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| Status |
Public on Apr 10, 2022 |
| Title |
Parsing the role of NSP1 in SARS-CoV-2 infection |
| Organisms |
Homo sapiens; Mesocricetus auratus; Chlorocebus sabaeus; Severe acute respiratory syndrome coronavirus 2 |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
NSP1 is a major shutoff factor of the SARS-CoV-2 coronavirus, which is responsible for the COVID-19 pandemic. The functions of NSP1 and its contribution to SARS-CoV-2 propagation is not well understood. We tackled these questions utilizing methods such as RNA sequencing, ribosome profiling, and SLAMseq.
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| Overall design |
To decipher SARS-CoV-2 NSP1's functions, we performed RNA sequencing following overexpression and fractionation of the wt protein and of two mutants. We also performed SLAMseq analysis on cell overexpressed with NSP1wt and with a mutated NSP1, and on cells infected with SARS-CoV-2 or with a SARS-CoV-2Δnsp1 mutated virus. Additionally, we performed ribosome profiling on cells infected with SARS-CoV-2 or with the SARS-CoV-2Δnsp1 mutant.
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| Contributor(s) |
Stern-Ginossar N, Fisher T, Gluck A, Kuroda M, Nachshon A, Hsu JC, Halfmann PJ, Yahalom-Ronen Y, Finkel Y, Schwartz M, Weiss S, Tseng CK, Israely T, Paran N, Kawaoka Y, Makino S |
| Citation(s) |
35671758 |
| |
| Submission date |
Apr 07, 2022 |
| Last update date |
Jul 10, 2022 |
| Contact name |
Noam Stern-Ginossar |
| E-mail(s) |
noam.stern-ginossar@weizmann.ac.il
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| Organization name |
Weizmann Institute
|
| Department |
Molecular Genetics
|
| Lab |
Noam Stern-Ginossar
|
| Street address |
234 herzel
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platforms (4)
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| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL30234 |
Illumina MiSeq (Homo sapiens; Severe acute respiratory syndrome coronavirus 2) |
| GPL32148 |
Illumina MiSeq (Chlorocebus sabaeus; Severe acute respiratory syndrome coronavirus 2) |
| GPL32149 |
Illumina MiSeq (Mesocricetus auratus; Severe acute respiratory syndrome coronavirus 2) |
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| Samples (159)
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| Relations |
| BioProject |
PRJNA824486 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE200422_Calu3_GrowthCurve_cds_reads.csv.gz |
607.4 Kb |
(ftp)(http) |
CSV |
| GSE200422_Fractionation_transcript_reads.csv.gz |
768.0 Kb |
(ftp)(http) |
CSV |
| GSE200422_Hamsters_cds_reads.csv.gz |
409.8 Kb |
(ftp)(http) |
CSV |
| GSE200422_Inf_del_HL.csv.gz |
55.7 Kb |
(ftp)(http) |
CSV |
| GSE200422_Inf_mock_HL.csv.gz |
61.7 Kb |
(ftp)(http) |
CSV |
| GSE200422_Inf_wt_HL.csv.gz |
68.9 Kb |
(ftp)(http) |
CSV |
| GSE200422_Infection_SLAMseq_cds_reads.csv.gz |
520.0 Kb |
(ftp)(http) |
CSV |
| GSE200422_OE_SLAMseq_cds_reads.csv.gz |
863.0 Kb |
(ftp)(http) |
CSV |
| GSE200422_OE_del_HL.csv.gz |
156.5 Kb |
(ftp)(http) |
CSV |
| GSE200422_OE_fractionation_transcript_reads.csv.gz |
832.1 Kb |
(ftp)(http) |
CSV |
| GSE200422_OE_gfp_HL.csv.gz |
163.3 Kb |
(ftp)(http) |
CSV |
| GSE200422_OE_rk_HL.csv.gz |
167.3 Kb |
(ftp)(http) |
CSV |
| GSE200422_OE_wt_HL.csv.gz |
180.0 Kb |
(ftp)(http) |
CSV |
| GSE200422_RibosomeProfiling_FP_cds_reads.csv.gz |
433.3 Kb |
(ftp)(http) |
CSV |
| GSE200422_RibosomeProfiling_mRNA_cds_reads.csv.gz |
624.1 Kb |
(ftp)(http) |
CSV |
| GSE200422_Ruxolitinib_cds_reads.csv.gz |
658.2 Kb |
(ftp)(http) |
CSV |
| GSE200422_Vero_GrowthCurve_cds_reads.csv.gz |
414.5 Kb |
(ftp)(http) |
CSV |
| GSE200422_cyt2nuc_ratios.csv.gz |
711.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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