Lysis plates for single cell mRNA sequencing were prepared as previous described2 (link). 96-well lysis plates were used for cells from the blood and mouse samples and contained 4 μL of lysis buffer instead of 0.4 μL.
Following negative selection against immune and endothelial cells by MACS, the remaining human lung cells were incubated with FcR Block (Becton Dickinson (BD) 564219) for 5 minutes and stained with directly conjugated anti-human CD45 (Biolegend 304006) and EPCAM (eBioscience 25–9326-42) antibodies on a Nutator for 30 minutes at the manufacturer’s recommended concentration. Cells were then pelleted (300 x g, 5 minutes, 4°C), washed with FACS buffer three times, then incubated with cell viability marker Sytox blue (1:3000, ThermoFisher S34857) and loaded onto a Sony SH800S cell sorter. Living single cells (Sytox blue-negative) were sorted into lysis plates based on three gates: EPCAM+CD45− (designated “epithelial”), EPCAM−CD45+ (designated “immune”), and EPCAM−CD45− (designated “endothelial or stromal”).
Immune cells from subject matched blood were incubated with FcR Block and Brilliant Violet buffer (BD 563794) for 20 minutes and then stained with directly conjugated anti-human CD3 (BD 563548), CD4 (BD 340443), CD8 (BD 340692), CD14 (BD 557831), CD19 (Biolegend 302234), CD47 (BD 563761), CD56 (BD 555516), and CD235a (BD 559944) antibodies for 30 minutes at the manufacturer’s recommended concentration. Cells were pelleted (300 x g, 5 minutes, 4°C), washed with FACS buffer twice, and then incubated with the viability marker propidium iodide and loaded onto a BD FACSAria II cell sorter. Living (propidium iodide-negative) single, non-red blood (CD235a−) cells were sorted into lysis plates along with specific immune populations: B cells (CD19+CD3−), CD8+ T cells (CD8+), CD4+ T cells (CD4+), NK cells (CD19−CD3−CD56+CD14−), classical monocytes (CD19− CD3−CD56−CD14+). After sorting, plates were quickly sealed, vortexed, spun down for 1 minute at 1000 x g, snap frozen on dry ice, and stored at −80 until cDNA synthesis.
Mouse cells were incubated with the viability marker DAPI and loaded onto a BD Influx cell sorter. Living (DAPI-negative) single cells were sorted into lysis plates based on presence or absence of the fluorescent lineage label (mEGFP for Axin2-Cre-ERT2, ZsGreen1 for Tbx4-LME-Cre).
Immune cells for bulk mRNA sequencing were incubated with FcR Block for 20 minutes and then stained with one of six panels of directly conjugated antibodies for 30 minutes at the manufacturers recommended concentration: anti-human CD16 (BD 558122), CD123 (BD 560826), CCR3 (R&D FAB155F), ITGB7 (BD 551082), CD3 (BD 555341), CD14 (Invitrogen MHCD1406), CD19 (BD 555414), and CD56 (BD 555517) (“basophils, neutrophils and eosinophils”); anti-human CD16 (BD 558122), CD14 (BD 347497), CD4 (BD 340443), CD3 (BD 555341), CD8 (BD 555368), CD19 (BD 555414), and CD56 (BD 555517) (“classical and nonclassical monocytes”); anti-human CD16 (BD 558122), CD1c (Miltenyi Biotec 130–098-007), CD11c (BD 340544), CCR3 (R&D FAB155F), CD123 (BD 560826), HLA-DR (BD 335796), CD3 (BD 555341), CD4 (BD 555348), CD8 (BD 555368), CD14 (Invitrogen MHCD1406), CD19 (BD 555414), and CD56 (BD 555517) (“pDCs, mDCs, CD16+ DCs”); anti-human IgM/IgD (BD 555778), CD19 (BD 557835), CD27 (BD 558664), CD20 (BD 335794), CD3 (BD 555341), CD4 (BD 555348), CD14 (Invitrogen MHCD1406), and CD56 (BD 555517) (“B cells”); anti-human CD16 (BD 558122), CD57 (BD 347393), CD56 (BD 557747), CD3 (BD 555341), CD4 (BD 555348), CD14 (Invitrogen MHCD1406), and CD19 (BD 555414) (“NK cells”); and anti-human CD45RA (Biolegend 304118), CCR7 (R&D FAB197F), CD62L (BD 555544), CD45RO (BD Pharmingen 560608), CD4 (BD 340443), CD8 (BD 340584), CD11b (BD 555389), CD14 (Invitrogen MHCD1406), CD19 (BD 555414), CD56 (BD 555517) (“T cells”). Cells were washed with FACS buffer twice, incubated with the viability marker propidium iodide and loaded onto a BD FACSAria II cell sorter. 40,000 cells from 21 canonical immune populations (Supplementary Table 3 ) were sorted in duplicate into Trizol LS (Invitrogen 10296010).
After sorting, all plates and samples were quickly sealed, vortexed, spun down for 1 minute at 1000 x g and then snap frozen on dry ice and stored at −80 until cDNA synthesis.
Following negative selection against immune and endothelial cells by MACS, the remaining human lung cells were incubated with FcR Block (Becton Dickinson (BD) 564219) for 5 minutes and stained with directly conjugated anti-human CD45 (Biolegend 304006) and EPCAM (eBioscience 25–9326-42) antibodies on a Nutator for 30 minutes at the manufacturer’s recommended concentration. Cells were then pelleted (300 x g, 5 minutes, 4°C), washed with FACS buffer three times, then incubated with cell viability marker Sytox blue (1:3000, ThermoFisher S34857) and loaded onto a Sony SH800S cell sorter. Living single cells (Sytox blue-negative) were sorted into lysis plates based on three gates: EPCAM+CD45− (designated “epithelial”), EPCAM−CD45+ (designated “immune”), and EPCAM−CD45− (designated “endothelial or stromal”).
Immune cells from subject matched blood were incubated with FcR Block and Brilliant Violet buffer (BD 563794) for 20 minutes and then stained with directly conjugated anti-human CD3 (BD 563548), CD4 (BD 340443), CD8 (BD 340692), CD14 (BD 557831), CD19 (Biolegend 302234), CD47 (BD 563761), CD56 (BD 555516), and CD235a (BD 559944) antibodies for 30 minutes at the manufacturer’s recommended concentration. Cells were pelleted (300 x g, 5 minutes, 4°C), washed with FACS buffer twice, and then incubated with the viability marker propidium iodide and loaded onto a BD FACSAria II cell sorter. Living (propidium iodide-negative) single, non-red blood (CD235a−) cells were sorted into lysis plates along with specific immune populations: B cells (CD19+CD3−), CD8+ T cells (CD8+), CD4+ T cells (CD4+), NK cells (CD19−CD3−CD56+CD14−), classical monocytes (CD19− CD3−CD56−CD14+). After sorting, plates were quickly sealed, vortexed, spun down for 1 minute at 1000 x g, snap frozen on dry ice, and stored at −80 until cDNA synthesis.
Mouse cells were incubated with the viability marker DAPI and loaded onto a BD Influx cell sorter. Living (DAPI-negative) single cells were sorted into lysis plates based on presence or absence of the fluorescent lineage label (mEGFP for Axin2-Cre-ERT2, ZsGreen1 for Tbx4-LME-Cre).
Immune cells for bulk mRNA sequencing were incubated with FcR Block for 20 minutes and then stained with one of six panels of directly conjugated antibodies for 30 minutes at the manufacturers recommended concentration: anti-human CD16 (BD 558122), CD123 (BD 560826), CCR3 (R&D FAB155F), ITGB7 (BD 551082), CD3 (BD 555341), CD14 (Invitrogen MHCD1406), CD19 (BD 555414), and CD56 (BD 555517) (“basophils, neutrophils and eosinophils”); anti-human CD16 (BD 558122), CD14 (BD 347497), CD4 (BD 340443), CD3 (BD 555341), CD8 (BD 555368), CD19 (BD 555414), and CD56 (BD 555517) (“classical and nonclassical monocytes”); anti-human CD16 (BD 558122), CD1c (Miltenyi Biotec 130–098-007), CD11c (BD 340544), CCR3 (R&D FAB155F), CD123 (BD 560826), HLA-DR (BD 335796), CD3 (BD 555341), CD4 (BD 555348), CD8 (BD 555368), CD14 (Invitrogen MHCD1406), CD19 (BD 555414), and CD56 (BD 555517) (“pDCs, mDCs, CD16+ DCs”); anti-human IgM/IgD (BD 555778), CD19 (BD 557835), CD27 (BD 558664), CD20 (BD 335794), CD3 (BD 555341), CD4 (BD 555348), CD14 (Invitrogen MHCD1406), and CD56 (BD 555517) (“B cells”); anti-human CD16 (BD 558122), CD57 (BD 347393), CD56 (BD 557747), CD3 (BD 555341), CD4 (BD 555348), CD14 (Invitrogen MHCD1406), and CD19 (BD 555414) (“NK cells”); and anti-human CD45RA (Biolegend 304118), CCR7 (R&D FAB197F), CD62L (BD 555544), CD45RO (BD Pharmingen 560608), CD4 (BD 340443), CD8 (BD 340584), CD11b (BD 555389), CD14 (Invitrogen MHCD1406), CD19 (BD 555414), CD56 (BD 555517) (“T cells”). Cells were washed with FACS buffer twice, incubated with the viability marker propidium iodide and loaded onto a BD FACSAria II cell sorter. 40,000 cells from 21 canonical immune populations (
After sorting, all plates and samples were quickly sealed, vortexed, spun down for 1 minute at 1000 x g and then snap frozen on dry ice and stored at −80 until cDNA synthesis.