|
| Status |
Public on Jun 12, 2023 |
| Title |
C_LP_Sub, rep 2 [T619_10078662] |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Peripheral blood
housing condition: Conventional
parity group: LP
dominance status: Subordinate
time: G98
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using NucleoSpin RNA Kit according to the manufacturer’s instructions. 500 ng of total RNA was used for library preparation.
RNA libraries were prepared following the QIAseq Stranded mRNA Library Kit (Qiagen) protocol, without modification, and using 12 cycles for amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Dragen RNA v3.8.4 (Illumina) was used for mapping and annotation against Sus scrofa reference genome GCF_000003025.6.
The data was analyzed using the R software (v. 4.1.2; http://www.r-project.org). Normalization, filtration, and statistical analysis were performed using the DESeq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: NCBI Sus scrofa reference genome sequence Sscrofa11.1
Supplementary files format and content: Tab-delimited text files containing the number of counts of the identified genes for each sample.
|
| |
|
| Submission date |
Jun 09, 2023 |
| Last update date |
Jun 12, 2023 |
| Contact name |
Mariana Mescouto Lopes |
| E-mail(s) |
mariana.mescouto-lopes@inrae.fr, marianamescouto@hotmail.com
|
| Phone |
+330789529872
|
| Organization name |
INRAe
|
| Department |
UMR Pegase
|
| Street address |
16 Le Clos Domaine de, La Prise
|
| City |
Saint-Gilles |
| ZIP/Postal code |
35590 |
| Country |
France |
| |
|
| Platform ID |
GPL32549 |
| Series (1) |
| GSE234561 |
Effects of housing environment, dominance status, and parity on the PBMC transcriptome of sows during gestation and lactation |
|
| Relations |
| BioSample |
SAMN35688891 |
| SRA |
SRX20650243 |
