Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | anti-CD4, clone SK3 (mouse monoclonal) | BD | Cat# 563,550 | 1.5 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD19, clone SJ25C1 (mouse monoclonal) | BD | Cat# 564,303 | 1 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD25, clone M-A251 (mouse monoclonal) | BD | Cat# 562,442 | 5 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-HLA-DR, clone B169414 (mouse monoclonal) | BioLegend | Cat# 307,637 | 0.625 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD56, clone HCD56 (mouse monoclonal) | BioLegend | Cat# 318,334 | 0.625 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD45RA, clone HI100 (mouse monoclonal) | BioLegend | Cat# 304,135 | 0.625 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD14, clone MφP9 (mouse monoclonal) | BD | Cat# 563,373 | 0.2 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CCR7, clone G043H7 (mouse monoclonal) | BioLegend | Cat# 353,229 | 4 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD57, clone NK-1 (mouse monoclonal) | BD | Cat# 555,619 | 5 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD8, clone SK1 (mouse monoclonal) | BD | Cat# 341,051 | 2 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-Vδ2 TCR, clone B6 (mouse monoclonal) | BioLegend | Cat# 331,408 | 0.156 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD3, clone UCHT1 (mouse monoclonal) | Beckman Coulter | Cat# IM2705U | 1 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD38, clone HIT2 (mouse monoclonal) | BD | Cat# 555,461 | 10 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-γ/δ TCR, clone 11F2 (mouse monoclonal) | BD | Cat# 655,434 | 1.25 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD127, clone A019D5 (mouse monoclonal) | BioLegend | Cat# 351,315 | 0.2 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-NKG2C, clone 134,591 (mouse monoclonal) | R&D Systems | Cat# FAB138N | 1.25 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD16, clone 3G8 (mouse monoclonal) | BD | Cat# 557,758 | 0.312 µl/50 µl staining volume; doi:10.1002/cyto.a.22580 |
| Antibody | anti-CD14, clone M5E2 (mouse monoclonal) | BioLegend | Cat# 301,842 | Fluorochrome: BV510 (detected in the same channel as AViD) |
| Antibody | anti-CD56, clone NCAM16.2 (mouse monoclonal) | BD | Cat# 564,447 | Fluorochrome: BUV737 |
| Antibody | anti-CD3, clone UCHT1 (mouse monoclonal) | BioLegend | Cat# 300,436 | Fluorochrome: BV570 |
| Antibody | anti-CD8, clone RPA-T8 (mouse monoclonal) | BD | Cat# 563,821 | Fluorochrome: BV650 |
| Antibody | anti-CD45RA, clone HI100 (mouse monoclonal) | BD | Cat# 560,674 | Fluorochrome: APC-H7 |
| Antibody | anti-CXCR5, clone J252D4 (mouse monoclonal) | BioLegend | Cat# 356,928 | Fluorochrome: PE-Dazzle594 |
| Antibody | anti-PD-1, clone eBioJ105 (mouse monoclonal) | eBioscience | Cat# 25-2799-42 | Fluorochrome: PE-Cy7 |
| Antibody | anti-IFN-γ, clone B27 (mouse monoclonal) | BD | Cat# 560,371 | Fluorochrome: V450 |
| Antibody | anti-IL-2, clone MQ1-17H12 (rat monoclonal) | BD | Cat# 559,334 | Fluorochrome: PE |
| Antibody | anti-IL-4, clone MP4-25D2 (rat monoclonal) | BioLegend | Cat# 500,822 | Fluorochrome: PerCP-Cy5.5 |
| Antibody | anti-IL-13, clone JES10-5A2 (rat monoclonal) | BD | Cat# 564,288 | Fluorochrome: BV711 |
| Antibody | anti-IL-21, clone 3A3-N2 (mouse monoclonal) | Miltenyi Biotec | Cat# 130-120-702 | Fluorochrome: APC |
| Antibody | anti-TNF-α, clone mAb11 (mouse monoclonal) | eBioscience | Cat# 11-7349-82 | Fluorochrome: FITC |
| Antibody | anti-CD40L, clone 24–31 (mouse monoclonal) (mouse monoclonal) | BioLegend | Cat# 310,825 | Fluorochrome: BV605 |
| Antibody | anti-Granzyme B, clone GB11 (mouse monoclonal) | BD | Cat# 560,213 | Fluorochrome: Alx700 |
| Chemical compound, drug | BD FACS Lyse Solution, 10× | BD | Cat #349,202 | doi:10.1002/cyto.a.22590 VC |
| Chemical compound, drug | BD FACS Perm II, 10× | BD | Cat #340,973 | doi:10.1002/cyto.a.22590VC |
| Chemical compound, drug | Brefeldin A | Sigma Chemical Co. | Cat #B-7651 | Final concentration of 10 µg/mldoi:10.1002/cyto.a.22590 VC |
| Chemical compound, drug | CD28/49d (BD Biosciences) | BD | Cat #347,690 | Final concentration of 1 µg/mldoi:10.1002/cyto.a.22590 VC |
| Chemical compound, drug | Golgi Stop containing monensin | BD | Cat #554,724 | doi:10.1002/cyto.a.22590 VC |
| Peptide, recombinant protein | Recombinant AMA1 | WRAIR | FVO strain, GMP produced in E. coli | |
| Peptide, recombinant protein | CSP peptide pool | doi: 10.3389/fimmu.2017.01008Biosynthan (RNA-sequencing stimulations) and Biosynthesis (ICS stimulations) | ||
| Peptide, recombinant protein | HBS peptide pool | doi: 10.3389/fimmu.2017.01008Biosynthan (RNAseq stimulations) and Biosynthesis (ICS stimulations) | ||
| Sequence-based reagent | Universal adapter E5V6NEXT: 5′-iCiGiCACACTCT TTCCCTACACGACGCrGrGrG-3′ |
Integrated DNA Technologies | iC: iso-dC, iG: iso-dG, rG: RNA G | |
| Sequence-based reagent | Barcoded adapter E3V6NEXT: 5′-/5Biosg/ACACTCTTTCCCT ACACGACGCTCTTCCGATC T[BC6]N10T30VN-3′ |
Integrated DNA Technologies | 5Biosg = 5′ biotin, [BC6] = 6 bp barcode specific to each cell/well, N10 = unique molecular identifiers, 10 bp | |
| Sequence-based reagent |
SINGV6 primer: 5′-/5Biosg/ACACTC TTTCCCTACACGACGC-3′ |
Integrated DNA Technologies | ||
| Sequence-based reagent | P5NEXTPT5 primer: 5′- AATGATACGGCGACC ACCGAGATCTACACT CTTTCCCTACACGAC GCTCTTCC*G*A*T*C*T-3′ |
Integrated DNA Technologies | * = phosphorothioate bonds | |
| Chemical compound, drug | SEB | Sigma Chemical Co. | Cat #S4881 | |
| Commercial assay or kit | SV96 Total RNA Isolation System | Promega | Cat# Z3500 | |
| Commercial assay or kit | DNA Clean & Concentrator-5 column | Zymo Research | Cat# D4004 | |
| Commercial assay or kit | Advantage 2 Polymerase Mix | Takara Bio | Cat# 639,202 | |
| Commercial assay or kit | dsDNA HS Assay | Life Technologies | Cat# Q32851 | |
| Commercial assay or kit | Nextera XT library preparation kit | Illumina | Cat# FC-131–1096 | |
| Commercial assay or kit | QIAquick Gel Extraction Kit | Qiagen | Cat# 28706 × 4 | |
| Chemical compound, drug | DMSO | Sigma | Cat# D2650 | |
| Software, algorithm | R | The R Foundation | R version 4.0.4 (2021-02-15) | |
| Software, algorithm | Burrows-Wheeler Aligner (BWA) | https://sourceforge.net/projects/bio-bwa/ | BWA Aln version 0.7.10 | |
| Software, algorithm | FlowJo | BD Life Sciences | FlowJo version 9.9 Tree Star | |
| Other | RLT buffer | Qiagen | Cat# 79,216 | |
| Other | RNA protect | Qiagen | Cat# 76,104 | |
| Other | 96-Well V-bottomed plate | Kisker, AttendBio | Cat# G096-VB | |
| Other | Adhesive foil | Kisker, AttendBio | Cat# G071-P | |
| Other | AviD | Invitrogen | Cat# L34957 | 0.5 µl reagent/50 µl staining volumedoi:10.1002/cyto.a.22590 VC |
| Other | Maxima H Minus Reverse Transcriptase | Thermo Scientific | Cat# EP0751 | |
| Other | Exonuclease I | New England BioLabs | Cat# M0293S | |
| Other | Agencourt AMPure XP magnetic beads | Beckman Coulter | Cat# A63881 | 0.6× |
| Other | E-Gel EX Gel, 2% | Thermo Fisher | Cat# G401002 | |
| Other | RNA 6000 Pico Chip | Agilent | Cat# 5067-1513 |