|
| Status |
Public on Jun 26, 2021 |
| Title |
23-Vero_E6-PC_plus_infection_lane1_20200605000 |
| Sample type |
SRA |
| |
|
| Source name |
VeroE6
|
| Organisms |
Chlorocebus aethiops; Severe acute respiratory syndrome coronavirus 2 |
| Characteristics |
cell line: VeroE6
sars-cov-2 infected: TRUE
treatment: 50 micromolar phosphatidylcholine liposomes
|
| Treatment protocol |
Liposome and inhibitors were prepared in DMEM + 10% fetal calf serum + 1% penicillin streptomycin at 1 micromolar (bemcentinib) or 50 micrmolar (PS or PC liposomes). SARS-CoV-2 was diluted and added to cells at MOI = 0.01 (VeroE6) or 0.5 (A549-ACE2). RNA was extracted 18 hours after infection (VeroE6) or 24 hours after infection (A549-ACE2)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Rneasy miniprep kit. Cells lysed in buffer RLT+betamercaptoethanol and homogenized with QIAshredder columns. RNA isolated accoring to protocol after DNAse digestion step with QIAgen kit. RNA integrity analyzed by Agilent Bioanalyzer.
Library prepared by University of Iowa Genomics Core using TruSeq Stranded mRNA kit protocol. Oligo-dT purification of polyA RNA, reverse transcription to cDNA, fragment purification, end polishing, followed by barcode ligation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end sequencing reads were subject to alignment to suitable reference genomes: human GRCh38 (GCA_000001405.15 - A549 cells), green monkey (Chlsab1/GCA_000409795.2 - Vero E6 cells) and SARS-CoV-2 (MN985325 - both A549 and Vero E6 cells). Alignments to human and monkey genomes were performed using hisat2 v2.0.5, while to viral genome using bowtie2 v2.2.9. Aligned reads were counted using featureCounts from subread package v1.5.2. Counted reads were normalized in R, using DESeq2 v1.30.0 and subjected to statistical analysis. The statistical analysis included computation of median based fold changes, Student t-test p values and false discovery rate (multiple testing correction).
The only analysis we performed was alignment to the human genome and SARS-CoV-2 genome. In the VeroE6 samples nearly 80% of the reads aligned to the viral genome, making analysis of the human mRNA changes difficult.
Genome_build: GRCh38 (GCA_000001405.15 - A549 cells), green monkey (Chlsab1/GCA_000409795.2 - Vero E6 cells) and SARS-CoV-2 (MN985325 - both A549 and Vero E6 cells)
Supplementary_files_format_and_content: Processed data consists of % reads mapped to AGM/human genome and reads mapped to SARS-CoV-2 genomes. Summary gene counts are also provided for A549-ACE2 samples.
|
| |
|
| Submission date |
Jun 25, 2021 |
| Last update date |
Jun 26, 2021 |
| Contact name |
Wendy Maury |
| Organization name |
University of Iowa
|
| Department |
Microbiology and Immunology
|
| Lab |
Maury Lab
|
| Street address |
51 Newton Rd, Bowen Science Building 3-615
|
| City |
Iowa City |
| State/province |
Iowa |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL29742 |
| Series (1) |
| GSE178942 |
SARS-CoV-2 infected and uninfected VeroE6 and A549-ACE2: Bemcentinib and liposome treatments |
|
| Relations |
| BioSample |
SAMN19876098 |
| SRA |
SRX11231264 |
