|
| Status |
Public on Aug 31, 2022 |
| Title |
Virus stock P2 |
| Sample type |
SRA |
| |
|
| Source name |
Rubella virus stock
|
| Organism |
Rubivirus rubellae |
| Characteristics |
infection: N/A
rubella virus strain: P2
sampling timepoint: N/A
|
| Treatment protocol |
Cells were infected with a MOI of 5.
|
| Growth protocol |
Human umbilical vein cells (HUVEC) from three donors (Promocell) were maintained in Endothelial Cell Growth Medium 2 (Promocell) and supplemented with 10% (v/v) Supplement Mix and 100 units/ml penicillin. The cells were cultivated in a humidified atmosphere with 5% CO2 at 37°C
Viruses were propagated on Vero E6 cells. After 6 days viral supernatant was concentrated by ultrafiltration through a 30 kDa filter and stored at −80°C. For every virus stock, a mock sample from uninfected cells was processed in parallel, which was then used as the mock control for the infections.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina Truseq stranded
adapter sequence: GATCGGAAGAGCACACGT
For RNA extraction, medium was removed and cells were lysed in Trizol (Thermo Fisher). Virus stocks were diluted 1:3 in Trizol LS (Thermo Fisher). RNA was extracted using the clean and concentrator kit 25 (Zymo) according to manufacturer's instruction.
RNA-sequencing library were prepared with polyA enrichment, or using the RiboZero kit (Illumina) for rRNA depletion, before continuing with the TruSeq stranded kit (Illumina)
rRNA depleted total RNA
polyA RNA-seq
total RNA from virus stocks
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
total RNA
|
| Data processing |
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the hg19 version of the human genome
Reads were then quantified using quasR (Gaidatzis et al, 2015).
For generating the viral genome sequences in the fasta files provided here, sequencing reads were aligned to the rubella virus sequence NC_001545.2 and differences recursively corrected. See JF727654.2 (Ervevax) and JN635289.1 (MA17) for previously available genome sequences.
Genome_build: hg19
Genome_build: Rubella virus NC_001545.2
Supplementary_files_format_and_content: tab-separated values
Supplementary_files_format_and_content: fasta
|
| |
|
| Submission date |
Dec 27, 2021 |
| Last update date |
Aug 31, 2022 |
| 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 |
GPL31148 |
| Series (1) |
| GSE192648 |
Rubella Virus wildtype and vaccine strains induce transcription of chemokines and components of innate immunity in human embryonic endothelial cells |
|
| Relations |
| BioSample |
SAMN24436361 |
| SRA |
SRX13510459 |
