KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
mouse anti-ZIKVE/anti-flavivirus group antigen	Millipore	Cat# MAB10216, RRID:AB_827205
rabbit anti-SOX2	Abcam	Cat# AB97959, RRID:AB_2341193
rabbit anti-NeuN	Millipore	Cat# ABN78, RRID:AB_10807945
AGO 2A8 antibody	Millipore	Cat# MABE56, RRID:AB_11214388
Bacterial and Virus Strains
ZIKV prototype MR766	National Institutes of Health	LC002520.1
ZIKV Brazilian strain Paraiba	Stevenson Laboratory, University of Miami Life Science and Technology Park	KX280026.1
Chemicals, Peptides, and Recombinant Proteins
StemPro Neural Supplement	ThermoFisher	A1050901
Eagle’s Minimum Essential Medium	ATCC	30–2003
RNase I	Ambion	AM2295
RNA phenol/chloroform	Ambion	9722
32P-γ-ATP	Perkin Elmer	blu002250uc
Critical Commercial Assays
iScript One-Step RT-PCR kit	Bio-Rad	1708892
NEBNext Ultra II Directional RNA Library Kit for Illumina	NEB	E7760L
Q5 master mix	NEB	M0494S
miRNeasy Mini Kit	QIAGEN	217004
iScript Mastermix	Bio-Rad	1708891
SYBR Green PCR Master Mix	Bio-Rad	1725270
protein A/G Dynabeads	ThermoFisher	88802
4–12% NuPAGE Bis-Tris gels	Invitrogen	NP0321BOX
Superscript III reverse transcriptase	Invitrogen	18080093
precast 6% Tris/Borate/EDTA-urea gels	Invitrogen	EC6265BOX
Circligase II	Epicenter	CL9021K
Deposited Data
Raw and processed data	GEO	GSE113640
Raw and processed RNA-seq data	GEO	GSE113636
Raw and processed AGO-iCLIP-seq data	GEO	GSE113638
Raw and processed miRNA-seq data	GEO	GSE113639
Experimental Models: Cell Lines
Human neural stem cells	ThermoFisher	A15654
Vero	ATCC	CCL-81
Experimental Models: Organisms/Strains
B6.129S2-Ifnar1tm1Agt/Mmjax	MMRC Jackson Laboratories	32045-JAX
Oligonucleotides
RT-qPCR ZIKV-F: TTGGTCATGATACTGCTGATTGC	IDT	N/A
RT-qPCR ZIKV-R: CCCTCCACGAAGTCTCTATTGC	IDT	N/A
L3 linker (HPLC-purified): /5rApp/AGATCGGAAGAGCG GTTCAG/3ddC/	IDT	N/A
Cut oligo (PAGE-purified): GTTCAGGATCCACGACGCT CTTC/3ddC/	IDT	N/A
P5 Solexa PCR primer: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC TTCCGATCT	IDT	N/A
P3 Solexa PCR primer: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAAC CGCTCTTCCGATCT	IDT	N/A
RT1: /5phos/NnaaccNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC	IDT	N/A
RT2: /5phos/NNacaaNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC	IDT	N/A
RT3: /5phos/NNattgNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC	IDT	N/A
RT4: /5phos/NNaggtNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC	IDT	N/A
RT5: /5phos/NNcgccNNNAGATCGGAAGAGCGTCGT GgatcCTGAACCGC	IDT	N/A
RT6: /5phos/NNccggNNNAGATCGGAAGAGCGTCGTGgatcCTGAACCGC	IDT	N/A
Software and Algorithms
TopHat v 1.4.1	(Trapnell et al., 2009)	https://ccb.jhu.edu/software/tophat/index.shtml
PRINSEQ v 0.20.3		http://prinseq.sourceforge.net
SAMtools	(Li et al., 2009)	http://samtools.sourceforge.net
DESeq2	(Love et al., 2014)	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Partek		http://www.partek.com
The Database for Annotation, Visualization and Integrated Discovery (DAVID)	(Huang et al., 2009)	https://david.ncifcrf.gov
Cytoscape	(Shannon et al., 2003)	https://cytoscape.org
TargetScan	(Agarwal et al., 2015)	http://www.targetscan.org/vert_72/
miRTarBase	(Chou et al., 2016)	http://mirtarbase.mbc.nctu.edu.tw/php/index.php
miRANDA	(Betel et al., 2008)	http://cbio.mskcc.org/microrna_data/manual.html
pyCRAC	(Webb et al., 2014)	http://sandergranneman.bio.ed.ac.uk/pyCRAC_software
flexbar	(Dodt et al., 2012)	https://github.com/seqan/flexbar/wiki/Manual
Novocraft		http://www.novocraft.com
ChIPpeakAnno	(Zhu et al., 2010)	https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html
rtracklayer	(Lawrence et al., 2009)	https://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html
Supermatcher		http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/supermatcher.html
GraphPad Prism		https://www.graphpad.com