organism: Homo sapiens
description: Protocols: 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).
attributes.tag: ELISA
attributes.value: ELISA: IgA positive; IgG positive
attributes.tag: ENA first public
attributes.value: 2021-03-23
attributes.tag: ENA last update
attributes.value: 2021-03-10
attributes.tag: External Id
attributes.value: SAMEA8226752
attributes.tag: INSDC center alias
attributes.value: ETH ZURICH
attributes.tag: INSDC center name
attributes.value: ETH ZURICH
attributes.tag: INSDC first public
attributes.value: 2021-03-23T08:54:54Z
attributes.tag: INSDC last update
attributes.value: 2021-03-10T12:42:37Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: IgA titer OD ratio
attributes.value: IgA titer OD ratio: 6.5
attributes.tag: IgG titer OD ratio
attributes.value: IgG titer OD ratio: 8.5
attributes.tag: Submitter Id
attributes.value: E-MTAB-10169:VDJ TC Sample 6
attributes.tag: age
attributes.value: 31
attributes.tag: body mass index
attributes.value: 23.2
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: T cell
attributes.tag: clinical history
attributes.value: previous Covid-19 infection for 9 days
attributes.tag: clinical information
attributes.value: no restrictions
attributes.tag: cohort
attributes.value: young patient group
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: disease staging
attributes.value: mild
attributes.tag: individual
attributes.value: individual 6
attributes.tag: infect
attributes.value: Severe acute respiratory syndrome coronavirus 2
attributes.tag: lateral flow test
attributes.value: lateral flow test: IgM negative; IgG positive
attributes.tag: organism part
attributes.value: blood
attributes.tag: protocol
attributes.value: VDJ-TCR enrichment
attributes.tag: sample name
attributes.value: E-MTAB-10169:VDJ TC Sample 6
attributes.tag: sampling timepoint
attributes.value: 34
attributes.tag: sex
attributes.value: male