1. Materials and methods flow chart.
Materials and methods flow chart. (A1) Four groups of mice were used for DNA/RNA extraction: a mouse that was Smad3+/+ and H. hepaticus negative (S+H−) (top left), a mouse that was Smad3−/− and H. hepaticus negative (S−H−) (top right), a mouse that was Smad3+/+ and H. hepaticus positive (S+H+) (bottom left), and a mouse that was Smad3−/− and H. hepaticus positive (S−H+) (bottom right, three panels from one histological section). These three panels display the types of lesions found in the S−H+ mice: hyperplasia, adenoma, and mucinous carcinoma. Inflammatory infiltrates are indicated by arrowheads. Four out of 10 mice in the S−H+ group had tumors at the time of sacrifice. The three double-headed red arrows indicate the Smad3−/−, H. hepaticus, and combined effects. (A2) Dissection of mouse large intestine from the S−H+ group showing tumor locations in dotted red lines and site of cecal matter removal. (B1) Flow chart showing number of reads at each step of DNA analysis. Reads were aligned to PATRIC (48) with Taxoner64 (95). The last step of the DNA analysis feeds into the second step of the RNA analysis. (B2) Flow chart showing number of reads at each step of RNA analysis. Reads were aligned with Bowtie2 (97) and quantified/normalized with cuffquant/cuffnorm, part of the Cufflinks suite of tools (99).
Scott G. Daniel et al. mSystems 2017; doi: /mSystems