|
| Status |
Public on Mar 01, 2022 |
| Title |
SARS-CoV-2 produces a diverse small viral RNA landscape capable of targeting host transcripts |
| Organisms |
Chlorocebus aethiops; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID-19) in humans, which may be lethal. In this study, we used a comparative transcriptomics approach to investigate the effects of SARS-CoV-2 infection on the host mRNA and sRNA expression programs in two primate cell lines. Upon infection, we observed global changes in host gene expression and differential expression of dozens of host miRNAs, many with known links to viral infection and immune response. Unexpectedly, we also discovered an expanded landscape of more than a hundred SARS-CoV-2-derived small viral RNAs (svRNAs), predicted to interact with differentially expressed host mRNAs and miRNAs. svRNAs are derived from distinct regions of the viral genome and sequence signatures suggest they are produced by a non-canonical biogenesis pathway. Our data suggest that svRNAs may play a role in SARS-CoV-2 propagation and antagonization of these svRNAs has potential for use as a therapeutic target.
|
| |
|
| Overall design |
For Calu-3 cell experiment: 30 total samples, 5 time points, 3 SARS-CoV-2-infected and 3 control human lung epithelial cell replicates per time point.
For Vero-E6 cell experiment: 21 total samples, 7 time points, 1-2 SARS-CoV-2 infected and 1 control African green monkey kidney cell replicates per time point.
|
| |
|
| Contributor(s) |
Neeb ZT, George AJ, Chauhan LV, Katzman S, Lipkin IW, Mishra N, Sanford JR |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Feb 26, 2022 |
| Last update date |
Mar 01, 2022 |
| Contact name |
Jeremy Sanford |
| E-mail(s) |
jsanfor2@ucsc.edu
|
| Phone |
8313345100
|
| Organization name |
UC Santa Cruz
|
| Department |
Molecular, Cell and Developmental Biology
|
| Lab |
Sanford Lab
|
| Street address |
1156 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL22915 |
Illumina HiSeq 4000 (Chlorocebus aethiops) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (99)
|
|
| Relations |
| BioProject |
PRJNA810734 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE197521_MIR_deseq.results.merge.withInfo_onlyMinAbs1L2FC.csv.gz |
4.3 Kb |
(ftp)(http) |
CSV |
| GSE197521_calu.deseq.results.merge.withInfo_onlyMinAbs1L2FC.csv.gz |
531.2 Kb |
(ftp)(http) |
CSV |
| GSE197521_caluPiranha0.95PeaksMerged.unique.bed.gz |
255 b |
(ftp)(http) |
BED |
| GSE197521_caluVs_mRNA.csv.gz |
127.8 Kb |
(ftp)(http) |
CSV |
| GSE197521_caluVs_miRNA.csv.gz |
2.4 Kb |
(ftp)(http) |
CSV |
| GSE197521_calu_sRNA_counts.csv.gz |
31.1 Kb |
(ftp)(http) |
CSV |
| GSE197521_vero.deseq.results.merge.withInfo_onlyMinAbs1L2FC.csv.gz |
124.3 Kb |
(ftp)(http) |
CSV |
| GSE197521_veroPiranha0.95PeaksMerged.unique.bed.gz |
292 b |
(ftp)(http) |
BED |
| GSE197521_veroVs_mRNA.csv.gz |
6.9 Kb |
(ftp)(http) |
CSV |
| GSE197521_vero_sRNA_counts.csv.gz |
21.1 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...