Computational protocol: Effect of vitamin C on azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced colitis-associated early colon cancer in mice

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Protocol publication

[…] The V3-V4 variable regions of 16S rRNA were targeted and amplified by PCR with barcode primers (27F and 518R). The following microbiome analysis steps were followed: barcode sorting, quality prescreening, trimming primer sequences, removing non-target sequences, assemble sequence for de-noise, taxonomic assignment, and chimera checking. The mechanisms were processed in Illumina Miseq software (ChunLab, Inc., Seoul, Korea). Operational taxonomic units (OTUs) were determined by XOR analysis in the CL community program (Chunlab Inc, Seoul, Korea). Microbiota were classified toxonomically based on the ExTaxon-e database with a 97% sequence similarity cutoff. The number of OTUs present in each sample was used to define species richness and diversity. In addition, the Chao 1 and Shannon estimator were used to calculate microbiota richness and diversity in Mothur and a distance matrix was created in Fast UniFrac (Chunlab Inc.: Seoul, Korea). […]

Pipeline specifications

Software tools mothur, Fast Unifrac
Application 16S rRNA-seq analysis
Organisms Mus musculus, Homo sapiens, Lactococcus
Chemicals Ascorbic Acid, Azoxymethane