KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Alexa Fluor® 488 anti-mouse FOXP3 (clone: MF-14) | BioLegend | Cat#126406, RRID:AB_1089113 |
| Alexa Fluor® 647 Anti-Mouse/Human FOXP3 (clone: 3G3) | eBioscience | Cat#MA5-18160, RRID:AB_2539534 |
| Alexa Fluor® 700 anti-mouse CD44 (clone: IM7) | BioLegend | Cat#103026, RRID:AB_493713 |
| Alexa Fluor® 700 anti-mouse CD45.1 (clone: A20) | BioLegend | Cat#110724, RRID:AB_493733 |
| Alexa Fluor® 700 anti-mouse CD8a (clone: 53-6.7) | BioLegend | Cat#100730, RRID:AB_493703 |
| Alexa Fluor® 700 anti-mouse TCR b chain (clone: H57-597) | BioLegend | Cat#109224, RRID:AB_1027648 |
| Anti-Human Interferon Alpha/Beta Receptor Chain 2 mAb (clone MMHAR-2) | R&D Systems | Cat#21385-1, RRID:AB_354167 |
| Anti-Mouse IFNAR-1 Purified (clone: MAR1-5A3) | Leinco Technologies | Cat#I-400, RRID: N/A |
| APC anti-mouse CD11c (clone: N418) | BioLegend | Cat#117310, RRID:AB_313779 |
| APC anti-mouse IFN-g (clone: XMG1.2) | BioLegend | Cat#505810, RRID:AB_315404 |
| APC anti-mouse IL-10 (clone: JES5-16E3) | BioLegend | Cat#505010, RRID:AB_315364 |
| APC anti-T-bet antibody (clone: 4B10) | BioLegend | Cat#644814, RRID:AB_10901173 |
| APC-conjugated I-Ab-PEPCK335-351 tetramer | NIH Tetramer Core Facility | N/A |
| APC/Cy7 anti-mouse CD4 (clone: RM4-5) | BioLegend | Cat#100526, RRID:AB_312727 |
| APC/Cy7 anti-mouse NK1.1 (clone: PK136) | BioLegend | Cat#108724, RRID:AB_830871 |
| BD Horizon BUV395 Rat Anti-Mouse CD4 (clone: GK1.1) | BD Biosciences | Cat#563790, RRID:AB_2738426 |
| BD Horizon BUV737 Hamster Anti-Mouse TCR b Chain (clone: H57-597) | BD Biosciences | Cat# 612821, RRID:N/A |
| BD Horizon BV395 Mouse Anti-Mouse CD45.2 (clone: 104) | BD Biosciences | Cat#564616, RRID:AB_2738867 |
| Brilliant Violet 421 anti-mouse I-A/I-E (clone: M5/114.15.2) | BioLegend | Cat#107631, RRID:AB_10900075 |
| Brilliant Violet 605 anti-mouse Ly-6C (clone: HK1.4) | BioLegend | Cat#128036, RRID:AB_2562353 |
| Brilliant Violet 650 anti-mouse TNF-a (clone: MP6-XT22) | BioLegend | Cat#506333, RRID:AB_2562450 |
| Brilliant Violet 711 anti-mouse CD11c (clone: N418) | BioLegend | Cat#117349, RRID:AB_2563905 |
| Brilliant Violet 421 anti-mouse TCR b chain (clone: H57-597) | BioLegend | Cat#109229, RRID:AB_10933263 |
| FITC anti-mouse CD11a (clone: M17/4) | BioLegend | Cat#101106, RRID:AB_312779 |
| FITC anti-mouse CD11a (clone: M17/4) | BioLegend | Cat#101106, RRID:AB_312779 |
| FITC anti-mouse CD45.2 (clone: 104) | BioLegend | Cat#109806, RRID:AB_313443 |
| FITC anti-mouse/human CD44 (clone: IM7) | BioLegend | Cat#103006, RRID:AB_312957 |
| InVivomAb anti-mouse CD4 (clone: GK1.1) | BioXCell | Cat#BE0003-1, RRID:AB_1107636 |
| InVivomAb anti-mouse IFNγ (clone: XMG1.2) | BioXCell | Cat#BP0055, RRID:AB_1107694 |
| Mouse IgG2A Isotype Control (clone: 20102) | R&D Systems | Cat#MAB003, RRID:AB_357345 |
| PE anti-mouse IL-10 (clone: JES5-16E3) | BioLegend | Cat#505008, RRID:AB_315362 |
| PE CD86 (clone: GL-1) | BioLegend | Cat#105008, RRID:AB_313151 |
| PE/Cy7 anti-mouse CD49d (clone: R1-2) | BioLegend | Cat#103618, RRID:AB_2563700 |
| PE/Cy7 anti-mouse IFN-g (clone: XMG1.2) | BioLegend | Cat#505826, RRID:AB_2295770 |
| PE/Cy7 anti-mouse Ly-6G (clone: 1A8) | BioLegend | Cat#127618, RRID:AB_1877261 |
| PE/Cy7 anti-mouse TNF-a (clone: MP6-XT22) | BioLegend | Cat#506324, RRID:AB_2256076 |
| PE/Dazzle 594 F4/80 (clone: BM8) | BioLegend | Cat#123146, RRID:AB_2564133 |
| PerCP/Cyanine5.5 anti-mouse CD4 (clone: RM4-5) | BioLegend | Cat#100540, RRID:AB_893326 |
| PerCP/Cyanine5.5 anti-mouse/human CD11b (clone: M1/70) | BioLegend | Cat#101228, RRID:AB_893232 |
| Ultra-LEAF Purified anti-human HLA-DR (clone: L243) | BioLegend | Cat#307648, RRID:AB_2561493 |
| Ultra-LEAF Purified Mouse IgG2a, K Isotype Control Antibody (clone: MOPC-173) | BioLegend | Cat#400264, RRID:AB_11148947 |
| Bacterial and Virus Strains | ||
| L. donovani amastigotes | Clinical isolates from VL patients at Kala-azar Medical Research Center, Muzaffapur, Bihar, India | N/A |
| L. donovani amastigotes (LV9; MHOM/ET/67/HU3) | Bradley and Kirkley (1977) | N/A |
| Biological Samples | ||
| PBMCs from healthy endemic controls | Kala-azar Medical Research Center, Muzaffapur, Bihar, India | N/A |
| PBMCs from visceral leishmaniasis patients | Kala-azar Medical Research Center, Muzaffapur, Bihar, India | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 2-Mercaptoethanol | Sigma-Aldrich | Cat#M6250 |
| Amphotericin liposomal 50 mg powder for injection, AmBisome® | Gilead Sciences | N/A |
| BD Cytofix Fixation Buffer Set | BD Biosciences | Cat#554714 |
| Brefeldin A | Sigma-Aldrich | Cat#6542 |
| DAPI for nucleic acid staining | Sigma-Aldrich | Cat#D9542 |
| Dextran, Fluorescein | Life Technologies | Cat#D7137 |
| eBioscience Foxp3/Transcription Factor Staining Buffer Set | Thermo Fisher Scientific | Cat#00-5523-00 |
| EDTA | Amresco | Cat#E177-500ML |
| Ficoll (Lymphoprep) | Stem Cell | Cat#7861 |
| Giemsa stain, modified | Sigma-Aldrich | Cat#GS500 |
| Medium 199, Hanks’ Balanced Salts | Thermo Fisher | Cat#12350039 |
| Monensin Solution (1,000X) | BioLegend | Cat#420701 |
| Neomycin trisulfate salt hydrate powder | Sigma-Aldrich | Cat#N1876-100G |
| N,N-Dimethylactamide anhydrous | Sigma-Aldrich | Cat#271012-100ML |
| N-acetyl-L-leucyl-L-leucyl-L-argininal | Amresco | Cat#J580-5MG |
| Percoll density gradient media | GE Healthcare | Cat#17089101 |
| Phenylmethanesulphonyl fluoride (PMSF) | HiMedia | Cat#RM1592 |
| Phorbol 12- myristate 13-acetate | Sigma-Aldrich | Cat#P8139 |
| ProLong Gold Antifade | Invitrogen | Cat#P36934 |
| Recombinant Mouse IFN-gamma Protein | R&D Systems | Cat#485-MI |
| Red blood cell lysing buffer Hybri-Max | Sigma-Aldrich | Cat#R7757 |
| RNAlater | Invitrogen | Cat#AM7021 |
| Ruxolitinib | ChemieTek | Cat#CT-INCB |
| Ruxolitinib, 5 mg | Santa Cruz Biotechnology | Cat#sc-364729 |
| Tissue-Tek® O.C.T. Compound | Sakura | Cat#4583 |
| Trizma® hydrochloride solution (TRIS-HCl) | Sigma-Aldrich | Cat#T2444 |
| Trypan blue stain (0.4%) for use with Countess Automated Cell Counter | Invitrogen | Cat#T10282 |
| Zombie Aqua fixable viability dye kit | BioLegend | Cat#423102 |
| Critical Commercial Assays | ||
| Agencourt AMPure XP | Beckman Coulter | Cat#A63881 |
| BD Cytometric Bead Array – Mouse IFN-γ Flex Set | BD Biosciences | Cat#558296 |
| BD Cytometric Bead Array – Mouse IL-10 Flex Set | BD Biosciences | Cat#558300 |
| BD Cytometric Bead Array – Mouse TNF Flex Set | BD Biosciences | Cat#558299 |
| DNA 1000 Kit | Agilent | Cat#5067-1504 |
| DNase Max Kit (50) | QIAGEN | Cat#15200-50 |
| ELISA MAX Deluxe Set Human IFNγ | BioLegend | Cat#430104 |
| High-capacity cDNA Reverse Transcription Kit | Thermo Fisher | Cat#4368814 |
| LS Columns | Miltenyi Biotec | Cat#130-042-401 |
| MACS CD1c (BDCA-1)+ Dendritic Cell Isolation Kit, human | Miltenyi Biotec | Cat#130-119-475 |
| MACS CD4 MicroBeads, human | Miltenyi Biotec | Cat#130-045-101 |
| MACS CD11c MicroBeads UltraPure, mouse | Miltenyi Biotec | Cat#130-108-338 |
| MACS CD14 MicroBeads, human | Miltenyi Biotec | Cat#130-050-201 |
| MACS CD19 MicroBeads, human | Miltenyi Biotec | Cat#130-050-301 |
| MS Columns | Miltenyi Biotec | Cat#130-042-201 |
| NextSeq 500/550 High Output Kit v2 (150 cycles) | Illumina | Cat#FC-404-2002 |
| QIAshredder (50) | QIAGEN | Cat#79654 |
| Qubit DNA HS Assay Kit | Life Technologies | Cat#Q32854 |
| Qubit RNA HS Assay Kit | Thermo Fisher | Cat#Q32852 |
| RNA 6000 Nano kit | Agilent Technologies | Cat#5067-1511 |
| RNase-Free DNase Set (50) | QIAGEN | Cat#79254 |
| RNeasy Mini Kit (50) | QIAGEN | Cat#74104 |
| Superscript III Reverse Transcriptase | Life Technologies | Cat#18080044 |
| TruSeq Stranded mRNA Library Prep Kit High Throughput (96 samples, 96 indexes) | Illumina | Cat#RS-122-2103 |
| Deposited Data | ||
| Peripheral blood CD4+ T cells isolated from L. donovani-infected patients, RNA-seq data | This paper | European Genome-phenome Archive (EGA) database accession number EGAS00001004152 |
| Experimental Models: Organisms/Strains | ||
| B6.129P2-Lyz2tm1(cre)lfo/J | Bred in house; Clausen et al. (1999) | RRID: IMSR_JAX:004781 |
| B6.129S4-Ccr2tm1lfc/J | Bred in house; Boring et al. (1997) | RRID: IMSR_JAX:004999 |
| B6.129S7-Rag1tm1Mom/J | Bred in house; Mombaerts et al. (1992) | RRID: IMSR_JAX:002216 |
| B6.(Cg)-Ifnar1tm1.1Ees/J | Bred in house; Prigge et al. (2015) | RRID: IMSR_JAX:028256 |
| B6.(Cg)-Ifnar1tm1.2Ees/J | Bred in house; Prigge et al. (2015) | RRID: IMSR_JAX:028288 |
| B6.Ifnar1ΔDC | Bred in house; This paper. | N/A |
| B6.Ifnar1ΔLysM | Bred in house; This paper. | N/A |
| B6.Cg-Tg(Itgax-cre)1-1Reiz/J | Bred in house; Caton et al. (2007) | RRID: IMSR_JAX:008068 |
| B6.SJL-PtprcaPepcb/BoyJArc | Australian Resource Centre | RRID: IMSR_JAX:002014 |
| C57BL/6JArc | Australian Resource Centre | RRID: IMSR_ARC:B6 |
| Oligonucleotides | ||
| Eukaryotic 18S rRNA Endogenous Control (VIC/MGB probe, primer limited) | Thermo Fisher | Cat#:4319413E |
| TaqMan Gene Expression Assay (FAM MGB) – human IFNB1 (Hs01077958_s1), human IFNA1 (Hs00855471_g1), human IFNAR1 (Hs01066118_m1), human IFNAR2 (Hs01022060_m1). | Thermo Fisher | Cat#4331182 |
| TaqMan MGB Probe - mouse Il12p40 (Mm00434174_m1), mouse Tnf (Mm0041889_m1), Il10 (Mm01288386_m1), Hprt (Mm01318743_m1), b2m (Mm00437762_m1) | Applied Biosciences | Cat#4331182 |
| Software and Algorithms | ||
| Adobe Illustrator, V23.0.3 | Adobe. https://www.adobe.com/ | N/A |
| Cutadapt, v1.11 | Martin, 2011 | N/A |
| EdgeR | Robinson et al. (2010) https://bioconductor.org/packages/release/bioc/html/edgeR.html | N/A |
| FACSDiva, v8.0 | BD Biosciences https://www.bdbiosciences.com/en-us/instruments/research-instruments/research-software/flow-cytometry-acquisition/facsdiva-software | N/A |
| FCAP Array Software, v3.0 | BD Biosciences. https://www.bdbiosciences.com/us/applications/research/bead-based-immunoassays/analysis-software/fcap-array-software-v30/p/652099 | Cat#652099 |
| FlowJo, v10 OSX | FlowJo, LLC. https://www.flowjo.com/ | N/A |
| GraphPad Prism 7, v7.0c | GraphPad Software. https://www.graphpad.com/scientific-software/prism/ | N/A |
| Ingenuity Pathway Analysis (IPA), winter 2018 release | QIAGEN https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/content-exploration-and-databases/qiagen-ipa/ | N/A |
| R Project for Statistical Computing | https://www.r-project.org/ | RRID: SCR_001905 |
| RNA-SeQC, v1.1.8 | DeLuca et al. (2012) | N/A |
| RSEM, V1.2.30 | Li and Dewey (2011) | N/A |
| RStudio Desktop, V1.0.136 - 1.2.1335 | https://rstudio.com/products/RStudio/ | N/A |
| Spliced Transcripts Alignment to a Reference (STAR), v2.5.2a | Dobin et al. (2013) https://github.com/alexdobin/STAR | N/A |
| Other | ||
| Ensembl (release 89) gene model | N/A | |
| GRCh37 assembly | https://m.ensembl.org/info/website/tutorials/grch37.html | N/A |