|
| Status |
Public on Apr 15, 2021 |
| Title |
Heat stress_Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Placenta
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Placenta
breed: Large White x Landrace
treatment: Heat stress
developmental stage: d60 of gestation
|
| Treatment protocol |
On d40 of gestation, pregnant pigs were either exposed to thermoneutral control (CON; constant 20 °C) or cyclic heat stress (HS; 28 °C between 0900h and 1700h, and 33 °C between 1700h and 0900h) conditions for 3 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Placental total RNA was extracted using ReliaPrep RNA tissue Miniprep System (Cat# Z6111; Promega, Madison, WI, USA) as per the manufacturer’s instructions.
The sequencing library was constructed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of sequencing reads was performed using FastQC software version 0.11.9. The raw reads were subjected to Illumina adaptor and low-quality base removals to obtain clean reads.
Clean reads were aligned/mapped to the pig reference genome (Sus scrofa 11.1) using Hisat2 version 2.1.0. The average alignment rate across all samples was 96.5 ± 0.15% (SD).
The aligned reads were then counted per gene using HTSeq software (version 0.11.3) with reversed strand interpretation.
Differential expression analysis using DESeq2 version 1.28.1.
Genome_build: Sus scrofa 11.1
Supplementary_files_format_and_content: Tab-delimited text files containing gene Ensembl ID and counts.
|
| |
|
| Submission date |
Mar 09, 2021 |
| Last update date |
Apr 15, 2021 |
| Contact name |
Weicheng Zhao |
| E-mail(s) |
weichengz89@gmail.com
|
| Organization name |
The University of Melbourne
|
| Street address |
Building 184, Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE168571 |
Maternal Heat Stress Alters Expression of Genes Associated with Nutrient Transport Activity and Metabolism in Female Placentae From Mid-Gestating Pigs |
|
| Relations |
| BioSample |
SAMN18229869 |
| SRA |
SRX10293473 |
