|
| Status |
Public on Jan 19, 2021 |
| Title |
Control2 |
| Sample type |
SRA |
| |
|
| Source name |
exsanguinated heart
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: heart
dose (mg/kg): 0
agent: none
Sex: male
tag: Wistar
|
| Treatment protocol |
Under halothane anesthesia, adult male Wistar rats (240-260 g) were made diabetic with a single dose of 55 (D55) or 100 (D100) mg/kg STZ into the tail vein. After 24 hours, hyperglycemia (>13 mmol/L) was confirmed using a glucometer and glucose test strips.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were followed for 4 days before termination at which time blood was collected and hearts exsanguinated.
Total RNA from 4 control, 6 D55, and 6 D100 rats was isolated using TRIzol. Sequencing libraries were prepared from 400 ng total RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA). Libraries were multiplexed and sequenced on the NextSeq 500 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
kallisto version 0.43.1 was first used to build an index file for the rat reference transcriptome Rnor_6.0 as downloaded from the Ensembl web site (www.ensembl.org). The sequence reads for each sample were then quantified with the quant function of kallisto.
For each sample, an in-house Perl script was used to sum the kallisto read counts at the transcript level for each gene.
Each sample was assessed with the quality control software RNA-SeQC (DeLuca et al., 2012) and the PtR script from the trinity suite (Grabherr et al., 2011).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab separated text file with ensembl gene id and counts from kallisto
|
| |
|
| Submission date |
Jan 22, 2019 |
| Last update date |
Jan 19, 2021 |
| Contact name |
Stephane Flibotte |
| Organization name |
University of British Columbia
|
| Department |
Faculty of Science
|
| Lab |
UBC/LSI Bioinformatics Core Facility
|
| Street address |
2370-6270 University Blvd.
|
| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE125451 |
Diabetes severity is reflected by changes in a cardiac gene expression signature characterized by metabolism and cell death processes |
|
| Relations |
| BioSample |
SAMN10788465 |
| SRA |
SRX5278211 |
