microbiome-in-DS

This repository contains the code allowing to reproduce the results of the analysis of the microbiome data, pre-published in the article: doi: https://doi.org/10.1101/2020.11.16.385989 Those data were obtained to determine the microbial content of the faecal microbiome samples from Wild Type and Down Syndrome model mice fed high-fat diet.

What is in the package?

• script to run seed-kraken
• python code to process the .csv files
• R code to analyse the data and visualise results (analysis.R)

The .csv files with microbial species counts generated by seed-kraken tool are available here: http://regulomics.mimuw.edu.pl/~ilona/microbiome_in_DS/

Usage

Run: analysis.R in RStudio to investigate all the steps of the analysis.

Content:

Figures:

• Differentially abundant species (DA) - DeSeq2
• Plotting the top DA species
• Plotting the most abundant species in DS and in WT mice
• Venn diagrams of species present in WT and DS
• Multidimensional Scaling Analysis (MDS)
• Hierarchical Clustering (HCL)
• Correlation of species within WT and DS mice
• Validation with total RNA HiSeq data - presence of species - Venn diagram
• Correlation of species abundances in 16S and total RNA HiSeq data

Supplementary Data and Figures:

• Numbers of reads per sample in 16S data
• Numbers of reads per sample in total RNA data
• Rarefaction curves in 16S data
• Rarefaction curves in total RNA data
• Validation with total RNA HiSeq data - presence of species - Venn diagram for each condition
• Correlation of species within WT and DS mice - validation in total RNA data