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Series GSE131607 Query DataSets for GSE131607
Status Public on Oct 22, 2019
Title Genetic mechanisms regulating the host response during mastitis
Organism Bos taurus
Experiment type Expression profiling by high throughput sequencing
Summary Mastitis is a very costly and common disease in the dairy industry. The study of the transcriptome from healthy and mastitic milk somatic cell samples using RNA-Sequencing technology (RNA-Seq) can provide measurements of transcript levels associated with the immune response to the infection. The objective of this study was to characterize the Holstein milk somatic cells transcriptome from 6 cows to determine host response to intramammary infections. RNA-Sequencing was performed on two samples from each cow from two separate quarters, one classified as healthy (n = 6) and one as mastitic (n = 6). In total, 449 genes were differentially expressed between the healthy and mastitic quarters (P-value < 0.01, FDR < 0.05, FC > ±2). Among the differentially expressed genes, the most expressed genes based on Reads Per Kilo base per Million mapped reads (RPKM) in the healthy group were associated with milk components (CSN2 and CSN3), and in the mastitic group they were associated with immunity (B2M and CD74). In-silico functional analysis was performed using the list of 449 differentially expressed genes, which identified 36 significantly enriched metabolic pathways (FDR < 0.01), some of which were associated with the immune system, such as cytokine-cytokine interaction and cell adhesion molecules. Seven functional candidate genes were selected, based on the criteria of being highly expressed and present in significant pathways that are relevant to the inflammatory process (GLYCAM1, B2M, CD74, BoLA DR-Alpha, FCER1G, SDS and NFKBIA). Lastly, we identified the differentially expressed genes that are located in QTL regions previously known to be associated with mastitis, specifically clinical mastitis, somatic cell count and somatic cell score. It was concluded that there are multiple genes within QTL regions that could potentially impact host response to mastitis causing agents, making some cows more susceptible to intramammary infections. The identification of key genes with functional, statistical, biological and positional relevance associated with host defense to infection, will contribute to a better understanding of the underlying genetic architecture associated with mastitis. This in turn will improve the sustainability of agricultural practices, by facilitating the selection of cows with improved host defense leading to increased resistance to mastitis.
 
Overall design RNA-Sequencing was performed on 6 Holstein dairy cows taking two samples from the same cow, one from a heathy quarter (n = 6) and one from the mastitic quarter (n = 6) to identify differentially expressed genes
 
Contributor(s) Asselstine V, Miglior F, Suárez-Vega A, Fonseca PA, Mallard B, Karrow N, Islas-Trejo A, Medrano J, Cánovas A
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Submission date May 21, 2019
Last update date Oct 22, 2019
Contact name Angela Cánovas
E-mail(s) acanovas@uoguelph.ca
Organization name University of Guelph
Department Animal Biosciences
Lab Cánovas Lab
Street address 50 Stone Road East
City Guelph
State/province ON
ZIP/Postal code N1G 2W1
Country Canada
 
Platforms (1)
GPL15749 Illumina HiSeq 2000 (Bos taurus)
Samples (12)
GSM3790859 H_2252_50A
GSM3790860 M_2252_50B
GSM3790861 H_2360_50C
Relations
BioProject PRJNA544129
SRA SRP199143

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE131607_global_count_genes_milk_somatic_cells.csv.gz 1.1 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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