1. Study overview.
Study overview. (A) Terminal ilea from conventional and GF mice were quantitatively compared to produce the "ileum data set." Transcriptomics was used with DNA microarrays to produce the "transcriptome data subset," and the same ileum samples were also quantitatively compared using shotgun mass spectrometry to produce the “proteome data subset.” In addition, the “meta-analysis data set” was produced by analyzing microarray data from previous publications (the meta-analysis did not use any of the ileum data set). Genes significantly affected by germ status were analyzed using Ingenuity pathway analysis. GAS, gamma interferon (IFN-y)-activating sequence; ISRE, IFN-stimulated response element; TC-PTP, T-cell protein tyrosine phosphatase. (B) The transcriptome data subset was analyzed using an HCA (both rows and columns were clustered; gray = missing value). Each row depicts a microarray probe that was significantly affected by germ status (n = 3,817), and each column depicts an array. Each array was used to analyze two ilea (one conventional and 1 GF; sex and strain matched). Each standard deviation (σst) was calculated across the columns independently for each strain using the log2-transformed GF/C ratios. F, female; M, male. (C) The proteome data subset was analyzed using an HCA (only rows were clustered; gray = missing value). Each row depicts a protein group that was significantly affected by germ status (n = 242), and each column depicts a mouse. Each z score was calculated across the columns independently for each strain using the log2-transformed abundance values.
Nathan P. Manes et al. mSystems 2017; doi: /mSystems