|
Antibodies
|
| APC-anti-mouse CD40L (clone SA047C3) |
Biolegend |
Cat#157009; RRID: AB_2890718 |
| Anti-VSV-G (clone 8G5F11) |
Millipore-Sigma |
Cat# MABF2337-100UG |
| PE-Cy™7 Mouse Anti-Human IgG, Clone G18-145 (RUO) |
BD Biosciences |
Cat# 561298;RRID: AB_10611712 |
| APC anti-human CD3 (clone HIT3a) |
Biolegend |
Cat#300312; RRID: AB_314048 |
| PE anti-human CD95 (Fas) |
Biolegend |
Cat#305607; RRID: AB_314545 |
| Anti-Fas Antibody (human, activating), clone CH11 |
Millipore-Sigma |
Cat#05-201; RRID:AB_309653 |
| APC Annexin V |
Biolegend |
Cat#640920; RRID: AB_2561515 |
| Human TruStain FcX |
Biolegend |
Cat#422302; RRID: AB_2818986 |
| APC anti-human CD19 (clone HIB19) |
Biolegend |
Cat#302212; RRID: AB_314242 |
| V450-CD20 (clone L27) |
BD Biosciences |
Cat#561163; RRID: AB_10563614 |
| BV711 anti-human CD8 (clone Sk1) |
Biolegend |
Cat#344734; RRID: AB_2565243 |
| TotalSeq™-C0063 anti-human CD45RA (clone HI100) |
Biolegend |
Cat# 304163; RRID: AB_2800764 |
| TotalSeq™-C0087 anti-human CD45RO (clone UCHL1) |
Biolegend |
Cat# 304259; RRID: AB_2800766 |
| TotalSeq™-C0390 anti-human CD127 (IL-7Rα) (clone A019D5) |
Biolegend |
Cat# 351356; RRID: AB_2800937 |
| TotalSeq™-C0251 anti-human Hashtag 1 |
Biolegend |
Cat# 394661; RRID: AB_2801031 |
| TotalSeq™-C0252 anti-human Hashtag 2 |
Biolegend |
Cat# 394663; RRID: AB_2801032 |
|
|
|
|
Bacterial and virus strains
|
| Stbl3 chemical competent cells |
Thermofisher |
Cat# C737303 |
|
|
|
|
Biological samples
|
|
|
| Human Blood buffy coat from LRS chambers |
Stanford Blood Center |
https://stanfordbloodcenter.org/research/buffy-coat-from-the-lrs-chamber/
|
|
|
|
|
Chemicals, peptides, and recombinant proteins
|
| Ganciclovir (GCV) |
InvivoGen |
Cat# sud-gcv |
| CellTrace Violet dye |
Thermofisher |
Cat#C34571
|
| IL2 |
PeproTech |
Cat#200-02-10ug |
| Synthesized peptides |
Elimbio |
Table S4
|
|
|
|
|
Critical commercial assays
|
| NEBuilder HiFi DNA Assembly Master Mix |
NEB |
Cat# E2621L |
| NEBNext High-Fidelity 2X PCR Master Mix |
NEB |
Cat# M0541L |
| Lenti-X GoStix Plus kit |
Takara |
Cat#631281 |
| Lenti-X Concentrator |
Takara |
Cat#631232 |
| Brilliant II SYBR Green qRT-PCR 1-Step Master Mix |
Agilent |
Cat#600825 |
| Quick-RNA miniprep kit |
Zymo |
Cat#R1055 |
| Annexin V Apoptosis Detection Kit |
Invitrogen |
Cat# 88-8006-72 |
| Lymphoprep |
STEMCELL Technologies |
Cat# 07811 |
| EasySep Human B Cell Enrichment Kit |
STEMCELL Technologies |
Cat#19844 |
| CellXVivo Human B cell expander |
R&D system |
Cat# CDK005 |
| EasySep human CD8+ T cell isolation kit |
STEMCELL Technologies |
Cat#17953 |
| TruSeq Stranded mRNA Library Prep Kit |
Illumina |
Cat# 20020594 |
| Chromium Next GEM Single Cell 5’ Kit v2 |
10xgenomics |
Cat#1000265 |
| Chromium Single Cell Human TCR Amplification Kit |
10xgenomics |
Cat#1000252 |
| 5’ Feature Barcode Kit |
10xgenomics |
Cat#1000256 |
| SPRISelect beads |
Beckman Coulter |
Cat# B23317
|
| DNA Clean & Concentrator-5 |
Zymo |
Cat#D4013 |
|
|
|
|
Deposited data
|
| Raw and processed sequencing data (single cell) |
This paper |
GEO database (GSE212998) |
| Raw and processed bulk RNA seq data |
This paper |
GEO database (GSE212998) |
|
|
|
|
Experimental models: Cell lines
|
| Raji |
ATCC |
CCL-86 |
| Ramos |
Lingwood lab |
N/A |
| HEK293T |
ATCC |
ATCC CRL-3216 |
| HLAKO HEK293T |
This paper |
N/A |
| Jurkat -76 |
Davis Lab |
N/A |
| Jurkat_CMV-TCR |
Davis Lab |
N/A |
| Jurkat_M1-TCR |
Davis Lab |
N/A |
| Ramos_HPV16-L2-BCR |
This paper |
N/A |
| Ramos_HER2-BCR |
This paper |
N/A |
| Ramos_SARS2-RBD-BCR |
This paper |
N/A |
| Jurkat_NYESO-1-TCR (1G4wt) |
This paper |
N/A |
| Jurkat_NYESO-1-TCR (1G4 a95:LY) |
This paper |
N/A |
| Jurkat-TCR5 |
This paper |
N/A |
| Jurkat_NYESO-1-TCR+mscarlet |
This paper |
N/A |
|
|
|
|
Oligonucleotides
|
| Primers for libraries preparation |
This paper |
Table S5
|
| shRNA oligo |
This paper |
Table S5
|
| CRISPR guide RNAs target HLA |
This paper |
Table S5
|
|
Recombinant DNA
|
| pMD2.G |
addgene |
Cat#12259 |
| psPAX2 |
addgene |
Cat#12260 |
| psPAX2-D64V-NC-MS2 |
addgene |
Cat#122944 |
| GFP-VPR |
addgene |
Cat#83374 |
| JWW-1 |
addgene |
Cat#66748 |
| pVITRO1-Trastuzumab-IgG1/κ |
addgene |
Cat#61883 |
| CMVTCRa_candidate5 |
addgene |
Cat#164999 |
| CMVTCRb_candidate5 |
addgene |
Cat#165000 |
| HER2 WT |
addgene |
Cat#16257 |
| pCCLc-MND-A0201-Mart1-SABR |
addgene |
Cat #119052 |
| HLA_A0101 |
addgene |
Cat#165009 |
| cEF.tk-GFP |
addgene |
Cat #33308 |
| pcDNA3.1-CD40L-mgSrtA |
addgene |
Cat#125795 |
| pcDNA3.1-CD40L-mutant |
addgene |
Cat #125796 |
| pMD2.G-VSV-G-mut |
This paper |
N/A |
| psPax2-MA-eGFP |
This paper |
N/A |
| psPax2-NC-eGFP |
This paper |
N/A |
| psPax2-NC-mNeon |
This paper |
N/A |
| plenti-sffv-tcr5-2a-hygro |
This paper |
N/A |
| plenti-EF1-NYESO_TCR-2a-hygro |
This paper |
N/A |
| PBCMV-HPV16_L2-BCR-2a-mCherry |
This paper |
N/A |
| plentiCMV-aCD19-Puro-2A-eGFP |
This paper |
N/A |
| plentiCMV-CD40L-Puro-2A-eGFP |
This paper |
N/A |
| plentiCMV-antigen-TM |
This paper |
N/A |
| plentiCMV-sp-HPV-TM |
This paper |
N/A |
| plentiCMV-sp-RBD-TM |
This paper |
N/A |
| plentiCMV-sp-HER2 |
This paper |
N/A |
| plentiCMV-sct-b2m-HLA-A0201 |
This paper |
N/A |
| plentiCMV-sct-p5-b2m-HLA-A0101 |
This paper |
N/A |
| plentiCMV10x-sct-b2m-HLA-A0201 |
This paper |
N/A |
| plentiCMV10x-sct-esp3i-b2m-HLA-A0201 |
This paper |
N/A |
|
|
|
|
Software and algorithms
|
| Cellranger |
10xgenomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome
|
| STAR |
60
|
|
| Htseq-count |
61
|
https://htseq.readthedocs.io/en/release_0.11.1/count.html
|
| DESeq2 |
62
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| Scanpy |
63
|
https://scanpy.readthedocs.io/en/stable/
|
| Scirpy |
64
|
https://github.com/scverse/scirpy
|
| Prism |
Graphpad |
https://www.graphpad.com/scientific-software/prism/
|
| Flowjo |
TreeStar |
https://www.flowjo.com/
|
|
Other
|
|
|
|
