single cell RNAseq of peripheral CD4+ T cells in the context SARS-CoV-2 infection
CD4+ T cells play a fundamental role in host defenses against viruses by orchestrating B cell development and/or by directly targeting pathogens. This dataset aimed at understanding the molecular profile of CD4+ T cells in the context of an acute and severe SARS-CoV-2 infection. The analyzed patient was recruited at Henri Mondor University Hospital (AP-HP, Paris France) in March 2020, and required oxygen as treatment. Peripheral (CD14-CD56-CD123-CD19-CD3+CD4+CD45RA-PD-1high) T cells were FACS-sorted using a Sony MA900 in PBS/0.08% FCS. 1.105 cells were obtained and 20000 were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. The scRNA-seq libraries were generated using the Chromium Next GEM Single Cell V(D)J Reagent Kit v.1.1 with Feature Barcoding (10x Genomics) according to the manufacturer's protocol. PBMCs were initially isolated from venous blood samples via standard density gradient centrifugation and used after cryopreservation at -150°C. Cells were thawed using RPMI-1640 (Gibco) 10% FBS, washed twice and incubated with fluorochrome-conjugated antibody cocktail and viable cells were identified using a LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Thermo Fisher Scientific) incubated with conjugated antibodies used for cell sorting (CD3/CD4/CD14/CD19/CD45/CD56/CD123/PD-1) as well as a panel of barcoded TotalSeqC® antibodies (CD11c/CD21/CD27/CD38/CD49d/CD69/CD71/CD73/CD95/CD103/CD138/CD305/CD307d/CD307e/CXCR3/CXCR4/CXCR5/HLA-DR/ICOS/ITB7/LAG-3/NKG2D/TIM3). A single sort was performed for this patient and 5'-transcriptomic, VDJ and ADT libraries were sequenced .