Computational protocol: Transcriptional profiling of the effect of lipopolysaccharide (LPS) pretreatment in blood from probiotics-treated dairy cows

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Protocol publication

[…] Hybridization was done on the Agilent Bovine v2 4x44K gene expression microarray slide (Agilent Technologies, Santa Clara CA, USA) for 17 h. Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan default settings for 4x44k array slides. Signal intensity data were extracted with the Agilent Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (GE1-v5_95_Feb07) according to the manufacturer's protocol. Signal intensity data were extracted with the Agilent Feature Extraction Software (v 9.5.1). Data normalization and statistical analysis were performed using GeneSpring software 13.0 (Agilent Technologies, Santa Clara CA, USA). Boxwhisker, matrix, and scatter plots displaying the log ratio distribution of microarray data after normalization is shown in , , and respectively. The raw data are available from the NCBI GEO repository, under the accession number GSE75240.In conclusion probiotics supplementation had an effect on the response to LPS exposure in bovine whole blood. Treatment with LPS resulted in 13,658 differentially expressed genes (fold change cutoff ≥ 2, P < 0.05), 3816 upregulated genes and 9842 downregulated genes. Exposure to LPS had specific effects on Toll-like receptors genes expression including TLR4, TLR2 and TLR7. Thus, probiotic supplementation may modulate the response to gram negative bacteria. […]

Pipeline specifications

Software tools Agilent Feature Extraction, GeneSpring GX
Application Gene expression microarray analysis
Organisms Bos taurus
Diseases Bacterial Infections