|
| Status |
Public on May 04, 2017 |
| Title |
SD_Wk7 post-sham_miRNASeq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Left ventricle tissue_Sham_7 weeks post surgery
|
| 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.
Small RNA libraries were constructed for Pools of 2-3 rats, 2 Pools per condition, using the TruSeq Small Sample Preparation RNA Kit. Samples were multiplexed sequenced with an Illumina HiSeq 2000 using the TruSeq SBS kit v2-HS.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Kriegel_Supplemental Table 3_ 5/6Nx vs. Sham_Wk7_miRNA
pool of 2-3 individuals
|
| Data processing |
Adapter sequences were first removed from the output reads by the tool cutadapt (http://code.google.com/p/cutadapt/); sequences with low quality (base quality < 13) at both ends of reads were further trimmed and trimmed reads with less than 25 bp were removed using the SolexaQA (http://solexaqa.sourceforge.net/).
The trimmed short sequencing reads were aligned to miRbase v20 to identify microRNAs using Bowtie, those that didn't map ewere mapped against Rfam and RepBase.
DESeq was implemented to identify differential expression.
The Benjamini-Hochberg method was used to control false discovery rate in differential expression analysis.
Genome_build: miRbase v20
Supplementary_files_format_and_content: Expression measurements are reported in normalized 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 |
| GSE98521 |
Molecular Mediators of Cardiac Pathology in Cardiorenal Syndrome Type 4 [miRNA] |
|
| Relations |
| BioSample |
SAMN06887346 |
| SRA |
SRX2781676 |
