| Antibodies |
|
| Monoclonal mouse anti-VEEV antibody 1A4A-1 |
Roehrig and Mathews104
|
N/A |
| TruStain FcX monoclonal rat anti-mouse CD16/32 |
BioLegend |
Cat#101320; RRID:AB_1574975 |
| FITC anti-mouse CD45.1 clone A20 |
BioLegend |
Cat#110705; RRID:AB_313494 |
| APC anti-mouse CD45.2 clone 104 |
BioLegend |
Cat#109813; RRID:AB_389210 |
| BV421 anti-mouse CD45 clone 30-F11 |
BioLegend |
Cat#103133; RRID:AB_10899570 |
| BV650 anti-mouse CD19 clone 6D5 |
BioLegend |
Cat#115541; RRID:AB_11204087 |
| BV421 anti-mouse TCR-β clone H57-597 |
BioLegend |
Cat#109229; RRID:AB_10933263 |
| BV570 anti-mouse CD8α clone 53-6.7 |
BioLegend |
Cat#100739; RRID:AB_10897645 |
| PerCP/Cyanine5.5 anti-mouse CD4 clone RM4-5 |
BioLegend |
Cat#100540; RRID:AB_893326 |
| PE/Cyanine7 anti-mouse NK1.1 clone PK136 |
BioLegend |
Cat#108713; RRID:AB_389363 |
| APC anti-mouse/human CD11b clone M1/70 |
BioLegend |
Cat#101211; RRID:AB_312794 |
| PE anti-mouse CD170 (Siglec-F) clone S17007L |
BioLegend |
Cat#155505; RRID:AB_2750234 |
| BV605 anti-mouse Ly6G clone 1A8 |
BioLegend |
Cat#127639; RRID:AB_2565880 |
| AF700 Ly6C clone HK1.4 |
BioLegend |
Cat#128023; RRID:AB_10640119 |
| Guinea pig polyclonal anti-NeuN clone A60 |
Millipore |
Cat#ABN90P; RRID:AB_2341095 |
| Rat monoclonal anti-GFAP clone 2.2B10 |
Thermo Fisher |
Cat#130300; RRID:AB_2532994 |
| Rabbit polyclonal anti-SOX9 |
Millipore |
Cat#AB5535; RRID:AB_2239761 |
| Rabbit polyclonal anti-Olig2 |
Millipore |
Cat#AB9610; RRID:AB_570666 |
| AF488 Donkey anti-guinea pig IgG |
Jackson ImmunoResearch |
Cat#706-545-148; RRID:AB_2340472 |
| AF647 Donkey anti-guinea pig IgG |
Jackson ImmunoResearch |
Cat#706-605-148; RRID:AB_2340476 |
| AF555 Donkey anti-rat IgG |
Thermo Fisher |
Cat#A48270; RRID:AB_2896336 |
| AF555 Donkey anti-rabbit IgG |
Thermo Fisher |
Cat#A31572; RRID:AB_162543 |
| AF546 Donkey anti-rabbit IgG |
Thermo Fisher |
Cat#A10040; RRID:AB_2534016 |
|
| Bacterial and virus strains |
|
| VEEV ZPC738 |
Anishchenko et al.,105 Hydeetal.,106 Ma et al.42
|
N/A |
| VEEV ZPC738-EGFP |
Sun et al.,107 Salimi et al.,62
|
N/A |
| SINV-VEEV TrD-GFP |
Paessler et al.,108 Ma et al.42
|
N/A |
| Madariaga Arg LL |
UTMB Arbovirus Reference Collection (Casals et al.,109 this paper) |
N/A |
|
| Critical commercial assays |
|
| MagMAX-96 Viral RNA Isolation Kit |
Applied Biosystems |
Cat#AM1836 |
| Taqman RNA-to-Ct 1-Step Kit |
ThermoFisher |
Cat#4392939 |
| RNA-Protein Co-Detection Ancillary kit |
Advanced Cell Diagnostics |
Cat#323180 |
| RNAscope H2O2 and Protease Reagents |
Advanced Cell Diagnostics |
Cat#322381 |
| RNAscope Multiplex Fluorescent Reagent Kit v2 |
Advanced Cell Diagnostics |
Cat#323100 |
| RNAscope Multiplex TSA Buffer |
Advanced Cell Diagnostics |
Cat#322809 |
| RNAscope 50X Wash Buffer |
Advanced Cell Diagnostics |
Cat#310091 |
| HRP-conjugated secondary Opal 650 Dye |
Akoya Biosciences |
Prod#FP1496A; Cat#OP-001005 |
| ViaDye Red Fixable Viability Dye Kit |
Cytek |
Cat#R7-60008 |
|
| Experimental models: Cell lines |
|
| Vero cells |
ATCC |
Cat#CCL-81; RRID:CVCL_0059 |
|
| Experimental models: Organisms/strains |
|
| C57BL/6J mice |
Jackson Laboratories |
Strain#000664; RRID:IMSR_JAX:000664 |
| C57BL/6J CD45.1 mice |
Jackson Laboratories |
Strain#002014; RRID:IMSR_JAX:002014 |
|
Ldlrad3Δ14/Δ14 mice |
Ma et al.42
|
N/A |
|
| Oligonucleotides |
|
| VEEV ZPC738 nsP3 forward: 5’-CAAGTCGAGGCAGACATTCA-3’ |
IDT PrimeTime Assay |
Custom (1 probe/2 primers) |
| VEEV ZPC738 nsP3 reverse: 5’-CAGGGTGTCAAGGATGGATAAA-3’ |
IDT PrimeTime Assay |
Custom (1 probe/2 primers) |
| VEEV ZPC738 nsP3 probe: 5’-/56-FAM/TGGTCCATT/ZEN/CCTCATGCATCCGAC/3IABkFQ/-3’ |
IDT PrimeTime Assay |
Custom (1 probe/2 primers) |
|
Mus musculus Gapdh primer + probe |
IDT PrimeTime Assay |
Mm.PT.39a.1 |
| VEEV ZPC738 RNAscope Probe |
ACD (Ma et al.42) |
Cat#876381 |
|
Ldlrad3 RNAscope Probe |
ACD (Ma et al.42) |
Cat#872101 |
|
| Software and algorithms |
|
| FlowJo |
BD Life Sciences |
V10.7.2; RRID:SCR_008520 |
| GraphPad Prism |
GraphPad |
V9.5.0; RRID:SCR_002798 |
| FIJI |
ImageJ2 |
V2.9.0/1.53t; RRID:SCR_002285 |
| NDP.view2 |
Hamamatsu |
V2 #U12388-01 |
| BioRender |
BioRender |
RRID:SCR_018361 |
|
| Other |
|
| Gibco 0.05% trypsin-EDTA |
Thermo Fisher |
Cat#25300054 |
| DNase I |
Sigma Aldrich |
Cat#D4263 |
