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. 2021 Oct 23;24(11):103325. doi: 10.1016/j.isci.2021.103325
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

smCD3-APC-H7 (clone SK7) Becton Dickinson (BD) Cat# 560176; RRID:AB_1645475
CD19-PC7 (clone J3-119) Becton Dickinson (BD) Cat# IM3628
CD20-V450 (clone 2H7) BioLegend Cat# 302320; RRID:AB_10638575
CD27-BV605 (clone L128) Becton Dickinson (BD) Cat# 562656
CD38-APC-R700 (clone HIT2) Becton Dickinson (BD) Cat# 564980

Biological samples

Peripheral blood of patients with active COVID-19 disease and after recovery This paper N/A
Peripheral blood of healthy individuals before and after vaccination with the seasonal flu vaccine (VaxxigripTetra2020/2021) This paper N/A

Chemicals, peptides, and recombinant proteins

Phusion HS II Thermo Fisher Cat# 564980

Critical commercial assays

LEGENDplex Human B Cell Panel (13-plex) BioLegend Cat# 740527
Anti-SARS-CoV-2-ELISA IgA Euroimmun AG Cat# EI 2606-9601 A
Anti-SARS-CoV-2-ELISA IgG Euroimmun AG Cat# EI 2606-9601 G
Anti-SARS-CoV-2-ELISA NCP Euroimmun AG Cat# EI 2606-9601-2 G
Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1 10X Genomics Cat# 1000167
Tube, Dynabeads™ MyOne™ SILANE 10X Genomics Cat# 2000048
Chromium Next GEM Chip G Single Cell Kit 10X Genomics Cat# 1000127
Chromium Single Cell V(D)J Enrichment Kit, Human B Cell 10X Genomics Cat# 1000016
Chromium Single Cell 5' Library Construction Kit, 10X Genomics Cat# 1000020
Single Index Kit T Set A 10X Genomics Cat# 1000213
ANAScreen Orgentec Cat# ORG 538
Rheumatoid Factor Screen Orgentec Cat# ORG 522S
Anti-Phospholipid Screen IgG/IgM Orgentec Cat# ORG 529

Deposited data

NGS single-cell RNA sequencing data This paper EMBL-EBI Array Express: E-MTAB-11011
IGH NGS Sequencing data from COVID-19 patients iReceptor Public Archive ID IR-Binder-000001
NGS Sequencing data of SARS-CoV-2-specific BCRs Ehling et al. (2021)
NGS Sequencing data of SARS-CoV-2-specific BCRs Galson et al. (2020)
NGS Sequencing data of SARS-CoV-2-specific BCRs Vita et al. (2019)
NGS Sequencing data of human B cells Dunn-Walters Lab (Stewart et al., 2021) EMBL-EBI: E-MTAB-9544

Oligonucleotides

BIOMED2-FR1 (IGH) van Dongen et al. (2003) N/A

Software and algorithms

R Studio version 3.5.1 RStudio, Boston, USA https://rstudio.com/products/rstudio/
GraphPad Prism 8.0.2 GraphPad Software, La Jolla, CA, USA https://www.graphpad.com/scientificsoftware/prism/
FlowJo v10 Becton Dickinson https://www.flowjo.com/solutions/flowjo
MiXCR (3.0.8) Bolotin et al. (2015) https://mixcr.readthedocs.io/en/master/
Cell Ranger software (v3.1.0) 10X Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Seurat (v 3.2.0) Satija Lab https://satijalab.org/seurat/
Slingshot 1.4.0 Street et al. (2018) https://bioconductor.org/packages/release/bioc/html/slingshot.html
IMGT/HighV-QUEST Brochet et al., 2008 http://www.imgt.org/HighV-QUEST/home.action
FastTreeMP Price et al., 2009 http://www.microbesonline.org/fasttree/
Archaeopteryx viewer (0.9928 beta) Han and Zmasek, 2009 https://sites.google.com/site/cmzmasek/home/software/archaeopteryx