|
| Status |
Public on Dec 31, 2020 |
| Title |
VERO_CEP_P2V_2 |
| Sample type |
SRA |
| |
|
| Source name |
vero cell CEP treatment first, then P2V treatment
|
| Organism |
Chlorocebus sabaeus |
| Characteristics |
treatment: vero cell CEP treatment first, then P2V treatment
cell line: Vero E6
|
| Treatment protocol |
Cells were treated with GX_P2V (2019-nCoVr at MOI = 0.01), CEP (5 uM), or CEP and virus, and then cultured for another 72h.
|
| Growth protocol |
Vero E6 cells (1.5×107 cells/flask) were plated in T75 culture flasks for 24h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and mRNA was isolated by using TRIzon (Invitrogen).
The libraries were constructed by using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
vero cell CEP treatment first, then P2V treatment
|
| Data processing |
The FastQC tools and fastx_trimmer wrapped in fastx toolkit were used to trim low-quality bases (Q<20) and adapter for raw sequences. Cleaned RNA-seq reads were mapped to the reference chlorocebus sabaeus genome ChlSab1.1 (GCA_000409795.2) by HISAT2 (v2.1.0)[14]. Duplicated reads for pair-end data were removed by SAMtools (v1.5)[15]. Counts for each gene were obtained by using HTseq. DESeq2 were used to identify differentially expressed genes between experimental groups [16]. False Discovery Rate (FDR q-value) was calculated by adjusting P-values with the Benjamini-Hochberg method. Genes with FDR q-value < 0.05 and |Log2 (Fold change)| > 1 were considered as differential expressed genes.
Genome_build: chlorocebus sabaeus genome ChlSab1.1 (GCA_000409795.2)
Supplementary_files_format_and_content: .txt, counts
|
| |
|
| Submission date |
Sep 16, 2020 |
| Last update date |
Dec 31, 2020 |
| Contact name |
Shasha Li |
| E-mail(s) |
shashal@umich.edu
|
| Phone |
01062798728
|
| Organization name |
University of Michigan
|
| Street address |
1109 Maiden Ln, ct apt 104
|
| City |
ANN ARBOR |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL18770 |
| Series (1) |
| GSE158050 |
Cepharanthine shows antiviral activities by modulating cellular stress responses triggered by a SARS-CoV2 related coronavirus |
|
| Relations |
| BioSample |
SAMN16180060 |
| SRA |
SRX9132490 |
