Code for using Silver and Bighead Carp cell lines for the identification of a unique metabolite fingerprint from thiram-specific chemical exposure

This was a joint project between:

Upper Midwest Environmental Sciences Center, U.S. Geological Survey, La Crosse, WI 54603

La Crosse Fish Health Center, U.S. Fish and Wildlife Service, Onalaska, WI 54650

This repository contains the raw data and R codes used in the metabolomics analysis for the manuscript which used silver and bighead carp fry cells exposed to thiram.

Species indclude in this manuscript

• Silver Carp (Hypophthalmichthys molitrix)
• Bighead Carp (Hypophthalmichthys nobilis)

The raw data is in:

• BHC thiram data.csv
• SVC thiram data labels.csv

The code used in the ordination analysis is in:

• figure_1_knit_code.Rmd

The code used in the principle component analysis is in:

• figure_2_knit_code.Rmd

The code used in graphing additional figures are in:

• Figure 5: figure_5_knit_code.Rmd
• Figure 6: figure_6_knit_code.Rmd
• Supplemental Figure 1: Supplemental thiram figure.Rmd
• Supplemental Figure 2: Supplemental DMSO figure.Rmd
• Supplemental Figure 3: Supplemental DMSO response.Rmd

The output from Profinder software which cross references molecular mass with retention time and chemical formula

• list.formula.csv

Known bugs

These R codes works specifically for data in the .csv file. The R codes were not designed to work with additionally data.