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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 04, 2020 |
| Title |
Gene expression profiling of SARS-CoV-1/2 infected human cell lines at bulk and single-cell level |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
To identify human genes and cellular pathways influencing SARS-CoV-1 and SARS-CoV-2 infection, we performed genome-wide measurements of different aspects of gene expression at the bulk and single-cell level.
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| Overall design |
Different human cell lines were infected with SARS-CoV-1 and SARS-CoV-2 and harvested at different time points. Gene expression profiling was measured using bulk and single-cell polyA RNA-sequencing, smallRNA sequencing, and totalRNA sequencing.
Raw data are not provided for AEC samples due to patient privacy concerns.
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| Contributor(s) |
Wyler E, Mösbauer K, Franke V, Diag A, Gottula LT, Arsie R, Klironomos F, Koppstein D, Ayoub S, Buccitelli C, Richter A, Legnini I, Ivanov A, Mari T, Del Giudice S, Papies JP, Praktiknjo S, Müller MA, Niemeyer D, Selbach M, Akalin A, Rajewsky N, Drosten C, Landthaler M |
| Citation(s) |
33585804 |
| Submission date |
Apr 15, 2020 |
| Last update date |
Mar 29, 2021 |
| Contact name |
Emanuel Wyler |
| E-mail(s) |
emanuel.wyler@mdc-berlin.de
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| Phone |
+49 30 9406 3009
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| Organization name |
Max Delbrück Center for Molecular Medicine
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| Department |
Berlin Institute for Medical Systems Biology
|
| Lab |
RNA Biology and Posttranscriptional Regulation
|
| Street address |
Robert Roessle Str 10
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| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platforms (3) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (203)
|
| GSM4477857 |
H1299_polyA_mock-4h-B |
| GSM4477858 |
H1299_polyA_S1-12h-A |
| GSM4477859 |
H1299_polyA_S1-12h-B |
| GSM4477860 |
H1299_polyA_S1-24h-A |
| GSM4477861 |
H1299_polyA_S1-24h-B |
| GSM4477862 |
H1299_polyA_S1-36h-A |
| GSM4477863 |
H1299_polyA_S1-36h-B |
| GSM4477864 |
H1299_polyA_S1-4h-A |
| GSM4477865 |
H1299_polyA_S1-4h-B |
| GSM4477866 |
H1299_polyA_S2-12h-A |
| GSM4477867 |
H1299_polyA_S2-12h-B |
| GSM4477868 |
H1299_polyA_S2-24h-A |
| GSM4477869 |
H1299_polyA_S2-24h-B |
| GSM4477870 |
H1299_polyA_S2-36h-A |
| GSM4477871 |
H1299_polyA_S2-36h-B |
| GSM4477872 |
H1299_polyA_S2-4h-A |
| GSM4477873 |
H1299_polyA_S2-4h-B |
| GSM4477874 |
H1299_polyA_untr-4h-A |
| GSM4477875 |
H1299_polyA_untr-4h-B |
| GSM4477876 |
Caco2_polyA-mock-24h-A |
| GSM4477877 |
Caco2_polyA-mock-24h-B |
| GSM4477878 |
Caco2_polyA-mock-4h-A |
| GSM4477879 |
Caco2_polyA-mock-4h-B |
| GSM4477880 |
Caco2_polyA-S1-12h-A |
| GSM4477881 |
Caco2_polyA-S1-12h-B |
| GSM4477882 |
Caco2_polyA-S1-24h-A |
| GSM4477883 |
Caco2_polyA-S1-24h-B |
| GSM4477884 |
Caco2_polyA-S1-4h-A |
| GSM4477885 |
Caco2_polyA-S1-4h-B |
| GSM4477886 |
Caco2_polyA-S2-12h-A |
| GSM4477887 |
Caco2_polyA-S2-12h-B |
| GSM4477888 |
Caco2_polyA-S2-24h-A |
| GSM4477889 |
Caco2_polyA-S2-24h-B |
| GSM4477890 |
Caco2_polyA-S2-4h-A |
| GSM4477891 |
Caco2_polyA-S2-4h-B |
| GSM4477892 |
Caco2_polyA-untr-4h-A |
| GSM4477893 |
Caco2_polyA-untr-4h-B |
| GSM4477894 |
Calu3_polyA_series1-untr-4h-A |
| GSM4477895 |
Calu3_polyA_series1-untr-4h-B |
| GSM4477896 |
Calu3_polyA_series1-mock-4h-A |
| GSM4477897 |
Calu3_polyA_series1-mock-4h-B |
| GSM4477898 |
Calu3_polyA_series1-mock-24h-A |
| GSM4477899 |
Calu3_polyA_series1-mock-24h-B |
| GSM4477900 |
Calu3_polyA_series1-S1-4h-A |
| GSM4477901 |
Calu3_polyA_series1-S1-4h-B |
| GSM4477902 |
Calu3_polyA_series1-S1-12h-A |
| GSM4477903 |
Calu3_polyA_series1-S1-12h-B |
| GSM4477904 |
Calu3_polyA_series1-S1-24h-A |
| GSM4477905 |
Calu3_polyA_series1-S1-24h-B |
| GSM4477906 |
Calu3_polyA_series1-S2-4h-A |
| GSM4477907 |
Calu3_polyA_series1-S2-4h-B |
| GSM4477908 |
Calu3_polyA_series1-S2-12h-A |
| GSM4477909 |
Calu3_polyA_series1-S2-12h-B |
| GSM4477910 |
Calu3_polyA_series1-S2-24h-A |
| GSM4477911 |
Calu3_polyA_series1-S2-24h-B |
| GSM4477912 |
Calu3_polyA_series1-S1-24h-A-detachedcells |
| GSM4477913 |
Calu3_polyA_series1-S1-24h-B-detachedcells |
| GSM4477914 |
Calu3_polyA_series1-S2-24h-A-detachedcells |
| GSM4477915 |
Calu3_polyA_series1-S2-24h-B-detachedcells |
| GSM4477916 |
Calu3_polyA_series2-12h-mock-1 |
| GSM4477917 |
Calu3_polyA_series2-12h-mock-2 |
| GSM4477918 |
Calu3_polyA_series2-12h-S1-1 |
| GSM4477919 |
Calu3_polyA_series2-12h-S1-2 |
| GSM4477920 |
Calu3_polyA_series2-12h-S2-1 |
| GSM4477921 |
Calu3_polyA_series2-12h-S2-2 |
| GSM4477922 |
Calu3_polyA_series2-4h-mock-1 |
| GSM4477923 |
Calu3_polyA_series2-4h-mock-2 |
| GSM4477924 |
Calu3_polyA_series2-4h-S1-1 |
| GSM4477925 |
Calu3_polyA_series2-4h-S1-2 |
| GSM4477926 |
Calu3_polyA_series2-4h-S2-1 |
| GSM4477927 |
Calu3_polyA_series2-4h-S2-2 |
| GSM4477928 |
Calu3_polyA_series2-8h-S1-1 |
| GSM4477929 |
Calu3_polyA_series2-8h-S1-2 |
| GSM4477930 |
Calu3_polyA_series2-8h-S2-1 |
| GSM4477931 |
Calu3_polyA_series2-8h-S2-2 |
| GSM4477932 |
Calu3_smallRNA-mock-24h-A |
| GSM4477933 |
Calu3_smallRNA-mock-24h-B |
| GSM4477934 |
Calu3_smallRNA-mock-4h-A |
| GSM4477935 |
Calu3_smallRNA-mock-4h-B |
| GSM4477936 |
Calu3_smallRNA-S1-12h-A |
| GSM4477937 |
Calu3_smallRNA-S1-12h-B |
| GSM4477938 |
Calu3_smallRNA-S1-24h-A |
| GSM4477939 |
Calu3_smallRNA-S1-24h-B |
| GSM4477940 |
Calu3_smallRNA-S1-4h-A |
| GSM4477941 |
Calu3_smallRNA-S1-4h-B |
| GSM4477942 |
Calu3_smallRNA-S2-12h-A |
| GSM4477943 |
Calu3_smallRNA-S2-12h-B |
| GSM4477944 |
Calu3_smallRNA-S2-24h-A |
| GSM4477945 |
Calu3_smallRNA-S2-24h-B |
| GSM4477946 |
Calu3_smallRNA-S2-4h-A |
| GSM4477947 |
Calu3_smallRNA-S2-4h-B |
| GSM4477948 |
Calu3_smallRNA-untr-4h-A |
| GSM4477949 |
Calu3_smallRNA-untr-4h-B |
| GSM4477950 |
Calu3_totalRNA-mock-24h-A |
| GSM4477951 |
Calu3_totalRNA-mock-24h-B |
| GSM4477952 |
Calu3_totalRNA-mock-4h-A |
| GSM4477953 |
Calu3_totalRNA-mock-4h-B |
| GSM4477954 |
Calu3_totalRNA-S1-12h-A |
| GSM4477955 |
Calu3_totalRNA-S1-12h-B |
| GSM4477956 |
Calu3_totalRNA-S1-24h-A |
| GSM4477957 |
Calu3_totalRNA-S1-24h-B |
| GSM4477958 |
Calu3_totalRNA-S1-4h-A |
| GSM4477959 |
Calu3_totalRNA-S1-4h-B |
| GSM4477960 |
Calu3_totalRNA-S2-12h-A |
| GSM4477961 |
Calu3_totalRNA-S2-12h-B |
| GSM4477962 |
Calu3_totalRNA-S2-24h-A |
| GSM4477963 |
Calu3_totalRNA-S2-24h-B |
| GSM4477964 |
Calu3_totalRNA-S2-4h-A |
| GSM4477965 |
Calu3_totalRNA-S2-4h-B |
| GSM4477966 |
Calu3_totalRNA-untr-4h-A |
| GSM4477967 |
Calu3_totalRNA-untr-4h-B |
| GSM4477968 |
H1299_scRNAseq-mock-36h-A |
| GSM4477969 |
H1299_scRNAseq-mock-36h-B |
| GSM4477970 |
H1299_scRNAseq-mock-4h-A |
| GSM4477971 |
H1299_scRNAseq-mock-4h-B |
| GSM4477972 |
H1299_scRNAseq-S1-12h-A |
| GSM4477973 |
H1299_scRNAseq-S1-12h-B |
| GSM4477974 |
H1299_scRNAseq-S1-24h-A |
| GSM4477975 |
H1299_scRNAseq-S1-24h-B |
| GSM4477976 |
H1299_scRNAseq-S1-36h-A |
| GSM4477977 |
H1299_scRNAseq-S1-36h-B |
| GSM4477978 |
H1299_scRNAseq-S2-12h-A |
| GSM4477979 |
H1299_scRNAseq-S2-12h-B |
| GSM4477980 |
H1299_scRNAseq-S2-24h-A |
| GSM4477981 |
H1299_scRNAseq-S2-24h-B |
| GSM4477982 |
H1299_scRNAseq-S2-36h-A |
| GSM4477983 |
H1299_scRNAseq-S2-36h-B |
| GSM4477984 |
Calu3_scRNAseq-mock-12h-A |
| GSM4477985 |
Calu3_scRNAseq-mock-12h-B |
| GSM4477986 |
Calu3_scRNAseq-mock-4h-A |
| GSM4477987 |
Calu3_scRNAseq-mock-4h-B |
| GSM4477988 |
Calu3_scRNAseq-S1-12h-A |
| GSM4477989 |
Calu3_scRNAseq-S1-12h-B |
| GSM4477990 |
Calu3_scRNAseq-S1-4h-A |
| GSM4477991 |
Calu3_scRNAseq-S1-4h-B |
| GSM4477992 |
Calu3_scRNAseq-S1-8h-A |
| GSM4477993 |
Calu3_scRNAseq-S1-8h-B |
| GSM4477994 |
Calu3_scRNAseq-S2-12h-A |
| GSM4477995 |
Calu3_scRNAseq-S2-12h-B |
| GSM4477996 |
Calu3_scRNAseq-S2-4h-A |
| GSM4477997 |
Calu3_scRNAseq-S2-4h-B |
| GSM4477998 |
Calu3_scRNAseq-S2-8h-A |
| GSM4477999 |
Calu3_scRNAseq-S2-8h-B |
| GSM4681394 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, mock infected, replicate 1 |
| GSM4681395 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, mock infected, replicate 2 |
| GSM4681396 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, mock infected, replicate 3 |
| GSM4681397 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, S2 infected, replicate 1 |
| GSM4681398 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, S2 infected, replicate 2 |
| GSM4681399 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, S2 infected, replicate 3 |
| GSM4681400 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , 800 nM Onalespib treated, S2 infected, replicate 1 |
| GSM4681401 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , 800 nM Onalespib treated, S2 infected, replicate 2 |
| GSM4681402 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , 800 nM Onalespib treated, S2 infected, replicate 3 |
| GSM4681403 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, mock infected, replicate 1 |
| GSM4681404 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, mock infected, replicate 2 |
| GSM4681405 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, mock infected, replicate 3 |
| GSM4681406 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, S2 infected, replicate 1 |
| GSM4681407 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, S2 infected, replicate 2 |
| GSM4681408 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, S2 infected, replicate 3 |
| GSM4681409 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM 17-AAG treated, S2 infected, replicate 1 |
| GSM4681410 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM 17-AAG treated, S2 infected, replicate 2 |
| GSM4681411 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM 17-AAG treated, S2 infected, replicate 3 |
| GSM4681412 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM Ganetespib treated, S2 infected, replicate 1 |
| GSM4681413 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM Ganetespib treated, S2 infected, replicate 2 |
| GSM4681414 |
polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM Ganetespib treated, S2 infected, replicate 3 |
| GSM5022796 |
polyA RNA from AEC, harvested at 24hpi, mock infected, DMSO (solvent) treated, replicate 1 |
| GSM5022797 |
polyA RNA from AEC, harvested at 24hpi, mock infected, DMSO (solvent) treated, replicate 2 |
| GSM5022798 |
polyA RNA from AEC, harvested at 24hpi, mock infected, DMSO (solvent) treated, replicate 3 |
| GSM5022799 |
polyA RNA from AEC, harvested at 24hpi, mock infected, 17-AAG (200 nM) treated, replicate 1 |
| GSM5022800 |
polyA RNA from AEC, harvested at 24hpi, mock infected, 17-AAG (200 nM) treated, replicate 2 |
| GSM5022801 |
polyA RNA from AEC, harvested at 24hpi, mock infected, 17-AAG (200 nM) treated, replicate 3 |
| GSM5022802 |
polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 1 |
| GSM5022803 |
polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 2 |
| GSM5022804 |
polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 3 |
| GSM5022805 |
polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 1 |
| GSM5022806 |
polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 2 |
| GSM5022807 |
polyA RNA from AEC, harvested at 24hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 3 |
| GSM5022808 |
polyA RNA from AEC, harvested at 48hpi, mock infected, DMSO (solvent) treated, replicate 1 |
| GSM5022809 |
polyA RNA from AEC, harvested at 48hpi, mock infected, DMSO (solvent) treated, replicate 2 |
| GSM5022810 |
polyA RNA from AEC, harvested at 48hpi, mock infected, DMSO (solvent) treated, replicate 3 |
| GSM5022811 |
polyA RNA from AEC, harvested at 48hpi, mock infected, 17-AAG (200 nM) treated, replicate 1 |
| GSM5022812 |
polyA RNA from AEC, harvested at 48hpi, mock infected, 17-AAG (200 nM) treated, replicate 2 |
| GSM5022813 |
polyA RNA from AEC, harvested at 48hpi, mock infected, 17-AAG (200 nM) treated, replicate 3 |
| GSM5022814 |
polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 1 |
| GSM5022815 |
polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 2 |
| GSM5022816 |
polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 3 |
| GSM5022817 |
polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 1 |
| GSM5022818 |
polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 2 |
| GSM5022819 |
polyA RNA from AEC, harvested at 48hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 3 |
| GSM5022820 |
polyA RNA from AEC, harvested at 72hpi, mock infected, DMSO (solvent) treated, replicate 1 |
| GSM5022821 |
polyA RNA from AEC, harvested at 72hpi, mock infected, DMSO (solvent) treated, replicate 2 |
| GSM5022822 |
polyA RNA from AEC, harvested at 72hpi, mock infected, DMSO (solvent) treated, replicate 3 |
| GSM5022823 |
polyA RNA from AEC, harvested at 72hpi, mock infected, 17-AAG (200 nM) treated, replicate 1 |
| GSM5022824 |
polyA RNA from AEC, harvested at 72hpi, mock infected, 17-AAG (200 nM) treated, replicate 2 |
| GSM5022825 |
polyA RNA from AEC, harvested at 72hpi, mock infected, 17-AAG (200 nM) treated, replicate 3 |
| GSM5022826 |
polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 1 |
| GSM5022827 |
polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 2 |
| GSM5022828 |
polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, DMSO (solvent) treated, replicate 3 |
| GSM5022829 |
polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 1 |
| GSM5022830 |
polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 2 |
| GSM5022831 |
polyA RNA from AEC, harvested at 72hpi, SARS-CoV-2 infected, 17-AAG (200 nM) treated, replicate 3 |
|
| Relations |
| BioProject |
PRJNA625518 |
| SRA |
SRP256479 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148729_AEC_SARSCoV2_17AAG_readcounts.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
| GSE148729_Caco2_polyA_readcounts.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
| GSE148729_Calu3_polyA_series1_readcounts.tsv.gz |
1.2 Mb |
(ftp)(http) |
TSV |
| GSE148729_Calu3_polyA_series2_readcounts_rev.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
| GSE148729_Calu3_scRNAseq_morethan1000genes_metadata.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
| GSE148729_Calu3_scRNAseq_morethan1000genes_rawcounts_tr.tsv.gz |
151.5 Mb |
(ftp)(http) |
TSV |
| GSE148729_Calu3_smallRNA_miRNAcounts.tsv.gz |
24.6 Kb |
(ftp)(http) |
TSV |
| GSE148729_Calu3_totalRNA_readcounts.tsv.gz |
792.2 Kb |
(ftp)(http) |
TSV |
| GSE148729_H1299_polyA_readcounts.tsv.gz |
1.3 Mb |
(ftp)(http) |
TSV |
| GSE148729_H1299_scRNAseq_morethan2000genes_metadata.tsv.gz |
593.9 Kb |
(ftp)(http) |
TSV |
| GSE148729_H1299_scRNAseq_morethan2000genes_rawcounts_tr.tsv.gz |
108.0 Mb |
(ftp)(http) |
TSV |
| GSE148729_Hsp90_gene_counts.tsv.gz |
1.1 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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