Period
2014 - 2019
Colaborators
Responsible: Raquel Pinho
PI: Dr.Elizabeth Maga, University of Californa, Davis, CA - United States
Colaborator: Dr. Lydia Garas, University of Californa, Davis, CA - United States
Colaborator: Dr. Elizabeth Maga, University of Californa, Davis, CA - United States
Colaborator: Dr. Bart Weimer, University of Californa, Davis, CA - United States
Colaborator: Dr. Carol Huang, University of Californa, Davis, CA - United States
Location
- University of California, Davis, CA - United States
Raquel Pinho’s main responsabilities
- Experiment design and project writing.
- Library construction for RNA-sequencing.
- RNA-seq data processing in Linux.
- RNA-seq data analysis in R.
- RNA-seq data visualization in R.
- Weighted co-expression network analysis using WGCNA.
- Integration of intestinal transcriptome, hepatic metabolome and intestinal microbiota 16S data using MixOmics.
- Validation of NGS results using qPCR for relative gene expression analysis.
Description
Goat milk containing human lysozyme (hLZ) has shown beneficial effects on microbiome composition, gastro-intestinal (GI) morphology and the clinical condition of pigs. To explore the effect of hLZ milk on intestinal gene expression in malnourished animals, RNA-seq was conducted with tissue from the duodenum, jejunum and ileum of malnourished piglets fed with hLZ milk, regular goat milk or with no milk supplementation. Gene co-expression analysis and pheno- typic correlations were made with WGCNA, while integration of transcriptome with microbiota information and the hepatic metabolite profile was done using mixOmics.
Data
BioProject: PRJNA823693
Publications
- PINHO, R. M.; GARAS L.C.; HUANG B.C; WEIMER B.C.; MAGA, E.A.. Lysozyme-rich milk affects gene expression along the length of porcine small intestine before and during enteropathogenic Escherichia coli infection. (submitted 2022).
- PINHO, R. M.; GARAS L.C.; HUANG B.C; WEIMER B.C.; MAGA, E.A. Milk from lysozyme transgenic goats influences gene expression in the intestine in a pig model of malnutrition. XII Transgenic Animal Research Conference (TARC), Lake Tahoe City, CA, United States. 2019.