KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies
| ||
| Anti-Human CD45 (clone HI30) | Biolegend | Cat#: 304002; |
| RRID: AB_314390 | ||
|
| ||
| Anti-Human HLA-ABC (clone W6/32) | Biolegend | Cat#: 311402; |
| RRID: AB_314871 | ||
|
| ||
| Anti-Human CD19 (clone HIB19) – 142Nd | Fluidigm | Cat#: 3142001B |
|
| ||
| Anti-Human CD117 (clone 104D2) – 143Nd | Fluidigm | Cat#: 3143001B |
|
| ||
| Anti-Human CD141 (clone BDCA-3) | Biolegend | Cat#: 344102; |
| RRID: AB_2201808 | ||
|
| ||
| Anti-PE (clone PE001) – 145Nd | Fluidigm | Cat#: 3145006B |
|
| ||
| Anti-Human CD64 (clone 10.1) – 146Nd | Fluidigm | Cat#: 3146006B |
|
| ||
| Anti-Human Gata6 (clone 2F10G3) | Abcam | Cat#: Ab175425 |
|
| ||
| Anti-Human CD16 (clone 3G8) – 148Nd | Fluidigm | Cat#: 3148004B |
|
| ||
| Anti-Human CD123 (clone 6H6) – 151Eu | Fluidigm | Cat#: 3151001B |
|
| ||
| Anti-Human CD66b (clone 80H3) – 152Sm | Fluidigm | Cat#: 3152011B |
|
| ||
| Anti-Human CD1c (clone BDCA-1) | Fluidigm | Cat#: 331502; |
| RRID: AB_1088995 | ||
|
| ||
| Anti-Human CD163 (clone GHI/61) – 154Sm | Fluidigm | Cat#: 3154007B |
|
| ||
| Anti-Human CD86 (clone IT2.2) – 156Gd | Fluidigm | Cat#: 3156008B |
|
| ||
| Anti-Human CD33 (clone WM53) – 158Gd | Fluidigm | Cat#: 3158001B |
|
| ||
| Anti-Human CD14 (clone M5E2) – 160Gd | Fluidigm | Cat#: 3160001B |
|
| ||
| Anti-Human CD11c (clone Bu15) – 162Dy | Fluidigm | Cat#: 3162005B |
|
| ||
| Anti-APC (clone APC003) – 163Dy | Fluidigm | Cat#: 3163001B |
|
| ||
| Anti-Human CCR3 (clone 5E8) | Biolegend | Cat#: 310702; |
| RRID: AB_345394 | ||
|
| ||
| Anti-Human CD116 (clone 4H1) | Biolegend | Cat#: 305902; |
| RRID: AB_314568 | ||
|
| ||
| Anti-Human CD24 (clone ML5) – 166Er | Fluidigm | Cat#: 3166007B |
|
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| Anti-Human CD206 (clone 15-2) – 168Er | Fluidigm | Cat#: 3168008B |
|
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| Anti-Human PPARγ (clones 3A4A9, 1E6A1) | Abcam | Cat#: Ab70405; |
| RRID: AB_1269873 | ||
|
| ||
| Anti-Human CD3 (clone UCHT1) – 170Er | Fluidigm | Cat#: 3170001B |
|
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| Anti-Human CD68 (clone Y1/82A) – 171Yb | Fluidigm | Cat#: 3171011B |
|
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| Anti-Human CD11b (clone M1/70) – 172Yb | Fluidigm | Cat#: 3172012B |
|
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| Anti-Human HLA-DR (clone L243) – 174Yb | Fluidigm | Cat#: 3174001B |
|
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| Ant-Human PD-L1 (clone 29E.2A3) -175Lu | Fluidigm | Cat#: 3175017B |
|
| ||
| Anti-Human CD56 (clone NCAM16.2) – 176Yb | Fluidigm | Cat#: 3176008B |
|
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| Anti-Human CCR2 PE (clone K036C2) | Biolegend | Cat#: 357026; |
| RRID: AB_2562059 | ||
|
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| Anti-Human CD115 APC (clone 9-4D2-1E4) | Biolegend | Cat#: 347306; |
| RRID: AB_2562441 | ||
|
| ||
| Anti-Human CCR6 (clone G034E3) – 141Pr | Fluidigm | Cat#: 3141003A |
|
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| Anti-Human CD45RA (clone HI100) -143Nd | Fluidigm | Cat#: 3143006B |
|
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| Anti-Human CD38 (clone HIT2) -144Nd | Fluidigm | Cat#: 3144014B |
|
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| Anti-Human CD4 (clone RPA-T4) – 145Nd | Fluidigm | Cat#: 3145001B |
|
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| Anti-Human CD8a (clone RPA-T8) – 146Nd | Fluidigm | Cat#: 3146001B |
|
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| Anti-Human CD73 (clone AD2) | Biolegend | Cat#: 344002; |
| RRID: AB_2154067 | ||
|
| ||
| Anti-Human CD127 (clone A019D5) – 149Sm | Fluidigm | Cat#: 3149011B |
|
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| Anti-Human LAG3 (clone874501) -150Nd | Fluidigm | Cat#: 3150016B |
|
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| Anti-Human ICOS (clone DX29) – 151Eu | Fluidigm | Cat#: 3151008B |
|
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| Anti-Human TCRγδ (clone 11F2) – 152Sm | Fluidigm | Cat#: 3152008B |
|
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| Anti-Human TIM3 (clone F38-2E2) – 153Eu | Fluidigm | Cat#: 3153008B |
|
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| Anti-Human CD27 (clone L128) – 155Gd | Fluidigm | Cat#: 3155001B |
|
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| Anti-Human CXCR3 (clone G025H7) – 156Gd | Fluidigm | Cat#: 3156004B |
|
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| Anti-Human CCR4 (clone 205410) – 158Gd | Fluidigm | Cat#: 3158006A |
|
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| Anti-Human CD39 (clone A1) – 160Gd | Fluidigm | Cat#: 3160004B |
|
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| Anti-Human CTLA4 (clone 14D3) – 161Dy | Fluidigm | Cat#: 3161004B |
|
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| Anti-Human Foxp3 (clone PCH101) – 162Dy | Fluidigm | Cat#: 3162011A |
|
| ||
| Anti-Human 41BB (clone 4B4-1) | Biolegend | Cat #: 309802; |
| RRID: AB_314781 | ||
|
| ||
| Anti-Human CD161 (clone HP-3G10) – 164Dy | Fluidigm | Cat#: 3164009B |
|
| ||
| Anti-Human BTLA (clone MIH26) | Biolegend | Cat#: 344502; |
| RRID: AB_2043950 | ||
|
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| Anti-Human CCR7 (clone G043H7) – 167Er | Fluidigm | Cat#: 3167009A |
|
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| Anti-Human CD25 (clone 2A3) – 169Tm | Fluidigm | Cat#: 3169003B |
|
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| Anti-Human Granzyme B (clone GB11) – 171Yb | Fluidigm | Cat#: 3171002B |
|
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| Anti-Human GITR (clone 621) | Biolegend | Cat#: 311602; |
| AB_314885 | ||
|
| ||
| Anti-Human PD-1 (clone EH12.2H7) – 175Lu | Fluidigm | Cat#: 3175008B |
|
| ||
| Anti-Human CD57 (clone HCD57) | Biolegend | Cat#: 322302; |
| RRID: AB_535988 | ||
|
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| Anti-Human CD326 (clone 9C4) | Fluidigm | Cat#: 3141006B |
|
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| Anti-Human CD19 (clone HIB19) | Biolegend | Cat#: 302202; |
| RRID: AB_314232 | ||
|
| ||
| Anti-Human CD45RA (clone HI100) | Biolegend | Cat#: 304102; |
| RRID: AB_314406 | ||
|
| ||
| Anti-Human CD4 (clone RPA-T4) | Biolegend | Cat#: 300501; |
| RRID: AB_314069 | ||
|
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| Anti-Human CD8a (clone RAP-T8) | Biolegend | Cat#: 301002; |
| RRID: AB_314120 | ||
|
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| Anti-Human IL-1ß (clone H1b-98) | Biolegend | Cat#: 511602; |
| RRID: AB_1236518 | ||
|
| ||
| Anti-Human CD16 (clone 3G8) | Biolegend | Cat#: 302002; |
| RRID: AB_314202 | ||
|
| ||
| Anti-Human CD127 (clone A019D5) | Biolegend | Cat#: 351302; |
| RRID: AB_10718513 | ||
|
| ||
| Anti-Human CD1c (BDCA-1) | Biolegend | Cat#: 331502; |
| RRID: AB_1088995 | ||
|
| ||
| Anti-Human CD123 (clone 6H6) | Biolegend | Cat#: 306002; |
| RRID: AB_314576 | ||
|
| ||
| Anti-Human CD66b (clone G10F5) | Biolegend | Cat#: 305102; |
| RRID: AB_314494 | ||
|
| ||
| Anti-Human TNFα (clone Mab11) | Biolegend | Cat#: 502902; |
| RRID: AB_315254 | ||
|
| ||
| Anti-Human CD86 (clone IT2.2) | Biolegend | Cat#: 305402; |
| RRID: AB_314522 | ||
|
| ||
| Anti-Human CD27 (clone O323) | Biolegend | Cat#: 302802; |
| RRID: AB_314294 | ||
|
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| Anti-Human IL-6 (clone MQ2-13A5) | Fluidigm | Cat#: 501102; |
| RRID: AB_315150 | ||
|
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| Anti-Human IFNγ (clone B27) | Fluidigm | Cat#: 506502; |
| RRID: AB_315435 | ||
|
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| Anti-Human CCL3 (clone 93342) | R&D Systems | Cat#: MAB2701; |
| RRID: AB_2259652 | ||
|
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| Anti-Human CD14 (clone M5E2) | Biolegend | Cat#: 301802; |
| RRID: AB_314184 | ||
|
| ||
| Anti-Human CD56 (clone B159) | BD Biosciences | Cat#: 555514; |
| RRID: AB_395904 | ||
|
| ||
| Anti-Human CD169 (clone 7-239) | Biolegend | Cat#: 346002; |
| RRID: AB_2189031 | ||
|
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| Anti-Human CD68 (clone Y1/82A) | Biolegend | Cat#: 333802; |
| RRID: AB_1089058 | ||
|
| ||
| Anti-Human CCL4 (clone 24006) | R&D Systems | Cat#: MAB271; |
| RRID: AB_2071178 | ||
|
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| Anti-Human CD25 (clone M-A251) | Biolegend | Cat#: 356102; |
| RRID: AB_2561752 | ||
|
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| Anti-Human CD11c (clone Bu15) | Biolegend | Cat#: 337202; |
| RRID: AB_1236381 | ||
|
| ||
| Anti-Human CD3 (clone UCHT1) | Biolegend | Cat#: 300402; |
| RRID: AB_314056 | ||
|
| ||
| Anti-Human PD-L1 (clone 29E.2A3) | Biolegend | Cat#: 329702; |
| RRID: AB_940372 | ||
|
| ||
| Anti-Human CD38 (clone HB-7) | Biolegend | Cat#: 356602; |
| RRID: AB_2561794 | ||
|
| ||
| Anti-Human CD161 (clone HP-3G10) | Biolegend | Cat#: 339902; |
| RRID: AB_1501090 | ||
|
| ||
| Anti-Human CD206 (clone 15-2) | Biolegend | Cat#: 321102; |
| RRID: AB_571923 | ||
|
| ||
| Anti-Human IL-8 (clone E8N1) | Biolegend | Cat#: 511402; |
| RRID: AB_893460 | ||
|
| ||
| Anti-Human HLADR (clone L243) | Biolegend | Cat#: 307602; |
| RRID: AB_314680 | ||
|
| ||
| Anti-Human PD-1 (clone EH12.2H7) | Biolegend | Cat#: 329902; |
| RRID: AB_940488 | ||
|
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| Anti-Human Granzyme B (clone GB11) | ThermoFisher | Cat#: MA1-80734; |
| RRID: AB_931084 | ||
|
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| Anti-Human CD11b (clone ICRF44) | Fluidigm | Cat#: 3209003B |
|
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| Anti-Human CD3 (clone 2GV6) | Ventana | Cat#: 790-4341 |
|
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| Anti-Human CD8 (clone C8/144b) | Dako | Cat#: M7103 |
|
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| Anti-Human CD20 (clone L26) | Dako | Cat#: 0755 |
|
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| Anti-Human DC-LAMP (clone 1010E1.01) | Novus Biologicals | Cat#: DDX0191P |
|
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| Anti-Human CD163 (clone EPR4166(2)) | Abcam | Cat#: ab129202 |
|
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| Anti-Human FoxP3 (clone 236A/E7) | Abcam | Cat#: ab20034 |
|
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| Anti-Human PD-L1 (E1L3N) | CST | Cat#: 13684 |
|
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| Anti-Human Pan-Cytokeratins (clone Ae1/Ae3) | Dako | Cat#: ab27988 |
|
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| Anti-Human Ki-67 (clone 30-9) | Ventana | Cat#: 790-4286 |
|
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| Anti-Human Granzyme B (clone GrB-7) | Dako | Cat#: M723501-2 |
|
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| Anti-Human HLA-ABC (clone EMR8-5) | Abcam | Cat#: ab70328 |
|
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| Anti-Human CD68 (clone KP1) | Dako | Cat#: M081401-2 |
|
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| Biological Samples
| ||
| Blood, non-involved lung, and tumor tissue | Fresh resections from patients with informed consent for an IRB-approved study. Surgeries were performed by the Department of Cardiothoracic Surgery, Mount Sinai Hospital. | N/A |
|
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| Chemicals, Peptides, and Recombinant Proteins
| ||
| Brefeldin A | Sigma-Aldrich | Cat#: B7651 |
|
| ||
| Phorbol 12-myristate 13-acetate | Sigma-Aldrich | Cat#: 79346 |
|
| ||
| Ionomycin | Sigma-Aldrich | Cat#: I0634 |
|
| ||
| Cell-ID Intercalator-103Rh | Fluidigm | Cat#: 201103A |
|
| ||
| Collagenase from Clostridium Histolyticum, Type IV | Sigma-Aldrich | Cat#: C5138 |
|
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| Ficoll-Paque™ PLUS | GE Healthcare | Cat#: 17144003 |
|
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| Critical Commercial Assays
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| Foxp3 / Transcription Factor | eBioscience | Cat#: 00-5521-00 |
| Fixation/Permeabilization Concentrate and Diluent | ||
|
| ||
| Permeabilization Buffer (10X) | eBioscience | Cat#: 00-8333-56 |
|
| ||
| Cytofix/Cytoperm | BD Biosciences | Cat#: 51-2090KZ |
|
| ||
| Perm/Wash | BD Biosciences | Cat#: 51-2091KZ |
|
| ||
| Maxpar® X8 Multimetal Labeling Kit | Fluidigm | Cat#: 201300 |
|
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| Deposited Data | ||
|
| ||
| Raw Data Files from MARS-Seq | NCBI Gene | GEO: GSE97168 |
| Expression Omnibus | ||
|
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| Experimental Models: Cell Lines
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| Experimental Models: Organisms/Strains
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| Recombinant DNA
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| Sequence-Based Reagents
| ||
| Software and Algorithms
| ||
| R | SOURCE: R Core Team (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL | https://www.R-project.org/. |
|
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| tidyverse | Hadley Wickham (2016). tidyverse: Easily Install and Load ’Tidyverse’ Packages. R package version 1.0.0. | https://CRAN.R-project.org/package=tidyverse |
|
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| ggplot2 | H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2009. | https://cran.r-project.org/web/packages/ggplot2/index.html |
|
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| viSNE | Nat Biotechnol. 2013 Jun; 31(6): 545–552. | N/A |
|
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| Phenograph | Cell. 2015 Jul 2;162(1):184-97. | N/A |
|
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| Other | ||