The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide
1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh EH25 9RG, United Kingdom
2 Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, 81679, Munich, Germany
3 Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
4 Innate Immunity Laboratory, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland QLD 4072, Australia
5 Department of Animal Science, Iowa State University, Ames, IA 50011, USA
BMC Genomics 2013, 14:581 doi:10.1186/1471-2164-14-581Published: 28 August 2013
Additional file 1:
Full list of clusters of pig macrophage gene expression using Biolayout. We analysed the 140 pigs micro-arrays (BMDM, MDM and AM - at 2 timepoint 0 h and 7 h using a Pearson correlation (R=0.91). The graph was composed of 5203 nodes and 29799 edges. In order to more easily differentiate the data from background noise, probesets with expression <50 in all samples have been removed from the analysis. List of all 505 clusters, using a MCL algorithm (MCL = 2.2), with the probeset number, the gene name, the gene description and the cluster number.
Format: XLSX Size: 196KB Download file
Additional file 2:
Full list of gene differentially regulated between compartment at homeostasis. Microarrays were analysed using the Partek software. (1) 49 probesets DR with a p adj. value < 0.01 and fold change > 30 or <-30 between AM and BMDM at homeostasis (0h) were listed. (2) List of the 144 probesets DR between MDM and BMDM at 0 h (p adj. value < 0.01 and fold change > 2 or <-2). (3) List of the 3322 probesets DR between AM and BMDM at 0h (p adj. value < 0.01 and fold change > 2 or <-2). (4) List of the 3058 probesets DR between AM and MDM at 0h (p adj. value < 0.01 and fold change > 2 or <-2).
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Additional file 3:
DR genes after LPS stimulation. Genes differentially expressed with p adj. value < 0.01 and upregulated (1) or down-regulated (2) (fold change > 2 or < -2) in the 3 types of macrophages between 0 h and 7 h after lps stimulation. Genes DR between the 5 breeds (p <0.01 and fold change >3 or <-3) in AM (3), BMDM (4) and MDM (5).
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Additional file 4:
Genes differentially regulated between the 5 breeds in BMDM and MDM. As in Figure 6, list of genes DR in BMDM and MDM after 7 h of LPS stimulation were grouped and included into a heat-maps (A and B respectively). DU is in red, HAM in blue, LR in green, LW in purple and PIE in yellow. The blue colour in the heat-map represents down-regulation of the gene and the red up-regulation of the gene in function to the average expression of the probeset. Duplicated probesets were removed, a total of 38 different genes for BMDM and 65 for MDM were plotted (p <0.01 and fold change >3 or <-3).
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Additional file 5:
Inter-species Comparison. (1) Using the human-mouse comparison data from Schroder et al. , we kept 2,058 genes with a known pig orthologue. From this list, we selected 834 genes for the analysis that are significantly different between human and mouse after 6 h of LPS stimulation (p<0.01). (2) Using Biolayout 3D, we could cluster genes expression into 8 groups using a Pearson correlation (R=0.85, MCL=2.2). (3) List of all neighbouring nodes of IDO1 (142 genes) and NOS2 (143 genes). 33 genes were found having a correlation higher than 0.95 with IDO1 and 40 genes had a correlation with NOS2A > 0.95.
Format: XLSX Size: 250KB Download file
Additional file 6:
The table have been sorted for each type of cell (MDM in blue, BMDM in red and AM in green) from the probeset with the largest variance to the smallest. The % of Variance id in the SED/Mean*100.
Format: XLSX Size: 73KB Download file