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Citation: Zhou et al., Nature Commun. 2019 10(1):1523.

7 technologies, 28 tissues and cell lines, 21 studies, 362 COVID gene lists.

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scRNA-seq comparison of PBMCs in severe, moderate, convalescent, and healthy donors.

 IsOMICS scRNA-seq, Single-cell T cell receptor (TCR) and B cell receptor (BCR) sequencing,  SampleType patient and healthy samples,  CellType ,  VirusStrain ,  Timepoints ,  Perturbations ,  HasCompleteData Yes,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined423       388 (92%)
COVID351 RNA_Zhang_Monocytes_severe-only_Up 47 scRNA-seq Monocytes Severe SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 severe patients (n=4) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value. 14 (30%) 44 (94%)
COVID352 RNA_Zhang_Monocytes_moderate-only_Up 26 scRNA-seq Monocytes Moderate SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 moderate patients (n=7) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value. 15 (58%) 22 (85%)
COVID353 RNA_Zhang_Monocytes_severe-and-moderate_Up 128 scRNA-seq Monocytes Severe and moderate SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 severe (n=4) and moderate patients (n=7) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value in severe patients. 87 (68%) 122 (95%)
COVID354 RNA_Zhang_NK-cells_severe-only_Up 45 scRNA-seq NK cells Severe SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 severe patients (n=4) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value. 40 (89%) 41 (91%)
COVID355 RNA_Zhang_NK-cells_moderate-only_Up 10 scRNA-seq NK cells Moderate SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 moderate patients (n=7) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value. 10 (100%) 8 (80%)
COVID356 RNA_Zhang_NK-cells_severe-and-moderate_Up 96 scRNA-seq NK cells Severe and moderate SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 severe (n=4) and moderate patients (n=7) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value in severe patients. 96 (100%) 87 (91%)
COVID357 RNA_Zhang_T-cells_severe-only_Up 79 scRNA-seq T cells Severe SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 severe patients (n=4) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value. 41 (52%) 69 (87%)
COVID358 RNA_Zhang_T-cells_moderate-only_Up 19 scRNA-seq T cells Moderate SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 moderate patients (n=7) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value. 11 (58%) 15 (79%)
COVID359 RNA_Zhang_T-cells_severe-and-moderate_Up 140 scRNA-seq T cells Severe and moderate SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 severe (n=4) and moderate patients (n=7) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value in severe patients. 114 (81%) 131 (94%)
COVID360 RNA_Zhang_B-cells_severe-only_Up 83 scRNA-seq B cells Severe SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 severe patients (n=4) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value. 21 (25%) 78 (94%)
COVID361 RNA_Zhang_B-cells_moderate-only_Up 28 scRNA-seq B cells Moderate SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 moderate patients (n=7) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value. 17 (61%) 27 (96%)
COVID362 RNA_Zhang_B-cells_severe-and-moderate_Up 75 scRNA-seq B cells Severe and moderate SARS-CoV-2 Healthy donors Post admission SARS-CoV-2 severe (n=4) and moderate patients (n=7) vs. healthy donors (n=5). Singificance defined by p-value < 0.01 and Log2FC >= 0.5. Features sorted by p-value in severe patients. 64 (85%) 69 (92%)

Interactome for CoV-1/CoV-2 NSP2 and NSP4.

 IsOMICS Interactome (AP-MS),  SampleType in vitro,  CellType HEK293T,  VirusStrain SARS-CoV-2 isolate Wuhan-Hu-1,  Timepoints 40h,  Perturbations ,  HasCompleteData ,  GeneListSource .

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined100       86 (86%)
COVID079 Interactome_Davis_HEK-293T_40h_NSP2 19 Interactome HEK-293T NSP2 40h 4 (21%) 16 (84%)
COVID080 Interactome_Davis_HEK-293T_40h_NSP4 85 Interactome HEK-293T NSP4 40h 4 (5%) 74 (87%)

Phosphoproteomics and proteomics study of CoV-2 infected Caco-2 cells.

 IsOMICS Phosphoproteome and Proteome,  SampleType in vitro,  CellType Caco-2,  VirusStrain SARS-CoV-2,  Timepoints 24h,  Perturbations ,  HasCompleteData ,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined902       761 (84%)
COVID234 Phosphoproteome_Klann_Caco-2_24h_Down 300 Phosphoproteome Caco-2 SARS-CoV-2 Mock 24h Significance defined by Abs(Log2FC)>1 and Adj P<0.05. Features sorted by pvalue. 65 (22%) 255 (85%)
COVID235 Phosphoproteome_Klann_Caco-2_24h_Up 300 Phosphoproteome Caco-2 SARS-CoV-2 Mock 24h Significance defined by Abs(Log2FC)>1 and Adj P<0.05. Features sorted by pvalue. 46 (15%) 249 (83%)
COVID236 Proteome_Klann_Caco-2_24h_Down 300 Proteome Caco-2 SARS-CoV-2 Mock 24h Significance defined by Abs(Log2FC)>0.5 and Adj P<0.05. Features sorted by pvalue. 32 (11%) 258 (86%)
COVID237 Proteome_Klann_Caco-2_24h_Up 75 Proteome Caco-2 SARS-CoV-2 Mock 24h Significance defined by Abs(Log2FC)>0.5 and Adj P<0.05. Features sorted by pvalue. 2 (3%) 66 (88%)

Calu-3 infection with SARS-CoV-2, SARS-CoV, and MERS-CoV.
Only SARS-CoV-2 results available in supplement
 IsOMICS RNA-Seq,  SampleType in vitro,  CellType Calu-3,  VirusStrain SARS-CoV-2, MERS CoV, SARS-CoV ,  Timepoints 7, 12, 24 h,  Perturbations ,  HasCompleteData Yes,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined1304       1089 (84%)
COVID035 RNA_Sun_Calu-3_0h_Down 172 RNA-seq Calu-3 SARS-CoV-2 uninfected 0h 9 (5%) 90 (52%)
COVID036 RNA_Sun_Calu-3_0h_Up 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 0h 89 (30%) 268 (89%)
COVID037 RNA_Sun_Calu-3_12h_Down 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 12h 129 (43%) 269 (90%)
COVID038 RNA_Sun_Calu-3_12h_Up 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 12h 199 (66%) 265 (88%)
COVID039 RNA_Sun_Calu-3_24h_Down 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 24h 130 (43%) 268 (89%)
COVID040 RNA_Sun_Calu-3_24h_Up 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 24h 193 (64%) 272 (91%)
COVID041 RNA_Sun_Calu-3_7h_Down 11 RNA-seq Calu-3 SARS-CoV-2 uninfected 7h 1 (9%) 9 (82%)
COVID042 RNA_Sun_Calu-3_7h_Up 65 RNA-seq Calu-3 SARS-CoV-2 uninfected 7h 59 (91%) 63 (97%)

5. Bojkova et al. SARS-CoV-2 infected host cell proteomics reveal potential therapy targets Nature peer reviewed (pre-proof)
Proteome and Translatome of SARS-CoV-2 infected CaCo-2 cells.
Extracted lists from supplement tables 1 & 2 (FC > 1.5, pvalue<0.05)
 IsOMICS Proteomics (abundance),  SampleType in vitro,  CellType CaCo-2,  VirusStrain SARS-CoV-2, clinical isolates, not specified,  Timepoints 2, 6, 10, 24 h,  Perturbations ,  HasCompleteData yes,  GeneListSource .

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined460       384 (83%)
COVID218 Proteome_Bojkova_Caco-2_10h_Down 13 Proteome Caco-2 SARS-CoV-2 Control 10h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 6 (46%) 7 (54%)
COVID219 Proteome_Bojkova_Caco-2_10h_Up 3 Proteome Caco-2 SARS-CoV-2 Control 10h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 2 (67%) 2 (67%)
COVID220 Proteome_Bojkova_Caco-2_24h_Down 73 Proteome Caco-2 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 25 (34%) 67 (92%)
COVID221 Proteome_Bojkova_Caco-2_24h_Up 42 Proteome Caco-2 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 9 (21%) 30 (71%)
COVID222 Proteome_Bojkova_Caco-2_2h_Down 3 Proteome Caco-2 SARS-CoV-2 Control 2h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 1 (33%) 0 (0%)
COVID223 Proteome_Bojkova_Caco-2_2h_Up 2 Proteome Caco-2 SARS-CoV-2 Control 2h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 2 (100%) 1 (50%)
COVID224 Proteome_Bojkova_Caco-2_6h_Down 3 Proteome Caco-2 SARS-CoV-2 Control 6h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 1 (33%) 2 (67%)
COVID225 Proteome_Bojkova_Caco-2_6h_Up 51 Proteome Caco-2 SARS-CoV-2 Control 6h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 13 (25%) 40 (78%)
COVID226 Translatome_Bojkova_Caco-2_10h_Down 84 Translatome Caco-2 SARS-CoV-2 Control 10h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 33 (39%) 70 (83%)
COVID227 Translatome_Bojkova_Caco-2_10h_Up 1 Translatome Caco-2 SARS-CoV-2 Control 10h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 0 (0%) 1 (100%)
COVID228 Translatome_Bojkova_Caco-2_24h_Down 174 Translatome Caco-2 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 47 (27%) 154 (89%)
COVID229 Translatome_Bojkova_Caco-2_24h_Up 44 Translatome Caco-2 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 4 (9%) 37 (84%)
COVID230 Translatome_Bojkova_Caco-2_2h_Down 18 Translatome Caco-2 SARS-CoV-2 Control 2h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 12 (67%) 15 (83%)
COVID231 Translatome_Bojkova_Caco-2_2h_Up 13 Translatome Caco-2 SARS-CoV-2 Control 2h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 2 (15%) 10 (77%)
COVID232 Translatome_Bojkova_Caco-2_6h_Down 19 Translatome Caco-2 SARS-CoV-2 Control 6h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 3 (16%) 14 (74%)
COVID233 Translatome_Bojkova_Caco-2_6h_Up 3 Translatome Caco-2 SARS-CoV-2 Control 6h Significance defined by Abs(Log2FC)>0.585 and P<0.05. Features sorted by pvalue. 3 (100%) 3 (100%)


 IsOMICS ,  SampleType patient samples,  CellType ,  VirusStrain ,  Timepoints ,  Perturbations ,  HasCompleteData Yes,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined1063       884 (83%)
COVID244 RNA_Wilk_CD14+Monocytes_patient-C1A-mild_Up 82 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 82 (100%) 82 (100%)
COVID245 RNA_Wilk_CD14+Monocytes_patient-C1A-mild_Down 58 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 56 (97%) 53 (91%)
COVID246 RNA_Wilk_CD14+Monocytes_patient-C1B-severe_Up 77 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 75 (97%) 75 (97%)
COVID247 RNA_Wilk_CD14+Monocytes_patient-C1B-severe_Down 62 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 62 (100%) 59 (95%)
COVID248 RNA_Wilk_CD14+Monocytes_patient-C2_Up 63 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 58 (92%) 61 (97%)
COVID249 RNA_Wilk_CD14+Monocytes_patient-C2_Down 65 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 62 (95%) 57 (88%)
COVID250 RNA_Wilk_CD14+Monocytes_patient-C3_Up 51 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 49 (96%) 48 (94%)
COVID251 RNA_Wilk_CD14+Monocytes_patient-C3_Down 61 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 61 (100%) 57 (93%)
COVID252 RNA_Wilk_CD14+Monocytes_patient-C4_Up 80 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 80 (100%) 78 (98%)
COVID253 RNA_Wilk_CD14+Monocytes_patient-C4_Down 102 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 97 (95%) 91 (89%)
COVID254 RNA_Wilk_CD14+Monocytes_patient-C5_Up 106 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 103 (97%) 101 (95%)
COVID255 RNA_Wilk_CD14+Monocytes_patient-C5_Down 146 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 117 (80%) 130 (89%)
COVID256 RNA_Wilk_CD14+Monocytes_patient-C6_Up 157 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 140 (89%) 145 (92%)
COVID257 RNA_Wilk_CD14+Monocytes_patient-C6_Down 89 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 83 (93%) 82 (92%)
COVID258 RNA_Wilk_CD14+Monocytes_patient-C7_Up 32 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 29 (91%) 29 (91%)
COVID259 RNA_Wilk_CD14+Monocytes_patient-C7_Down 34 scRNA-seq CD14+ Monocytes SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 34 (100%) 31 (91%)
COVID260 RNA_Wilk_CD16+Monocytes_patient-C1A-mild_Up 75 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 67 (89%) 71 (95%)
COVID261 RNA_Wilk_CD16+Monocytes_patient-C1A-mild_Down 17 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 17 (100%) 16 (94%)
COVID262 RNA_Wilk_CD16+Monocytes_patient-C1B-severe_Up 49 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 43 (88%) 48 (98%)
COVID263 RNA_Wilk_CD16+Monocytes_patient-C1B-severe_Down 12 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 12 (100%) 12 (100%)
COVID264 RNA_Wilk_CD16+Monocytes_patient-C3_Up 39 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 35 (90%) 36 (92%)
COVID265 RNA_Wilk_CD16+Monocytes_patient-C3_Down 1 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 1 (100%) 1 (100%)
COVID266 RNA_Wilk_CD16+Monocytes_patient-C4_Up 77 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 71 (92%) 77 (100%)
COVID267 RNA_Wilk_CD16+Monocytes_patient-C4_Down 16 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 16 (100%) 15 (94%)
COVID268 RNA_Wilk_CD16+Monocytes_patient-C5_Up 101 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 73 (72%) 91 (90%)
COVID269 RNA_Wilk_CD16+Monocytes_patient-C5_Down 6 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 6 (100%) 6 (100%)
COVID270 RNA_Wilk_CD16+Monocytes_patient-C6_Up 31 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 27 (87%) 28 (90%)
COVID271 RNA_Wilk_CD16+Monocytes_patient-C7_Up 26 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 26 (100%) 26 (100%)
COVID272 RNA_Wilk_CD16+Monocytes_patient-C7_Down 27 scRNA-seq CD16+ Monocytes SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 20 (74%) 24 (89%)
COVID273 RNA_Wilk_Dendritic-cells_patient-C1A-mild_Up 40 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 40 (100%) 40 (100%)
COVID274 RNA_Wilk_Dendritic-cells_patient-C1A-mild_Down 2 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 2 (100%) 2 (100%)
COVID275 RNA_Wilk_Dendritic-cells_patient-C1B-severe_Up 15 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 14 (93%) 15 (100%)
COVID276 RNA_Wilk_Dendritic-cells_patient-C1B-severe_Down 2 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 2 (100%) 2 (100%)
COVID277 RNA_Wilk_Dendritic-cells_patient-C2_Up 74 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 3 (4%) 31 (42%)
COVID278 RNA_Wilk_Dendritic-cells_patient-C3_Up 12 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 12 (100%) 9 (75%)
COVID279 RNA_Wilk_Dendritic-cells_patient-C3_Down 1 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 1 (100%) 1 (100%)
COVID280 RNA_Wilk_Dendritic-cells_patient-C4_Up 25 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 25 (100%) 25 (100%)
COVID281 RNA_Wilk_Dendritic-cells_patient-C4_Down 18 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 18 (100%) 15 (83%)
COVID282 RNA_Wilk_Dendritic-cells_patient-C5_Up 73 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 67 (92%) 72 (99%)
COVID283 RNA_Wilk_Dendritic-cells_patient-C5_Down 23 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 22 (96%) 19 (83%)
COVID284 RNA_Wilk_Dendritic-cells_patient-C6_Up 18 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 13 (72%) 14 (78%)
COVID285 RNA_Wilk_Dendritic-cells_patient-C7_Up 29 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 27 (93%) 27 (93%)
COVID286 RNA_Wilk_Dendritic-cells_patient-C7_Down 27 scRNA-seq Dendritic cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 22 (81%) 25 (93%)
COVID287 RNA_Wilk_NK-cells_patient-C1A-mild_Up 34 scRNA-seq NK cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 34 (100%) 32 (94%)
COVID288 RNA_Wilk_NK-cells_patient-C1A-mild_Down 16 scRNA-seq NK cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 16 (100%) 15 (94%)
COVID289 RNA_Wilk_NK-cells_patient-C1B-severe_Up 12 scRNA-seq NK cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 8 (67%) 8 (67%)
COVID290 RNA_Wilk_NK-cells_patient-C1B-severe_Down 14 scRNA-seq NK cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 14 (100%) 12 (86%)
COVID291 RNA_Wilk_NK-cells_patient-C2_Up 5 scRNA-seq NK cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 4 (80%) 4 (80%)
COVID292 RNA_Wilk_NK-cells_patient-C2_Down 7 scRNA-seq NK cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 5 (71%) 7 (100%)
COVID293 RNA_Wilk_NK-cells_patient-C3_Up 25 scRNA-seq NK cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 23 (92%) 24 (96%)
COVID294 RNA_Wilk_NK-cells_patient-C3_Down 8 scRNA-seq NK cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 8 (100%) 7 (88%)
COVID295 RNA_Wilk_NK-cells_patient-C4_Up 24 scRNA-seq NK cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 23 (96%) 23 (96%)
COVID296 RNA_Wilk_NK-cells_patient-C4_Down 22 scRNA-seq NK cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 22 (100%) 21 (95%)
COVID297 RNA_Wilk_NK-cells_patient-C5_Up 52 scRNA-seq NK cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 43 (83%) 48 (92%)
COVID298 RNA_Wilk_NK-cells_patient-C5_Down 29 scRNA-seq NK cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 26 (90%) 27 (93%)
COVID299 RNA_Wilk_NK-cells_patient-C6_Up 31 scRNA-seq NK cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 29 (94%) 31 (100%)
COVID300 RNA_Wilk_NK-cells_patient-C6_Down 4 scRNA-seq NK cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 4 (100%) 4 (100%)
COVID301 RNA_Wilk_NK-cells_patient-C7_Up 5 scRNA-seq NK cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 5 (100%) 5 (100%)
COVID302 RNA_Wilk_NK-cells_patient-C7_Down 30 scRNA-seq NK cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 20 (67%) 27 (90%)
COVID303 RNA_Wilk_CD8+T-cells_patient-C1A-mild_Up 19 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 19 (100%) 19 (100%)
COVID304 RNA_Wilk_CD8+T-cells_patient-C1A-mild_Down 23 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 20 (87%) 18 (78%)
COVID305 RNA_Wilk_CD8+T-cells_patient-C1B-severe_Up 10 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 10 (100%) 9 (90%)
COVID306 RNA_Wilk_CD8+T-cells_patient-C1B-severe_Down 9 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 9 (100%) 8 (89%)
COVID307 RNA_Wilk_CD8+T-cells_patient-C2_Up 11 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 11 (100%) 10 (91%)
COVID308 RNA_Wilk_CD8+T-cells_patient-C2_Down 10 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 9 (90%) 8 (80%)
COVID309 RNA_Wilk_CD8+T-cells_patient-C3_Up 34 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 32 (94%) 32 (94%)
COVID310 RNA_Wilk_CD8+T-cells_patient-C3_Down 5 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 5 (100%) 5 (100%)
COVID311 RNA_Wilk_CD8+T-cells_patient-C4_Up 22 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 22 (100%) 22 (100%)
COVID312 RNA_Wilk_CD8+T-cells_patient-C4_Down 31 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 31 (100%) 30 (97%)
COVID313 RNA_Wilk_CD8+T-cells_patient-C5_Up 43 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 41 (95%) 42 (98%)
COVID314 RNA_Wilk_CD8+T-cells_patient-C5_Down 45 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 39 (87%) 39 (87%)
COVID315 RNA_Wilk_CD8+T-cells_patient-C6_Up 43 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 39 (91%) 42 (98%)
COVID316 RNA_Wilk_CD8+T-cells_patient-C6_Down 11 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 11 (100%) 11 (100%)
COVID317 RNA_Wilk_CD8+T-cells_patient-C7_Up 4 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 4 (100%) 2 (50%)
COVID318 RNA_Wilk_CD8+T-cells_patient-C7_Down 12 scRNA-seq CD8+ T cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 10 (83%) 10 (83%)
COVID319 RNA_Wilk_CD4+T-cells_patient-C1A-mild_Up 40 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 40 (100%) 40 (100%)
COVID320 RNA_Wilk_CD4+T-cells_patient-C1A-mild_Down 34 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 33 (97%) 28 (82%)
COVID321 RNA_Wilk_CD4+T-cells_patient-C1B-severe_Up 13 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 13 (100%) 13 (100%)
COVID322 RNA_Wilk_CD4+T-cells_patient-C1B-severe_Down 7 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 7 (100%) 7 (100%)
COVID323 RNA_Wilk_CD4+T-cells_patient-C2_Up 22 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 19 (86%) 21 (95%)
COVID324 RNA_Wilk_CD4+T-cells_patient-C2_Down 10 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 10 (100%) 9 (90%)
COVID325 RNA_Wilk_CD4+T-cells_patient-C3_Up 15 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 14 (93%) 15 (100%)
COVID326 RNA_Wilk_CD4+T-cells_patient-C3_Down 6 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 6 (100%) 6 (100%)
COVID327 RNA_Wilk_CD4+T-cells_patient-C4_Up 24 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 24 (100%) 24 (100%)
COVID328 RNA_Wilk_CD4+T-cells_patient-C4_Down 31 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 30 (97%) 27 (87%)
COVID329 RNA_Wilk_CD4+T-cells_patient-C5_Up 39 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 39 (100%) 39 (100%)
COVID330 RNA_Wilk_CD4+T-cells_patient-C5_Down 32 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 31 (97%) 29 (91%)
COVID331 RNA_Wilk_CD4+T-cells_patient-C6_Up 39 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 33 (85%) 36 (92%)
COVID332 RNA_Wilk_CD4+T-cells_patient-C6_Down 12 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 11 (92%) 11 (92%)
COVID333 RNA_Wilk_CD4+T-cells_patient-C7_Up 8 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 7 (88%) 7 (88%)
COVID334 RNA_Wilk_CD4+T-cells_patient-C7_Down 11 scRNA-seq CD4+ T cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 10 (91%) 10 (91%)
COVID335 RNA_Wilk_B-cells_patient-C1A-mild_Up 64 scRNA-seq B cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 64 (100%) 63 (98%)
COVID336 RNA_Wilk_B-cells_patient-C1A-mild_Down 62 scRNA-seq B cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 62 (100%) 52 (84%)
COVID337 RNA_Wilk_B-cells_patient-C1B-severe_Up 107 scRNA-seq B cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 99 (93%) 96 (90%)
COVID338 RNA_Wilk_B-cells_patient-C1B-severe_Down 78 scRNA-seq B cells SARS-CoV-2 Healthy 11d post onset SARS-CoV-2 patient C1, male, 60-69 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 17. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 78 (100%) 69 (88%)
COVID339 RNA_Wilk_B-cells_patient-C2_Up 35 scRNA-seq B cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 34 (97%) 35 (100%)
COVID340 RNA_Wilk_B-cells_patient-C2_Down 21 scRNA-seq B cells SARS-CoV-2 Healthy 16d post onset SARS-CoV-2 patient C2, male, 40-49 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 21 (100%) 18 (86%)
COVID341 RNA_Wilk_B-cells_patient-C3_Up 84 scRNA-seq B cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 82 (98%) 80 (95%)
COVID342 RNA_Wilk_B-cells_patient-C3_Down 30 scRNA-seq B cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C3, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 25. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 30 (100%) 28 (93%)
COVID343 RNA_Wilk_B-cells_patient-C4_Up 126 scRNA-seq B cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 109 (87%) 118 (94%)
COVID344 RNA_Wilk_B-cells_patient-C4_Down 172 scRNA-seq B cells SARS-CoV-2 Healthy 9d post onset SARS-CoV-2 patient C4, male, 30-39 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 16. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 169 (98%) 146 (85%)
COVID345 RNA_Wilk_B-cells_patient-C5_Up 119 scRNA-seq B cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 110 (92%) 112 (94%)
COVID346 RNA_Wilk_B-cells_patient-C5_Down 184 scRNA-seq B cells SARS-CoV-2 Healthy 15d post onset SARS-CoV-2 patient C5, male, 50-59 yr, ventilated/ARDS: no, admission level: ICU, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 167 (91%) 157 (85%)
COVID347 RNA_Wilk_B-cells_patient-C6_Up 114 scRNA-seq B cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 54 (47%) 102 (89%)
COVID348 RNA_Wilk_B-cells_patient-C6_Down 34 scRNA-seq B cells SARS-CoV-2 Healthy 2d post onset SARS-CoV-2 patient C6, male, >80 yr, ventilated/ARDS: yes, admission level: ICU, days intubated: 11. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 34 (100%) 32 (94%)
COVID349 RNA_Wilk_B-cells_patient-C7_Up 5 scRNA-seq B cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 5 (100%) 5 (100%)
COVID350 RNA_Wilk_B-cells_patient-C7_Down 42 scRNA-seq B cells SARS-CoV-2 Healthy 12d post onset SARS-CoV-2 patient C7, male, 20-29 yr, ventilated/ARDS: no, admission level: floor, days intubated: 0. Singificance defined by p-value < 0.05 and abs(log2FC) >= 0.25. Features sorted by log2FC. 40 (95%) 39 (93%)

Nasopharyngeal swabs from 430 SARS-CoV-2 patients and 54 controls.

 IsOMICS RNA-seq,  SampleType patient samples,  CellType SARS CoV2 patients,  VirusStrain SARS-CoV2,  Timepoints ,  Perturbations ,  HasCompleteData ,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined416       345 (83%)
COVID238 RNA_Lieberman_Nasopharynx_Infected_vs_Neg_Down 43 RNA-seq Nasopharynx SARS-CoV-2 Negative Significance defined by Abs(Log2FC)>1 and Adj P<0.1. Features sorted by pvalue. 9 (21%) 41 (95%)
COVID239 RNA_Lieberman_Nasopharynx_Infected_vs_Neg_Up 41 RNA-seq Nasopharynx SARS-CoV-2 Negative Significance defined by Abs(Log2FC)>1 and Adj P<0.1. Features sorted by pvalue. 22 (54%) 39 (95%)
COVID240 RNA_Lieberman_Nasopharynx_High_vs_Low_Down 190 RNA-seq Nasopharynx SARS-CoV-2 High Viral Load SARS-CoV-2 Low Viral Load Significance defined by Adj P<0.1. Features sorted by pvalue. 10 (5%) 149 (78%)
COVID241 RNA_Lieberman_Nasopharynx_High_vs_Low_Up 173 RNA-seq Nasopharynx SARS-CoV-2 High Viral Load SARS-CoV-2 Low Viral Load Significance defined by Adj P<0.1. Features sorted by pvalue. 21 (12%) 146 (84%)

Processed RNAseq data from mock-infected and SARS-CoV-2 infected Vero E6 cells (MOI=0.3) collected 24 hpi (“RNAseq_Vero E6”).

 IsOMICS RNA-seq,  SampleType in vitro,  CellType Vero-E6 cells,  VirusStrain SARS-CoV-2 USA-WA1/2020,  Timepoints 24h,  Perturbations ,  HasCompleteData ,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined381       314 (82%)
COVID242 RNA_Riva_Vero-E6_24h_Down 81 RNA-seq Vero-E6 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>1 and Adj P<0.01. Features sorted by pvalue. 0 (0%) 58 (72%)
COVID243 RNA_Riva_Vero-E6_24h_Up 300 RNA-seq Vero-E6 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>1 and Adj P<0.01. Features sorted by pvalue. 0 (0%) 256 (85%)

Phosphoproteomics study of CoV-2 infected Vero-E6 cells.

 IsOMICS Phosphoproteomics,  SampleType in vitro,  CellType Vero-E6 cells,  VirusStrain SARS-CoV2,  Timepoints 0 to 24h,  Perturbations ,  HasCompleteData ,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined1276       1020 (80%)
COVID055 Phosphoproteome_Bouhaddou_Vero_E6_0h_Down 283 Phosphoproteome Vero_E6 SARS-CoV-2 Control 0h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 222 (78%) 236 (83%)
COVID056 Phosphoproteome_Bouhaddou_Vero_E6_0h_Up 184 Phosphoproteome Vero_E6 SARS-CoV-2 Control 0h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 143 (78%) 151 (82%)
COVID057 Phosphoproteome_Bouhaddou_Vero_E6_12h_Down 300 Phosphoproteome Vero_E6 SARS-CoV-2 Control 12h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 290 (97%) 247 (82%)
COVID058 Phosphoproteome_Bouhaddou_Vero_E6_12h_Up 300 Phosphoproteome Vero_E6 SARS-CoV-2 Control 12h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 276 (92%) 245 (82%)
COVID059 Phosphoproteome_Bouhaddou_Vero_E6_24h_Down 300 Phosphoproteome Vero_E6 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 254 (85%) 244 (81%)
COVID060 Phosphoproteome_Bouhaddou_Vero_E6_24h_Up 300 Phosphoproteome Vero_E6 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 228 (76%) 248 (83%)
COVID061 Phosphoproteome_Bouhaddou_Vero_E6_2h_Down 300 Phosphoproteome Vero_E6 SARS-CoV-2 Control 2h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 248 (83%) 244 (81%)
COVID062 Phosphoproteome_Bouhaddou_Vero_E6_2h_Up 300 Phosphoproteome Vero_E6 SARS-CoV-2 Control 2h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 272 (91%) 244 (81%)
COVID063 Phosphoproteome_Bouhaddou_Vero_E6_4h_Down 201 Phosphoproteome Vero_E6 SARS-CoV-2 Control 4h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 191 (95%) 168 (84%)
COVID064 Phosphoproteome_Bouhaddou_Vero_E6_4h_Up 263 Phosphoproteome Vero_E6 SARS-CoV-2 Control 4h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 246 (94%) 211 (80%)
COVID065 Phosphoproteome_Bouhaddou_Vero_E6_8h_Down 300 Phosphoproteome Vero_E6 SARS-CoV-2 Control 8h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 276 (92%) 250 (83%)
COVID066 Phosphoproteome_Bouhaddou_Vero_E6_8h_Up 300 Phosphoproteome Vero_E6 SARS-CoV-2 Control 8h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 280 (93%) 244 (81%)
COVID067 Proteome_Bouhaddou_Vero_E6_0h_Down 10 Proteome Vero_E6 SARS-CoV-2 Control 0h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 4 (40%) 9 (90%)
COVID068 Proteome_Bouhaddou_Vero_E6_0h_Up 1 Proteome Vero_E6 SARS-CoV-2 Control 0h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 0 (0%) 1 (100%)
COVID069 Proteome_Bouhaddou_Vero_E6_12h_Down 53 Proteome Vero_E6 SARS-CoV-2 Control 12h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 50 (94%) 49 (92%)
COVID070 Proteome_Bouhaddou_Vero_E6_12h_Up 6 Proteome Vero_E6 SARS-CoV-2 Control 12h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 6 (100%) 3 (50%)
COVID071 Proteome_Bouhaddou_Vero_E6_24h_Down 97 Proteome Vero_E6 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 61 (63%) 86 (89%)
COVID072 Proteome_Bouhaddou_Vero_E6_24h_Up 16 Proteome Vero_E6 SARS-CoV-2 Control 24h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 8 (50%) 10 (62%)
COVID073 Proteome_Bouhaddou_Vero_E6_2h_Down 43 Proteome Vero_E6 SARS-CoV-2 Control 2h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 40 (93%) 39 (91%)
COVID074 Proteome_Bouhaddou_Vero_E6_2h_Up 6 Proteome Vero_E6 SARS-CoV-2 Control 2h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 4 (67%) 3 (50%)
COVID075 Proteome_Bouhaddou_Vero_E6_4h_Down 33 Proteome Vero_E6 SARS-CoV-2 Control 4h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 33 (100%) 29 (88%)
COVID076 Proteome_Bouhaddou_Vero_E6_4h_Up 3 Proteome Vero_E6 SARS-CoV-2 Control 4h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 3 (100%) 0 (0%)
COVID077 Proteome_Bouhaddou_Vero_E6_8h_Down 45 Proteome Vero_E6 SARS-CoV-2 Control 8h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 42 (93%) 41 (91%)
COVID078 Proteome_Bouhaddou_Vero_E6_8h_Up 6 Proteome Vero_E6 SARS-CoV-2 Control 8h Significance defined by Abs(Log2FC)>1 and Adj P<0.05 as in the publication. Features sorted by pvalue. 5 (83%) 3 (50%)

10. Blanco-Melo et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19 Cell peer reviewed (pre-proof)

 IsOMICS RNA-Seq,  SampleType in vitro, in vivo model, patient samples,  CellType primary human lung epithelium (NHBE), A549, Calu-3, ferrets, patient samples,  VirusStrain SARS-CoV-2 (USA-WA1/2020),  Timepoints multiple, depending on model system,  Perturbations ,  HasCompleteData yes,  GeneListSource GEO read counts.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined1801       1408 (78%)
COVID007 RNA_Blanco-Melo_A549_Down 300 RNA-seq A549 SARS-CoV-2 uninfected 9h 138 (46%) 237 (79%)
COVID008 RNA_Blanco-Melo_A549_Up 300 RNA-seq A549 SARS-CoV-2 uninfected 9h 108 (36%) 244 (81%)
COVID009 RNA_Blanco-Melo_A549-ACE2_Down 207 RNA-seq A549 w/ exogenous ACE2 SARS-CoV-2 uninfected 9h 54 (26%) 162 (78%)
COVID010 RNA_Blanco-Melo_A549-ACE2_Up 300 RNA-seq A549 w/ exogenous ACE2 SARS-CoV-2 uninfected 9h 88 (29%) 234 (78%)
COVID011 RNA_Blanco-Melo_A549-ACE2-ruxolitinib_Down 234 RNA-seq A549 w/ exogenous ACE2 SARS-CoV-2 and ruxolitinib SARS-CoV-2 9h 142 (61%) 211 (90%)
COVID012 RNA_Blanco-Melo_A549-ACE2-ruxolitinib_Up 8 RNA-seq A549 w/ exogenous ACE2 SARS-CoV-2 and ruxolitinib SARS-CoV-2 9h 5 (62%) 6 (75%)
COVID013 RNA_Blanco-Melo_A549-low-MOI_Down 1 RNA-seq A549 SARS-CoV-2 (low MOI) uninfected 9h 1 (100%) 1 (100%)
COVID014 RNA_Blanco-Melo_A549-low-MOI_Up 35 RNA-seq A549 SARS-CoV-2 (low MOI) uninfected 9h 35 (100%) 35 (100%)
COVID015 RNA_Blanco-Melo_Calu-3_Down 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 9h 130 (43%) 240 (80%)
COVID016 RNA_Blanco-Melo_Calu-3_Up 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 9h 218 (73%) 287 (96%)
COVID017 RNA_Blanco-Melo_Lung_Down 262 RNA-seq Lung SARS-CoV-2 uninfected post-mortem 73 (28%) 186 (71%)
COVID018 RNA_Blanco-Melo_Lung_Up 84 RNA-seq Lung SARS-CoV-2 uninfected post-mortem 23 (27%) 63 (75%)
COVID019 RNA_Blanco-Melo_NHBE_Down 11 RNA-seq NHBE SARS-CoV-2 uninfected 24h 1 (9%) 8 (73%)
COVID020 RNA_Blanco-Melo_NHBE_Up 86 RNA-seq NHBE SARS-CoV-2 uninfected 24h 63 (73%) 79 (92%)

Proteomics comparison of sera samples from healthy, severe and non-severe COVID-19 patients, and non-COVID-19 patients.

 IsOMICS Proteomics and metabolomics,  SampleType patient and healthy samples,  CellType Healthy, non-COVID-19, and SARS CoV2 patient sera,  VirusStrain ,  Timepoints N/A,  Perturbations ,  HasCompleteData Yes,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined137       107 (78%)
COVID210 Proteome_Shen_Serum-severe-vs-nonsevere_Up 26 Proteome Serum SARS-CoV-2 (severe) SARS-CoV-2 (mild) Significance defined by Supp Table. Features sorted by pvalue. 26 (100%) 20 (77%)
COVID211 Proteome_Shen_Serum-severe-vs-nonsevere_Down 16 Proteome Serum SARS-CoV-2 (severe) SARS-CoV-2 (mild) Significance defined by Supp Table. Features sorted by pvalue. 15 (94%) 13 (81%)
COVID212 Proteome_Shen_Serum-severe-vs-healthy_Up 63 Proteome Serum SARS-CoV-2 (severe) Healthy Significance defined by Supp Table. Features sorted by pvalue. 35 (56%) 52 (83%)
COVID213 Proteome_Shen_Serum-severe-vs-healthy_Down 59 Proteome Serum SARS-CoV-2 (severe) Healthy Significance defined by Supp Table. Features sorted by pvalue. 37 (63%) 42 (71%)
COVID214 Proteome_Shen_Serum-nonCovid-vs-healthy_Up 15 Proteome Serum Non-SARS-CoV-2 patient Healthy Significance defined by Supp Table. Features sorted by pvalue. 11 (73%) 14 (93%)
COVID215 Proteome_Shen_Serum-nonCovid-vs-healthy_Down 13 Proteome Serum Non-SARS-CoV-2 patient Healthy Significance defined by Supp Table. Features sorted by pvalue. 13 (100%) 9 (69%)
COVID216 Proteome_Shen_Serum-nonsevere-vs-healthy_Up 21 Proteome Serum SARS-CoV-2 (mild) Healthy Significance defined by Supp Table. Features sorted by pvalue. 15 (71%) 16 (76%)
COVID217 Proteome_Shen_Serum-nonsevere-vs-healthy_Down 23 Proteome Serum SARS-CoV-2 (mild) Healthy Significance defined by Supp Table. Features sorted by pvalue. 20 (87%) 18 (78%)

Gene expression profiling of SARS-CoV-1/2 infected human cell lines at bulk and single-cell level.
Includes small RNA-seq in addition to polyA/total RNA. H1299 cell line ignored since few genes change overall.
 IsOMICS RNA-Seq, scRNA-seq,  SampleType in vitro,  CellType Calu-3, Caco-2, H1299,  VirusStrain SARS-CoV-2,  Timepoints 4, 8, 12, 24, 36 h,  Perturbations ,  HasCompleteData Yes,  GeneListSource GEO read counts.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined1048       818 (78%)
COVID043 RNA_Wyler_Caco-2_12h_Down 126 RNA-seq Caco-2 SARS-CoV-2 uninfected 12h 38 (30%) 85 (67%)
COVID044 RNA_Wyler_Caco-2_12h_Up 29 RNA-seq Caco-2 SARS-CoV-2 uninfected 12h 17 (59%) 22 (76%)
COVID045 RNA_Wyler_Caco-2_24h_Down 33 RNA-seq Caco-2 SARS-CoV-2 uninfected 24h 21 (64%) 24 (73%)
COVID046 RNA_Wyler_Caco-2_24h_Up 97 RNA-seq Caco-2 SARS-CoV-2 uninfected 24h 39 (40%) 77 (79%)
COVID047 RNA_Wyler_Calu-3_12h_Down 195 RNA-seq Calu-3 SARS-CoV-2 uninfected 12h 41 (21%) 122 (63%)
COVID048 RNA_Wyler_Calu-3_12h_Up 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 12h 214 (71%) 286 (95%)
COVID049 RNA_Wyler_Calu-3_24h_Down 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 24h 49 (16%) 222 (74%)
COVID050 RNA_Wyler_Calu-3_24h_Up 300 RNA-seq Calu-3 SARS-CoV-2 uninfected 24h 218 (73%) 285 (95%)

13. Li et al. Urine Proteome of COVID-19 Patients medRxiv pre-print
Proteomics analysis of urine samples from healthy, mild, and severe COVID-19 patients.

 IsOMICS Proteomics,  SampleType patient and healthy samples,  CellType Healthy and SARS CoV2 patient urine,  VirusStrain ,  Timepoints N/A,  Perturbations ,  HasCompleteData Yes,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined494       385 (78%)
COVID204 Proteome_Li_Urine-severe-vs-healthy_Up 84 Proteome Urine SARS-CoV-2 (severe) Healthy Significance defined by Supp Table. Features sorted by pvalue. 53 (63%) 70 (83%)
COVID205 Proteome_Li_Urine-severe-vs-healthy_Down 171 Proteome Urine SARS-CoV-2 (severe) Healthy Significance defined by Supp Table. Features sorted by pvalue. 107 (63%) 125 (73%)
COVID206 Proteome_Li_Urine-mild-vs-healthy_Up 86 Proteome Urine SARS-CoV-2 (mild) Healthy Significance defined by Supp Table. Features sorted by pvalue. 54 (63%) 71 (83%)
COVID207 Proteome_Li_Urine-mild-vs-healthy_Down 99 Proteome Urine SARS-CoV-2 (mild) Healthy Significance defined by Supp Table. Features sorted by pvalue. 86 (87%) 70 (71%)
COVID208 Proteome_Li_Urine-recovery-vs-healthy_Up 153 Proteome Urine SARS-CoV-2 (in recovery) Healthy Significance defined by Supp Table. Features sorted by pvalue. 45 (29%) 123 (80%)
COVID209 Proteome_Li_Urine-recovery-vs-healthy_Down 127 Proteome Urine SARS-CoV-2 (in recovery) Healthy Significance defined by Supp Table. Features sorted by pvalue. 63 (50%) 96 (76%)

14. Lamers et al. SARS-CoV-2 productively infects human gut enterocytes Science peer reviewed
Bulk RNA sequencing of SARS-CoV and SARS-CoV-2 infected human intestinal organoids.

 IsOMICS RNA-Seq,  SampleType in vitro,  CellType human intestinal organoids,  VirusStrain SARS-CoV-2,  Timepoints 24, 60 h,  Perturbations ,  HasCompleteData Yes,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined485       375 (77%)
COVID025 RNA_Lamers_intestinal-organoid_differentiated_Down 46 RNA-seq intestinal organoid (differentiation medium) SARS-CoV-2 uninfected 60h 22 (48%) 34 (74%)
COVID026 RNA_Lamers_intestinal-organoid_differentiated_Up 36 RNA-seq intestinal organoid (differentiation medium) SARS-CoV-2 uninfected 60h 14 (39%) 27 (75%)
COVID027 RNA_Lamers_intestinal-organoid_expansion_Down 267 RNA-seq intestinal-organoid (expansion medium) SARS-CoV-2 uninfected 60h 20 (7%) 203 (76%)
COVID028 RNA_Lamers_intestinal-organoid_expansion_Up 172 RNA-seq intestinal-organoid (expansion medium) SARS-CoV-2 uninfected 60h 16 (9%) 141 (82%)

SARS-CoV-2-Human Protein-Protein Interaction Map.

 IsOMICS Proteomics (APMS),  SampleType in vitro,  CellType HEK293T,  VirusStrain SARS-CoV-2 (USA-WA1/2020),  Timepoints n/a,  Perturbations ,  HasCompleteData yes,  GeneListSource .

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined333       247 (74%)
COVID081 Interactome_Gordon_HEK-293T_38h_E 6 Interactome HEK-293T E 38h 0 (0%) 5 (83%)
COVID082 Interactome_Gordon_HEK-293T_38h_M 30 Interactome HEK-293T M 38h 0 (0%) 22 (73%)
COVID083 Interactome_Gordon_HEK-293T_38h_N 15 Interactome HEK-293T N 38h 0 (0%) 13 (87%)
COVID084 Interactome_Gordon_HEK-293T_38h_NSP1 6 Interactome HEK-293T NSP1 38h 0 (0%) 6 (100%)
COVID085 Interactome_Gordon_HEK-293T_38h_NSP10 5 Interactome HEK-293T NSP10 38h 0 (0%) 4 (80%)
COVID086 Interactome_Gordon_HEK-293T_38h_NSP11 1 Interactome HEK-293T NSP11 38h 0 (0%) 0 (0%)
COVID087 Interactome_Gordon_HEK-293T_38h_NSP12 20 Interactome HEK-293T NSP12 38h 0 (0%) 15 (75%)
COVID088 Interactome_Gordon_HEK-293T_38h_NSP13 41 Interactome HEK-293T NSP13 38h 0 (0%) 24 (59%)
COVID089 Interactome_Gordon_HEK-293T_38h_NSP14 3 Interactome HEK-293T NSP14 38h 0 (0%) 3 (100%)
COVID090 Interactome_Gordon_HEK-293T_38h_NSP15 3 Interactome HEK-293T NSP15 38h 0 (0%) 2 (67%)
COVID091 Interactome_Gordon_HEK-293T_38h_NSP2 7 Interactome HEK-293T NSP2 38h 0 (0%) 5 (71%)
COVID092 Interactome_Gordon_HEK-293T_38h_NSP4 8 Interactome HEK-293T NSP4 38h 0 (0%) 6 (75%)
COVID093 Interactome_Gordon_HEK-293T_38h_NSP5 1 Interactome HEK-293T NSP5 38h 0 (0%) 1 (100%)
COVID094 Interactome_Gordon_HEK-293T_38h_NSP5_C145A 2 Interactome HEK-293T NSP5_C145A 38h 0 (0%) 1 (50%)
COVID095 Interactome_Gordon_HEK-293T_38h_NSP6 4 Interactome HEK-293T NSP6 38h 0 (0%) 3 (75%)
COVID096 Interactome_Gordon_HEK-293T_38h_NSP7 32 Interactome HEK-293T NSP7 38h 0 (0%) 24 (75%)
COVID097 Interactome_Gordon_HEK-293T_38h_NSP8 24 Interactome HEK-293T NSP8 38h 0 (0%) 18 (75%)
COVID098 Interactome_Gordon_HEK-293T_38h_NSP9 16 Interactome HEK-293T NSP9 38h 0 (0%) 13 (81%)
COVID099 Interactome_Gordon_HEK-293T_38h_ORF10 9 Interactome HEK-293T ORF10 38h 0 (0%) 9 (100%)
COVID100 Interactome_Gordon_HEK-293T_38h_ORF3A 8 Interactome HEK-293T ORF3A 38h 0 (0%) 7 (88%)
COVID101 Interactome_Gordon_HEK-293T_38h_ORF3B 1 Interactome HEK-293T ORF3B 38h 0 (0%) 1 (100%)
COVID102 Interactome_Gordon_HEK-293T_38h_ORF6 3 Interactome HEK-293T ORF6 38h 0 (0%) 2 (67%)
COVID103 Interactome_Gordon_HEK-293T_38h_ORF7A 2 Interactome HEK-293T ORF7A 38h 0 (0%) 2 (100%)
COVID104 Interactome_Gordon_HEK-293T_38h_ORF8 47 Interactome HEK-293T ORF8 38h 0 (0%) 32 (68%)
COVID105 Interactome_Gordon_HEK-293T_38h_ORF9B 11 Interactome HEK-293T ORF9B 38h 0 (0%) 10 (91%)
COVID106 Interactome_Gordon_HEK-293T_38h_ORF9C 26 Interactome HEK-293T ORF9C 38h 0 (0%) 17 (65%)
COVID107 Interactome_Gordon_HEK-293T_38h_S 2 Interactome HEK-293T S 38h 0 (0%) 2 (100%)


 IsOMICS RNA-Seq,  SampleType patient samples,  CellType BALF, PBMC,  VirusStrain SARS-CoV-2,  Timepoints n/a,  Perturbations ,  HasCompleteData yes,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined1151       774 (67%)
COVID051 RNA_Xiong_BALF_Down 300 RNA-seq BALF SARS-CoV-2 uninfected 3 (1%) 245 (82%)
COVID052 RNA_Xiong_BALF_Up 300 RNA-seq BALF SARS-CoV-2 uninfected 9 (3%) 214 (71%)
COVID053 RNA_Xiong_PBMC_Down 263 RNA-seq PBMC SARS-CoV-2 uninfected 7 (3%) 117 (44%)
COVID054 RNA_Xiong_PBMC_Up 300 RNA-seq PBMC SARS-CoV-2 uninfected 5 (2%) 206 (69%)


 IsOMICS Transcriptomics,  SampleType in vitro,  CellType pHAE cultures,  VirusStrain SARS-CoV-2, 2019-nCoV/WA1,  Timepoints 48 h,  Perturbations ,  HasCompleteData Yes,  GeneListSource Processed from GEO read counts.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined351       235 (67%)
COVID202 RNA_Vanderheiden_pHAE_48h_Down 193 RNA-seq pHAE SARS-CoV-2 Mock 48h Significance defined by Log2FC >= 1.0 and adjusted p-value < 0.01. Features sorted by pvalue. 0 (0%) 125 (65%)
COVID203 RNA_Vanderheiden_pHAE_48h_Up 158 RNA-seq pHAE SARS-CoV-2 Mock 48h Significance defined by Log2FC >= 1.0 and adjusted p-value < 0.01. Features sorted by pvalue. 0 (0%) 110 (70%)

SARS-CoV2 infection in Huh7 cell line and performed transcriptomics and proteomics analysis in uninfected and 24,48,72 hours post infection to identify the host cellular response against SARS-CoV2.

 IsOMICS RNA-Seq, proteomics,  SampleType in vitro,  CellType Huh-7,  VirusStrain SARS-CoV-2,  Timepoints 24, 48, 72 h,  Perturbations ,  HasCompleteData Yes,  GeneListSource Processed from raw reads.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined631       410 (65%)
COVID001 RNA_Appelberg_Huh-7_24h_Down 6 RNA-seq Huh-7 SARS-CoV-2 uninfected 24h 2 (33%) 4 (67%)
COVID002 RNA_Appelberg_Huh-7_24h_Up 8 RNA-seq Huh-7 SARS-CoV-2 uninfected 24h 2 (25%) 7 (88%)
COVID003 RNA_Appelberg_Huh-7_48h_Down 23 RNA-seq Huh-7 SARS-CoV-2 uninfected 48h 17 (74%) 17 (74%)
COVID004 RNA_Appelberg_Huh-7_48h_Up 97 RNA-seq Huh-7 SARS-CoV-2 uninfected 48h 83 (86%) 41 (42%)
COVID005 RNA_Appelberg_Huh-7_72h_Down 300 RNA-seq Huh-7 SARS-CoV-2 uninfected 72h 16 (5%) 231 (77%)
COVID006 RNA_Appelberg_Huh-7_72h_Up 300 RNA-seq Huh-7 SARS-CoV-2 uninfected 72h 84 (28%) 162 (54%)

Gene expression in CD21low and CD21pos B cells from CVID patients.

 IsOMICS RNA-Seq,  SampleType patient samples,  CellType B cells,  VirusStrain SARS-CoV-2,  Timepoints N/A,  Perturbations ,  HasCompleteData Yes,  GeneListSource GEO read counts.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined792       496 (63%)
COVID021 RNA_Keller_B-cells-CD21pos_infection_Down 24 RNA-seq B cells SARS-CoV-2 (CD21+) uninfected (CD21+) 5 (21%) 17 (71%)
COVID022 RNA_Keller_B-cells-CD21pos_infection_Up 275 RNA-seq B cells SARS-CoV-2 (CD21+) uninfected (CD21+) 86 (31%) 175 (64%)
COVID023 RNA_Keller_B-cells-Infected_CD21pos_Down 284 RNA-seq B cells SARS-CoV-2 (CD21+) SARS-CoV-2 (CD21 low) 82 (29%) 182 (64%)
COVID024 RNA_Keller_B-cells-Infected_CD21pos_Up 300 RNA-seq B cells SARS-CoV-2 (CD21+) SARS-CoV-2 (CD21 low) 9 (3%) 175 (58%)

Comprehensive SARS-CoV-2 infection profiling using proteomics and RNASeq, particularly for different SARS-CoV-2 proteins.

 IsOMICS Interactome, Proteomics, Ubiquitome, Phosphoproteome, RNA-seq,  SampleType in vitro,  CellType A549-ACE2,  VirusStrain SARS-CoV-2-MUC-IMB-1,  Timepoints 6 to 72h,  Perturbations ,  HasCompleteData ,  GeneListSource Supplemental table.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined4695       2816 (60%)
COVID108 Interactome_Stukalov_A549_72h_E 11 Interactome A549 E 72h Significance defined by Supp Table. Features sorted by pvalue. 7 (64%) 6 (55%)
COVID109 Interactome_Stukalov_A549_72h_M 139 Interactome A549 M 72h Significance defined by Supp Table. Features sorted by pvalue. 68 (49%) 71 (51%)
COVID110 Interactome_Stukalov_A549_72h_N 9 Interactome A549 N 72h Significance defined by Supp Table. Features sorted by pvalue. 6 (67%) 6 (67%)
COVID111 Interactome_Stukalov_A549_72h_NSP1 3 Interactome A549 NSP1 72h Significance defined by Supp Table. Features sorted by pvalue. 3 (100%) 2 (67%)
COVID112 Interactome_Stukalov_A549_72h_NSP12 1 Interactome A549 NSP12 72h Significance defined by Supp Table. Features sorted by pvalue. 1 (100%) 1 (100%)
COVID113 Interactome_Stukalov_A549_72h_NSP13 1 Interactome A549 NSP13 72h Significance defined by Supp Table. Features sorted by pvalue. 0 (0%) 0 (0%)
COVID114 Interactome_Stukalov_A549_72h_NSP14 2 Interactome A549 NSP14 72h Significance defined by Supp Table. Features sorted by pvalue. 0 (0%) 1 (50%)
COVID115 Interactome_Stukalov_A549_72h_NSP15 4 Interactome A549 NSP15 72h Significance defined by Supp Table. Features sorted by pvalue. 0 (0%) 3 (75%)
COVID116 Interactome_Stukalov_A549_72h_NSP16 2 Interactome A549 NSP16 72h Significance defined by Supp Table. Features sorted by pvalue. 1 (50%) 2 (100%)
COVID117 Interactome_Stukalov_A549_72h_NSP2 1 Interactome A549 NSP2 72h Significance defined by Supp Table. Features sorted by pvalue. 0 (0%) 1 (100%)
COVID118 Interactome_Stukalov_A549_72h_NSP3_MACROD 2 Interactome A549 NSP3_MACROD 72h Significance defined by Supp Table. Features sorted by pvalue. 0 (0%) 1 (50%)
COVID119 Interactome_Stukalov_A549_72h_NSP4 11 Interactome A549 NSP4 72h Significance defined by Supp Table. Features sorted by pvalue. 9 (82%) 9 (82%)
COVID120 Interactome_Stukalov_A549_72h_NSP6 81 Interactome A549 NSP6 72h Significance defined by Supp Table. Features sorted by pvalue. 44 (54%) 46 (57%)
COVID121 Interactome_Stukalov_A549_72h_NSP7 5 Interactome A549 NSP7 72h Significance defined by Supp Table. Features sorted by pvalue. 5 (100%) 3 (60%)
COVID122 Interactome_Stukalov_A549_72h_NSP8 3 Interactome A549 NSP8 72h Significance defined by Supp Table. Features sorted by pvalue. 2 (67%) 2 (67%)
COVID123 Interactome_Stukalov_A549_72h_NSP9 6 Interactome A549 NSP9 72h Significance defined by Supp Table. Features sorted by pvalue. 4 (67%) 4 (67%)
COVID124 Interactome_Stukalov_A549_72h_ORF3 300 Interactome A549 ORF3 72h Significance defined by Supp Table. Features sorted by pvalue. 199 (66%) 190 (63%)
COVID125 Interactome_Stukalov_A549_72h_ORF7A 56 Interactome A549 ORF7A 72h Significance defined by Supp Table. Features sorted by pvalue. 39 (70%) 24 (43%)
COVID126 Interactome_Stukalov_A549_72h_ORF7B 300 Interactome A549 ORF7B 72h Significance defined by Supp Table. Features sorted by pvalue. 203 (68%) 173 (58%)
COVID127 Interactome_Stukalov_A549_72h_ORF8 29 Interactome A549 ORF8 72h Significance defined by Supp Table. Features sorted by pvalue. 18 (62%) 25 (86%)
COVID128 Interactome_Stukalov_A549_72h_ORF9B 2 Interactome A549 ORF9B 72h Significance defined by Supp Table. Features sorted by pvalue. 1 (50%) 2 (100%)
COVID129 Interactome_Stukalov_A549_72h_S 2 Interactome A549 S 72h Significance defined by Supp Table. Features sorted by pvalue. 1 (50%) 2 (100%)
COVID130 Phosphoproteome_Stukalov_A549-ACE2_24h_Down 300 Phosphoproteome A549-ACE2 SARS-CoV-2 Mock 24h Significance defined by Supp Table. Features sorted by pvalue. 169 (56%) 213 (71%)
COVID131 Phosphoproteome_Stukalov_A549-ACE2_24h_Up 300 Phosphoproteome A549-ACE2 SARS-CoV-2 Mock 24h Significance defined by Supp Table. Features sorted by pvalue. 190 (63%) 229 (76%)
COVID132 Phosphoproteome_Stukalov_A549-ACE2_6h_Down 70 Phosphoproteome A549-ACE2 SARS-CoV-2 Mock 6h Significance defined by Supp Table. Features sorted by pvalue. 52 (74%) 61 (87%)
COVID133 Phosphoproteome_Stukalov_A549-ACE2_6h_Up 70 Phosphoproteome A549-ACE2 SARS-CoV-2 Mock 6h Significance defined by Supp Table. Features sorted by pvalue. 44 (63%) 58 (83%)
COVID134 Proteome_Stukalov_A549-ACE2_24h_Down 300 Proteome A549-ACE2 SARS-CoV-2 Mock 24h Significance defined by Supp Table. Features sorted by pvalue. 178 (59%) 200 (67%)
COVID135 Proteome_Stukalov_A549-ACE2_24h_Up 133 Proteome A549-ACE2 SARS-CoV-2 Mock 24h Significance defined by Supp Table. Features sorted by pvalue. 92 (69%) 103 (77%)
COVID136 Proteome_Stukalov_A549-ACE2_6h_Down 10 Proteome A549-ACE2 SARS-CoV-2 Mock 6h Significance defined by Supp Table. Features sorted by pvalue. 9 (90%) 9 (90%)
COVID137 Proteome_Stukalov_A549-ACE2_6h_Up 8 Proteome A549-ACE2 SARS-CoV-2 Mock 6h Significance defined by Supp Table. Features sorted by pvalue. 8 (100%) 5 (62%)
COVID138 Proteome_Stukalov_A549_72h_E_Down 242 Proteome A549 E Control 72h Significance defined by Supp Table. Features sorted by pvalue. 206 (85%) 135 (56%)
COVID139 Proteome_Stukalov_A549_72h_E_Up 190 Proteome A549 E Control 72h Significance defined by Supp Table. Features sorted by pvalue. 144 (76%) 112 (59%)
COVID140 Proteome_Stukalov_A549_72h_M_Down 173 Proteome A549 M Control 72h Significance defined by Supp Table. Features sorted by pvalue. 147 (85%) 97 (56%)
COVID141 Proteome_Stukalov_A549_72h_M_Up 103 Proteome A549 M Control 72h Significance defined by Supp Table. Features sorted by pvalue. 82 (80%) 69 (67%)
COVID142 Proteome_Stukalov_A549_72h_NSP10_Down 32 Proteome A549 NSP10 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 26 (81%) 16 (50%)
COVID143 Proteome_Stukalov_A549_72h_NSP10_Up 48 Proteome A549 NSP10 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 38 (79%) 32 (67%)
COVID144 Proteome_Stukalov_A549_72h_NSP12_Down 211 Proteome A549 NSP12 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 145 (69%) 111 (53%)
COVID145 Proteome_Stukalov_A549_72h_NSP12_Up 41 Proteome A549 NSP12 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 32 (78%) 16 (39%)
COVID146 Proteome_Stukalov_A549_72h_NSP13_Down 96 Proteome A549 NSP13 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 57 (59%) 69 (72%)
COVID147 Proteome_Stukalov_A549_72h_NSP13_Up 121 Proteome A549 NSP13 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 95 (79%) 73 (60%)
COVID148 Proteome_Stukalov_A549_72h_NSP14_Down 38 Proteome A549 NSP14 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 29 (76%) 23 (61%)
COVID149 Proteome_Stukalov_A549_72h_NSP14_Up 45 Proteome A549 NSP14 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 32 (71%) 29 (64%)
COVID150 Proteome_Stukalov_A549_72h_NSP15_Down 34 Proteome A549 NSP15 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 29 (85%) 16 (47%)
COVID151 Proteome_Stukalov_A549_72h_NSP15_Up 69 Proteome A549 NSP15 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 56 (81%) 39 (57%)
COVID152 Proteome_Stukalov_A549_72h_NSP16_Down 39 Proteome A549 NSP16 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 36 (92%) 19 (49%)
COVID153 Proteome_Stukalov_A549_72h_NSP16_Up 65 Proteome A549 NSP16 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 54 (83%) 38 (58%)
COVID154 Proteome_Stukalov_A549_72h_NSP1_Down 213 Proteome A549 NSP1 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 127 (60%) 116 (54%)
COVID155 Proteome_Stukalov_A549_72h_NSP1_Up 129 Proteome A549 NSP1 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 83 (64%) 70 (54%)
COVID156 Proteome_Stukalov_A549_72h_NSP2_Down 121 Proteome A549 NSP2 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 87 (72%) 71 (59%)
COVID157 Proteome_Stukalov_A549_72h_NSP2_Up 70 Proteome A549 NSP2 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 47 (67%) 37 (53%)
COVID158 Proteome_Stukalov_A549_72h_NSP3_MACROD_Down 48 Proteome A549 NSP3_MACROD Control 72h Significance defined by Supp Table. Features sorted by pvalue. 38 (79%) 34 (71%)
COVID159 Proteome_Stukalov_A549_72h_NSP3_MACROD_Up 79 Proteome A549 NSP3_MACROD Control 72h Significance defined by Supp Table. Features sorted by pvalue. 53 (67%) 55 (70%)
COVID160 Proteome_Stukalov_A549_72h_NSP4_Down 42 Proteome A549 NSP4 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 31 (74%) 23 (55%)
COVID161 Proteome_Stukalov_A549_72h_NSP4_Up 82 Proteome A549 NSP4 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 56 (68%) 43 (52%)
COVID162 Proteome_Stukalov_A549_72h_NSP6_Down 68 Proteome A549 NSP6 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 52 (76%) 36 (53%)
COVID163 Proteome_Stukalov_A549_72h_NSP6_Up 65 Proteome A549 NSP6 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 44 (68%) 36 (55%)
COVID164 Proteome_Stukalov_A549_72h_NSP7_Down 34 Proteome A549 NSP7 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 26 (76%) 18 (53%)
COVID165 Proteome_Stukalov_A549_72h_NSP7_Up 40 Proteome A549 NSP7 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 25 (62%) 26 (65%)
COVID166 Proteome_Stukalov_A549_72h_NSP8_Down 61 Proteome A549 NSP8 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 47 (77%) 40 (66%)
COVID167 Proteome_Stukalov_A549_72h_NSP8_Up 52 Proteome A549 NSP8 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 40 (77%) 27 (52%)
COVID168 Proteome_Stukalov_A549_72h_NSP9_Down 42 Proteome A549 NSP9 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 35 (83%) 26 (62%)
COVID169 Proteome_Stukalov_A549_72h_NSP9_Up 55 Proteome A549 NSP9 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 47 (85%) 31 (56%)
COVID170 Proteome_Stukalov_A549_72h_N_Down 139 Proteome A549 N Control 72h Significance defined by Supp Table. Features sorted by pvalue. 116 (83%) 84 (60%)
COVID171 Proteome_Stukalov_A549_72h_N_Up 102 Proteome A549 N Control 72h Significance defined by Supp Table. Features sorted by pvalue. 82 (80%) 62 (61%)
COVID172 Proteome_Stukalov_A549_72h_ORF3_Down 300 Proteome A549 ORF3 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 211 (70%) 189 (63%)
COVID173 Proteome_Stukalov_A549_72h_ORF3_Up 293 Proteome A549 ORF3 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 205 (70%) 203 (69%)
COVID174 Proteome_Stukalov_A549_72h_ORF6_Down 79 Proteome A549 ORF6 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 64 (81%) 52 (66%)
COVID175 Proteome_Stukalov_A549_72h_ORF6_Up 91 Proteome A549 ORF6 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 62 (68%) 48 (53%)
COVID176 Proteome_Stukalov_A549_72h_ORF7A_Down 67 Proteome A549 ORF7A Control 72h Significance defined by Supp Table. Features sorted by pvalue. 54 (81%) 42 (63%)
COVID177 Proteome_Stukalov_A549_72h_ORF7A_Up 74 Proteome A549 ORF7A Control 72h Significance defined by Supp Table. Features sorted by pvalue. 56 (76%) 38 (51%)
COVID178 Proteome_Stukalov_A549_72h_ORF7B_Down 123 Proteome A549 ORF7B Control 72h Significance defined by Supp Table. Features sorted by pvalue. 95 (77%) 73 (59%)
COVID179 Proteome_Stukalov_A549_72h_ORF7B_Up 130 Proteome A549 ORF7B Control 72h Significance defined by Supp Table. Features sorted by pvalue. 95 (73%) 71 (55%)
COVID180 Proteome_Stukalov_A549_72h_ORF8_Down 63 Proteome A549 ORF8 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 44 (70%) 37 (59%)
COVID181 Proteome_Stukalov_A549_72h_ORF8_Up 80 Proteome A549 ORF8 Control 72h Significance defined by Supp Table. Features sorted by pvalue. 50 (62%) 45 (56%)
COVID182 Proteome_Stukalov_A549_72h_ORF9B_Down 219 Proteome A549 ORF9B Control 72h Significance defined by Supp Table. Features sorted by pvalue. 116 (53%) 115 (53%)
COVID183 Proteome_Stukalov_A549_72h_ORF9B_Up 116 Proteome A549 ORF9B Control 72h Significance defined by Supp Table. Features sorted by pvalue. 67 (58%) 61 (53%)
COVID184 Proteome_Stukalov_A549_72h_S_Down 48 Proteome A549 S Control 72h Significance defined by Supp Table. Features sorted by pvalue. 36 (75%) 25 (52%)
COVID185 Proteome_Stukalov_A549_72h_S_Up 63 Proteome A549 S Control 72h Significance defined by Supp Table. Features sorted by pvalue. 46 (73%) 37 (59%)
COVID186 RNA_Stukalov_A549-ACE2_12h_Down 19 RNA-seq A549-ACE2 SARS-CoV-2 Mock 12h Significance defined by Supp Table. Features sorted by pvalue. 18 (95%) 13 (68%)
COVID187 RNA_Stukalov_A549-ACE2_12h_Up 13 RNA-seq A549-ACE2 SARS-CoV-2 Mock 12h Significance defined by Supp Table. Features sorted by pvalue. 10 (77%) 11 (85%)
COVID188 RNA_Stukalov_A549-ACE2_18h_Down 33 RNA-seq A549-ACE2 SARS-CoV-2 Mock 18h Significance defined by Supp Table. Features sorted by pvalue. 27 (82%) 14 (42%)
COVID189 RNA_Stukalov_A549-ACE2_18h_Up 66 RNA-seq A549-ACE2 SARS-CoV-2 Mock 18h Significance defined by Supp Table. Features sorted by pvalue. 54 (82%) 63 (95%)
COVID190 RNA_Stukalov_A549-ACE2_24h_Down 39 RNA-seq A549-ACE2 SARS-CoV-2 Mock 24h Significance defined by Supp Table. Features sorted by pvalue. 26 (67%) 26 (67%)
COVID191 RNA_Stukalov_A549-ACE2_24h_Up 96 RNA-seq A549-ACE2 SARS-CoV-2 Mock 24h Significance defined by Supp Table. Features sorted by pvalue. 81 (84%) 87 (91%)
COVID192 RNA_Stukalov_A549-ACE2_30h_Down 102 RNA-seq A549-ACE2 SARS-CoV-2 Mock 30h Significance defined by Supp Table. Features sorted by pvalue. 47 (46%) 58 (57%)
COVID193 RNA_Stukalov_A549-ACE2_30h_Up 297 RNA-seq A549-ACE2 SARS-CoV-2 Mock 30h Significance defined by Supp Table. Features sorted by pvalue. 166 (56%) 232 (78%)
COVID194 RNA_Stukalov_A549-ACE2_3h_Down 2 RNA-seq A549-ACE2 SARS-CoV-2 Mock 3h Significance defined by Supp Table. Features sorted by pvalue. 2 (100%) 1 (50%)
COVID195 RNA_Stukalov_A549-ACE2_3h_Up 16 RNA-seq A549-ACE2 SARS-CoV-2 Mock 3h Significance defined by Supp Table. Features sorted by pvalue. 8 (50%) 15 (94%)
COVID196 RNA_Stukalov_A549-ACE2_6h_Down 16 RNA-seq A549-ACE2 SARS-CoV-2 Mock 6h Significance defined by Supp Table. Features sorted by pvalue. 15 (94%) 10 (62%)
COVID197 RNA_Stukalov_A549-ACE2_6h_Up 6 RNA-seq A549-ACE2 SARS-CoV-2 Mock 6h Significance defined by Supp Table. Features sorted by pvalue. 6 (100%) 5 (83%)
COVID198 Ubiquitinome_Stukalov_A549-ACE2_24h_Down 202 Ubiquitinome A549-ACE2 SARS-CoV-2 Mock 24h Significance defined by Supp Table. Features sorted by pvalue. 148 (73%) 142 (70%)
COVID199 Ubiquitinome_Stukalov_A549-ACE2_24h_Up 300 Ubiquitinome A549-ACE2 SARS-CoV-2 Mock 24h Significance defined by Supp Table. Features sorted by pvalue. 198 (66%) 202 (67%)
COVID200 Ubiquitinome_Stukalov_A549-ACE2_6h_Down 255 Ubiquitinome A549-ACE2 SARS-CoV-2 Mock 6h Significance defined by Supp Table. Features sorted by pvalue. 170 (67%) 173 (68%)
COVID201 Ubiquitinome_Stukalov_A549-ACE2_6h_Up 103 Ubiquitinome A549-ACE2 SARS-CoV-2 Mock 6h Significance defined by Supp Table. Features sorted by pvalue. 83 (81%) 74 (72%)


 IsOMICS scRNA-seq, TCR-seq,  SampleType patient samples,  CellType BALF,  VirusStrain SARS-CoV-2,  Timepoints ,  Perturbations ,  HasCompleteData yes,  GeneListSource GEO read counts.

COVID IDList NameSizeTechnologySourceTreatmentReferenceTimePointsComments#Found Multiple Times#Found in Other Studies
 Combined1375       786 (57%)
COVID029 RNA_Liao_BALF-mild_Down 300 RNA-seq BALF SARS-CoV-2 (mild) uninfected 123 (41%) 165 (55%)
COVID030 RNA_Liao_BALF-mild_Up 300 RNA-seq BALF SARS-CoV-2 (mild) uninfected 106 (35%) 132 (44%)
COVID031 RNA_Liao_BALF-severe_Down 300 RNA-seq BALF SARS-CoV-2 (severe) uninfected 233 (78%) 145 (48%)
COVID032 RNA_Liao_BALF-severe_Up 300 RNA-seq BALF SARS-CoV-2 (severe) uninfected 156 (52%) 248 (83%)
COVID033 RNA_Liao_BALF-severe-vs-mild_Down 300 RNA-seq BALF SARS-CoV-2 (severe) SARS-CoV-2 (mild) 141 (47%) 118 (39%)
COVID034 RNA_Liao_BALF-severe-vs-mild_Up 300 RNA-seq BALF SARS-CoV-2 (severe) SARS-CoV-2 (mild) 74 (25%) 226 (75%)