Search

Lists of IPA canonical pathways significantly enriched for differentially expressed genes in non-depleted (0) and depleted RNA samples (protocol variants A and B) from pathogen-challenged and non-challenged udder quarters. Pathways are classified for being observed across all protocols (0, A or B) or shared between two or all three protocols. (PDF 214 kb)

Distribution of gene expression level (FPKM) for the depleted and non-depleted RNA samples from non-challenged udder samples. 0, A, and B represent the non-depleted or the depleted RNA samples (protocol variant A and B), respectively. (PDF 283 kb)

IGV screen shot of the read distribution across the PAEP gene for the E. coli challenged udder sample from cow 2. O, A and B represent the non-depleted or the depleted RNA samples (protocol variant A and B), respectively. Exon 6 is zoomed in for better demonstration of the position of the antisense capture oligonucleotide (see red line). (PDF 235 kb)

Additional file 2. Cell counts by parity. This file contains a table summarizing descriptive analysis of cell count by parity group (Results).

Additional file 1. Complete dataset. This file contains a table of the complete dataset from all enrolled cows used for descriptive analysis and statistical analysis (Materials and methods).

Additional file 3. Modulated mRNA concentrations after stimulating pbMEC, pbMFC, RAW 264.7 or MAC-T with E. coli 1303 for various times to illustrate basic and full-scale mRNA expression in these cell types. Values are means from two biological replica experiments, each assayed in duplicate (Âą SEM) of relative copy numbers; grey underlay, significant induction; red underlay, significant down regulation, fold change > 2, P < 0.05 vs. unstimulated control. Bonferroniâ s correction for multiple analyses was applied.

Additional file 4. Extent and kinetics of modulated mRNA concentrations after stimulating pbMEC, pbMFC, RAW 264.7 or boMdM (#434 and #561) with E. coli 1303 , S. aureus 1027 or S. uberis 233 for various times. Values are means from two biological replica experiments, each assayed in duplicate (± SEM) of fold changes relative to unstimulated controls; grey underlay, significant induction; red underlay significant down regulation, fold change > 2, P < 0.05 vs. unstimulated control. Bonferroni’s correction for multiple analyses was applied.

Additional file 1. Pathogen specific regulated gene expression in primary bovine monocyte-derived macrophages (boMdM). Extent and kinetics of modulated mRNA expression of TNF, IL6 and CCL20 after stimulating boMdM from three different animals (#434, #561, #996) with E. coli 1303, S. aureus 1027 or S. uberis 233 for various times. Values are means from two technical replicas (Âą SEM) of fold changes relative to unstimulated controls. Data are taken from Additional file 5.

Additional file 5. Pathogen specific regulated gene expression in primary bovine monocyte-derived macrophages (boMdM). Extent and kinetics of modulated mRNA concentrations after stimulating boMdM from three different animals (#434, #561, #996) with E. coli 1303, S. aureus 1027 or S. uberis 233 for various times. Values are means from two technical replicas (Âą SEM) of fold changes relative to unstimulated controls; grey underlay, significant induction, fold change > 2, P < 0.05 vs. unstimulated control. Bonferroniâ s correction for multiple analyses was applied.

Additional file 2. Sequences of the oligonucleotide primers used for real-time PCR quantification. List of the primers used for RT-qPCR, of the pertinent source files and the resulting amplicon sizes.