|
| Status |
Public on Jul 31, 2019 |
| Title |
373 |
| Sample type |
SRA |
| |
|
| Source name |
Gastrocnemius muscle
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL6/J
genotype: fl/fl; Tg/+
Sex: Male
tissue: Gastrocnemius muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gastrocnemius muscles were carefully removed, visibly cleared of any adipose or connective tissue and immediately flash frozen in liquid nitrogen. RNA was extracted using TRIzol reagent and column purified using a PureLink RNA mini kit. Sample quality was determined using an Agilent bioanalyzer. Sequencing libraries were prepared from 1 ug of the purified RNA extract.
500ng of total RNA was enriched for Poly (A) RNA and then barcoded libraries for sequencing were prepared using the Lexogen mRNA Sense kit for Ion Torrent according to manufacturer’s standard protocol. Libraries were amplified 13 cycles and the quality of each library was checked on an Agilent Bioanalyzer DNA High Sensitivity chip. A 1ul aliquot of each sample was pooled and run on the Ion Torrent PGM 314 chip. The libraries were then pooled based on read counts from the PGM 314 chip, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an ABI 5500 Wildfire sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Data processing |
Reads were aligned to the mouse genome using TopHat v2.0.10 and bowtie v1.0.0 with these parameters -p 11 --bowtie1 --color --qual
Counts were generated using HTSeq v0.5.4p5 with parameters --strand=no --mode=intersection-nonempty
Genome_build: GRCm38.75
Supplementary_files_format_and_content: text file with read counts.
|
| |
|
| Submission date |
Jul 12, 2016 |
| Last update date |
Jul 31, 2019 |
| Contact name |
Quynh Tran |
| E-mail(s) |
qtran@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place, C4029, Mail Stop 250
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL16790 |
| Series (1) |
| GSE84312 |
RNAseq analysis of quadriceps muscles from adult mice with constitutively active skeletal and cardiac muscle mTORC1 (through conditional knockout of Tsc1 under the Mck Cre) and their wild type litter mates |
|
| Relations |
| BioSample |
SAMN05382228 |
| SRA |
SRX1936381 |
