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["Table S1. Basic information and demography of multiple single-cell datasets. "]
["tissue","disease","dataset source","technology","number of cells"]
["colon","healthy","Smillie, et al, Cell, 2019","10X Genomics",35670]
["colon","non-inflamed ulcerative colitis","Smillie, et al, Cell, 2019","10X Genomics",50275]
["colon","inflamed ulcerative colitis","Smillie, et al, Cell, 2019","10X Genomics",54124]
["ileum","Crohn's disease","Martin, et al, Cell, 2019","10X Genomics",45198]
["synovium","osteoarthritis","Zhang, et al, Nature Immunology, 2019","CEL-Seq2",471]
["synovium","rheumatoid arthritis","Zhang, et al, Nature Immunology, 2019","CEL-Seq2",2316]
["synovium","rheumatoid arthritis","Stephenson, et al, Nature Communication, 2018","Dropseq",8871]
["kidney","healthy","Arazi, et al, Nature Immunology, 2019","CEL-Seq2",155]
["kidney","SLE","Arazi, et al, Nature Immunology, 2019","CEL-Seq2",2523]
["lung","systemic sclerosis","Reyfman, et al, AJRCCM, 2019","10X Genomics",8607]
["lung","healthy","Reyfman, et al, AJRCCM, 2019","10X Genomics",24231]
["lung","hypersensitivity pneumonitis","Reyfman, et al, AJRCCM, 2019","10X Genomics",3906]
["lung","polymyositis","Reyfman, et al, AJRCCM, 2019","10X Genomics",4819]
["BALF","healthy","Liao, et al, Nature Medicine, 2020","10X Genomics",21435]
["BALF","mild COVID-19","Liao, et al, Nature Medicine, 2020","10X Genomics",7249]
["BALF","severe COVID-19","Liao, et al, Nature Medicine, 2020","10X Genomics",37234]

{"sheet":"demograhic characteristics","index":1,"n_rows":54,"n_cols":17,"rows_kept":54,"merged":[[10,0,15,0],[35,1,35,2]],"flags":["formulas_cached_only"]}
["Table S1. Basic information and demography of multiple single-cell datasets. "]
["Zhang, et al, RA ",{"$nulls":5},"Martin, et al, CD"]
["Summary",null,"OA","leukocyte-poor RA ","leukocyte-rich RA ",null,"Summary","Characteristic","Patients"]
["Demographic variables","Age, mean",71,64.2,57.3,null,null,"General data"]
[null,"(Range)","(64-81)","(42-79)","(36-71)",null,null,"Age (y.o.; mean ± sd)","32.7 ± 12.9"]
[null,"Females, n (%)","10 (66.7)","15 (82.4)","14 (73.7)",null,null,"Sex (M/F)","10/4"]
["RA-related variables","Mean years of disease duration",null,15.7,"5.5*",null,null,"Disease duration (y.; mean ± sd)","9.1 ± 9.3"]
[null,"(range)",null,"(<1-51)","(<1-29)",null,null,"Smokers - no. (%)","1 (7)"]
[null,"RF positive, n (%)",null,"8 (47.1)","16* (84.2)",null,null,"Montreal classification"]
[null,"CCP positive, n (%)",null,"10 (58.8)","14 (73.7)",null,null,"Age at diagnosis - no. (%)"]
["DMARDs","Prednisone, n (%)",null,"10 (55.6)","4* (22.2)",null,null,"A1 below 16 y.o.","3 (21)"]
[null,"Methotrexate, n (%)",null,"7 (41.2)","3 (15.8)",null,null,"A2 between 17 and 40 y.o.","10 (71)"]
[null,"TNFi, n (%)",null,"4 (23.5)","2 (10.5)",null,null,"A3 above 40 y.o.","1 (7)"]
[null,"Rituximab, n (%)",null,"0 (0)","1 (5.3)",null,null,"Behavior - no. (%)"]
[null,"Abatacept, n (%)",null,"1 (5.9)","1 (5.3)",null,null,"B1 non-stricturing, non-penetrating","0 (0)"]
[null,"Tofacitinib, n (%)",null,"2 (11.8)","1 (5.3)",null,null,"B2 stricturing","12 (86)"]
[{"$nulls":7},"B3 penetrating","2 (15)"]
["Arazi, et al, SLE",{"$nulls":6},"Lab data"]
["Summary","SLE Patients ","Controls ",{"$nulls":4},"Hemoglobin (g/dL; mean ± sd)","13.2 ± 1.6"]
["Age, years","34 ± 11","35 ± 7",{"$nulls":4},"Platelets (G/L; mean ± sd)","286 ± 102"]
["Female, n (%)","21 (88)","6 (60)",{"$nulls":4},"Albumin (g/dL; mean ± sd)","3.7 ± 0.5"]
["SLEDAI","13.5 ± 7","ND",{"$nulls":4},"CRP (mg/L; mean ± sd)","25.5 ± 24.7"]
["dsDNA IU/mL","298 ± 407","ND",{"$nulls":4},"Medication at time of surgery - no. (%)"]
["C3 mg/dL","70 ± 25","ND",{"$nulls":4},"Antibiotics","4 (29)"]
["C4 mg/dL","11 ± 7.5","ND",{"$nulls":4},"5-ASA","6 (36)"]
["Hydroxychloroquine, n (%)","18 (75)",0,{"$nulls":4},"6-mercaptorurine","4 (29)"]
["Mycophenolate mofetil, n (%)","16 (67)",0,{"$nulls":4},"Corticosteroids","7 (50)"]
["Azathioprine, n (%)","3 (13)",0,{"$nulls":4},"Anti-TNF⍺","10 (71)"]
["Cyclophosphamide, n (%)","1 (4)",0]
["Tacrolimus, n (%)","1 (4)",0]
[]
["Smillie, et al, UC"]
["Summary","Colitis","Healthy "]
["Sex (M/F)","10/7","7/6"]
["Smoking (Yes/No)","7/10","7/6"]
["Age","Aa range of ages (20 – 77 years)"]
[]
[]
["Liao, et al, COVID-19 BALF"]
["Patient","M1","M2","M3","S1","S2","S3","S4","S5","S6","S7","S8","S9","S10","HC1","HC2","HC3"]
["Severity","Moderate","Moderate","Moderate","Severee","Critical","Critical","Critical","Critical","Critical","Severe","Critical","Critical","Critical","-","-","-"]
["Age",36,37,35,62,66,63,65,57,46,52,73,67,65,38,24,22]
["Gender","Male","Female","Male","Male","Male","Male","Female","Female","Male","Male","Male","Male","Male","Female","Male","Male"]
["Wuhan exposure","Yes ","Yes","Yes","Yes","Yes","Yes","Yes","Yes","Yes","No","Yes","Yes","Yes","-","-","-"]
["Symptom onset date / First symptom","2020-1-9 / Cough","2020-1-11 / Fever/Cough","2020-1-9 / Fever/Muscle aches","2020-1-11 / Fever/Cough","2020-1-3 / Fever/Cough","2020-1-8 / Fever/Cough","2020-1-4 / Fever/Cough/Chest distress ","2020-1-21 / Dizziness/Fever/Chest distress","2020-1-21 / Fever/Cough","2020-2-8 / Fever","2020-1-20 / Fever","2020-1-17 / Fever/diarrhea","2020-1-20 / Bloating/Fever","-","-","-"]
["Hospitalization date","2020-01-16","2020-01-16","2020-01-15","2020-01-18","2020-01-11","2020-01-15","2020-01-20","2020-01-23","2020-01-22","2020-2-11","2020-1-22","2020-1-22","2020-1-30","-","-","-"]
["BALF sampling data ","2020-01-20","2020-01-20","2020-01-22","2020-01-22","2020-01-21","2020-01-22","2020-01-29","2020-01-29","2020-02-02","2020-2-13","2020-2-2, 2-8 ","2020-1-29","2020-2-21","2019-1-29 ","2019-2-14","2019-9-12 "]
["Chronic basic disease","None","None","None","None","Hypertension","Sleep apnea","Diabetes","None","None","None","Hypertension","Hypertension","Diabetes & Hypertension","None","None","None"]
["Medication history","None","None","None","None","Amlodipine Besylate","None","None","None","None","None","None","L-amlodipine & Bisoprolol","None","None","None","None"]
["SARS-CoV-2 RT-qPCR (Ct) / Sample / Date","+(33.8) / Sputum / 2020-1-24","Negative","+(30) / Throat swab / 2020-01-20","+(29) / Throat swab / 2020-01-20","+(26) / Sputum / 2020-01-20","+(28.5) / Sputum / 2020-1-21","+(24.2) / Sputum / 2020-1-21","+(22.5) / Throat swab / 2020-1-21","+(30) / Sputum / 2020-1-23","+(26) / Nasal swab / 2020-2-15","+(23) / Nasal swab / 2020-1-23","+(30.9) / Throat swab / 2020-1-24","+(30.44) / Throat swab / 2020-1-30","ND","ND","ND"]
["RBD-antibody (C.O.I.) / Date","+ (6.01) / 2020-1-22","+ (25.39) / 2020-1-30","+ (2.36) / 2020-1-29","Negative (0.55) / 2020-1-29","+ (33.59) / 2020-1-31","+ (26.1) / 2020-1-29","+ (69.49) / 2020-1-28","+ (2.72) / 2020-1-29","+ (9.36) / 2020-2-2","+ (5.98) / 2020-2-20","+ (1.19) / 2020-2-2","+ (48.92) / 2020-1-28","+ (46.16) / 2020-2-20","ND","ND","ND"]
["Interferon aromization","2020-1-16","None","2020-1-18","2020-1-16","2020-1-14","2020-1-15","2020-1-20","2020-1-23","2020-1-22","2020-2-11","2020-1-22","2020-1-22","2020-1-30","-","-","-"]
["Ribavirin","2020-1-16","No","2020-1-18","2020-1-16","2020-1-14","2020-1-15","2020-1-20","No","2020-1-23","2020-2-11","2020-1-22","no","no","-","-","-"]
["Methyl-prednisolone","No","No","No","No","Yes","Yes","Yes","Yes","No","No","Yes","Yes","Yes","-","-","-"]