REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD71 M-A712 BV421	BD Biosciences	Cat#562995; RRID: AB_2737939
CD4 SK3 BV650	BD Biosciences	Cat#563875; RRID: AB_2744425
CD27 L128 BV711	BD Biosciences	Cat#563167; RRID: AB_2738042
CD38 HIT2 BV786	BD Biosciences	Cat#563964; RRID: AB_2738515
CCR7 150503 AF700	BD Biosciences	Cat#561143; RRID: AB_10562031
CD14 MΦP9 APC-H7	BD Biosciences	Cat#560180; RRID: AB_1645464
CD19 SJ25C1 APC-H7	BD Biosciences	Cat#560177; RRID: AB_1645470
CD45RA HI100 FITC	BD Biosciences	Cat#555488; RRID: AB_395879
CD8a SK1 PerCP-Cy5.5	BD Pharmingen	Cat#565310; RRID: AB_2687497
CD95 DX2 PE-CF594	BD Biosciences	Cat#562395; RRID: AB_11153666
PD-1 EH12.1 PE-Cy7	BD Biosciences	Cat#561272; RRID: AB_10611585
CD3 OKT3 BV510	BioLegend	Cat#317332; RRID: AB_2561943
HLA-DR L243 BV605	BioLegend	Cat#307640; RRID: AB_2561913
CXCR5 RF8B2 BV421	BD Biosciences	Cat#562747; RRID: AB_2737766
CD19 SJ25C1 BV510	BD BioSciences	Cat#562947; RRID: AB_2737912
CCR6 11A9 BV650	BD Biosciences	Cat#563922; RRID: AB_2738488
CD20 2H7 BV711	BD Biosciences	Cat#563126; RRID: AB_2313579
CD27 M-T271 AF700	BD Biosciences	Cat#560611; RRID: AB_1727454
CD4 RPA-T4 APC-H7	BD Biosciences	Cat#560158; RRID: AB_1645478
CD3 UCHT1 PE-CF594	BD Biosciences	Cat#562280; RRID: AB_11153674
CXCR3 (CD183) 1C6 APC	BD Biosciences	Cat#550967; RRID: AB_398481
CD8 SK1 FITC	BD Biosciences	Cat#555634; RRID: AB_395996
CD45 HI30 PerCPCy5.5	BD Biosciences	Cat#340953; RRID: AB_400194
ICOS (CD278) DX29 PE	BD Biosciences	Cat#557802; RRID: AB_396878
CD8a SK1 BV605	BD Biosciences	Cat#564116; RRID: AB_2869551
CD25 2A3 BV711	BD Biosciences	Cat#563159; RRID: AB_2738037
CXCR3 G025H7 BV785	BioLegend	Cat#353738; RRID: AB_2565924
APC (4-1BB) 4B4-1 CD137	BioLegend	Cat#309810; RRID: AB_830672
CD69 FN50 PerCPCy5.5	BioLegend	Cat#310926; RRID: AB_2074956
CD134 L106 PE	BD Biosciences	Cat#340420; RRID: AB_400027
CD45RA L48 PECy7	BD Biosciences	Cat#337167; RRID: AB_647424
CD19 J4.119 ECD	Beckman Coulter	Cat#IM2708U; RRID:AB_130854
IgM G20-127 BUV395	BD Biosciences	Cat#563903; RRID:AB_2721269
CD21 B-ly4 BUV737	BD Biosciences	Cat#564437; RRID:AB_2738807
IgD IA6-2 PE-Cy7	BD Biosciences	Cat#561314; RRID:AB_10642457
IgG G18-145 BV786	BD Biosciences	Cat#564230; RRID:AB_2738684
CD27 O323 BV605	BioLegend	Cat#302829; RRID:AB_11204431
Streptavidin PE	BD Biosciences	Cat#554061, RRID:AB_10053328
Streptavidin APC	BD Biosciences	Cat#554067, RRID:AB_10050396
Peroxidase AffiniPure goat anti-human IgG, Fcγ fragment specific	Jackson ImmunoResearch	Cat#109-035-098; RRID: AB_2337586
Biological samples
Blood samples (peripheral blood mononuclear cells (PBMCs) and plasma samples) from COVID-19-vaccinated adult haematological malignancy patients and healthy control individuals	The Royal Melbourne Hospital, The Austin Hospital, St Vincent’s Hospital, and The Peter McCallum Cancer Center	N/A
Chemicals, peptides, and recombinant proteins
3,3′,5,5′-Tetramethylbenzidine (TMB) Liquid Substrate System for ELISA, peroxidase substrate	Sigma	Cat#T0440-1L
Alkaline phosphatase yellow (pNPP) liquid substrate for ELISA	Sigma	Cat#P7998-100ML
Pierce High Sensitivity Streptavidin-HRP	Thermo Fisher Scientific	Cat#21130
SARS-CoV-2 RBD protein	Amanat et al.,40	N/A
SARS-CoV-2 Spike protein	Juno et al.,37	N/A
SARS-CoV-2 peptides – A1/ORF1a1637 TTDPSFLGRY; A1/S865-873 LTDEMIAQY; A2/S269 YLQPRTFLL; A3/N361 KTFPPTEPK; A3/S378 KTFPPTEPK; A24/S1208 QYIKWPWYI; B7/N105-113 SPRWYFYYL; B15/S919-927 NQKLIANQF; B35/S321-329 QPTESIVRF; and DPB4/S167 TFEYVSQPFLMDLE	GenScript	N/A
HLA-A∗01:01/S865 monomer (SARS-CoV-2, S865, LTDEMIAQY)	Peptide sequence30, monomer [Rossjohn Laboratory]	N/A
HLA-A∗01:01/ORF1a1637 monomer (SARS-CoV-2, ORF1a1637, TTDPSFLGRY)	Peptide sequence41, monomer21	N/A
HLA-A∗03:01/S378 monomer (SARS-CoV-2, S378, KCYGVSPTK)	Peptide sequence41, monomer [Rossjohn Laboratory]	N/A
HLA-A∗03:01/N361 monomer (SARS-CoV-2, N361, KTFPPTEPK)	Peptide sequence42, monomer21	N/A
HLA-B∗07:02/N105 monomer (SARS-CoV-2, N105, SPRWYFYYL)	Peptide sequence42, monomer18	N/A
HLA-B∗15:01/S919 monomer (SARS-CoV-2, S919, NQKLIANQF)	Peptide sequence23, monomer [Rossjohn Laboratory]	N/A
HLA-A∗02:01/S269 monomer (SARS-CoV-2, S269, YLQPRTFLL)	Peptide sequence/monomer19	N/A
HLA-B∗35:01/S321 monomer (SARS-CoV-2, S321, QPTESIVRF)	Peptide sequence33, monomer [Rossjohn Laboratory]	N/A
HLA-A∗24:02/S1208 monomer (SARS-CoV-2, S1208, QYIKWPWYI)	Peptide sequence31, monomer20	N/A
HLA-DPA1∗01:03/DPB1∗04:01/S167 monomer (SARS-CoV-2, S167, TFEYVSQPFLMDLE)	Peptide sequence/monomer22	N/A
Software and algorithms
R v4.2.1	R Core Team,43	https://cran.r-project.org
conga package	Schattgen et al.44	https://github.com/phbradley/conga
igraph R package v1.3.2	Csárdi and Nepusz45	https://igraph.org/r/
TCRdist pipeline	Dash et al.46	https://github.com/phbradley/tcr-dist
Gephi v0.9.7	Jacomy et al.47	https://gephi.org/
Corrplot v0.92	Wei and Simko48	https://github.com/taiyun/corrplot
rstatix pacakage v0.7.0	Kassambara49	https://CRAN.R-project.org/package=rstatix
EnhancedVolcano v1.14.0	Blighe et al.50	https://github.com/kevinblighe/EnhancedVolcano
FlowJo v10.5.3	FlowJo	https://www.flowjo.com
Prism v8.3.1 or v9.1.0	GraphPad	https://www.graphpad.com
BD FACS Diva v8.0.1	BD Biosciences	https://www.bdbiosciences.com/en-us/instruments/research-instruments/research-software/flow-cytometry-acquisition/facsdiva-software
Other
Anti-PE Micro-Beads	Miltenyi Biotec	Cat# 130-048-801, RRID:AB_244373
Anti-APC Micro-Beads	Miltenyi Biotec	Cat# 130-090-855, RRID:AB_244367