This folder contains files and information associated with the publication "Antibody responses to Zika virus proteins in pregnant and non-pregnant macaques"

Manuscript byline: 

Antibody responses to Zika virus proteins in pregnant and non-pregnant macaques

Anna S. Heffron1*, Emma L. Mohr2*, Amelia Haj1, Connor R. Buechler1, Adam Bailey1, Dawn M. Dudley1, Christina M. Newman1, Mariel S. Mohns1, Michelle Koenig1, Meghan E. Breitbach1, Mustafa Rasheed1, Laurel M. Stewart1, Jens Eickhoff3, Richard S. Pinapati4, Erica Beckman4, Hanying Li4, Jigar Patel4, John C. Tan4, David H. O’Connor1

1Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison

2Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison

3Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison

4Roche Sequencing Solutions, Madison

Biorxiv link: https://doi.org/10.1101/352880

Journal link:

Animals:

• A1 - cy0879, Pegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection.
• A2 - cy0886, Pegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection.
• B1 - 411359, ZIKV-004
• C1 - 295022, ZIKV-002
• D1 - 448436, ZIKV-008
• D2 - 861138, ZIKV-011
• F1 - 393422, ZIKV-024
• F2 - 826226, ZIKV-024
• F3 - 912116, ZIKV-024
• G1 - 660875, ZIKV-005
• G2 - 827577, ZIKV-003
• H1 - 146523, ZIKV-019
• H2 - 858972, ZIKV-019
• H3 - 419969, ZIKV-019
• I1 - 776301, ZIKV-021

Datasets:

Please see the files stored below in the folders "analysis" and "Code and Data"

To generate the plots form the Peptide Arrays,

1. Download the zip file: R_Script and_Data Antibody responses to the Zika virus polypeptide.zip
2. Uncompress the file R_Script and Data Antibody Responses to the Zika Virus Polypeptide.zip file 351.3 MB (~4.25 GB)
3. • This compressed folder contains the raw data from the peptide arrays.
4. Open the R Markdown File (.RMD type) in R Studio and Run All
5. • The libraries should auto install if you have admin rights to the computer and the folders your libraries install.  
   • You may need to manually install some libraries that your computer was unable to automatically install.
6. The script maps the relative paths to where the script resides automatically with the rstudioapi.  

Recommended minimum 16GB RAM (8GB of available RAM to run the script), 8 GB of HD Space for data, Plots, RStudio, R and required libraries, and macOS 10.11+ operating system.

A processed dataset is included in the file "Code and Data" as "Peptide microarray compiled data.csv.zip."

1. This compressed CSV dataset was generated by the above script. 
2. For this data, the Log2 of fluorescence data of the peptide array was computed, and the corresponding Log2 Background Fluorescence Intensity was subtracted.  
3. The Sequences ID's, Protein Positions, Virus names, and select Regions were merged into this file using the 16-mer probe sequences. The file can be searched or sorted using any of these parameters.

Array designs:

Two array designs were used in this study. They are stored below in the folder "Array designs."