|
| Status |
Public on Mar 04, 2021 |
| Title |
F3996-Meth-abs-2 |
| Sample type |
SRA |
| |
|
| Source name |
Left ventricular tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
Sex: F
treatment: Methamphetamine
abstinence: Yes
|
| Treatment protocol |
Adult male and female rats (8 weeks of age) received daily (10:00) subcutaneous injections with methamphetamine (5 mg/ kg/day) or saline for 10 consecutive days.
|
| Growth protocol |
Male and female Sprague Dawley rats (Charles River Laboratories, strain code 001) were pair housed in standard cages with free access to food and water and were maintained on a 12 hour / 12 hour light / dark schedule (lights on at 07:00).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were either isolated on day 11 (24 hours after the last saline /methamphetamine injection) or isolated 30 days after the last saline / methamphetamine injection to investigate the effects of a 30 day period of abstinence on myocardial gene expression. Total RNA was isolated using Trizol (Thermo Fisher, Waltham, MA) according to the manufacturer’s instructions.
RNA libraries were prepared from each heart using the Truseq RNA mRNA library prep kit from Illumina (San Diego, CA). RNA sequencing (2 x 50 paired end reads; 20 million reads / sample) was performed on an Illumina HiSeq1500 sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
raw_counts.csv
normalized_counts.csv
|
| Data processing |
Reads were trimmed to remove adapter sequence and low-quality base calls using Trimmomatic v0.38
Reads were aligned to the rat genome rn06 using HISAT2 v2.1.0
Aligned reads were mapped to known transcripts from Ensembl genes version 94 using GenomicAlignments v1.16.0
Differentially epxressed genes were identified using DESeq2 v1.20.0 with a Benjamini-Hochberg estimated false discovery rate of 0.1 used as a threshold for statistical significance.
Sample F4329-Sal-3 failed to cluster with other samples and was omitted from further processing.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Counts per gene per sample in CSV format.
|
| |
|
| Submission date |
Sep 28, 2020 |
| Last update date |
Mar 04, 2021 |
| Contact name |
James Denvir |
| E-mail(s) |
denvir@marshall.edu
|
| Organization name |
Marshall University School of Medicine
|
| Department |
Biochemistry and Microbiology
|
| Lab |
Genomics and Bioinformatics Core Facility
|
| Street address |
One John Marshall Drive
|
| City |
Huntington |
| State/province |
WV |
| ZIP/Postal code |
25755 |
| Country |
USA |
| |
|
| Platform ID |
GPL18404 |
| Series (1) |
| GSE158655 |
Methamphetamine Induces Sex-Dependent Changes in Gene Expression in Male and Female Hearts |
|
| Relations |
| BioSample |
SAMN16280348 |
| SRA |
SRX9202765 |
