|
| Status |
Public on May 04, 2017 |
| Title |
SD_Wk4 post-sham_RNASeq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Left ventricle tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: heart
heart region: left ventricle
strain: Sprague Dawley
Sex: male
age: 10 weeks of age at surgery
diet: 0.4% Dyets chow
|
| Treatment protocol |
At 10 weeks of age rats were subjected to sham or 5/6Nx surgery.
|
| Growth protocol |
Rats were delivered from Harlan (Envigo) at 9 weeks of age and placed on 0.4% Dyets chow and provided food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Left ventricle tissues were isolated and flash frozen in liquid nitrogen. They were then ground into powder under liquid nitrogen which was thawed in Trizol for chloroform-based RNA isolation.
mRNA libraries were constructed for these pools using the Illumina TruSeq Stranded Total RNA Kit. Samples were multiplexed seven per lane on a 300 Gb flow cell and paired-end sequenced with an Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
pool of 2-3 individuals
Supplemental Table 1_5-6Nx vs. Sham_Wk4
Pool_1_ATGTCA
|
| Data processing |
Adapter sequences were first removed from the output reads by the tool cutadapt (http://code.google.com/p/cutadapt/).
The trimmed short sequencing reads were aligned to the rat reference (rn5) using Tophat v2.0.10 with mammalian default parameters.
We used the rat Ensembl transcripts (release 76) to guide RABT assembly by Cufflinks v2.0.10.
Cuffdiff was used to determine differences in transcript/isoform abundance between groups.
The Benjamini-Hochberg method was used to control false discovery rate in differential expression analysis.
Genome_build: rn5
Supplementary_files_format_and_content: Gene-level or isoform expression measurements are reported in fragments per kilobase per million reads.
|
| |
|
| Submission date |
May 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Alison J. Kriegel |
| E-mail(s) |
akriegel@mcw.edu
|
| Phone |
(414)955-4835
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Physiology
|
| Lab |
Kriegel
|
| Street address |
8701 Watertown Plank Rd.
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (2) |
| GSE97950 |
Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 |
| GSE98520 |
Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 [mRNA] |
|
| Relations |
| BioSample |
SAMN06887365 |
| SRA |
SRX2781686 |
