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Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

Joy S Xiang, Jasmine R Mueller, En-Ching Luo, Brian A Yee, Danielle Schafer, Jonathan C Schmok, Frederick E Tan, Katherine Rothamel, Rachael N McVicar, Elizabeth M Kwong, Krysten L Jones, Hsuan-Lin Her, Chun-Yuan Chen, Anthony Q Vu, Wenhao Jin, Samuel S Park, Phuong Le, Kristopher W Brannan, Eric R Kofman, Yanhua Li, Alexandra T Tankka, Kevin D Dong, Yan Song, Aaron F Carlin, Eric L Van Nostrand, Sandra L Leibel, Gene W Yeo

bioRxiv : the preprint server for biology · 2022

PubMed ↗ DOI ↗ PMC full text ↗

Abstract

The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/β. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.

Linked datasets 4

GSE173498 GSE · via ncbi_elink
GEO ↗

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [eCLIP]

Homo sapiens

299 data files
FileTypeSize
E-IN1_S86_L002_R1_001.fastq.gz OTHER 525.9 MB
E-IN2_S87_L002_R1_001.fastq.gz OTHER 766.1 MB
E-IP1_S65_L002_R1_001.fastq.gz OTHER 2.1 GB
E-IP2_S66_L002_R1_001.fastq.gz OTHER 1.1 GB
M-IN1_S53_L002_R1_001.fastq.gz OTHER 519.3 MB
M-IN2_S54_L002_R1_001.fastq.gz OTHER 537.8 MB
M-IP1_S97_L002_R1_001.fastq.gz OTHER 661.8 MB
M-IP2_S98_L002_R1_001.fastq.gz OTHER 605.7 MB
N-IN1_S74_L002_R1_001.fastq.gz OTHER 406.4 MB
N-IN2_S76_L002_R1_001.fastq.gz OTHER 560.1 MB
N-IP1_S75_L002_R1_001.fastq.gz OTHER 474.7 MB
N-IP2_S77_L002_R1_001.fastq.gz OTHER 798.6 MB
nsp10-IN1__S63_L002_R1_001.fastq.gz OTHER 743.9 MB
nsp10-IN1_S64_L002_R1_001.fastq.gz OTHER 1.1 GB
nsp10-IP1_S103_L002_R1_001.fastq.gz OTHER 813.4 MB
nsp10-IP2_S104_L002_R1_001.fastq.gz OTHER 721.5 MB
Nsp11-1-IN_S28_L007_R1_001.fastq.gz OTHER 407.0 MB
NSP11_1_IP_S47_L003_R1_001.fastq.gz OTHER 734.6 MB
NSP11_2_iN_S18_L003_R1_001.fastq.gz OTHER 847.0 MB
NSP11_2_IP_S44_L003_R1_001.fastq.gz OTHER 727.6 MB
NSP1-1-IN_S1_L002_R1_001.fastq.gz OTHER 343.2 MB
NSP1-1-IP_S2_L002_R1_001.fastq.gz OTHER 1.4 GB
nsp12-1-IN_S24_L004_R1_001.fastq.gz OTHER 1.9 GB
nsp12-1-IP_S42_L004_R1_001.fastq.gz OTHER 1.4 GB
nsp12-2-IN_S26_L004_R1_001.fastq.gz OTHER 2.6 GB
nsp12-2-IP_S43_L004_R1_001.fastq.gz OTHER 1.4 GB
NSP1-2-IP_S4_L002_R1_001.fastq.gz OTHER 533.0 MB
NSP13_1_IN_S36_L003_R1_001.fastq.gz OTHER 811.0 MB
NSP13_1_IP_S45_L003_R1_001.fastq.gz OTHER 771.9 MB
Nsp13-2-IN_S29_L007_R1_001.fastq.gz OTHER 388.5 MB
NSP13_2_IP_S38_L003_R1_001.fastq.gz OTHER 804.8 MB
NSP14_1_IN_S2_L003_R1_001.fastq.gz OTHER 717.5 MB
NSP14_1_IP_S31_L003_R1_001.fastq.gz OTHER 641.1 MB
NSP14_2_iN_S3_L003_R1_001.fastq.gz OTHER 810.5 MB
NSP14_2_IP_S22_L003_R1_001.fastq.gz OTHER 719.3 MB
nsp15-IN1_S78_L002_R1_001.fastq.gz OTHER 307.1 MB
nsp15-IN2_S79_L002_R1_001.fastq.gz OTHER 673.1 MB
nsp15-IP1_S45_L002_R1_001.fastq.gz OTHER 613.1 MB
nsp15-IP2_S46_L002_R1_001.fastq.gz OTHER 470.8 MB
NSP16-1-IN_S9_L002_R1_001.fastq.gz OTHER 442.0 MB
NSP16-1-IP_S10_L002_R1_001.fastq.gz OTHER 465.3 MB
NSP16-2-IN_S11_L002_R1_001.fastq.gz OTHER 389.8 MB
NSP16-2-IP_S12_L002_R1_001.fastq.gz OTHER 436.8 MB
nsp2-1-IN_S3_L004_R1_001.fastq.gz OTHER 1.8 GB
nsp2-1-IP_S8_L004_R1_001.fastq.gz OTHER 1.6 GB
nsp2-2-IN_S4_L004_R1_001.fastq.gz OTHER 1.7 GB
nsp2-2-IP_S11_L004_R1_001.fastq.gz OTHER 1.6 GB
nsp3-1-IN_S5_L004_R1_001.fastq.gz OTHER 1.8 GB
nsp3-1-IP_S9_L004_R1_001.fastq.gz OTHER 1.9 GB
nsp3-2-IN_S6_L004_R1_001.fastq.gz OTHER 1.8 GB
nsp3-2-IP_S12_L004_R1_001.fastq.gz OTHER 1.6 GB
NSP4_1_IN_S5_L003_R1_001.fastq.gz OTHER 743.2 MB
Nsp4-1-IP_S27_L007_R1_001.fastq.gz OTHER 396.0 MB
NSP4_2_iN_S4_L003_R1_001.fastq.gz OTHER 731.3 MB
NSP4_2_IP_S28_L003_R1_001.fastq.gz OTHER 737.6 MB
nsp5-1-IN_S20_L004_R1_001.fastq.gz OTHER 1.1 GB
nsp5-1-IP_S44_L004_R1_001.fastq.gz OTHER 1.7 GB
nsp5-2-IN_S17_L004_R1_001.fastq.gz OTHER 1.9 GB
nsp5-2-IP_S39_L004_R1_001.fastq.gz OTHER 2.7 GB
nsp5_C145A-IN1_S47_L002_R1_001.fastq.gz OTHER 557.6 MB
nsp5_C145A-IN2_S49_L002_R1_001.fastq.gz OTHER 628.0 MB
nsp5_C145A-IP1_S48_L002_R1_001.fastq.gz OTHER 522.0 MB
nsp5_C145A-IP2_S50_L002_R1_001.fastq.gz OTHER 528.5 MB
nsp6-1-IN_S2_L004_R1_001.fastq.gz OTHER 1.6 GB
nsp6-1-IP_S10_L004_R1_001.fastq.gz OTHER 1.6 GB
nsp6-2-IN_S1_L004_R1_001.fastq.gz OTHER 1.7 GB
nsp6-2-IP_S7_L004_R1_001.fastq.gz OTHER 1.9 GB
nsp7-1-IN_S13_L004_R1_001.fastq.gz OTHER 968.5 MB
nsp7-1-IP_S16_L004_R1_001.fastq.gz OTHER 829.7 MB
nsp7-2-IN_S14_L004_R1_001.fastq.gz OTHER 1.8 GB
nsp7-2-IP_S15_L004_R1_001.fastq.gz OTHER 1.2 GB
NSP8_1_IN_S35_L003_R1_001.fastq.gz OTHER 649.7 MB
NSP8_1_IP_S39_L003_R1_001.fastq.gz OTHER 1.0 GB
NSP8_2_iN_S33_L003_R1_001.fastq.gz OTHER 757.6 MB
NSP8_2_IP_S43_L003_R1_001.fastq.gz OTHER 942.8 MB
nsp8-IP2_S57_L002_R1_001.fastq.InvRNA2.fq.gz OTHER 407.6 MB
nsp9-1-IN_S5_L001_R1_001.fastq.gz OTHER 958.0 MB
nsp9-1-IP_S36_L001_R1_001.fastq.gz OTHER 775.2 MB
nsp9-2-IN_S4_L001_R1_001.fastq.gz OTHER 872.3 MB
nsp9-2-IP_S31_L001_R1_001.fastq.gz OTHER 1.1 GB
ORF10_1_IN_S14_L003_R1_001.fastq.gz OTHER 661.7 MB
ORF10_1_IP_S48_L003_R1_001.fastq.gz OTHER 673.3 MB
ORF10_2_iN_S7_L003_R1_001.fastq.gz OTHER 738.7 MB
ORF10_2_IP_S41_L003_R1_001.fastq.gz OTHER 762.8 MB
ORF3a-IN1_S82_L002_R1_001.fastq.gz OTHER 481.0 MB
ORF3a-IN2_S81_L002_R1_001.fastq.gz OTHER 538.6 MB
ORF3a-IP1_S51_L002_R1_001.fastq.gz OTHER 601.0 MB
ORF3a-IP2_S52_L002_R1_001.fastq.gz OTHER 632.0 MB
orf3b-1-IN_S23_L004_R1_001.fastq.gz OTHER 1.3 GB
orf3b-1-IP_S46_L004_R1_001.fastq.gz OTHER 1.2 GB
orf3b-2-IN_S22_L004_R1_001.fastq.gz OTHER 1.9 GB
orf3b-2-IP_S40_L004_R1_001.fastq.gz OTHER 1.5 GB
ORF6-IN1_S88_L002_R1_001.fastq.gz OTHER 512.9 MB
ORF6-IN2_S89_L002_R1_001.fastq.gz OTHER 522.2 MB
ORF6-IP1_S67_L002_R1_001.fastq.gz OTHER 874.8 MB
ORF6-IP2_S68_L002_R1_001.fastq.gz OTHER 956.5 MB
ORF7a-IN1_S59_L002_R1_001.fastq.gz OTHER 1.9 GB
ORF7a-IN2_S60_L002_R1_001.fastq.gz OTHER 1.3 GB
ORF7a-IP1_S101_L002_R1_001.fastq.gz OTHER 590.3 MB
ORF7a-IP2_S102_L002_R1_001.fastq.gz OTHER 774.5 MB
orf7b-1-IN_S29_L004_R1_001.fastq.gz OTHER 1.8 GB
orf7b-1-IP_S52_L004_R1_001.fastq.gz OTHER 1.5 GB
orf7b-2-IN_S21_L004_R1_001.fastq.gz OTHER 1.8 GB
orf7b-2-IP_S38_L004_R1_001.fastq.gz OTHER 1.6 GB
orf8-1-IN_S47_L004_R1_001.fastq.gz OTHER 1.3 GB
orf8-1-IP_S57_L004_R1_001.fastq.gz OTHER 1.6 GB
orf8-2-IN_S37_L004_R1_001.fastq.gz OTHER 1.3 GB
orf8-2-IP_S55_L004_R1_001.fastq.gz OTHER 1.5 GB
orf9b-1-IN_S30_L004_R1_001.fastq.gz OTHER 1.2 GB
orf9b-1-IP_S54_L004_R1_001.fastq.gz OTHER 1.2 GB
orf9b-2-IN_S32_L004_R1_001.fastq.gz OTHER 1.5 GB
orf9b-2-IP_S41_L004_R1_001.fastq.gz OTHER 3.2 GB
orf9c-1-IN_S27_L004_R1_001.fastq.gz OTHER 2.4 GB
orf9c-1-IP_S34_L004_R1_001.fastq.gz OTHER 1.6 GB
orf9c-2-IN_S35_L004_R1_001.fastq.gz OTHER 1.7 GB
orf9c-2-IP_S53_L004_R1_001.fastq.gz OTHER 1.8 GB
SPIKE_1_IN_S16_L003_R1_001.fastq.gz OTHER 750.8 MB
SPIKE_1_IP_S42_L003_R1_001.fastq.gz OTHER 1002.8 MB
SPIKE_2_iN_S17_L003_R1_001.fastq.gz OTHER 675.1 MB
SPIKE_2_IP_S34_L003_R1_001.fastq.gz OTHER 668.7 MB
SRR14343981_GSM5268670 OTHER 1.4 GB
SRR14343982_GSM5268671 OTHER 533.0 MB
SRR14343983_GSM5268672 OTHER 1.6 GB
SRR14343984_GSM5268673 OTHER 1.6 GB
SRR14343985_GSM5268674 OTHER 1.9 GB
SRR14343986_GSM5268675 OTHER 1.6 GB
SRR14343987_GSM5268676 OTHER 396.0 MB
SRR14343988_GSM5268677 OTHER 737.0 MB
SRR14343989_GSM5268678 OTHER 1.7 GB
SRR14343990_GSM5268679 OTHER 2.7 GB
SRR14343991_GSM5268680 OTHER 522.0 MB
SRR14343992_GSM5268681 OTHER 528.0 MB
SRR14343993_GSM5268682 OTHER 1.6 GB
SRR14343994_GSM5268683 OTHER 1.9 GB
SRR14343995_GSM5268684 OTHER 829.0 MB
SRR14343996_GSM5268685 OTHER 1.2 GB
SRR14343997_GSM5268686 OTHER 1.0 GB
SRR14343998_GSM5268687 OTHER 942.0 MB
SRR14343999_GSM5268688 OTHER 775.0 MB
SRR14344000_GSM5268689 OTHER 1.1 GB
SRR14344001_GSM5268690 OTHER 813.0 MB
SRR14344002_GSM5268691 OTHER 721.0 MB
SRR14344003_GSM5268692 OTHER 734.0 MB
SRR14344004_GSM5268693 OTHER 727.0 MB
SRR14344005_GSM5268694 OTHER 1.4 GB
SRR14344006_GSM5268695 OTHER 1.4 GB
SRR14344007_GSM5268696 OTHER 771.0 MB
SRR14344008_GSM5268697 OTHER 804.0 MB
SRR14344009_GSM5268698 OTHER 641.0 MB
SRR14344010_GSM5268699 OTHER 719.0 MB
SRR14344011_GSM5268700 OTHER 613.0 MB
SRR14344012_GSM5268701 OTHER 470.0 MB
SRR14344013_GSM5268702 OTHER 465.0 MB
SRR14344014_GSM5268703 OTHER 436.0 MB
SRR14344015_GSM5268704 OTHER 1002.0 MB
SRR14344016_GSM5268705 OTHER 668.0 MB
SRR14344017_GSM5268706 OTHER 601.0 MB
SRR14344018_GSM5268707 OTHER 631.0 MB
SRR14344019_GSM5268708 OTHER 1.2 GB
SRR14344020_GSM5268709 OTHER 1.5 GB
SRR14344021_GSM5268710 OTHER 2.1 GB
SRR14344022_GSM5268711 OTHER 1.1 GB
SRR14344023_GSM5268712 OTHER 661.0 MB
SRR14344024_GSM5268713 OTHER 605.0 MB
SRR14344025_GSM5268714 OTHER 874.0 MB
SRR14344026_GSM5268715 OTHER 956.0 MB
SRR14344027_GSM5268716 OTHER 590.0 MB
SRR14344028_GSM5268717 OTHER 774.0 MB
SRR14344029_GSM5268718 OTHER 1.5 GB
SRR14344030_GSM5268719 OTHER 1.6 GB
SRR14344031_GSM5268720 OTHER 1.6 GB
SRR14344032_GSM5268721 OTHER 1.5 GB
SRR14344033_GSM5268722 OTHER 474.0 MB
SRR14344034_GSM5268723 OTHER 798.0 MB
SRR14344035_GSM5268724 OTHER 1.2 GB
SRR14344036_GSM5268725 OTHER 3.2 GB
SRR14344037_GSM5268726 OTHER 1.6 GB
SRR14344038_GSM5268727 OTHER 1.8 GB
SRR14344039_GSM5268728 OTHER 673.0 MB
SRR14344040_GSM5268729 OTHER 762.0 MB
SRR14344041_GSM5268730 OTHER 884.0 MB
SRR14344042_GSM5268731 OTHER 407.0 MB
SRR14344043_GSM5268732 OTHER 1.0 GB
SRR14344044_GSM5268733 OTHER 1.1 GB
SRR14344045_GSM5268734 OTHER 689.0 MB
SRR14344046_GSM5268735 OTHER 447.0 MB
SRR14344047_GSM5268736 OTHER 393.0 MB
SRR14344048_GSM5268737 OTHER 686.0 MB
SRR14344049_GSM5268738 OTHER 1.6 GB
SRR14344050_GSM5268739 OTHER 1.8 GB
SRR14344051_GSM5268740 OTHER 2.2 GB
SRR14344052_GSM5268741 OTHER 2.2 GB
SRR14344053_GSM5268742 OTHER 3.2 GB
SRR14344054_GSM5268743 OTHER 1.9 GB
SRR14344055_GSM5268744 OTHER 343.0 MB
SRR14344056_GSM5268745 OTHER 1.8 GB
SRR14344057_GSM5268746 OTHER 1.7 GB
SRR14344058_GSM5268747 OTHER 1.8 GB
SRR14344059_GSM5268748 OTHER 1.8 GB
SRR14344060_GSM5268749 OTHER 743.0 MB
SRR14344061_GSM5268750 OTHER 731.0 MB
SRR14344062_GSM5268751 OTHER 1.1 GB
SRR14344063_GSM5268752 OTHER 1.9 GB
SRR14344064_GSM5268753 OTHER 557.0 MB
SRR14344065_GSM5268754 OTHER 627.0 MB
SRR14344066_GSM5268755 OTHER 1.6 GB
SRR14344067_GSM5268756 OTHER 1.7 GB
SRR14344068_GSM5268757 OTHER 968.0 MB
SRR14344069_GSM5268758 OTHER 1.8 GB
SRR14344070_GSM5268759 OTHER 649.0 MB
SRR14344071_GSM5268760 OTHER 757.0 MB
SRR14344072_GSM5268761 OTHER 957.0 MB
SRR14344073_GSM5268762 OTHER 872.0 MB
SRR14344074_GSM5268763 OTHER 1.1 GB
SRR14344075_GSM5268764 OTHER 743.0 MB
SRR14344076_GSM5268765 OTHER 407.0 MB
SRR14344077_GSM5268766 OTHER 847.0 MB
SRR14344078_GSM5268767 OTHER 1.9 GB
SRR14344079_GSM5268768 OTHER 2.6 GB
SRR14344080_GSM5268769 OTHER 810.0 MB
SRR14344081_GSM5268770 OTHER 388.0 MB
SRR14344082_GSM5268771 OTHER 717.0 MB
SRR14344083_GSM5268772 OTHER 810.0 MB
SRR14344084_GSM5268773 OTHER 307.0 MB
SRR14344084.lite OTHER 307.1 MB
SRR14344085_GSM5268774 OTHER 673.0 MB
SRR14344086_GSM5268775 OTHER 442.0 MB
SRR14344087_GSM5268776 OTHER 389.0 MB
SRR14344088_GSM5268777 OTHER 750.0 MB
SRR14344089_GSM5268778 OTHER 675.0 MB
SRR14344090_GSM5268779 OTHER 480.0 MB
SRR14344091_GSM5268780 OTHER 538.0 MB
SRR14344092_GSM5268781 OTHER 1.3 GB
SRR14344093_GSM5268782 OTHER 1.9 GB
SRR14344093.lite OTHER 1.9 GB
SRR14344094_GSM5268783 OTHER 525.0 MB
SRR14344095_GSM5268784 OTHER 766.0 MB
SRR14344096_GSM5268785 OTHER 519.0 MB
SRR14344097_GSM5268786 OTHER 537.0 MB
SRR14344098_GSM5268787 OTHER 512.0 MB
SRR14344098.lite OTHER 512.9 MB
SRR14344099_GSM5268788 OTHER 522.0 MB
SRR14344100_GSM5268789 OTHER 1.9 GB
SRR14344101_GSM5268790 OTHER 1.3 GB
SRR14344102_GSM5268791 OTHER 1.8 GB
SRR14344103_GSM5268792 OTHER 1.8 GB
SRR14344104_GSM5268793 OTHER 1.3 GB
SRR14344105_GSM5268794 OTHER 1.3 GB
SRR14344106_GSM5268795 OTHER 406.0 MB
SRR14344107_GSM5268796 OTHER 560.0 MB
SRR14344108_GSM5268797 OTHER 1.2 GB
SRR14344109_GSM5268798 OTHER 1.5 GB
SRR14344110_GSM5268799 OTHER 2.4 GB
SRR14344110.lite OTHER 2.4 GB
SRR14344111_GSM5268800 OTHER 1.7 GB
SRR14344112_GSM5268801 OTHER 661.0 MB
SRR14344113_GSM5268802 OTHER 738.0 MB
SRR14344114_GSM5268803 OTHER 580.0 MB
SRR14344115_GSM5268804 OTHER 494.0 MB
SRR14344116_GSM5268805 OTHER 459.0 MB
SRR14344117_GSM5268806 OTHER 569.0 MB
SRR14344118_GSM5268807 OTHER 631.0 MB
SRR14344119_GSM5268808 OTHER 765.0 MB
SRR14344120_GSM5268809 OTHER 610.0 MB
SRR14344121_GSM5268810 OTHER 558.0 MB
SRR14344122_GSM5268811 OTHER 1.9 GB
SRR14344123_GSM5268812 OTHER 1.4 GB
SRR14344124_GSM5268813 OTHER 2.0 GB
SRR14344125_GSM5268814 OTHER 2.0 GB
SRR14344126_GSM5268815 OTHER 2.3 GB
SRR14344127 OTHER 2.7 GB
SRR14344127_GSM5268816 OTHER 2.7 GB
Vero_N-1-IN_S13_L001_R1_001.fastq.gz OTHER 1.9 GB
Vero_N-1-IP_S5_L001_R1_001.fastq.gz OTHER 1.6 GB
Vero_N-2-IN_S14_L001_R1_001.fastq.gz OTHER 1.4 GB
Vero_N-2-IP_S6_L001_R1_001.fastq.gz OTHER 1.8 GB
Vero_NSP12-1-IN_S11_L001_R1_001.fastq.gz OTHER 2.3 GB
Vero_NSP12-1-IP_S3_L001_R1_001.fastq.gz OTHER 2.2 GB
Vero_NSP12-2-IN_S12_L001_R1_001.fastq.gz OTHER 2.7 GB
Vero_NSP12-2-IP_S4_L001_R1_001.fastq.gz OTHER 1.9 GB
Vero_NSP8-1-IN_S9_L001_R1_001.fastq.gz OTHER 2.0 GB
Vero_NSP8-1-IP_S1_L001_R1_001.fastq.gz OTHER 2.2 GB
Vero_NSP8-2-IN_S10_L001_R1_001.fastq.gz OTHER 2.0 GB
Vero_NSP8-2-IP_S2_L001_R1_001.fastq.gz OTHER 3.2 GB
WTH_1_IN_S13_L003_R1_001.fastq.gz OTHER 631.3 MB
WTH_1_IP_S30_L003_R1_001.fastq.gz OTHER 689.2 MB
WTH_2_iN_S12_L003_R1_001.fastq.gz OTHER 765.8 MB
WTH_2_IP_S24_L003_R1_001.fastq.gz OTHER 447.4 MB
WT-high-IN1_S92_L002_R1_001.fastq.gz OTHER 580.9 MB
WT-high-IN2_S93_L002_R1_001.fastq.gz OTHER 494.1 MB
WT-high-IP1_S71_L002_R1_001.fastq.gz OTHER 884.3 MB
WTL_1_IN_S10_L003_R1_001.fastq.gz OTHER 610.6 MB
WTL_1_IP_S11_L003_R1_001.fastq.gz OTHER 393.3 MB
WTL_2_iN_S20_L003_R1_001.fastq.gz OTHER 558.5 MB
WTL_2_IP_S21_L003_R1_001.fastq.gz OTHER 686.8 MB
WT-low-IN1_S90_L002_R1_001.fastq.gz OTHER 459.6 MB
WT-low-IN2_S91_L002_R1_001.fastq.gz OTHER 569.8 MB
WT-low-IP1_S69_L002_R1_001.fastq.gz OTHER 1.0 GB
WT-low-IP2_S70_L002_R1_001.fastq.gz OTHER 1.1 GB
GSE173508 GSE · via ncbi_elink
GEO ↗

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins

Homo sapiens

GSE173507 GSE · via ncbi_elink
GEO ↗

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [RNA-Seq]

Homo sapiens

8 data files
FileTypeSize
A549-APO-moi-3_S9_L004_R1_001.fastq.gz RNA-Seq 11.7 GB
SRR14346737_GSM5268956 RNA-Seq 11.7 GB
SRR14346738_GSM5268957 RNA-Seq 14.2 GB
SRR14346739_GSM5268958 RNA-Seq 635.0 MB
SRR14346740_GSM5268959 RNA-Seq 6.0 GB
Veros-APO-moi-0p1_S1_L004_R1_001.fastq.gz RNA-Seq 14.2 GB
WT-1__S34_L004_R1_001.fastq.gz RNA-Seq 635.4 MB
WT-2_S21_L004_R1_001.fastq.gz RNA-Seq 6.0 GB
GSE198899 GSE · via ncbi_elink
GEO ↗

Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins [Ribo-Seq]

Homo sapiens

16 data files
FileTypeSize
Ctrl-input-1_S43_L002_R1_001.fastq.gz OTHER 1.3 GB
Ctrl-input-2_S44_L002_R1_001.fastq.gz OTHER 1.3 GB
Ctrl-poly-1_S49_L002_R1_001.fastq.gz OTHER 2.0 GB
Ctrl-poly-2_S50_L002_R1_001.fastq.gz OTHER 1.8 GB
ORF9c-input-1_S41_L002_R1_001.fastq.gz OTHER 1.4 GB
ORF9c-input-2_S42_L002_R1_001.fastq.gz OTHER 1.6 GB
ORF9c-poly-1_S47_L002_R1_001.fastq.gz OTHER 1.6 GB
ORF9c-poly-2_S48_L002_R1_001.fastq.gz OTHER 1.6 GB
SRR18360416_GSM5959190 OTHER 1.3 GB
SRR18360417_GSM5959189 OTHER 1.3 GB
SRR18360418_GSM5959188 OTHER 1.8 GB
SRR18360419_GSM5959187 OTHER 2.0 GB
SRR18360420_GSM5959186 OTHER 1.6 GB
SRR18360421_GSM5959185 OTHER 1.4 GB
SRR18360422_GSM5959184 OTHER 1.6 GB
SRR18360423_GSM5959183 OTHER 1.6 GB

Potentially related datasets 1

These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.

Accession Source Title
GSE173508 GSE · GEO GEO ↗ Discovery and functional interrogation of the virus and host RNA interactome of SARS-CoV-2 proteins

Analysis pipelines 4

Pipeline Assay Steps Dataset
GSE173498 eCLIP Data Processing geo_data_processing eCLIP 19 GSE173498
GSE173507 RNA-seq Data Processing geo_data_processing RNA-seq 4 GSE173507
GSE173508 eCLIP Data Processing geo_data_processing eCLIP 19 GSE173508
GSE198899 Ribo-seq Data Processing geo_data_processing Ribo-seq 6 GSE198899
Funding 4 grants
Grant Funder
S10 OD026929 NIH HHS (United States)
T32 CA067754 NCI NIH HHS (United States)
R00 HG009530 NHGRI NIH HHS (United States)
K08 AI130381 NIAID NIH HHS (United States)