|
| Status |
Public on May 01, 2024 |
| Title |
WT-718 |
| Sample type |
SRA |
| |
|
| Source name |
CD8+ T Cells
|
| Organism |
Bos taurus |
| Characteristics |
cell type: CD8+ T Cells
treatment: Bovine Turbinates Cells infected with WT strain of AlHV-1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CD8+ T lymphocytes filtered through a 40 μm cell strainer and the concentration adjusted to 1200 cells/μL before single cell capture using the Chromium controller (10x Genomics)
Cells were loaded on the Chromium Controller (10x Genomics) and Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5ʹ v1 Reagent Kit (10x Genomics) according to manufacturer’s protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end reads were mapped to mouse genome bosTau9 with Bowtie2 using default parameters for paired-end reads. Reads that mapped several regions, or with insufficient mapping quality, were removed with samtools view. Duplicate reads were removed with MarkDuplicates tools (Picard suite). Peaks were called with MACS2
Assembly: bosTau9
Supplementary files format and content: bigwig files
|
| |
|
| 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 |
GPL26012 |
| Series (2) |
| GSE253727 |
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 [ATAC-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 |
SAMN39510712 |
| SRA |
SRX23331546 |
