library_construction_protocol: Cells were washed with 0.04% w/v bovine serum albumin (BSA) in PBS and counted. Feature Barcoding was performed on moDCs prior to single cell RNAseq to label mock and ZIKV treated cells. Cells were blocked with Human TruStain FcX on ice for 10 minutes and then surface stained with BioLegend antibodies (TotalSeq™-C0253 anti-human Hashtag 3 Antibody and TotalSeq™-C0252 anti-human Hashtag 2 Antibody) on ice for 20 minutes. The 10X Genomics Chromium Next GEM Single Cell 5' v2 assay protocol (PN-1000264) was modified to be ZIKV-inclusive by adding a ZIKV-specific primer to the reverse transcription reaction mixture (Fig 1). All other steps were followed according to the manufacturer's protocol. The ZIKV-specific primer (5'-AAGCAGTGGTATCAACGCAGAGTACCCTTCCACAAAGTCCCTATTGC-3') was previously published by Lanciotti et al. (49) and modified to contain the non-poly-dT tag (underlined sequence) for cDNA amplification. After bead cleanup, cDNA was amplified 13 cycles, and gene expression (5' GEX) and feature barcoded libraries were generated using the 5' v2 Library Construction Kit (PN-1000190). 5' GEX libraries were constructed using cDNA that was first fragmented at 32ºC for 5 min. Each sample was indexed with the Dual Index Kit TT Set A plate (PN-1000215) for 14 cycles of 98ºC for 20s, 54ºC for 30s, 72ºC for 20s, with a final extension of 72ºC for 1 min. Amplified feature barcoded libraries were constructed using DNA from supernatant cleanup. Each sample was indexed with the Dual Index Kit TN Set A plates (PN-1000250) for cycles of 98ºC for 20s, 54ºC for 30s, and 72ºC for 20s, with a final extension of 72ºC for 1 min. For QC, final libraries un on a HS DNA chip on an Agilent Bioanalyzer 2100. The 5'GEX and feature barcoded libraries were pooled separately and then combined at an appropriate ratio in order to obtain the targeted read depth of 50,000/cell and 5,000/cell for the 5' GEX and feature barcoded libraries, respectively.