|
| Status |
Public on Jul 31, 2019 |
| Title |
IonXpress_RNA_062 |
| Sample type |
SRA |
| |
|
| Source name |
Quadriceps
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
feeding 16h before sacrifice: Fasted
diet during week 6-7: High Fat Diet
tissue: Quadriceps
age: 22 weeks of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using PureLink RNA Mini kit by Life Tech
1ug of total RNA was enriched for Poly A RNA using Ambion Dynabeads mRNA Direct Micro kit and barcoded libraries for sequencing were prepared using the Life Technologies RNAseq V2 kit for Ion Torrent according to manufacturer’s standard protocol. Libraries were amplified 14 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 an Ion Torrent PGM 314 chip. The libraries were equally pooled based on PGM 314 read data, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an Ion Torrent Proton sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Aligned first via tophat v2.1.0, allowing for 5 mismatches and setting strandedness to second strand
Took unmapped reads and re-alined with bowtie v2.2.5 under local very sensitive settings to get the remaining ~40% of reads mapped
Merged the tophat and bowtie results files into merged.bam
Counts were generated using Htseq v0.6.0 with parameters stranded=yes, mode=intersection-nonempty with default cutoff score of 10.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include htseq counts for each Sample.
|
| |
|
| 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 |
GPL18635 |
| Series (1) |
| GSE84313 |
Gene expression profiles of mice with juvenile HFD exposure for one week |
|
| Relations |
| BioSample |
SAMN05382223 |
| SRA |
SRX1936366 |
