KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Fixable Viability Dye eFluor780 | Thermo Fisher Scientific | Cat #65-0865-18 |
| Viability Dye Aqua Blue | Invitrogen | Cat # L34965 |
| Mouse anti-human CD4 BV650 (clone: OKT-4) | BioLegend | Cat # 317436 |
| Mouse anti-human CD20 ECD (clone: B9E9) | Beckman Coulter | Cat # IM3607U |
| Mouse anti-human PD1 BV605 (clone: EH12.2H7) | BioLegend | Cat # 329924 |
| Mouse anti-human CD8a Qdot705 (clone: 3B5) | Thermo Fisher Scientific | Cat # Q10059 |
| Mouse anti-human Ki67 Alexa Fluor 700 (clone: B56) | BD Biosciences | Cat # 561277 |
| Mouse anti-human CXCR5 PE (clone: MU5UBEE) | Thermo Fisher Scientific | Cat # 12-9185-42 |
| Mouse anti-human Bcl6 BV421 (Clone: K112-91) | BD Biosciences | Cat # 563363 |
| Mouse anti-human CD95 PE-Cy5 (clone: DX2) | BD Biosciences | Cat # 559773 |
| Mouse anti-human IgG PE-Cy7 (clone: G18-145) | BD Biosciences | Cat # 561298 |
| Mouse anti-human CD4 BV421 (clone: OKT-4) | BioLegend | Cat # 317434 |
| Mouse anti-human CD20 PE-Cy7 (clone: 2H7) | Thermo Fisher Scientific | Cat # 25-0209-42 |
| Mouse anti-human CD38 PE (Clone: OKT10) | NHP Reagents | Cat # PR-3802 |
| Mouse anti-human CD71 PE-CF594 (Clone: L01.1) | BD Biosciences | Custom conjugate |
| Mouse anti-human CD8 APC eFluor 780 (clone: RPA-T8) | Thermo Fisher Scientific | Cat # 47-0088-42 |
| Mouse anti-human CD20 BV650 (Clone: 2H7) | BioLegend | Cat # 302336 |
| Mouse anti-human PD1 BV785 (Clone: EH12.2H7) | BioLegend | Cat # 329930 |
| Mouse anti-human CXCR5 PE-Cy7 (clone: MU5UBEE) | Thermo Fisher Scientific | Cat # 25-9185-42 |
| Mouse anti-human CD25 FITC (Clone: BC96) | BioLegend | Cat # 302604 |
| Mouse anti-human OX40 PE (Clone: L106) | BD Biosciences | Cat # 340420 |
| Mouse anti-human 4-1BB APC (Clone:4B4-1) | BioLegend | Cat # 309810 |
| Goat anti-rhesus IgG (H+L) - HRP | Southern Biotech | Cat # 6200-05 |
| Recombinant Ab Rh60mer1 HC | Genscript | Custom |
| QVQLVQSGAEVKKPGSSVKVSCTASGYTFIDYYIHWLRQAPRQGLEWMGWINPYNGNTKYGQKFQDRVTMTRDTSTNTAYMELSSLRSEDTAVYYCARETWIQMQLRGFEYWGQGVLVTVSS | ||
| Recombinant Ab Rh60mer1 LC | Genscript | Custom |
| QAALTQSPSVSGSPGQSVTISCTGHGSNIGGYNRVSWYQQHPGKAPKLMIYEVSNRPSGVSDRFSGSTSGNTASLIISGLQAEDEADYYCNSYAVFGGGTRLTVL | ||
| Recombinant Ab Rh60mer2 HC | Genscript | Custom |
| QVQLVQSGAEVKKPGSSVKVSCTASGYTFIDYYIHWLRQAPRQGLEWMGWINPYNGNTKYGQKFQDRVTMTRDTSTNTAYMELSSLRSEDTAVYYCARETWIQMQLRGFEYWGQGVLVTVSS | ||
| Recombinant Ab Rh60mer2 LC | Genscript | Custom |
| QAALTQSPSVSGSPGQSVTISCTGTSSDIGGYNRVSWYQQHPGKAPKLMIYEVSKRPSGVSDRFSGSKSGNTASLTISGLQAEDEADYYCNSYAVFGGGTRLTVL | ||
| Recombinant Ab Rh60mer3 HC | Genscript | Custom |
| QVQLVQSGAEVKKPGASVKVSCKASGFTFGSYGINWVRQAPGQGLEWMGGIVPLVGVTNYAQKFQGRVTITADTSTRTAYMELSSLRSEDMAVYYCVRCGQYSSWSIWYFDLWGPGTPITISS | ||
| Recombinant Ab Rh60mer3 LC | Genscript | Custom |
| AALTQSPSVSGSPGQSVTISCTGHGSNIGGYNRVSWYQQHPGKAPKLMIYEVSNRPSGVSDRFSGSTSGNTASLIISGLQAEDEADYYCNSYAVFGGGTRLTVL | ||
| Recombinant Ab Rh60mer4 HC | Genscript | Custom |
| QVQLVQSGAEVKKPGASVKVSCKASGFTFGSYGINWVRQAPGQGLEWMGGIVPLVGVTNYAQKFQGRVTITADTSTRTAYMELSSLRSEDMAVYYCVRCGQYSSWSIWYFDLWGPGTPITISS | ||
| Recombinant Ab Rh60mer4 LC | Genscript | Custom |
| QAALTQSPSVSGSPGQSVTISCTGTSSDIGGYNRVSWYQQHPGKAPKLMIYEVSKRPSGVSDRFSGSKSGNTASLTISGLQAEDEADYYCNSYAVFGGGTRLTVL | ||
| Recombinant Ab Rh60mer5 HC | Genscript | Custom |
| QVQLVQSGAEITQPGASVKLSCKASGYTFTGYYMHWVRQAPGQGLEWIGLIYPYKGDKGYAQNFQGRVTITTDTSTSTGYMELSSLRSEDTAVYYCTRDRGLDGFDYWGQGVLVTVSS | ||
| Recombinant Ab Rh60mer5 LC | Genscript | Custom |
| AALTQSPSVSGSPGQSVTISCTGHGSNIGGYNRVSWYQQHPGKAPKLMIYEVSNRPSGVSDRFSGSTSGNTASLIISGLQAEDEADYYCNSYAVFGGGTRLTVL | ||
| Recombinant Ab Rh60mer6 HC | Genscript | Custom |
| QVQLVQSGAEITQPGASVKLSCKASGYTFTGYYMHWVRQAPGQGLEWIGLIYPYKGDKGYAQNFQGRVTITTDTSTSTGYMELSSLRSEDTAVYYCTRDRGLDGFDYWGQGVLVTVSS | ||
| Recombinant Ab Rh60mer6 LC | Genscript | Custom |
| QAALTQSPSVSGSPGQSVTISCTGTSSDIGGYNRVSWYQQHPGKAPKLMIYEVSKRPSGVSDRFSGSKSGNTASLTISGLQAEDEADYYCNSYAVFGGGTRLTVL | ||
| Bacterial and Virus Strains | ||
| HXB2 ENV HIV pseudovirus | NIH AIDS Reagent Program | Cat # 1069 |
| HXB2 N276A ENV HIV pseudovirus | Mutant made by Burton Lab; Sok et al., 2016 | NA |
| Chemicals, Peptides, and Recombinant Proteins | ||
| eOD-GT8 60-mer | Produced inhouse; Jardine et al., 2016a | NA |
| ISCOMATRIX | CSL | N/A |
| Soluble saponin-based ISCOMs-class adjuvant | Adjuvant made by Irvine Lab; Pauthner et al., 2019 | NA |
| Alexa Fluor 488 Protein Labeling Kit | Thermo Fisher Scientific | Cat # A10235 |
| Alexa Fluor 647 Protein Labeling Kit | Thermo Fisher Scientific | Cat # A20173 |
| eOD-GT8 lumazine overlapping peptides | A&A Labs LLC | Cat # 17127902 |
| Staphylococcal enterotoxin B (SEB) | Toxin Technology Inc. | Cat # BT202 |
| TMB Substrate | Thermo Fisher Scientific | Cat # 34021 |
| Evan’s Blue Dye | Millipore Sigma | Cat # E2129 |
| RLT lysis buffer | QIAGEN | Cat #79216 |
| Critical Commercial Assays | ||
| eBioscience FoxP3/ Transcription Factor Staining Buffer Set | Thermo Fisher Scientific | Cat # 00-5523-00 |
| RNeasy kits | QIAGEN | Cat #74104 |
| KAPA Real-Time Library Amplification Kit | Roche | Cat # KK2702 |
| Deposited Data | ||
| eOD-GT8 60-mer specific Bulk BCR sequencing reads | NCBI SRA | SRA: SRP199928 |
| Experimental Models: Cell Lines | ||
| TZM-bl cells | NIH AIDS Reagent Program | Cat #8129 |
| Experimental Models: Organisms/Strains | ||
| Indian-origin rhesus macaques (outbred) | Yerkes National Primate Research Center | N/A |
| Olionucleotides | ||
| CDS Oligo (dT): TTTTTTTTTTTTTTTTTTTTTTTTVN | Integrated DNA Technologies, Inc. | N/A |
| SMARTer II A Oligo: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG | Integrated DNA Technologies, Inc. | N/A |
| IgG Constant Primer: GCCAGGGGGAAGACCGATGGGCCCTTGGTGGA | Integrated DNA Technologies, Inc. | N/A |
| IgK Constant Primer: GCGGGAAGATGAAGACAGATGGTGCAGCCACAG | Integrated DNA Technologies, Inc. | N/A |
| IgL Constant Primer: GGCCTTGTTGGCTTGAAGCTCCTCAGAGGAGGG | Integrated DNA Technologies, Inc. | N/A |
| P5_Seq BC_XX 5PIIA: CACGACGCTCTTCCGATCT4-8xNAACCACTA AAGCAGTGGTATCAACGCAGAGT | Integrated DNA Technologies, Inc. | N/A |
| P7_ i7_XX IgG: CAAGCAGAAGACGGCATACGAGATTAGTGGTT GCCAGGGGGAAGACCGATGGGCCCTTGGTGGA | Integrated DNA Technologies, Inc. | N/A |
| P7_ i7_XX IgK: CAAGCAGAAGACGGCATACGAGATTAGTGGTT GCGGGAAGATGAAGACAGATGGTGCAGCCACAG | Integrated DNA Technologies, Inc. | N/A |
| P7_ i7_XX IgL: CAAGCAGAAGACGGCATACGAGATTAGTGGTT GGCCTTGTTGGCTTGAAGCTCCTCAGAGGAGGG | Integrated DNA Technologies, Inc. | N/A |
| P5_Graft P5_seq: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT | Integrated DNA Technologies, Inc. | N/A |
| Software and Algorithms | ||
| Prism v7.0/v8.0 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo v10.4 | FlowJo LLC | https://www.flowjo.com |
| ImageJ | National Institute of Health | https://imagej.nih.gov/ij/ |
| pRESTO | https://presto.readthedocs.io/en/latest/ | |
| ChangeO | https://changeo.readthedocs.io/en/stable/ | |
| Alakazam | https://alakazam.readthedocs.io/en/stable/ | |
| SHazaM | https://shazam.readthedocs.io/en/stable/ | |
| seqtk | https://github.com/lh3/seqtk | |
| MUSCLE | https://www.drive5.com/muscle/ | |
| EMBOSS 6.6.0.0 | ftp://emboss.open-bio.org/pub/EMBOSS/ | |
| CD-HIT | http://weizhongli-lab.org/cd-hit/ | |
| IgBLAST | https://ncbi.github.io/igblast/ | |
| blastn | ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ | |
| DomainGapAlign | IMGT® | http://www.imgt.org/IMGTindex/IMGTDomainGapAlign.php |
| parallel | https://www.gnu.org/software/parallel/ | |
| Other | ||
| Repertoire analysis and resources | This paper 10.5281/zenodo.3239472 |
https://github.com/BosingerLab/NHP_eOD-GT8_manuscript |
| Corning® 96 Well Half-Area Microplate | Sigma Millipore | Cat # CLS3690 |