SRX11515803 GSM5465083 SRP329309 SRS9553619 GSM5465083 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465083 GSM5465083 GEO Accession GSM5465083 SRX11515804 GSM5465084 SRP329309 SRS9553618 GSM5465084 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465084 GSM5465084 GEO Accession GSM5465084 SRX11515805 GSM5465085 SRP329309 SRS9553620 GSM5465085 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465085 GSM5465085 GEO Accession GSM5465085 SRX11515806 GSM5465086 SRP329309 SRS9553621 GSM5465086 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465086 GSM5465086 GEO Accession GSM5465086 SRX11515807 GSM5465087 SRP329309 SRS9553622 GSM5465087 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465087 GSM5465087 GEO Accession GSM5465087 SRX11515808 GSM5465088 SRP329309 SRS9553623 GSM5465088 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465088 GSM5465088 GEO Accession GSM5465088 SRX11515809 GSM5465089 SRP329309 SRS9553624 GSM5465089 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465089 GSM5465089 GEO Accession GSM5465089 SRX11515810 GSM5465090 SRP329309 SRS9553625 GSM5465090 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465090 GSM5465090 GEO Accession GSM5465090 SRX11515811 GSM5465091 SRP329309 SRS9553626 GSM5465091 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465091 GSM5465091 GEO Accession GSM5465091 SRX11515812 GSM5465092 SRP329309 SRS9553627 GSM5465092 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465092 GSM5465092 GEO Accession GSM5465092 SRX11515813 GSM5465093 SRP329309 SRS9553628 GSM5465093 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465093 GSM5465093 GEO Accession GSM5465093 SRX11515814 GSM5465094 SRP329309 SRS9553629 GSM5465094 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465094 GSM5465094 GEO Accession GSM5465094 SRX11515815 GSM5465095 SRP329309 SRS9553630 GSM5465095 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465095 GSM5465095 GEO Accession GSM5465095 SRX11515816 GSM5465096 SRP329309 SRS9553631 GSM5465096 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465096 GSM5465096 GEO Accession GSM5465096 SRX11515817 GSM5465097 SRP329309 SRS9553633 GSM5465097 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465097 GSM5465097 GEO Accession GSM5465097 SRX11515818 GSM5465098 SRP329309 SRS9553632 GSM5465098 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465098 GSM5465098 GEO Accession GSM5465098 SRX11515819 GSM5465099 SRP329309 SRS9553634 GSM5465099 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465099 GSM5465099 GEO Accession GSM5465099 SRX11515820 GSM5465100 SRP329309 SRS9553635 GSM5465100 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465100 GSM5465100 GEO Accession GSM5465100 SRX11515821 GSM5465101 SRP329309 SRS9553636 GSM5465101 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465101 GSM5465101 GEO Accession GSM5465101 SRX11515822 GSM5465102 SRP329309 SRS9553638 GSM5465102 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465102 GSM5465102 GEO Accession GSM5465102 SRX11515823 GSM5465103 SRP329309 SRS9553637 GSM5465103 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465103 GSM5465103 GEO Accession GSM5465103 SRX11515824 GSM5465104 SRP329309 SRS9553640 GSM5465104 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465104 GSM5465104 GEO Accession GSM5465104 SRX11515825 GSM5465105 SRP329309 SRS9553639 SAMN20342766 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465105 GSM5465105 GEO Accession GSM5465105 SRX11515826 GSM5465106 SRP329309 SRS9553641 GSM5465106 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465106 GSM5465106 GEO Accession GSM5465106 SRX11515827 GSM5465107 SRP329309 SRS9553642 GSM5465107 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465107 GSM5465107 GEO Accession GSM5465107 SRX11515828 GSM5465108 SRP329309 SRS9553643 GSM5465108 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465108 GSM5465108 GEO Accession GSM5465108 SRX11515829 GSM5465109 SRP329309 SRS9553644 GSM5465109 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465109 GSM5465109 GEO Accession GSM5465109 SRX11515830 GSM5465110 SRP329309 SRS9553645 GSM5465110 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465110 GSM5465110 GEO Accession GSM5465110 SRX11515831 GSM5465111 SRP329309 SRS9553646 GSM5465111 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465111 GSM5465111 GEO Accession GSM5465111 SRX11515832 GSM5465112 SRP329309 SRS9553648 GSM5465112 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465112 GSM5465112 GEO Accession GSM5465112 SRX11515833 GSM5465113 SRP329309 SRS9553647 GSM5465113 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465113 GSM5465113 GEO Accession GSM5465113 SRX11515834 GSM5465114 SRP329309 SRS9553649 GSM5465114 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465114 GSM5465114 GEO Accession GSM5465114 SRX11515835 GSM5465115 SRP329309 SRS9553650 GSM5465115 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465115 GSM5465115 GEO Accession GSM5465115 SRX11515836 GSM5465116 SRP329309 SRS9553651 GSM5465116 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465116 GSM5465116 GEO Accession GSM5465116 SRX11515837 GSM5465117 SRP329309 SRS9553652 GSM5465117 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465117 GSM5465117 GEO Accession GSM5465117 SRX11515838 GSM5465118 SRP329309 SRS9553654 GSM5465118 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465118 GSM5465118 GEO Accession GSM5465118 SRX11515839 GSM5465119 SRP329309 SRS9553653 GSM5465119 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465119 GSM5465119 GEO Accession GSM5465119 SRX11515840 GSM5465120 SRP329309 SRS9553655 GSM5465120 OTHER TRANSCRIPTOMIC other Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465120 GSM5465120 GEO Accession GSM5465120 SRX11515841 GSM5465121 SRP329309 SRS9553656 GSM5465121 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465121 GSM5465121 GEO Accession GSM5465121 SRX11515842 GSM5465122 SRP329309 SRS9553657 GSM5465122 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465122 GSM5465122 GEO Accession GSM5465122 SRX11515843 GSM5465123 SRP329309 SRS9553658 GSM5465123 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465123 GSM5465123 GEO Accession GSM5465123 SRX11515844 GSM5465124 SRP329309 SRS9553659 GSM5465124 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465124 GSM5465124 GEO Accession GSM5465124 SRX11515845 GSM5465125 SRP329309 SRS9553660 GSM5465125 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465125 GSM5465125 GEO Accession GSM5465125 SRX11515846 GSM5465126 SRP329309 SRS9553661 GSM5465126 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465126 GSM5465126 GEO Accession GSM5465126 SRX11515847 GSM5465127 SRP329309 SRS9553662 GSM5465127 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465127 GSM5465127 GEO Accession GSM5465127 SRX11515848 GSM5465128 SRP329309 SRS9553664 GSM5465128 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465128 GSM5465128 GEO Accession GSM5465128 SRX11515849 GSM5465129 SRP329309 SRS9553663 GSM5465129 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465129 GSM5465129 GEO Accession GSM5465129 SRX11515850 GSM5465130 SRP329309 SRS9553666 GSM5465130 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465130 GSM5465130 GEO Accession GSM5465130 SRX11515851 GSM5465131 SRP329309 SRS9553665 GSM5465131 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465131 GSM5465131 GEO Accession GSM5465131 SRX11515852 GSM5465132 SRP329309 SRS9553667 GSM5465132 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465132 GSM5465132 GEO Accession GSM5465132 SRX11515853 GSM5465133 SRP329309 SRS9553668 GSM5465133 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465133 GSM5465133 GEO Accession GSM5465133 SRX11515854 GSM5465134 SRP329309 SRS9553669 GSM5465134 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465134 GSM5465134 GEO Accession GSM5465134 SRX11515855 GSM5465135 SRP329309 SRS9553670 GSM5465135 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465135 GSM5465135 GEO Accession GSM5465135 SRX11515856 GSM5465136 SRP329309 SRS9553672 GSM5465136 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465136 GSM5465136 GEO Accession GSM5465136 SRX11515857 GSM5465137 SRP329309 SRS9553671 GSM5465137 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465137 GSM5465137 GEO Accession GSM5465137 SRX11515858 GSM5465138 SRP329309 SRS9553673 GSM5465138 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465138 GSM5465138 GEO Accession GSM5465138 SRX11515859 GSM5465139 SRP329309 SRS9553674 GSM5465139 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465139 GSM5465139 GEO Accession GSM5465139 SRX11515860 GSM5465140 SRP329309 SRS9553675 GSM5465140 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465140 GSM5465140 GEO Accession GSM5465140 SRX11515861 GSM5465141 SRP329309 SRS9553676 GSM5465141 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465141 GSM5465141 GEO Accession GSM5465141 SRX11515862 GSM5465142 SRP329309 SRS9553677 GSM5465142 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465142 GSM5465142 GEO Accession GSM5465142 SRX11515863 GSM5465143 SRP329309 SRS9553678 GSM5465143 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465143 GSM5465143 GEO Accession GSM5465143 SRX11515864 GSM5465144 SRP329309 SRS9553679 GSM5465144 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465144 GSM5465144 GEO Accession GSM5465144 SRX11515865 GSM5465145 SRP329309 SRS9553681 GSM5465145 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465145 GSM5465145 GEO Accession GSM5465145 SRX11515866 GSM5465146 SRP329309 SRS9553680 GSM5465146 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465146 GSM5465146 GEO Accession GSM5465146 SRX11515867 GSM5465147 SRP329309 SRS9553682 GSM5465147 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465147 GSM5465147 GEO Accession GSM5465147 SRX11515868 GSM5465148 SRP329309 SRS9553684 GSM5465148 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465148 GSM5465148 GEO Accession GSM5465148 SRX11515869 GSM5465149 SRP329309 SRS9553683 GSM5465149 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465149 GSM5465149 GEO Accession GSM5465149 SRX11515870 GSM5465150 SRP329309 SRS9553685 GSM5465150 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465150 GSM5465150 GEO Accession GSM5465150 SRX11515871 GSM5465151 SRP329309 SRS9553686 GSM5465151 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465151 GSM5465151 GEO Accession GSM5465151 SRX11515872 GSM5465152 SRP329309 SRS9553687 GSM5465152 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465152 GSM5465152 GEO Accession GSM5465152 SRX11515873 GSM5465153 SRP329309 SRS9553688 GSM5465153 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465153 GSM5465153 GEO Accession GSM5465153 SRX11515874 GSM5465154 SRP329309 SRS9553689 GSM5465154 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465154 GSM5465154 GEO Accession GSM5465154 SRX11515875 GSM5465155 SRP329309 SRS9553690 GSM5465155 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465155 GSM5465155 GEO Accession GSM5465155 SRX11515876 GSM5465156 SRP329309 SRS9553692 GSM5465156 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465156 GSM5465156 GEO Accession GSM5465156 SRX11515877 GSM5465157 SRP329309 SRS9553691 GSM5465157 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465157 GSM5465157 GEO Accession GSM5465157 SRX11515878 GSM5465158 SRP329309 SRS9553693 GSM5465158 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465158 GSM5465158 GEO Accession GSM5465158 SRX11515879 GSM5465159 SRP329309 SRS9553694 GSM5465159 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465159 GSM5465159 GEO Accession GSM5465159 SRX11515880 GSM5465160 SRP329309 SRS9553695 GSM5465160 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465160 GSM5465160 GEO Accession GSM5465160 SRX11515881 GSM5465161 SRP329309 SRS9553696 GSM5465161 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465161 GSM5465161 GEO Accession GSM5465161 SRX11515882 GSM5465162 SRP329309 SRS9553697 GSM5465162 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465162 GSM5465162 GEO Accession GSM5465162 SRX11515883 GSM5465163 SRP329309 SRS9553698 GSM5465163 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465163 GSM5465163 GEO Accession GSM5465163 SRX11515884 GSM5465164 SRP329309 SRS9553700 GSM5465164 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465164 GSM5465164 GEO Accession GSM5465164 SRX11515885 GSM5465165 SRP329309 SRS9553699 GSM5465165 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465165 GSM5465165 GEO Accession GSM5465165 SRX11515886 GSM5465166 SRP329309 SRS9553703 GSM5465166 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465166 GSM5465166 GEO Accession GSM5465166 SRX11515887 GSM5465167 SRP329309 SRS9553702 GSM5465167 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465167 GSM5465167 GEO Accession GSM5465167 SRX11515888 GSM5465168 SRP329309 SRS9553701 GSM5465168 RNA-Seq TRANSCRIPTOMIC cDNA Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse. Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols. Illumina NovaSeq 6000 gds 305465168 GSM5465168 GEO Accession GSM5465168