Lists of DEGs between LPS stimulated and unstimulated PBMCs. For every effect studied (LPS, and interaction effects: LPS:Fam1, LPS:Fam2) the list of genes differentially expressed at false discovery rate < 0.001 with log 2 fold changes is given. (XLSX 198 kb

Alicja Pacholewska

Eliane Marti

Tosso Leeb

Vidhya Jagannathan

Vincent Gerber

PubMed

Springer - Publisher Connector

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

Alicja Pacholewska (705841)

Eliane Marti (157764)

Tosso Leeb (81674)

Vidhya Jagannathan (13914)

Vincent Gerber (171558)

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Additional file 4: of LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

Background

Lipopolysaccharide (endotoxin, LPS) is a strong inducer of the innate immune response. It is widespread in our environment, e.g. in house dust and contributes to asthma. Compared to humans, horses are even more sensitive to LPS. However, data on LPS effects on the equine transcriptome are very limited. Using RNA-seq we analysed LPS-induced differences in the gene expression in equine peripheral blood mononuclear cells at the gene and gene-network level in two half-sib families and one group of unrelated horses.



Results

24 h-LPS challenge of equine immune cells resulted in substantial changes in the transcriptomic profile (1,265 differentially expressed genes) showing partial overlap with human data. One of the half-sib families showed a specific response different from the other two groups of horses. We also identified co-expressed gene modules that clearly differentiated 24 h-LPS- from non-stimulated samples. These modules consisted of 934 highly interconnected genes and included genes involved in the immune response (e.g. IL6, CCL22, CXCL6, CXCL2), however, none of the top ten hub genes of the modules have been annotated as responsive to LPS in gene ontology.



Conclusions

Using weighted gene co-expression network analysis we identified ten co-expressed gene modules significantly regulated by in vitro stimulation with LPS. Apart from 47 genes (5%) all other genes highly interconnected within the most up- and down-regulated modules were also significantly differentially expressed (FDR < 0.05). The LPS-regulated module hub genes have not yet been described as having a role in the immune response to LPS (e.g. VAT1 and TTC25)

Pacholewska, Alicja

Marti, Eliane Isabelle

Leeb, Tosso

Jagannathan, Vidhya

Gerber, Vinzenz

Bern Open Repository and Information System (BORIS)

Data used for the analysis in R. An RData file that contains compressed objects required for the differential expression and co-expression analyses with the script from Additional file 1. It contains the count and design tables. (RDATA 2007Â kb

Additional file 2: of LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

http://dx.doi.org/10.1186/s12864-016-3390-y

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells

Abstract

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