Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE162323
Status 2021/4/1
Title SARS-CoV-2 utilizes a multipronged strategy to suppress host protein synthesis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing;Other
Summary Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 19 (COVID-19) pandemic. Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis and its ability to antagonize innate immune responses. Here, we use RNA-sequencing and ribosome profiling along SARS-CoV-2 infection and comprehensively define the mechanisms that are utilized by SARS-CoV-2 to shutoff cellular protein synthesis. We show SARS-CoV-2 infection leads to a global reduction in translation but that viral transcripts are not preferentially translated. Instead, we reveal that infection leads to accelerated degradation of cytosolic cellular mRNAs which facilitates viral takeover of the mRNA pool in infected cells. Moreover, we show that the translation of transcripts whose expression is induced in response to infection, including innate immune genes, is impaired, implying infection prevents newly transcribed cellular mRNAs from accessing the ribosomes. Overall, our results uncover the multipronged strategy employed by SARS-CoV-2 to commandeer the translation machinery and to suppress host defenses.
Samples
GSM ID Sample info Characteristics Description
GSM4949729 Calu3_mrna_8hpi_2_total virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:8 RNA-seq without polyA selection
GSM4949730 Calu3_fp_uninf_1 virus strain:--; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected Ribo-seq after treatment with Cycloheximide
GSM4949731 Calu3_fp_uninf_2 virus strain:--; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected Ribo-seq after treatment with Cycloheximide
GSM4949732 Calu3_fp_3hpi virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:3 Ribo-seq after treatment with Cycloheximide
GSM4949733 Calu3_fp_5hpi virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:5 Ribo-seq after treatment with Cycloheximide
GSM4949734 Calu3_fp_8hpi_1 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:8 Ribo-seq after treatment with Cycloheximide
GSM4949735 Calu3_fp_8hpi_2 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:8 Ribo-seq after treatment with Cycloheximide
GSM5049221 slam_uninf_no4sU cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq after 4sU labeling;slam_uninf_params.txt
GSM5049222 slam_uninf_1h_4sU cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq after 4sU labeling;slam_uninf_params.txt
GSM5049223 slam_uninf_2h_4sU_rep1 cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq after 4sU labeling;slam_uninf_params.txt
GSM5049224 slam_uninf_2h_4sU_rep2 cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq after 4sU labeling;slam_uninf_params.txt
GSM5049225 slam_uninf_3h_4sU cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq after 4sU labeling;slam_uninf_params.txt
GSM5049226 slam_uninf_4h_4sU cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq after 4sU labeling;slam_uninf_params.txt
GSM5049227 slam_inf_no4sU virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:7 RNA-seq after 4sU labeling;slam_inf_params.txt
GSM5049228 slam_inf_4hpi_1h_4sU virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:4 RNA-seq after 4sU labeling;slam_inf_params.txt
GSM5049229 slam_inf_5hpi_2h_4sU_rep1 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:5 RNA-seq after 4sU labeling;slam_inf_params.txt
GSM5049230 slam_inf_5hpi_2h_4sU_rep2 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:5 RNA-seq after 4sU labeling;slam_inf_params.txt
GSM5049231 slam_inf_6hpi_3h_4sU virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:6 RNA-seq after 4sU labeling;slam_inf_params.txt
GSM5049232 slam_inf_7hpi_4h_4sU virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:7 RNA-seq after 4sU labeling;slam_inf_params.txt
GSM5049233 frac_uninf_cyto_rep1 cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049234 frac_uninf_nuc_rep1 cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049235 frac_uninf_total_rep1 cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049236 frac_uninf_cyto_rep2 cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049237 frac_uninf_nuc_rep2 cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049238 frac_uninf_total_rep2 cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049239 frac_inf_7hpi_cyto_rep1 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:7 RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049240 frac_inf_7hpi_nuc_rep1 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:7 RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049241 frac_inf_7hpi_total_rep1 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:7 RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049242 frac_inf_7hpi_cyto_rep2 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:7 RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049243 frac_inf_7hpi_nuc_rep2 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:7 RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM5049244 frac_inf_7hpi_total_rep2 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:7 RNA-seq of the cytosolic, nuclear and total cell fractions.;frac_reads.txt
GSM4949718 Calu3_mrna_uninf_1 virus strain:--; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq with polyA selection
GSM4949719 Calu3_mrna_uninf_2 virus strain:--; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq with polyA selection
GSM4949720 Calu3_mrna_3hpi virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:3 RNA-seq with polyA selection
GSM4949721 Calu3_mrna_5hpi virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:5 RNA-seq with polyA selection
GSM4949722 Calu3_mrna_8hpi_1 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:8 RNA-seq with polyA selection
GSM4949723 Calu3_mrna_8hpi_2 virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:8 RNA-seq with polyA selection
GSM4949724 Calu3_mrna_uninf_1_total virus strain:--; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq without polyA selection
GSM4949725 Calu3_mrna_uninf_2_total virus strain:--; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:uninfected RNA-seq without polyA selection
GSM4949726 Calu3_mrna_3hpi_total virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:3 RNA-seq without polyA selection
GSM4949727 Calu3_mrna_5hpi_total virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:5 RNA-seq without polyA selection
GSM4949728 Calu3_mrna_8hpi_1_total virus strain:BetaCoV/Germany/BavPat1/2020 Ref-SKU: 026V-03883; cell line:Calu 3 cells, ATCC HTB-55; hours post infection:8 RNA-seq without polyA selection
Platform GPL24676  GPL29320  : Illumina NovaSeq 6000 (Homo sapiens);Illumina NovaSeq 6000 (Homo sapiens; Severe acute respiratory syndrome coronavirus 2)
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* p<0.05 ** p<0.01