DOI: 10.5061/dryad.kwh70rzd1
title: ZAP affects Zika virus RNA interactome- supplemental datasets 1 and 2

description: One of the most recent advances in the analysis of viral RNA–cellular
 protein interactions is the Comprehensive Identification of RNA-binding
 Proteins by Mass Spectrometry (ChIRP-MS). Here, we used ChIRP-MS in
 mock-infected and Zika-infected wild-type cells and cells knockout for the
 zinc finger CCCH-type antiviral protein 1 (ZAP). We characterized
 “ZAP-independent” and “ZAP-dependent” cellular protein interactomes
 associated with flavivirus RNA and found that ZAP affects cellular
 proteins associated with Zika virus RNA. The ZAP-dependent interactome
 identified with ChIRP-MS provides potential ZAP co-factors for antiviral
 activity against Zika virus and possibly other viruses. Identifying the
 full spectrum of ZAP co-factors and mechanisms of how they act will be
 critical to understanding the ZAP antiviral system and may contribute to
 the development of antivirals.
description: # ZAP affects Zika virus RNA interactome - supplemental datasets 1 and 2
 [https://doi.org/10.5061/dryad.kwh70rzd1](https://doi.org/10.5061/dryad.kwh70rzd1) Supplementary data ## Description of the data and file structure **Table S1** **- ChIRP-MS data** Table S1 ChIRP_MS data, **sheet** “**C Extended Zika interactome**” – Proteins with top 15 Spectral Counts are highlighted in red. RNA helicases are highlighted in yellow. Table S1 ChIRP_MS data, **sheet** “**D Reference Ooi et al., 2019**” – The same proteins in both studies are highlighted in red. Table S1 ChIRP_MS data, **sheet** “**F ZAP-independent interactome**” – Proteins with top 15 Spectral Counts are highlighted in red. Table S1 ChIRP_MS data, **sheet** “**H ZAP-dependent interactome**” – Proteins with top 15 Spectral Counts are highlighted in red. RNA helicases are highlighted in yellow. The empty cells in files are a result of the programs used. **Supplemental Materials and Methods.** The file contains experimental details. **Supplemental Dataset 1.** This dataset contains 26 raw fastq files representing paired-end NGS data for input and enriched samples described in results and in Figure 2D. The dataset also contains the "Zika virus NGS sample IDs" file which provides identifications for raw files and experimental conditions (VERO-ZAP-WT or VERO-ZAP-KO cells; MOCK or Zika virus; input or enriched samples; replicate number). **Supplemental Dataset 2.** This dataset contains the folder “RAWfiles” with 12 Mass spectrometry RAW data files representing three biological replicates for MOCK and Zika virus-infected VERO-ZAP-WT and VERO-ZAP-KO cells. The folder “MSFragger” contains the output of FragPipe v18.0 which was used to analyze Mass spectrometry RAW data files as described in Supplemental Materials and Methods. The folder “MSFragger” contains data for individual samples, and the “combined_protein.tsv” file (also represented in Table S1B), which was used for the identification of Extended, ZAP-independent, and ZAP-dependent Zika virus RNA interactomes from ChIRP-MS results as described in Supplemental Materials and Methods. The "Zika virus ChIRP-MS sample IDs" file provides identifications for raw files and experimental conditions (VERO-ZAP-WT or VERO-ZAP-KO cells; MOCK or Zika virus; biological replicate number). “combined_protein.tsv” file is the output of FragPipe v18.0 and contains Spectral Counts from all experimental conditions. The empty cells in files are a result of the programs used. NA - not available.