|
| Status |
Public on May 01, 2024 |
| Title |
Del8 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood mononuclear cells
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Peripheral blood mononuclear cells
cell type: CD8+ T Cells
treatment: Bovine Turbinates Cells infected with ORF73-deficient strain of AlHV-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were subjected to a microbead-based negative selection protocol. Total RNA was purified from 2 millions of CD8+ T lymphocytes using an RNeasy Mini Kit. A total of 1 μg of total RNA was used as input for the Truseq stranded mRNA sample kit (Illumina)
A total of 1 μg of total RNA was used as input for the Truseq stranded mRNA sample kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the NCBI Bos taurus Annotation Release 106 and the AlHV-1 BAC genome from (KX905135.1) using STAR.
Subsequently the analysis was performed with R Bioconductor packages Rsamtools and GenomicAlignments were used to count the reads by exons, and gene count datasets were then analyzed to determine differentially expressed genes (DEGs) using DESeq2.
Assembly: bosTau9
Supplementary files format and content: row count text file per sample
|
| |
|
| Submission date |
Jan 19, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Abdulkader AZOUZ |
| E-mail(s) |
Abdulkader.azouz@ulb.be
|
| Organization name |
Université Libre de Bruxelles
|
| Street address |
Rue Adrienne Bolland, 8
|
| City |
GOSSELIES |
| ZIP/Postal code |
6041 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL23055 |
| Series (2) |
| GSE253728 |
Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever [RNA-seq] |
| GSE253729 |
Deep sequencing after alcelaphine gammaherpesvirus 1 infection reveals the nature of CD8+ T cell expansion and identify an essential viral protein for fatal bovine malignant catarrhal fever |
|
| Relations |
| BioSample |
SAMN39510814 |
| SRA |
SRX23331566 |
