|
| Status |
Public on Apr 27, 2020 |
| Title |
Pig2_scar |
| Sample type |
SRA |
| |
|
| Source name |
Left ventricular myocardial tissue
|
| Organism |
Sus scrofa |
| Characteristics |
surgery: Ischemia/reperfusion (IR)
zone: Scar
Sex: Female
|
| Treatment protocol |
Ischemia/reperfusion= 1-hour occlusion of the left anterior descending artery, just below the second diagonal branch, following by reperfusion. Sham= same procedure but no occlusion of artery.
|
| Growth protocol |
None- tissue was extracted when pigs were 4-weeks post surgery and rapidly frozen before RNA extracted.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Myocardial tissue was harvested 4-weeks following surgery and cut into zonal sections. Tissue was washed in PBS and rapidly frozen in liquid nitrogen, before transfer to a -80C freezer for storage. RNA was then extracted using a commercially available kit (NucleoSpin RNA kit (740955, Macherey-Nagel) and eluted in RNAse free H20 prior to submission to CCHMC DNA Core for processing.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq files were trimmed to remove adapter and loq quality sequences using Trimmomatic V 0.33
Trimmed reads were mapped to the reference (Sscrofa11) using hisat2 V 2.0.5
After trimming the reads were quantified using Kallisto V 0.43.1, this gives us TPM and Counts
Genome_build: Sscrofa11
Supplementary_files_format_and_content: tab-delimited text files include TPM and COUNTS for all samples
|
| |
|
| Submission date |
Sep 11, 2019 |
| Last update date |
Apr 27, 2020 |
| Contact name |
Katherine E Yutzey |
| E-mail(s) |
katherine.yutzey@cchmc.org
|
| Phone |
513-636-8340
|
| Organization name |
Cinicnnati Children's Hospital Medical Center
|
| Department |
Divison of Molecular Cardiovascular Biology
|
| Street address |
240 Albert Sabin Way
|
| City |
Cinicnnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE137293 |
RNA-seq analysis of young swine following cardiac ischemia/reperfusion injury. |
|
| Relations |
| BioSample |
SAMN12730808 |
| SRA |
SRX6832212 |
