ Kit (Qiagen). Sequencing libraries were prepared after PolyA RNA isolation using mRNA-sequencing kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
WT_Hippocampus-3
|
| Data processing |
Raw sequence reads were mapped back to the mouse reference genome (mm9) together with a comprehensive database of annotated exon junctions compiled from mouse, human, and rat mRNA/EST data. The program tophat (v1.3.2) with bowtie (v3.4.6) was used for alignment (parameters: -a 5 -F 0.05 -r 150 -j <junction.hmr.raw>)
After read mapping, transcript structure between the sequenced ends could be ambiguous due to alternative splicing, and if this occurs, the structure was inferred using a bayes method by modeling the size distribution of cDNA fragments
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format, with the four columms representing chromosome, start (0-based), end (1-based), and normalized read coverage (FPKM)
|
| |
|
| Submission date |
Jun 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Ranjan Batra |
| E-mail(s) |
[email protected]
|
| Phone |
352-222-9209
|
| Organization name |
University of California San Diego
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Yeo Lab
|
| Street address |
2880 Torrey Pines Scenic Drive
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE38497 |
Muscleblind-Like 2 mediated alternative splicing in the developing bain by mRNA sequencing |
|
| Relations |
| SRA |
SRX151659 |
| BioSample |
SAMN01037008 |
