|
| Status |
Public on May 08, 2024 |
| Title |
Time Point_3dpc_Group_12dv_Sample1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Blood
|
| Organism |
Sus scrofa domesticus |
| Characteristics |
age: 27 weeks old
diet: ad libitum
tissue: Whole Blood
cell line: primary
cell type: Peripheral Blood Mononuclear Cells (PBMCs)
time: 3 days post-challenge
treatment: Vaccination and challenge
|
| Treatment protocol |
Whole blood was kept at -80˚C in TRIzol Reagent (Invitrogen) until use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol-chloroform method, and further purified using RNeasy mini Kit, QIAGEN (RNAse-free water) following the manufacturer’s protocol. DNase I (RNase-Free DNase Set, Qiagen) treatment for 15 min at room temperature was performed to ensure RNA quality. Total RNA from whole blood was submitted for sequencing to the Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain. Total RNA was quantified by Qubit RNA BR Assay kit (Thermo Fisher Scientific) and the RNA integrity was estimated by using RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
The RNASeq libraries were prepared with KAPA mRNA HyperPrep Kit (Roche) following the manufacturer´s recommendations starting with 500 ng of total RNA as the input material. The library was quality controlled on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp, following the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads mapped with STAR v2.7.8a
Genes quantified with RSEM v1.3.0
Assembly: Concatenation of Sscrofa11.1 and KP055815
Supplementary files format and content: Tab-delimited text file with raw counts for each sample
|
| |
|
| Submission date |
May 03, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Jordi Argilaguet Marqués |
| E-mail(s) |
jordi.argilaguet@irta.cat
|
| Organization name |
IRTA-CReSA
|
| Street address |
CAMPUS UAB EDIF.CRESA
|
| City |
Bellaterra |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL29562 |
| Series (1) |
| GSE266565 |
Elucidating the Onset of Cross-protective Immunity after Intranasal Vaccination with the Attenuated African Swine Fever Vaccine Candidate BA71ΔCD2 |
|
| Relations |
| BioSample |
SAMN41192849 |
| SRA |
SRX24448727 |
