|
| Status |
Public on Aug 29, 2019 |
| Title |
VZV1 |
| Sample type |
SRA |
| |
|
| Source name |
MeWo (ATCC® HTB-65™)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MeWo
cell type: Melanoma cells
vzv infection: VZV (strain pOka) infected
treatment: None
|
| Treatment protocol |
Nutlin-3 treatment (10 mm) for the duration for 48 hours.
|
| Growth protocol |
MeWo cells were cultured in MEM media (Sigma) supplemented with 10% FBS, 1% non-essential amino acid solution (Sigma) and 1% penicillin/streptomycin. MeWo cells infected with pOka at passage 24 at MOI of 0.01 were used for further analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from MeWo cells infected with pOka at passage 24 +/- Nutlin-3 treatment, normal MeWo cells and uninfected MeWo cells treated with Nutlin-3 using Tri Reagent (Zymo Research) followed by RNA extraction using the Direct-zol RNA MiniPrep kit (Direct-zol RNA MiniPrep, Zymo Research). The extracted RNA was further purified with the RNeasy Kit (Qiagen).
PolyA-selected stranded RNASeq libraries were generated using the Agilent SureSelect Strand Specific RNA Library Kit. 2µg of high quality total RNA was used per sample (RIN score >8), in accordance with manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
pOka 24-1
processed data file: RNAseq_data.txt
|
| Data processing |
Final libraries were pooled and sequenced across two runs on an Illumina NextSeq (75 cycle v2 high output kit).
Sequence read datasets were demultiplexed using bcl2fastq v2.17 under strict conditions (--barcode-mismatches 0), trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Aligned first against the human transcriptome (Homo sapiens (release 84) reference sequence (GRCh38)) and then against the VZV reference genome Dumas (GenBank accession number NC_001348.1) using Tophat2 (http://ccb.jhu.edu/software/tophat/index.shtml).
Transcript abundances were assessed using featureCounts and all data were normalised using TMM normalisation and followed by differential expression analysis using the edgeR package in Bioconductor.
FPKM values for each sample were then calculated from the edgeR output.
Genome_build: GRCh38
Supplementary_files_format_and_content: RNAseq_data.txt: Tab-delimited text file of normalised FPKM values.
|
| |
|
| Submission date |
Aug 28, 2019 |
| Last update date |
Aug 29, 2019 |
| Contact name |
Ryan O'Shaughnessy |
| E-mail(s) |
[email protected]
|
| Organization name |
Queen Mary University of London
|
| Street address |
4 Newark Street
|
| City |
London |
| ZIP/Postal code |
E12AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE136586 |
Kallikrein-mediated cytokeratin 10 degradation is required for VZV propagation in skin |
|
| Relations |
| BioSample |
SAMN12628646 |
| SRA |
SRX6755703 |
