| Antibodies, conventional flow cytometry, and sorting |
|
|
|
| Anti-Human CCR7 Alexa Fluor 488 |
BioLegend |
G043H7; Cat No.: 353205; RRID:AB_10918624 |
| Anti-Human CCR7 APC-Cy7 |
BioLegend |
G043H7; Cat No.: 353212; RRID:AB_10916390 |
| Anti-Human CD103 BUV395 |
BD Biosciences |
Ber-act8; Cat No.: 564346; RRID:AB_2738759 |
| Anti-Human CD103 BV421 |
BD Biosciences |
Ber-act8; Cat No.: 566257; RRID:AB_2739635 |
| Anti-Human CD107a BUV395 |
BD Biosciences |
H4A3; Cat No.: 565113; RRID:AB_2739073 |
| Anti-Human CD14 PerCP-Cy5.5 |
BD Biosciences |
M5E2; Cat No.: 550787; RRID:AB_393884 |
| Anti-Human CD19 PerCP-Cy5.5 |
Tonbo |
HIB19; Cat No.: 65-0199; RRID:AB_2621888 |
| Anti-Human CD3 BUV496 |
BD Biosciences |
UCHT1; Cat No.: 612940; RRID:AB_2870222 |
| Anti-Human CD3 BV650 |
BioLegend |
OKT3; Cat No.: 317323; RRID:AB_2563352 |
| Anti-Human CD4 BUV737 |
BD Biosciences |
SK3; Cat No.: 564305; RRID:AB_2713927 |
| Anti-Human CD4 PE-Cy7 |
Tonbo |
RPA-T4; Cat No.: 60-0049; RRID:AB_2621831 |
| Anti-Human CD45 Alexa Fluor 700 |
BioLegend |
HI30; Cat No.: 304023; RRID:AB_493761 |
| Anti-Human CD45 BV711 |
BioLegend |
HI30; Cat No.: 304050; RRID:AB_2563466 |
| Anti-Human CD45RA Alexa Fluor 700 |
BioLegend |
HI100; Cat No.: 304120; RRID:AB_493763 |
| Anti-Human CD45RA BV605 |
BioLegend |
HI100; Cat No.: 304134; RRID:AB_2563814 |
| Anti-Human CD56 PE-Cy5 |
BioLegend |
5.1H11; Cat No.: 362515; RRID:AB_2564088 |
| Anti-Human CD69 BV711 |
BioLegend |
FN50; Cat No.: 310944; RRID:AB_2566466 |
| Anti-Human CD8 BUV496 |
BD Biosciences |
RPA-T8; Cat No.: 564805; RRID:AB_2869614 |
| Anti-Human CD8 BV510 |
BioLegend |
SK1; Cat No.: 344732; RRID:AB_2564624 |
| Anti-Human GzmB Alexa Fluor 700 |
BD Biosciences |
GB11; Cat No.: 560213; RRID:AB_1645453 |
| Anti-Human IFN-γ BB700 |
BD Biosciences |
B27; Cat No.: 566394; RRID:AB_2744484 |
| Anti-Human Perforin BV510 |
BioLegend |
dG9; Cat No.: 308120; RRID:AB_2563829 |
| Anti-Human TNF-α PE-Cy7 |
BD Biosciences |
MAb11; Cat No.: 557647; RRID:AB_396764 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| LIVE/DEAD Fixable Blue Dead Cell Stain |
Thermo Fisher Scientific |
Cat No.: L23105
|
| Fixable Viability Dye eFluor 780 |
Thermo Fisher Scientific |
Cat No.: 65-0865-18 |
| Human TruStain FcX |
BioLegend |
Cat No.: 422302; RRID:AB_2818986 |
| RPMI 1640 |
Corning |
Cat No.: 10-040-CM |
|
| Human HLA-multimer reagents |
|
|
|
| HLA-A*0101[YSEHPTFTSQY]-CMV pp65 |
ProImmune |
F266-4A-D (APC) |
| HLA-A*0101[VTEHDTLLY]-CMV pp50 |
ProImmune |
F739-4A-D (APC) |
| HLA-A*0201[NLVPMVATV]-CMV pp65 |
Immudex |
WB2132-APC (APC) |
| HLA-A*0201[VLEETSVML]-CMV IE-1 |
Immudex |
WB2658-APC (APC) |
| HLA-A*2402[QYDPVAALF]-CMV pp65 |
ProImmune |
F414-4A-D (APC) |
| HLA-A*2402[VYALPLKML]-CMV pp65 |
ProImmune |
F380-4A-D (APC) |
| HLA-B*0702[TPRVTGGGAM]-CMV pp65 |
ProImmune |
F045-4A-D (APC) |
| HLA-B*0702[RPHERNGFTVL]-CMV pp65 |
ProImmune |
F308-4A-D (APC) |
| HLA-A*0101[VSDGGPNLY]-Flu PB1 |
ProImmune |
F540-4A-D (APC) |
| HLA-A*0101[CTELKLSDY]-Flu NP |
Immudex |
WA3410-APC (APC) |
| HLA-A*0101[CTELKLSDY]-Flu NP |
Immudex |
WA3410-PE (PE) |
| HLA-A*0201[GILGFVFTL]-Flu MP |
Immudex |
WB2161-APC (APC) |
| HLA-A*0201[GILGFVFTL]-Flu MP |
Immudex |
WB2161-PE (PE) |
| HLA-B*0702[SPIVPSFDM]-Flu NP |
Immudex |
F1744-4A-D (APC) |
| HLA-B*0702[SPIVPSFDM]-Flu NP |
Immudex |
F1744-4B-D (PE) |
| HLA-B*0702[QPEWFRNVL]-Flu PB1 |
Immudex |
F1743-4A-D (APC) |
| HLA-B*0702[QPEWFRNVL]-Flu PB1 |
Immudex |
F1743-4B-D (PE) |
| HLA-A*0201[ALIAPVHAV]-negative control |
Immudex |
WB2666-APC (APC) |
| HLA-A*0201[ALIAPVHAV]-negative control |
Immudex |
WB2666-PE (PE) |
|
| Deposited data |
|
|
|
| Raw and analyzed data |
This paper |
N/A |
| Flow cytometry and TCR sequencing data |
Immunology Database and Analysis Portal |
accession number SDY1885 |
| Single-cell RNA sequencing data |
NCBI Gene Expression Omnibus |
accession number GSE178837
|
|
| Software and algorithms |
|
|
|
| Python version 3.7 |
Python (2020) |
https://www.python.org/downloads/release/python-370/
|
| Anaconda version 4 |
Anaconda (2020) |
https://www.anaconda.com/products/individual
|
| VDJtools |
Shugay et al., 2015
|
https://vdjtools-doc.readthedocs.io/en/master/
|
| MiXCR |
Bolotin et al., 2015
|
https://mixcr.readthedocs.io/en/master/
|
| tcR |
Nazarov et al., 2015
|
http://imminfo.github.io/tcr/
|
| Seurat |
Stuart et al., 2019
|
https://github.com/satijalab/seurat/
|
| RStudio version 1.3.1073 |
RStudio, Inc. (2020) |
https://www.rstudio.com
|
| R version 4.0.3 |
R Foundation for Statistical Computing (2020) |
https://www.R-project.org
|
| FlowJo V 10.7 software |
Tree Star |
https://www.flowjo.com/
|
| Prism 8.4.3 |
GraphPad Software, LLC |
https://www.graphpad.com/
|
|
| Other |
|
|
|
| EasySep Dead Cell Removal (Annexin V) Kit |
STEMCELL Technologies |
Cat No.: 17899 |
| EasySep Human CD8+ T Cell Enrichment Kit |
STEMCELL Technologies |
Cat No.: 19053 |
| Immunocult Human CD3/CD28 T cell activator |
STEMCELL Technologies |
Cat No.: 10971 |
| IFN-y Secretion Assay – Detection Kit, human (PE) |
Miltenyi Biotec |
Cat No.: 130-054-202 |
