KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Alexa Fluor 700 mouse anti-human CD3, clone SP34-2 | BD Biosciences | Cat#557917; RRID:AB_396938 |
| AmCyan mouse anti-human CD4, clone L200 | BD Biosciences | Cat#561488; RRID:AB_10693557 |
| PerCP-Cy5.5, mouse anti-human CD8α, clone SK1 | BD Biosciences | Cat#341051; RRID:AB_400209 |
| FITC, mouse anti-human TNFα, clone MAb11 | eBioscience | Cat#11-7349-82; RRID:AB_465424 |
| APC, mouse anti-human IFNγ, clone B27 | BD Biosciences | Cat#554702; RRID:AB_398580 |
| PE, mouse anti-human CD69, clone FN50 | BD Biosciences | Cat#557050; RRID:AB_396566 |
| PE-TexasRed, mouse anti-human CD28, clone CD28.2 | BD Biosciences | Cat#562296; RRID:AB_11151918 |
| mouse anti-human CCR7, clone 150503 | R&D systems | Cat#MAB197-100 |
| Pacific Blue, mouse anti-human CD3, clone SP34-2 | BD Biosciences | Cat#558124; RRID:AB_397044 |
| PE-Cy7 mouse anti-human CD4, clone L200 | BD Biosciences | Cat#560644; RRID:AB_1727474 |
| PE-Cy7 mouse anti-human CD4, clone L200 | BD Biosciences | Cat#564107; RRID:AB_2738596 |
| PE, mouse anti-human CD28, clone CD28.2 | BD Biosciences | Cat#561793; RRID:AB_396072 |
| FITC, mouse anti-human CD95, clone DX2 | BD Biosciences | Cat#555673; RRID:AB_2100496 |
| ECD, mouse anti-human CD69, clone FN50 | Biolegend | Cat#310942; RRID:AB_2564277 |
| Pacific Blue, mouse anti-human CCR7, clone 150503 | BD Biosciences | Cat#562555; RRID:AB_2728119 |
| FITC, mouse anti-human IFNγ, clone B27 | BD Biosciences | Cat#554700; RRID:AB_395517 |
| Alexa Fluor 700, mouse anti-human TNFα, clone MAb11 | BD Biosciences | Cat#557996; RRID:AB_396978 |
| mouse anti-human CD28, clone CD28.2 | BD Biosciences | Cat#555726; RRID:AB_396069 |
| mouse anti-human CD49d, clone L25 | BD Biosciences | Cat#340976; RRID:AB_400198 |
| mouse anti-human MHC-I, clone W6/32 | Lab-generated from hybridoma | N/A |
| mouse anti-human HLA-DR, clone G46.6 | BD Biosciences | Cat#556642; RRID:AB_396508 |
| PerCP-eFluor710, mouse anti-human CD8a, clone SK1 | Life Tech | Cat#46-0087-42; RRID:AB_1834411 |
| BV510, mouse anti-human CD4, Clone L200 | BD Biosciences | Cat#563094; RRID:AB_2738001 |
| PE, mouse anti-human CD69, Clone FN50 | eBioscience | Cat#12-0699-42; RRID:AB_10733526 |
| FITC, mouse anti-human TNFa, Clone MAB11 | BD Biosciences | Cat#552889m; RRID:AB_394518 |
| Bacterial and Virus Strains | ||
| SIVmac239 (in vitro) | Lab-generated | N/A |
| SIVmac239 (in vivo) | Lab-generated | Stock 20082 |
| E. coli DH10β | ThermoFisher Scientific | Cat#EC0113 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Pacific Blue, Streptavidin | BD Biosciences | Cat#563259, RRID:AB_2869475 |
| SIVmac239 Gag, Pol, Rev/Tat/Nef, Vif, Env peptides (15mer with 11 a.a. overlap) | NIH HIV Reagent Program | Gag=ARP-6204 Pol=ARP-6443 Rev=ARP-6448 Tat=ARP-6207 Nef=ARP-8762 Vif=ARP-6205 Env=ARP-6883 |
| VL9 peptide (VMAPRTLLL) | Genscript USA incorporated | N/A |
| Recombinant SIVmac251 pr55 Gag protein | NIH AIDS Reagent Program | ARP-13384 |
| Recombinant SIVmac239 gp120 Env protein | lab generated | N/A |
| Recombinant interleukin-2 | Genscript USA incorporated | Cat# Z00368-1 |
| Deposited Data | ||
| whole blood mRNA-seq data | GEO (Gene Expression Omnibus) | GSE205080 |
| Experimental Models: Cell Lines | ||
| Primary embryonic rhesus fibroblasts | Lab-generated | N/A |
| K562 cell line | ATCC | CCL-243 |
| RM3 cell line | Shared from the laboratory of Dr. David I. Watkins. | Described in publication: PMID 3116083 |
| Experimental Models: Organisms/Strains | ||
| Mauritian-origin Macaca fascicularis | Accredited vendors for each MCM listed in Table S1 | N/A |
| Macaca mulatta | Oregon National Primate Research Center | N/A |
| Oligonucleotides | ||
| sGAG21: 5′-GTCTGCGTCAT(dP)TGGTGCATTC-3′ | Biosearch Technologies | N/A |
| sGAG22: 5′-CACTAG(dK)TGTCTCTGCACTAT(dP)TGTTTTG-3′ | Biosearch Technologies | N/A |
| psGAG23: 5′-FAM-CTTC(dP)TCAGT(dK)TGTTTCACTTTCTCTTCTGCG-BHQ1-3′ | Biosearch Technologies | N/A |
| SIVnestF01: 5′-GATTTGGATTAGCAGAAAGCCTGTTG-3′ | Biosearch Technologies | N/A |
| SIVnestR01: 5′-GTTGGTCTACTTGTTTTTGGCATAGTTTC-3′ | Biosearch Technologies | N/A |
| Recombinant DNA | ||
| CyCMV 31908 bacterial artificial chromosome | Lab-generated | GenBank accession #ON109535 |
| pCEP4 mammlian expression vector | ThermoFisher | Cat# V04450 |
| Mafa-E*02:01:02 | Lab-generated | Described in publication: PMID 29150562 PMCID: PMC5736429 DOI: 10.4049/jimmunol.1700841 |
| Mafa-DR Alleles | Lab-generated | Described in publication: PMID 17384942 PMCID: PMC2836927 DOI: 10.1007/s00251-007-0209-7 |
| Software and Algorithms | ||
| FlowJo v10.8.1 | BD Biosciences | N/A |
| Prism v9.3.1 | GraphPad Software | N/A |
| FastQC | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | PMC4243306 |
| STAR v2.7.5 | https://github.com/alexdobin/STAR | PMC3530905 |
| R markdown code | https://github.com/galelab/Malouli_Signature_of_ddCyCMV-SIV_protection | Malouli_Signature_of_ddCyCMV-SIV_protection |
| Bowtie 2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | PMC3322381 |
| HTSeq v0.12 | Anders et al., Bioinformatics. 2015 | PMC4287950 |