|
|
|
|
Antibody
|
| Goat anti-human IgG(H+L)/HRP |
Fisher Scientific |
Cat # 31412 |
| Goat anti-mouse IgG(H+L)/HRP |
Fisher Scientific |
Cat # A-10677 |
| PE–anti-human FC antibody |
Biolegend |
Cat#409304 |
| Anti-SARS-CoV-2 mAb (Clone 2) |
Sidi Chen Lab |
Peng et al. 2022 |
| Anti-SARS-CoV-2 mAb (Clone 6) |
Sidi Chen Lab |
Peng et al. 2022 |
| Anti-SARS-CoV-2 mAb (Clone 13A) |
Sidi Chen Lab |
Peng et al. 2022 |
| Anti-Omicron mAb (MB.02) |
Sidi Chen Lab |
This study |
| Anti-Omicron mAb (MB.08) |
Sidi Chen Lab |
This study |
| Anti-Omicron mAb (PB.03) |
Sidi Chen Lab |
This study |
|
|
|
|
Bacterial and Virus Strains
|
|
|
| B.1.1.529 variant (Omicron) pseudovirus |
Sidi Chen Lab |
This study |
| B.1.617 variant (Delta) pseudovirus |
Sidi Chen Lab |
This study |
| Omicron sub-variant BA.1.1 pseudovirus |
Sidi Chen Lab |
This study |
| Omicron sub-variant BA.2 pseudovirus |
Sidi Chen Lab |
Fang et al. 2022 |
| Omicron sub-variant BA.2.12.1pseudovirus |
Sidi Chen Lab |
This study |
| Omicron sub-variant BA.3 pseudovirus |
Sidi Chen Lab |
This study |
| Omicron sub-variant BA.5 pseudovirus |
Sidi Chen Lab |
This study |
|
|
|
|
Chemicals, Peptides, and Recombinant Proteins
|
|
|
| DPBS |
Kline |
Cat#14190144 |
| RPMI 1640 Medium |
Gibco |
Cat#11875-093 |
| Fetal Bovine Serum |
Sigma Aldrich |
Cat#F4135-500ML |
| DMEM |
Kline |
Cat#11995065 |
| Penicillin-Streptomycin (10,000 U/mL) |
Gibco |
Cat#15140122 |
| Glutamax |
Med School |
Cat#35050061 |
| TWEEN-20 |
Sigma-Aldrich |
Cat# P1379 |
| 50TS microplate washer |
Fisher Scientific |
Cat#BT50TS16 |
| ACK Lysing Buffer |
Lonza |
Cat#BP10-548E |
| Gibson Assembly Master Mix - 50 rxn |
NEB |
Cat#E2611L |
| HiscribeTM T7 ARCA mRNA Kit (with tailing) |
NEB |
Cat#E2060S |
| Phusion Flash High-Fidelity PCR Master Mix |
ThermoFisher |
Cat#F548L |
| E-Gel™ Low Range Quantitative DNA Ladder |
ThermoFisher |
Cat#12373031 |
| QIAquick Gel Extraction Kit |
Qiagen |
Cat#28706 |
| EndoFree® Plasmid Maxi Kit |
Qiagen |
Cat#12362 |
| Quant-iT™ RiboGreen™ RNA Assay Kit |
ThermoFisher |
Cat#R11490
|
| Tetramethylbenzidine substrate |
Biolegend |
Cat#421101 |
| RNeasy® Plus Mini Kit |
Qiagen |
Cat#74134 |
| Library Construction Kit, 16 rxns |
10X Genomics |
Cat#1000190 |
| Live/Dead aqua fixable stain |
Thermofisher |
Cat#L34976
|
| BSA |
Fisher Scientific |
BP1600-100 |
| 100 μm cell strainer |
Corning |
Cat#352360 |
| 40 μm cell strainer |
Corning |
Cat#352340 |
| Bovine Serum Albumin |
Sigma Aldrich |
Cat#A9418-100G |
| EDTA |
Kline |
Cat#AB00502-01000 |
| Tris-Cl pH 8.5 |
TENOVA |
Cat#15085 |
| N1-Methylpseudouridine-5’-Triphosphate - (N-1081) |
TriLink (NC) |
Cat#N-1081-1 |
| Sucrose |
Thomas |
Cat#C987K85 (EA/1) |
| Lymphoprep |
STEMCELL |
Cat # 07851 |
| Memory B Cell Isolation Kit, mouse |
Miltenyi Biotec |
Cat#130-095-838 |
| CD138+ Plasma Cell Isolation Kit, mouse |
Miltenyi Biotec |
Cat#130-095-530 |
| rProtein A Sepharose Fast Flow |
GE healthcare |
Cat#17-1279-01 |
| Octet Anti-Penta-HIS (HIS1K) Biosensors |
SARTORIUS |
Cat#18-5120 |
| Octet Anti-Human Fc Capture (AHC) Biosensors |
SARTORIUS |
Cat#18-5060 |
| SARS-COV RBD protein (His-tag) |
Fisher Scientific |
Cat#50-196-4017 |
| SARS-COV2 Delta RBD protein (His-tag) |
SINO |
Cat#40592-V08H90 |
| SARS-COV2 Omicron RBD protein (His-tag) |
SINO |
Cat#40592-V08H121 |
| MERS-COV RBD protein (His-tag) |
Fisher Scientific |
Cat#50-201-9463 |
| ACE2 protein, Human, Recombinant (His Tag) |
SINO |
Cat # 10108-H08H |
| ACE2 protein, Human, Recombinant (mFc Tag) |
SINO |
Cat # 10108-H05H |
| Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns PN-1000263 |
10X Genomics |
Cat#PN-1000263 |
| Chromium Next GEM Chip K Single Cell Kit, 16 rxns PN-1000287 |
10X Genomics |
Cat#PN-1000287 |
| CD22-ECD protein (His-tag) |
SINO |
Cat#11958-HNAH |
|
|
|
|
Experimental Models: Cell Lines
|
|
|
| HEK293T |
ThermoFisher |
Catalog Number: R70007
|
| K562-CD22-O/E-GFP |
Sidi Chen Lab |
This study |
| K562-GPRC5D-O/E-GFP |
Sidi Chen Lab |
This study |
|
|
|
|
Experimental Models: Organisms/Strains
|
|
|
| ATX-GK+ Human Transgenic Mouse |
Alloy |
N/A |
|
|
|
|
Oligo name and sequence
|
|
|
| Various oligos (See Table S3 - supplemental oligos file) |
Sidi Chen Lab |
This study |
|
|
|
|
Recombinant DNA
|
|
|
| pcDNA3.1 plasmids |
Addgene |
Cat# V790-20 |
| pHIVNLGagPol |
Schmidt et al., 2020 |
Gift from Dr Bieniasz’ lab |
| pCCNanoLuc2AEGFP |
Schmidt et al., 2020 |
Gift from Dr Bieniasz’ lab |
| pSARS-CoV-2 SΔ19 |
Schmidt et al., 2022 |
Gift from Dr Bieniasz’ lab |
| pFZ47 (B.1.1.529 variant (6P)) |
Sidi Chen Lab |
Fang et al. 2022 |
| pVP29b (B.1.617 variant (6P)) |
Sidi Chen Lab |
Peng et al. 2022 |
| pCCNanoLuc2AEGFP plasmid |
Schmidt et al. |
Gift from Dr Bieniasz’ lab |
| Polyethylenimine |
POLYSCIENCES INC |
Cat#24765-1 |
| pFZ57 (Omicron BA.2 subvariant (6P)) |
Sidi Chen Lab |
Fang et al. 2022 |
| pPR158 (Omicron BA.1.1 subvariant (6P)) |
Sidi Chen Lab |
This study |
| pPR185 (Omicron BA.2.12.1 subvariant (6P)) |
Sidi Chen Lab |
This study |
| pPR186 (Omicron BA.3 subvariant (6P)) |
Sidi Chen Lab |
This study |
| pPR187 (Omicron BA.5 subvariant (6P)) |
Sidi Chen Lab |
This study |
| pZF46 (B.1.1.529 Omicron spike hexapro mRNA) |
Sidi Chen Lab |
Fang et al. 2022 |
| pPR128 (CD22-mRNA) |
Sidi Chen Lab |
This study |
| pPR109 (GPRC5D-mRNA) |
Sidi Chen Lab |
This study |
|
|
|
|
Software and Algorithms
|
|
|
| FlowJo software 9.9.6 |
FlowJo, LLC |
https://www.flowjo.com
|
| GraphPad Prism 8.0 |
GraphPad Software Inc |
https://www.graphpad.com/scientific-software/prism/
|
| Pymol |
Schrödinger |
http://www.pymol.org/
|
| Cell Ranger v3.1.0 |
10X Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation
|
| Loupe V(D)J Browser |
10X Genomics |
https://support.10xgenomics.com/single-cell-vdj/software/visualization/latest/installation
|
| R |
R project |
https://www.r-project.org
|
| plyr R package |
Wickham. (2011). Journal of Statistical Software |
http://www.jstatsoft.org/v40/i01/
|
| dplyr R package |
Wickham et al., (2021). dplyr: A Grammar of Data Manipulation. R package version 1.0.7 |
https://CRAN.R-project.org/package=dplyr
|
| ggplot2 R package |
Wickham. (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York |
https://ggplot2.tidyverse.org
|
| stringr R package |
Hadley Wickham (2019). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.4.0 |
https://CRAN.R-project.org/package=stringr
|
| Circlize R package |
Gu et al., Bioinformatics, 2014 |
https://cran.r-project.org/package=circlize
|
| Pheatmap R package |
Kolde, 2019 |
https://cran.r-project.org/package=pheatmap
|
|
|
|
|
Deposited Data
|
|
|
| Single cell BCR-seq |
This study |
GEO: GSE203030
|
| Flow data |
This study |
Mendeley Data, DOI: 10.17632/4dcgs8mvzx.3
|
|
Other
|
|
|
|
|
|
