Supporting data and methods for "Evidence for NMN deamidation by host-microbiome interactions" by Kim LJ et al, FEBS Letters 2023
Raw data, analytical methods and statistics contained in submission "Nicotinamide mononucleotide (NMN) deamidation by host-microbiome interactions" by Kim LJ et al 2023.
Steps to reproduce
MICROBIOME SEQUENCING Download the two QZA files and the R script "microbiome_analysis.R" to the root folder of a new project in RStudio. The script is annotated to show steps used in data processing, and provides options for generating figures at different taxonomic levels - Supp Fig 1 is shown at the genus level. It may be necessary to install packages listed in the script under the "library()" commands, these can be downloaded using "install.packages()" for the package of interest, before running the rest of the script. METABOLOMICS Download the CSV files which contain all data extracted from mass spectrometry runs (also available in .mat files) as well as the R scripts "Lynn_paper_cleaner_FEBS_R2.R" and "permutational_t_test_protocol.R" to a root folder of a new project in RStudio. Note that there are two versions of most CSV files, a second version with the suffix "_corrected". These readings have been subject to natural isotope correction using the isocorrectoR algorithm, as described in methods of the paper. Data shown in Fig. 7 and Supp. Fig. 3 of the paper were generated in GraphPad Prism, with the file for this containing data, figures and illustrations also attached. GIT stands for "gastrointestinal tissue".
National Health and Medical Research Council
American Federation for Aging Research
AFAR/Hevolution New Investigator