Additional file 1: Figure S1. of Epithelial response to a high-protein diet in rat colon

Plot of the first and the second principal component (PC1 and PC2) of the PCA analysis of microarray data. a - Results of the PCA with all the samples (n = 16). #: Samples considered as outliers. b – Results of the PCA after removal of the two outliers (n = 14). Samples of rats fed a high-protein diet are in black and samples from rats fed a normal-protein diet are in red. (PDF 27 kb

Primers used in real time PCR assays.

<p>Primers used in real time PCR assays.</p

Immunohistochemical detection of influenza A antigen in chicken embryos at 24-inoculation.

<p>(A) Brain; Wt group. Extensive immunostaining was observed in endothelial cells (arrowheads) and well as multifocal areas of brain parenchyma involving neurons (arrow). (B) Brain; ΔF2 group. There were occasional small foci of endothelial (arrows) and parenchymal (arrowhead) staining. (C) Liver; Wt group. There is extensive immunostaining of sinusoidal lining cells as well as scattered hepatocytes. (D) Liver, ΔF2 group. There was mild immunostaining of individual sinusoidal lining cells (arrows).</p

Global analysis of PB1-F2-dependant gene expression changes in the lungs of influenza infected chickens at day 2 pi.

<p>(A) Distribution of genes differentially regulated between wt- and ΔF2-infected chicken lungs. Major functions according to GO annotated function are indicated for each category of regulated genes. (B) Canonical pathways associated to differentially expressed genes were compared using Ingenuity Pathways Analysis. Canonical pathways are ranked using the p-value obtained using the right-tailed Fisher's exact test, it represents the probability of each biological function to be involved in the group of analyzed genes.</p

Additional file 8: Figure S5. of Epithelial response to a high-protein diet in rat colon

Tight-junction signaling canonical pathway diagram. This pathway was significantly enriched in the set of genes regulated by the high-protein diet. The diagram was obtained from Ingenuity Pathway Analysis software and depicts genes implicated in this pathway and their interactions. Expression of genes colored in green were downregulated (q < 0.1) in colonocytes of rats fed a high-protein diet when compared to a normal-protein diet. (PDF 465 kb

Comparison of Nig06 PB1-F2 impact on the lung host-response in chicken and mouse.

<p>(A) Scatter plot comparing wt-infected chickens vs. ΔF2-infected chicken lung transcriptomes at day 2 pi. Genes selected for ontological analysis are highlighted. (B) Scatterplot comparing wt-infected mice vs. ΔF2-infected mice lung transcriptomes at day 2 pi. (C) Distribution of major GO functions associated to genes regulated by PB1-F2 in infected chicken lungs. (D) Distribution of major GO functions associated to genes regulated by PB1-F2 in infected mouse lungs. (E) Canonical pathways associated to differentially expressed genes in chicken and mouse were compared using Ingenuity Pathways Analysis and ranked with the p-value obtained using the right-tailed Fisher's exact test.</p

Additional file 6: Table S3. of Epithelial response to a high-protein diet in rat colon

List of Ingenuity Pathway Analysis software canonical pathways significantly enriched (p < 0.05) in the set of genes differentially expressed in colonocytes of rats fed a high-protein diet compared to rats fed a normal protein diet. (.xls). (XLSX 67 kb

Additional file 5: Table S2. of Epithelial response to a high-protein diet in rat colon

List of Ingenuity Pathway Analysis software biological categories and functions significantly enriched (p < 0.05) in the set of genes differentially expressed in colonocytes of rats fed a high-protein diet compared to rats fed a normal protein diet. (.xls). (XLSX 125 kb