|
| Status |
Public on Feb 07, 2020 |
| Title |
Pig 7697 – Naive – Sac day 3 |
| Sample type |
SRA |
| |
|
| Source name |
Naive Heart
|
| Organism |
Sus scrofa |
| Characteristics |
injured / naive: Naive
injured postnatal day: N/A
age at tissue collection (day): 3
|
| Treatment protocol |
MI was induced via permanent ligation of the left descending coronary artery, and animals in the Age-matched normals group underwent all surgical procedures for MI induction except the ligation step.
|
| Growth protocol |
Pigs (Prestage Farms, Inc, West Point, MS) were fed every 4 hours with bovine colostrum on P1-P2, with a 1:1 ratio of colostrum:sow’s milk on P3, and with cow’s milk from P4 until sample collection. Supplemental iron was provided on P7, and the animals were housed in an incubator at ~85 °F with room air until P28 days of age.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from tissue samples (~30 mg) colle cted from the border zone of ischemia in the hearts of MI animals and from the corresponding region of hearts in Age-matched normal animals.
Libraries were quantified via qPCR with equal amounts of RNA for all samples, and RNA concentrations were diluted to 3 nM before loading equimolar amounts onto the flow cells.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Pig heart tissue, naive, tissue collected on day 3
|
| Data processing |
Trimming: Paired-end fastq files were evaluated with the trim-galore [48] package for quality assessments of the input sequencing files
Mapping: mapping was conducted with the Ensembl pig genome assembly (Sscrofa11.1) and STAR package v2.5.2 to produce the sorted BAM (Binary Alignment Map) file format.
Convert from BAM format to SAM format: SAMtool
Counting: mapped transcripts (raw expression) were counted with the HTSeq/0.6.1 package
Normalization: Expression levels were normalized and differential gene expressions (log2 of the fold-change ) were analyzed with Deseq2
Genome_build: Ensembl pig genome assembly (Sscrofa11.1)
Supplementary_files_format_and_content: tab-delimited text files include expression values for each sample.
|
| |
|
| Submission date |
Feb 06, 2020 |
| Last update date |
Feb 08, 2020 |
| Contact name |
Thanh Minh Nguyen |
| E-mail(s) |
[email protected]
|
| Phone |
3174108458
|
| Organization name |
University of Alabama at Birmingham
|
| Department |
Department of Biomedical Engineering
|
| Street address |
1670 University Blvd, Volker Hall G094
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35233 |
| Country |
USA |
| |
|
| Platform ID |
GPL20983 |
| Series (1) |
| GSE144883 |
Identifying the Key Regulators that Promote Cell-cycle Activity in the Hearts of Early Neonatal Pigs after Myocardial Injury |
|
| Relations |
| BioSample |
SAMN14051856 |
| SRA |
SRX7691581 |
