ERX5227245 E-MTAB-10169:Sample 1_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913303 SAMEA8226731 Sample 1_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type mononuclear cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol gene expression ERX5227246 E-MTAB-10169:Sample 2_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913304 SAMEA8226732 Sample 2_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type mononuclear cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol gene expression ERX5227247 E-MTAB-10169:Sample 3_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913305 SAMEA8226733 Sample 3_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type mononuclear cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol gene expression ERX5227248 E-MTAB-10169:Sample 4_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913306 SAMEA8226734 Sample 4_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type mononuclear cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol gene expression ERX5227249 E-MTAB-10169:Sample 5_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913307 SAMEA8226735 Sample 5_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type mononuclear cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol gene expression ERX5227250 E-MTAB-10169:Sample 6_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913308 SAMEA8226736 Sample 6_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type mononuclear cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol gene expression ERX5227251 E-MTAB-10169:Sample 7_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913309 SAMEA8226737 Sample 7_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type mononuclear cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol gene expression ERX5227252 E-MTAB-10169:Sample 8_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913310 SAMEA8226738 Sample 8_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type mononuclear cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol gene expression ERX5227253 E-MTAB-10169:VDJ Sample 1_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913311 SAMEA8226739 VDJ Sample 1_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type B cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol VDJ-BCR enrichment ERX5227254 E-MTAB-10169:VDJ Sample 2_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913312 SAMEA8226740 VDJ Sample 2_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type B cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol VDJ-BCR enrichment ERX5227255 E-MTAB-10169:VDJ Sample 3_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913313 SAMEA8226741 VDJ Sample 3_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type B cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol VDJ-BCR enrichment ERX5227256 E-MTAB-10169:VDJ Sample 4_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913314 SAMEA8226742 VDJ Sample 4_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type B cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol VDJ-BCR enrichment ERX5227257 E-MTAB-10169:VDJ Sample 5_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913315 SAMEA8226743 VDJ Sample 5_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type B cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol VDJ-BCR enrichment ERX5227258 E-MTAB-10169:VDJ Sample 6_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913316 SAMEA8226744 VDJ Sample 6_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type B cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol VDJ-BCR enrichment ERX5227259 E-MTAB-10169:VDJ Sample 7_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913317 SAMEA8226745 VDJ Sample 7_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type B cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol VDJ-BCR enrichment ERX5227260 E-MTAB-10169:VDJ Sample 8_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913318 SAMEA8226746 VDJ Sample 8_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type B cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol VDJ-BCR enrichment ERX5227261 E-MTAB-10169:VDJ TC Sample 1_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913319 SAMEA8226747 VDJ TC Sample 1_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type T cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol VDJ-TCR enrichment ERX5227262 E-MTAB-10169:VDJ TC Sample 2_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913320 SAMEA8226748 VDJ TC Sample 2_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type T cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol VDJ-TCR enrichment ERX5227263 E-MTAB-10169:VDJ TC Sample 3_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913321 SAMEA8226749 VDJ TC Sample 3_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type T cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol VDJ-TCR enrichment ERX5227264 E-MTAB-10169:VDJ TC Sample 4_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913322 SAMEA8226750 VDJ TC Sample 4_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type T cell Experimental Factor: disease staging moderate Experimental Factor: cohort older patient group Experimental Factor: protocol VDJ-TCR enrichment ERX5227265 E-MTAB-10169:VDJ TC Sample 5_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913323 SAMEA8226751 VDJ TC Sample 5_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type T cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol VDJ-TCR enrichment ERX5227266 E-MTAB-10169:VDJ TC Sample 6_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913324 SAMEA8226752 VDJ TC Sample 6_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type T cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol VDJ-TCR enrichment ERX5227267 E-MTAB-10169:VDJ TC Sample 7_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913325 SAMEA8226753 VDJ TC Sample 7_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type T cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol VDJ-TCR enrichment ERX5227268 E-MTAB-10169:VDJ TC Sample 8_p ERP127548 PRJEB43580 A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients ERS5913326 SAMEA8226754 VDJ TC Sample 8_p RNA-Seq TRANSCRIPTOMIC SINGLE CELL PCR PBMC samples were thawed, washed in complete media (RPMI 1640, 10%(v/v) FBS) and pelleted by centrifugation. Cells were resuspended in 0.5 mL complete media, counted and treated with 10 U ml−1 DNAse I (Stemcell Technologies, #) for 15 min at RT in order to prevent cell clumping. After DNase I digestion, cells were washed twice in complete media, pelleted by centrifugation and resuspended in 0.5 mL flow cytometry buffer (PBS, 2%(v/v) FBS, 2 mM EDTA). The cell suspension was filtered through a 40 μM cell strainer prior to immunomagnetic isolation. As a first step, plasma cells were isolated using the EasySep Human CD138 Positive Selection Kit II (Stemcell Technologies, #17877) for analysis in a companion study (manuscript in preparation). The negative fraction of the above selections was divided into two aliquots that were subjected to negative immunomagnetic isolation of either B cells (EasySep Human Pan-B cell Enrichment Kit, Stemcell Technologies, #19554) or T cells (EasySep Human T cell Isolation Kit, Stemcell Technologies, #17951). After isolation, B cells and T cells were pelleted by centrifugation, resuspended in PBS, 0.4%(v/v) BSA, filtered through a 40 μM cell strainer and counted. T cells and B cells originating from the same patient were pooled in equal numbers and the final suspension was counted and assessed for viability using a fluorescent cell counter (Cellometer Spectrum, Nexcelom). Whenever possible, cells were adjusted to a concentration of 1×106 live cells/mL in PBS, 0.04%(v/v) BSA before proceeding with droplet generation. Encapsulation of lymphocytes and DNA-barcoded gel beads was performed using the Chromium controller (10x Genomics, PN-110203). Briefly, 1.4×104 to 1.7×104 cells (in reverse transcription mix) were loaded per channel for a targeted recovery of 8×103 to 1×104 cells per sample. Reverse transcription and preparation of single-cell transcriptome, BCR and TCR libraries was performed according to the manufacturer's instructions (CG000086 manual, RevM, 10x Genomics) and using the following kits: Chromium Single Cell 5' Library & Gel Bead Kit (PN-1000006), Chromium Single Cell 5' Library Construction Kit (PN-1000020), Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (PN-1000005), Chromium Single Cell V(D)J Enrichment Kit, Human B Cell (PN-1000016), Chromium Single Cell A Chip Kit (PN-1000009), Chromium i7 Multiplex Kit (PN-120262). Illumina NovaSeq 6000 Experimental Factor: cell type T cell Experimental Factor: disease staging mild Experimental Factor: cohort young patient group Experimental Factor: protocol VDJ-TCR enrichment