|
| Status |
Public on May 15, 2023 |
| Title |
RCMV_UV_3 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organisms |
Rattus norvegicus; Murid betaherpesvirus 8 |
| Characteristics |
strain: Sprague Dawley rats
tissue: spleen
cell type: Dendritic cells
treatment: UV-irradiated RCMV wt
timepoint: 24h
|
| Treatment protocol |
DCs were enriched from spleen homogenates using OX-62 (CD103) microbeads (Miltenyi Biotec), and RNA was either directly extracted after enrichment or 24h hours later following infection with wt/∆vXLC1/UV-irradiated rat CMV at an MOI of 3 or mock infection, as indicated.
|
| Growth protocol |
Sprague Dawley rats were bred at the animal facility of the Robert Koch Institute and sacrificed by an isoflurane overdose.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were resuspended in Trizol LS (Thermo Fisher) and RNA isolated using the Zymo Clean and Concetrator Kit (Zymo).
PolyA enriched RNA-sequencing library were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
polyA enrichment
|
| Data processing |
Sequencing reads were aligned to the rn6 version of the rat genome using hisat2 (Kim et al, 2015) with standard parameters.
Reads were then quantified using quasR (Gaidatzis et al, 2015).
Assembly: rn6
Supplementary files format and content: tab-separated values
|
| |
|
| Submission date |
May 10, 2023 |
| Last update date |
Feb 22, 2024 |
| Contact name |
Emanuel Wyler |
| E-mail(s) |
emanuel.wyler@mdc-berlin.de
|
| Phone |
+49 30 9406 3009
|
| Organization name |
Max Delbrück Center for Molecular Medicine
|
| Department |
Berlin Institute for Medical Systems Biology
|
| Lab |
RNA Biology and Posttranscriptional Regulation
|
| Street address |
Robert Roessle Str 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL34220 |
| Series (1) |
| GSE232184 |
Rat cytomegalovirus efficiently replicates within dendritic cells and affects both surface marker and gene expression |
|
| Relations |
| BioSample |
SAMN35026849 |
| SRA |
SRX20281060 |
