KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Fixable Viability Dye eFluor506 | Thermo Fisher Scientific | Cat # 65–0866-18 |
| Fixable Viability Dye eFluor780 | Thermo Fisher Scientific | Cat # 65–0865-18 |
| Mouse anti-human CD20 PE-Texas Red (clone: 2H7) | Beckman Coulter | Cat # IM3607U |
| Mouse anti-human CD4 BV650 (clone: OKT-4) | BioLegend | Cat # 317436 |
| Mouse anti-human CD8a Qdot705 (clone: 3B5) | Thermo Fisher Scientific | Cat # Q10059 |
| Mouse anti-human IgG PE-Cy7 (clone: G18–145) | BD Biosciences | Cat # 561298 |
| Mouse anti-human CXCR5 PE (clone: MU5UBEE) | Thermo Fisher Scientific | Cat # 12–9185-42 |
| Mouse anti-human PD1 BV605 (clone: EH12.2H7) | BioLegend | Cat # 329924 |
| Mouse anti-human CD3 BV786 (clone: SP34–2) | BD Biosciences | Cat # 563918 |
| Mouse anti-human IgM PerCP-Cy5.5 (clone:G20–127) | BD Biosciences | Cat # 561285 |
| Mouse anti-human Ki67 Alexa Fluor 700 (clone: B56) | BD Biosciences | Cat # 561277 |
| Mouse anti-human Ki67 Alexa Fluor 488 (clone: B56) | BD Biosciences | Cat # 558616 |
| Mouse anti-human Bcl6 Alexa Fluor 488 (clone: K112–91) | BD Biosciences | Cat # 561524 |
| Mouse anti-human CD4 APC eFluor 780 (clone: SK3) | Thermo Fisher Scientific | Cat # 47–0047-42 |
| Mouse anti-human CD8 APC eFluor 780 (clone: RPA-T8) | Thermo Fisher Scientific | Cat # 47–0088-42 |
| Mouse anti-human CD16 APC eFluor 780 (clone: ebioCB16) | Thermo Fisher Scientific | Cat # 47–0168-42 |
| Mouse anti-human CD20 Alexa Fluor 488 (clone: 2H7) | BioLegend | Cat # 302316 |
| Mouse anti-human CD38 PE (Clone: OKT) | NHP Reagents | Cat # PR-3802 |
| Mouse anti-human CD71 PE-CF594 (Clone: L01.1) | BD Biosciences | Custom conjugate |
| Mouse anti-human CD4 BV650 (Clone: OKT4) | BioLegend | Cat # 317436 |
| Mouse anti-human CD20 BV570 (Clone: 2H7) | BioLegend | Cat # 302332 |
| 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 |
| Mouse anti-human CD14 APC/Cy7 (Clone: M5E2) | BioLegend | Cat # 301820 |
| Mouse anti-human CD16 APC/Cy7 (Clone: 3G8) | BioLegend | Cat # 302018 |
| Mouse anti-human CD20 BV650 (Clone: 2H7) | BioLegend | Cat # 302336 |
| Mouse anti-human CD4 APC (Clone: OKT4) | BioLegend | Cat # 317416 |
| Mouse anti-human Bcl6 BV421 (Clone: K112–91) | BD Biosciences | Cat # 563363 |
| Mouse anti-human Bcl6 Alexa Fluor 647 (Clone: K112–91) | BD Biosciences | Cat # 561525 |
| Mouse anti-human IgM BV421 (Clone: G20–127) | BD Biosciences | Cat # 562618 |
| Mouse anti-human IgG PE (Clone: G18–145) | BD Biosciences | Cat # 560951 |
| Mouse anti-human IgD Alexa Fluor 488 | Southern Biotech | Cat # 2030–30 |
| Mouse anti-human Lambda biotin (Clone: IS7–24C7) | Miltenyi | Cat # 130–093-025 |
| Mouse anti-human CD35 (Clone: E11) | BD Biosciences | Cat # 565327 |
| Streptavidin-Alexa Fluor 647 | Thermo Fisher Scientific | Cat # S32357 |
| Streptavidin-BV421 | BioLegend | Cat # 405225 |
| Streptavidin-BV711 | BioLegend | Cat # 405241 |
| Goat anti-rhesus IgG (H+L) - HRP | Southern Biotech | Cat # 6200–05 |
| Goat anti-Human IgG, Fcγ fragment specific-HRP | Jackson ImmunoResearch | Cat # 109–035-098 |
| 19R | Thermo Fisher Scientific, unpublished | Custom |
| BDA1 HC:QVQLQESGPGLVKPSETLSLTCAVSGASISIYWWGWIRQPPGKGLEWIGEIIGSSGSTNSNPSFKSRVTISKDASKNQFSLNLNSVTAADTAVYYCVRVGAAISLPFDYWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWFQQKPGQSPVLIIYEDNKRPSGIPERFSGSSSGTVATLTISGAQVEDEGDYYCYSRHSSGNHGLFGGGTRLTVL |
Genscript | Custom |
| BDA2 HC:QVQLQESGPGLLKPSETLSLTCAVSGGSFSSYWWSWIRQPPGKGLEWIGEINGNSGSTHYNPSLKSRVTISKDASKNQFSLKLNSVTAADTAVYYCARWGPTGVTQGEPDFDYWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITYSGDALPKRYAYWFQQKPGQSPVLIIYEDSKRPSGIPERFSGSSSGTVATLTISGAQVEDEADYYCYSTDSSGNHFFGAGTRLTVL |
Genscript | Custom |
| BDA3 HC:QVQLQESGPGLVKPSETLSLTCAVSGHSVSSGYGWGWIRQPPGKGLEWIGQIYGYSGSTSYNPSLKSRVTVSTDTSKNQFSLRLSSLTAADTAVYYCARWHHGSFDIWGPGTPITISS LC:SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWFQQKPGQSPVLIIYEDNKRPSGIPERFSGSSSGTVATLTINGAQVEDEGDYYCYSRHSSGNHGLFGGGTRLTVL |
Genscript | Custom |
| BDA4 HC:QVQLQESGPGLVKPSETLSLTCAVSGASIRIYWWGWIRQPPGKGLEWIGEIIGSSGSTNSNPSFKSRVTISKDASKNQFSLNLNSVTAADTAVYYCVRVGAAISFPFDYWGQGVLVTVSS LC:SSELTQPPSVSVSPGQTARITCSGDALPKKYAYWFQQKPGQSPVLIIYEDNKRPSGIPERFSGSSSGTVATLTISGAQVEDEGDFYCYSRHSSGNHGLFGGGTRLTVL |
Genscript | Custom |
| BDA5 HC:QVQLQESGPGLLKPSETLSLTCAVSGGSFSSYWWSWIRQPPGKGLEWIGEINGNSGNTHYNPSLKSRVTISKDASKNHFSLKLSSVTAADTAVYYCARWGPTGVTQGEPDFDYWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITYSGDALPKKYAYWFQQKPGQSPVLIIYEDNKRPSGIPERFSGSSSGTVATLTISGAQVEDEADYYCYSTDSSGNHFFGAGTRLTVL |
Genscript | Custom |
| BDA6 HC:QVQLQESGPGLLKPSETLSLTCAVSGGSFSSYWWSWIRQPPGKGLEWIGEINGNSGSTHYNPSLKSRVTISKDASKNQFSLKLNSVTAADTAVYYCARWGPTGVTQGEPDFDYWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITCSGDALPKKYVYWFQQKPGQSPVLIIYEDSKRPSGIPERFSGSSSGTVATLTISGAQVEDEADYYCYSTISSGNDRIFGAGTRLTVL |
Genscript | Custom |
| BDA7 HC:QVQLQESGPGLVKPSETLSLTCAVSGASISIYWWSWIRQPPGKGLEWIGEIIGNSGSTNSNPSFKSRVTISKDASKNQFSLKLSSVTAADTAVYYCVRVGAAISLPYDYWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWFQQKPGQSPVLIIYEDNKRPSGIPERFSGSSSGTVATLTISGAQVEDEGDYYCYSRHSSGNHGLFGGGTRLTVL |
Genscript | Custom |
| BDA8 HC:QVQLQESGPGLLKPSETLSLTCAVSGGSFSSYWWSWIRQPPGKGLEWIGEINGNSGNTHYNPSLKSRVTISKDASKNQFSLKLSSVTAADTAVYYCARWGPTGVTQGEPEFDYWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITYSGDALPKKYAYWFQQKPGQSPVLIIYEDNKRPSGIPERFSGSSSGTVATLTISGAQVEDEADYYCYSTDSSGNHFFGAGTRLTVL |
Genscript | Custom |
| BDA9 HC:QVQLQESGPGLLKPSETLSLTCAVSGGSFSNYWWSWIRQPPGKGLEWIGEINGNSGSTHYNPSLKSRVTISKDASKNQFSLKLNSVTAADTAVYYCARWGPTGVTQGEPDFDFWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITYSGDALPKRYAYWFQQKPGQSPVLIIYEDSKRPSGIPERFSGSSSGTVATLTISGAQVEDEADYYCYSTDSSGNHFFGVGTRLTVL |
Genscript | Custom |
| BDA10 HC:QVQLQESGPGLVKPSETLSLTCAVSGVSISIYWWSWIRQPPGKGLEWIGEIIGNSGNTNSSPSFKSRVTISKDASKNQFSLKLSSVTAADTAVYYCVRVGAAISLPFDYWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITCSGDALPEKYAYWFQQKPGQSPVLIIYDDNIRPSGIPERFSGSSSGTVATLTISGAQVEDEGDYYCYSRHSSGNHGLFGGGTRLTVL |
Genscript | Custom |
| BDA11 HC:QVQLQESGPGLVKPSETLSLTCAVSGGSFSSYWWSWIRQPPGKGLEWIGEINGNSGSTNYNPSLKSRVTISKDASKNQFSLKLSSVTAADTAVYYCARVRVGAAISLPFDYWGQGVLVTVSS LC:SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWFQQKPGQSPVLIIYEDNKRPSGIPERFSGSSSGTVATLTISGAQVEDEGDYYCYSRHISGNHGLFGGGTRLTVL |
Genscript | Custom |
| BDA12 HC: BDA1HC LC:SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWFQQKPGQSPVLIIYEDNKRPSGIPERFSGSSSGTVATLTISGAQVEDEGDYYCFSRHSSGNHGLFGGGTRLTVL |
Genscript | Custom |
| BDA13 HC: BDA1 HC LC:SYELTQPPSVSVSPGQTARITCSGDALPKKYAYWFQQKPGQSPVLIIYDDSQRPSGIPERFSGSSSGTVATLTISGAQVEDEGDYYCFSRHSSGNHGLFGGGTRLTVL |
Genscript | Custom |
| Bacterial and Virus Strains | ||
| BG505.W6M.ENV.C2 | Wu et al., 2006 / NIH AIDS Reagent Program | Cat # 11518 |
| 12 virus panel – global isolates | (deCamp et al., 2014) | |
| Chemicals, Peptides, and Recombinant Proteins | ||
| BG505 Olio6 | Produced inhouse (Kulp et al., 2017) | |
| BG505 Olio6CD4-KO | Produced inhouse (Kulp et al., 2017) | |
| BG505 MD39 | Produced inhouse (Kulp et al., 2017) | |
| BG505 Olio6CD4-KO – Biotin | Produced inhouse | |
| BG505 Olio6 – Biotin | Produced inhouse | |
| BG505 MD39 – Biotin | Produced inhouse | |
| BG505 SOSIP – Biotin | Produced inhouse | |
| BG505 gp120 - Biotin | Produced inhouse | |
| BG505 SOSIP.664 v5.2 | Produced inhouse (Torrents de la Peña et al., 2017) | |
| His-Tag biotin peptide biotin - ALDGGGGSHHHHHHHH | A&A Labs LLC | N/A |
| Recombinant Protein A Sepharose | GE Healthcare | Cat # 17127902 |
| Lectin from Galanthus nivalis (snowdrop), lyophilized powder | Sigma-Aldrich | Cat # L9275–5mg |
| Olio6-CD4ko peptide megapool | A&A Labs LLC | N/A |
| Staphylococcal enterotoxin B (SEB) | Toxin Technology Inc. | Cat # BT202 |
| DNAse I Solution | Stemcell Technologies | Cat # 07900 |
| Streptavidin | Jackson ImmunoResearch Laboratories, Inc | Cat # 016–000-084 |
| TMB Substrate | Thermo Fisher Scientific | Cat # 34021 |
| Cholesterol | Avanti Polar Lipids | Cat # 700000 |
| 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (16:0 PC (DPPC)) | Avanti Polar Lipids | Cat # 850355 |
| N-Decanoyl-N-methylglucamine (MEGA-10) | Sigma-Aldrich | Cat # D6277 |
| Quil-A® saponin | InvioGen | Cat # vac-quil |
| Critical Commercial Assays | ||
| Pierce™ Fab Preparation Kit | Thermo Fisher Scientific | Cat # 44985 |
| eBioscience FoxP3/ Transcription Factor Staining Buffer Set | Thermo Fisher Scientific | Cat # 00–5523-00 |
| QCL-1000™ Endpoint Chromogenic LAL Assay | Lonza | Cat # 50–647U |
| BirA biotin-protein ligase standard reaction kit | Avidity Inc | Cat # BirA500 |
| Cholesterol Quantitation Kit | Sigma- Aldrich | Cat # MAK043–1KT |
| AMPure XP beads | Beckman Coulter | Cat # A63882 |
| KAPA HiFi HotStart Real-time PCR Master Mix (2X) | Kapa Biosystems, Inc. | Cat # KK2702 |
| Deposited Data | ||
| Rhesus macaque genomic raw sequences | NCBI SRA | PRJNA509445 |
| Rhesus macaque genome assembly | NCBI Assembly | SBKD01000000 |
| Week 7 single-cell RNA-seq sequences | NCBI SRA | PRJNA520929 |
| IgG BCR sequence reads from 224–13 (bolus) right LN | NCBI SRA, GenBank | PRJNA520929, KCVI00000000 |
| IgG BCR sequence reads from 224–13 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCVJ00000000 |
| IgK BCR sequence reads from 224–13 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCVK00000000 |
| IgL BCR sequence reads from 224–13 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCVL00000000 |
| IgG BCR sequence reads from RCn16 (bolus) right LN | NCBI SRA, GenBank | PRJNA520929, KCVM00000000 |
| IgK BCR sequence reads from RCn16 (bolus) right LN | NCBI SRA, GenBank | PRJNA520929, KCVN00000000 |
| IgL BCR sequence reads from RCn16 (bolus) right LN | NCBI SRA, GenBank | PRJNA520929, KCVO00000000 |
| IgG BCR sequence reads from RCn16 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCVP00000000 |
| IgK BCR sequence reads from RCn16 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCVQ00000000 |
| IgL BCR sequence reads from RCn16 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCVR00000000 |
| IgG BCR sequence reads from RRk16 (bolus) right LN | NCBI SRA, GenBank | PRJNA520929, KCWO00000000 |
| IgK BCR sequence reads from RRk16 (bolus) right LN | NCBI SRA, GenBank | PRJNA520929, KCWP00000000 |
| IgL BCR sequence reads from RRk16 (bolus) right LN | NCBI SRA, GenBank | PRJNA520929, KCWQ00000000 |
| IgG BCR sequence reads from RRk16 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCWR00000000 |
| IgK BCR sequence reads from RRk16 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCWS00000000 |
| IgL BCR sequence reads from RRk16 (bolus) left LN | NCBI SRA, GenBank | PRJNA520929, KCWT00000000 |
| IgG BCR sequence reads from RVh16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCVS00000000 |
| IgK BCR sequence reads from RVh16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCVT00000000 |
| IgL BCR sequence reads from RVh16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCVU00000000 |
| IgG BCR sequence reads from RVh16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCVV00000000 |
| IgK BCR sequence reads from RVh16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCVW00000000 |
| IgL BCR sequence reads from RVh16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCVX00000000 |
| IgG BCR sequence reads from RYm16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXA00000000 |
| IgK BCR sequence reads from RYm16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXB00000000 |
| IgL BCR sequence reads from RYm16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXC00000000 |
| IgG BCR sequence reads from RYm16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXD00000000 |
| IgK BCR sequence reads from RYm16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXE00000000 |
| IgL BCR sequence reads from RYm16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXF00000000 |
| IgG BCR sequence reads from RWr16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWU00000000 |
| IgK BCR sequence reads from RWr16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWV00000000 |
| IgL BCR sequence reads from RWr16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWW00000000 |
| IgG BCR sequence reads from RWr16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWX00000000 |
| IgK BCR sequence reads from RWr16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWY00000000 |
| IgL BCR sequence reads from RWr16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWZ00000000 |
| IgG BCR sequence reads from RQq16 (2w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCVY00000000 |
| IgG BCR sequence reads from RQq16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCVZ00000000 |
| IgK BCR sequence reads from RQq16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWA00000000 |
| IgL BCR sequence reads from RQq16 (2w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWB00000000 |
| IgG BCR sequence reads from RWh16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXG00000000 |
| IgK BCR sequence reads from RWh16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXH00000000 |
| IgL BCR sequence reads from RWh16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXI00000000 |
| IgG BCR sequence reads from RWh16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXJ00000000 |
| IgK BCR sequence reads from RWh16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXK00000000 |
| IgL BCR sequence reads from RWh16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXL00000000 |
| IgG BCR sequence reads from ROw16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXM00000000 |
| IgK BCR sequence reads from ROw16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXN00000000 |
| IgL BCR sequence reads from ROw16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCXO00000000 |
| IgG BCR sequence reads from ROw16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXP00000000 |
| IgK BCR sequence reads from ROw16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXQ00000000 |
| IgL BCR sequence reads from ROw16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCXR00000000 |
| IgG BCR sequence reads from RTh16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWI00000000 |
| IgK BCR sequence reads from RTh16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWJ00000000 |
| IgL BCR sequence reads from RTh16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWK00000000 |
| IgG BCR sequence reads from RTh16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWL00000000 |
| IgK BCR sequence reads from RTh16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWM00000000 |
| IgL BCR sequence reads from RTh16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWN00000000 |
| IgG BCR sequence reads from RFr16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWC00000000 |
| IgK BCR sequence reads from RFr16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWD00000000 |
| IgL BCR sequence reads from RFr16 (4w pumps) right LN | NCBI SRA, GenBank | PRJNA520929, KCWE00000000 |
| IgG BCR sequence reads from RFr16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWF00000000 |
| IgK BCR sequence reads from RFr16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWG00000000 |
| IgL BCR sequence reads from RFr16 (4w pumps) left LN | NCBI SRA, GenBank | PRJNA520929, KCWH00000000 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM 224–13 (bolus) | EMDataBank | EMD-9175 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RCn16 (bolus) | EMDataBank | EMD-9176 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RRk16 (bolus) | EMDataBank | EMD-9180 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RVh16 (2w pumps) | EMDataBank | EMD-9181 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RYm16 (2w pumps) | EMDataBank | EMD-9185 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RWr16 (2w pumps) | EMDataBank | EMD-9184 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RQq16 (2w pumps) | EMDataBank | EMD-9179 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RWh16 (4w pumps) | EMDataBank | EMD-9183 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM ROw16 (4w pumps) | EMDataBank | EMD-9178, EMD-9186 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RTh16 (4w pumps) | EMDataBank | EMD-9182 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RFr16 (4w pumps) | EMDataBank | EMD-9177 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM 145–11 (bolus) | EMDataBank | EMD-0571 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RHw16(bolus) | EMDataBank | EMD-0580 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RAa14 (bolus) | EMDataBank | EMD-0575 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM 5N6 (bolus) | EMDataBank | EMD-05694e |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM REj15 (bolus) | EMDataBank | EMD-0578 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM REv16 (bolus) | EMDataBank | EMD-0579 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RAv16 (ED) | EMDataBank | EMD-0576, EMD-0577 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM B077(ED) | EMDataBank | EMD-0573, EMD-0574 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM BM57 (ED) | EMDataBank | EMD-0572 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM 99–13(ED) | EMDataBank | EMD-0570 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RMI15 (ED) | EMDataBank | EMD-0581 |
| Negative stain EM map of polyclonal serum in complex with BG505 SOSIP.664 from RM RWo15 (ED) | EMDataBank | EMD-0582 |
| Negative stain EM map of BDA1 in complex with BG505 SOSIP.664 | EMDataBank | EMD-9138 |
| 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 | |
| Olionucleotides | ||
| CDS Oligo (dT): TTTTTTTTTTTTTTTTTTTTTTTTTVN | Integrated DNA Technologies, Inc. | |
| SMARTer II A Oligo: AAGCAGTGGTATCAACGCAGAGTACATrGrGrG | Integrated DNA Technologies, Inc. | |
| IgG Constant Primer: GCCAGGGGGAAGACCGATGGGCCCTTGGTGGA | Integrated DNA Technologies, Inc. | |
| IgK Constant Primer: GCGGGAAGATGAAGACAGATGGTGCAGCCACAG | Integrated DNA Technologies, Inc. | |
| IgL Constant Primer: GGCCTTGTTGGCTTGAAGCTCCTCAGAGGAGGG | Integrated DNA Technologies, Inc. | |
| P5_Seq BC_XX 5PIIA: CACGACGCTCTTCCGATCT 4–8xN AACCACTA AAGCAGTGGTATCAACGCAGAGT | Integrated DNA Technologies, Inc. | |
| P7_ i7_XX IgG: CAAGCAGAAGACGGCATACGAGATTAGTGGTT GCCAGGGGGAAGACCGATGGGCCCTTGGTGGA | Integrated DNA Technologies, Inc. | |
| P7_ i7_XX IgK: CAAGCAGAAGACGGCATACGAGATTAGTGGTT GCGGGAAGATGAAGACAGATGGTGCAGCCACAG | Integrated DNA Technologies, Inc. | |
| P7_ i7_XX IgL: CAAGCAGAAGACGGCATACGAGATTAGTGGTT GGCCTTGTTGGCTTGAAGCTCCTCAGAGGAGGG | Integrated DNA Technologies, Inc. | |
| P5_Graft P5_seq: AATGATACGGCGACCACCGAGATCTACAC TCTTTCCCTACACGACGCTCTTCCGATCT | 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 |
| Appion database | (Lander et al., 2009) | |
| Leginon | (Suloway et al., 2005) | |
| DoG Picker | (Voss et al., 2009) | |
| Relion | (Scheres, 2012) | |
| FALCON-Unzip | (Chin et al., 2016) | |
| IMGT | http://www.imgt.org | |
| BLAT | (Kent, 2002) | |
| BLASR | (Chaisson and Tesler, 2012) | |
| BLAST | https://blast.ncbi.nlm.nih.gov/Blast.cgi | |
| MsPAC | https://bitbucket.org/oscarlr/mspac | |
| Integrated Genomics Viewer | (Robinson et al., 2011; Thorvaldsdóttir et al., 2013) | https://software.broadinstitute.org/software/igv/ |
| BALDR | (Upadhyay et al., 2018) | |
| FastQC v0.11.5 | (Andrew, 2010) | |
| Immcantation | (Gupta et al., 2015; Vander Heiden et al., 2014) | |
| IgBLAST v1.6.1 | (Ye et al., 2013) | |
| MUSCLE v3.8.1551 | (Edgar, 2004) | |
| CD-HIT v4.7 | (Fu et al., 2012) | |
| IMGT DomainGAPAlign | (Ehrenmann and Lefranc, 2011; Ehrenmann et al., 2010) | |
| MAFFT | (Katoh and Standley, 2013) | |
| FastTree2 | (Price et al., 2010) | |
| FigTree | http://tree.bio.ed.ac.uk/software/figtree/ | |
| ImageJ | https://imagej.nih.gov/ij/ | |
| Other | ||
| Mini-osmotic pumps (0.5uL/hr, 14 day release) | ALZET | Model 2002 |
| Mini-osmotic pumps (0.25uL/hr, 28 day release) | ALZET | Model 2004 |
| Costar Assay Plate, 96 well flat-bottom, half area, high binding | Corning | Cat # 3690 |