Computational protocol: Resistant Starches Protect against Colonic DNA Damage and Alter Microbiota and Gene Expression in Rats Fed a Western Diet123

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Protocol publication

[…] Data on body, organ, and digesta weights, digesta pH, and biochemistry are presented as the mean ± SEM for each treatment group. The effect of treatments was determined by 1-way ANOVA and differences between treatments were analyzed post hoc by Tukey’s honestly significant difference test. Relationships between measures were determined by Pearson correlation analysis. Analyses were performed using a SigmaStat statistical software program (SigmaStat 2.0 for Windows, SPSS). For the gene expression microarray array data, 1-way ANOVA and post hoc pairwise comparisons using Tukey’s honestly significant difference test were performed on the normalized gene expression data using R (R version 2.11.0, R Foundation for Statistical Computing). The gene expression qRT-PCR data were normalized (to the endogenous controls) and analyzed for differential expression by the same method.Principal components analysis (PCA) was carried out on normalized array signal intensities from the microbiota microarray using the Genespring 7.3 software program (Agilent Technologies). P < 0.05 was considered significant for all datasets. […]

Pipeline specifications

Software tools SPSS, GeneSpring GX
Applications Miscellaneous, Gene expression microarray analysis
Organisms Zea mays, Rattus norvegicus, Triticum aestivum
Diseases Colonic Diseases
Chemicals Ammonia, Butyrates, Phenol