Murine colon: IL-10-/- versus BALB/c
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ABSTRACT:
ORGANISM(S): Mus musculus Rattus norvegicus Human gammaherpesvirus 8 JC polyomavirus Betapolyomavirus macacae Homo sapiens Human immunodeficiency virus 1 Murid gammaherpesvirus 4 Human betaherpesvirus 5 Human alphaherpesvirus 1 Betapolyomavirus hominis human gammaherpesvirus 4 Murid betaherpesvirus 1
PROVIDER: GSE31706 | GEO | 2012/01/01
SECONDARY ACCESSION(S): PRJNA145451
REPOSITORIES: GEO
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Project description:MicroRNA profiling of mouse colonic tissue comparing severe colon pathology with mild and no pathology. Three condition experiment: BALB/c (No Pathology Control), IL-10-/- with Pathology = 1, IL-10-/- with Pathology > 3. Biological replicates were pooled RNA samples of 3 separate mice per condition.
2012-01-01 | E-GEOD-31706 | biostudies-arrayexpress
Project description:Inappropriate response to normal intestinal bacteria is involved in the development of Inflammatory Bowel Diseases (IBD, e.g. Crohn’s Disease (CD), ulcerative colitis (UC)) and variations in the host genome may mediate this process. IL-10-/- mice develop CD-like colitis mainly in the colon, in part due to inappropriate responses to normal intestinal bacteria including Enterococcus strains. Comprehensive characterization of changes in gene expression associated with the observed inflammation in the IL-10-/- mouse model has yet to be reported. Our aim was to characterize changes in colonic gene expression in IL-10-/- and C57BL/6J (C57; control) mice resulting from oral bacterial inoculation with 12 Enterococcus faecalis and faecium (EF) strains isolated from calves or poultry, complex intestinal flora (CIF) collected from healthy control mice, or a mixture of the two (EF•CIF). At 12 weeks of age, total RNA extracted from intact colon was hybridized to Agilent 44k mouse arrays. Lists of differentially expressed genes were generated using linear models for microarray analysis (Bioconductor), and genes clustered using GeneSpring GX and Ingenuity Pathways Analysis software. Intestinal inflammation was increased in IL-10-/- mice as a result of inoculation, with the strongest effect being in the EF and EF.CIF groups; expression of >4,000 gene probes was altered in colon tissue compared with similarly inoculated C57 mice. Genes differentially expressed in IL-10-/- mice as a result of EF or EF.CIF inoculation were associated with the following pathways: inflammatory disease (111 genes differentially expressed), immune response (209 genes), antigen presentation (11 genes, particularly major histocompatability complex Class II), fatty acid metabolism (30 genes) and detoxification (31 genes). Our results suggest that the colonic inflammation in EF and EF.CIF-inoculated IL-10-/- mice is mediated by mechanisms similar to those of human IBD, in particular CD. Example logFC calculation This example describes the calculation of the fold-change value (logFC) for a single spot (in this case, spot 27222) for a single comparison. This calculation method was applied to generate all of the comparison data shown in the supplementary data files. The comparison in question is for: colon tissue from C57BL/6J mouse with EF.CIF treatment (represented by duplicate samples GSM307282 (Title: C57BL/6J_Colon_EF.CIF_Rep1_(Pool17)) and GSM307283 (Title: C57BL/6J_Colon_EF.CIF_Rep2_(Pool18)) vs. colon tissue from C57BL/6J mouse under conventional conditions (represented by duplicate samples GSM307270 (Title: C57BL/6J_Colon_Conventional_Rep1_(Pool5)) and GSM307271 (Title: C57BL/6J_Colon_Conventional_Rep2_(Pool6)) Important Note: Limma analysis maps the treatments on each slide to the M values which are by convention always log2(R) - log2(G). Because this experiment is a reference design, with the reference RNA always Cy5 (i.e. red, channel 2) and the treatment sample Cy3 (i.e. green, channel 1), and we are interested in the values of the treatment samples compared with the reference, the M values in the data files are displayed as log2(G) - log2(R) The average expression is what is important here, which is calculated from the normalized M values for the appropriate comparison of interest as follows: [1] Mean value for Spot 27222, for each treatment: C57BL/6J mouse, EF.CIF: = mean (0.26363587 (GSM307282), 0.05084283 (GSM307283)) = 0.15723935 C57BL/6J mouse, conventional = mean (1.42951674 (GSM307270),1.15444106 (GSM307271)) = 1.2919789 [2] Calculation of LogFC for the comparison of interest: The contrast of interest is C57BL/6J: EF.CIF vs Conventional, so by performing a subtraction of these values for the comparison of interest (i.e. (mean for EF.CIF) - (mean for Conventional), the common reference is cancelled out, thus: C57BL/6J: EF.CIF vs Conventional = 0.15723935 - 1.2919789 = -1.13473955 So, the fold-change value (logFC) for spot 27222 for the comparison in question (C57BL/6J: EF.CIF vs. Conventional) is: -1.13473955
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