Transcriptome Analysis of Three Sheep Intestinal Regions reveals Key Pathways and Hub Regulatory Genes of Large Intestinal Lipid Metabolism

[1]  Martin G. Frasch,et al.  RNAseq profiling of primary microglia and astrocyte cultures in near-term ovine fetus: A glial in vivo-in vitro multi-hit paradigm in large mammalian brain , 2017, Journal of Neuroscience Methods.

[2]  A. Palou,et al.  Cpt1a gene expression in peripheral blood mononuclear cells as an early biomarker of diet-related metabolic alterations , 2016, Food & nutrition research.

[3]  D. Carreño,et al.  Fish oil-induced milk fat depression and associated downregulation of mammary lipogenic genes in dairy ewes. , 2016, Journal of dairy science.

[4]  Limin Sun,et al.  Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep , 2016, Scientific Reports.

[5]  Fei Li,et al.  Effects of early feeding on the host rumen transcriptome and bacterial diversity in lambs , 2016, Scientific Reports.

[6]  T. Spencer,et al.  Analysis of the Uterine Epithelial and Conceptus Transcriptome and Luminal Fluid Proteome During the Peri-Implantation Period of Pregnancy in Sheep1 , 2016, Biology of reproduction.

[7]  Kristina M. Hettne,et al.  Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington’s disease peripheral blood samples , 2016, Metabolomics.

[8]  Z. Ji,et al.  Identification and Classification of New Transcripts in Dorper and Small-Tailed Han Sheep Skeletal Muscle Transcriptomes , 2016, PloS one.

[9]  Christophe Klopp,et al.  Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome , 2016, Scientific Data.

[10]  Y. Kamisaka,et al.  Modulation of gluconeogenesis and lipid production in an engineered oleaginous Saccharomyces cerevisiae transformant , 2016, Applied Microbiology and Biotechnology.

[11]  Takao Shimizu,et al.  Lysophosphatidylethanolamine acyltransferase 1/membrane‐bound O‐acyltransferase 1 regulates morphology and function of P19C6 cell‐derived neurons , 2016, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[12]  G. Barton,et al.  How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? , 2015, RNA.

[13]  B. Dalrymple,et al.  Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues , 2016, PeerJ.

[14]  G. Barton,et al.  Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? , 2016, RNA.

[15]  C. Robert-Granié,et al.  Characterization and Comparative Analysis of the Milk Transcriptome in Two Dairy Sheep Breeds using RNA Sequencing , 2015, Scientific Reports.

[16]  Y. Yue,et al.  De novo assembly and characterization of skin transcriptome using RNAseq in sheep (Ovis aries). , 2015, Genetics and molecular research : GMR.

[17]  Davide Heller,et al.  STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..

[18]  G. Mithieux,et al.  Intestinal glucose metabolism revisited. , 2014, Diabetes research and clinical practice.

[19]  Bronwen L. Aken,et al.  The sheep genome illuminates biology of the rumen and lipid metabolism , 2014, Science.

[20]  D. Russell,et al.  Regulation of Fatty Acid Oxidation in Mouse Cumulus-Oocyte Complexes during Maturation and Modulation by PPAR Agonists , 2014, PloS one.

[21]  Jie Zhou,et al.  RNA-seq differential expression studies: more sequence or more replication? , 2014, Bioinform..

[22]  J. Loor,et al.  Central Role of the PPARγ Gene Network in Coordinating Beef Cattle Intramuscular Adipogenesis in Response to Weaning Age and Nutrition , 2014, Gene regulation and systems biology.

[23]  P. Portincasa,et al.  New insights into the molecular mechanism of intestinal fatty acid absorption , 2013, European journal of clinical investigation.

[24]  Z. Ji,et al.  Characterization and Comparative Analyses of Muscle Transcriptomes in Dorper and Small-Tailed Han Sheep Using RNA-Seq Technique , 2013, PloS one.

[25]  P. Kellman,et al.  MultiContrast Delayed Enhancement (MCODE) improves detection of subendocardial myocardial infarction by late gadolinium enhancement cardiovascular magnetic resonance: a clinical validation study , 2012, Journal of Cardiovascular Magnetic Resonance.

[26]  Susan R. Wilson,et al.  Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing , 2012, BMC Genomics.

[27]  R. Eckel,et al.  Tissue‐Specific Responses of Lipoprotein Lipase to Dietary Macronutrient Composition as a Predictor of Weight Gain Over 4 Years , 2012, Obesity.

[28]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[29]  Paras Gupta,et al.  The peroxisome proliferator-activated receptor: A family of nuclear receptors role in various diseases , 2011, Journal of advanced pharmaceutical technology & research.

[30]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[31]  Wei Sun,et al.  The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. , 2011, Cell metabolism.

[32]  L. Armentano,et al.  Ruminant Nutrition Symposium: Productivity, digestion, and health responses to hindgut acidosis in ruminants. , 2011, Journal of animal science.

[33]  G. Breves,et al.  Transepithelial transport and intraepithelial metabolism of short-chain fatty acids (SCFA) in the porcine proximal colon are influenced by SCFA concentration and luminal pH. , 2011, Comparative biochemistry and physiology. Part A, Molecular & integrative physiology.

[34]  John Turk,et al.  Identification of a Physiologically Relevant Endogenous Ligand for PPARα in Liver , 2009, Cell.

[35]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[36]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[37]  R. Murphy,et al.  Lysophospholipid Acyltransferases and Arachidonate Recycling in Human Neutrophils* , 2008, Journal of Biological Chemistry.

[38]  J. Peters,et al.  Quantitative expression patterns of peroxisome proliferator-activated receptor-beta/delta (PPARbeta/delta) protein in mice. , 2008, Biochemical and biophysical research communications.

[39]  S. Stymne,et al.  A family of eukaryotic lysophospholipid acyltransferases with broad specificity , 2008, FEBS letters.

[40]  J. Peters,et al.  Quantitative expression patterns of peroxisome proliferator-activated receptor- β / δ (PPAR β / δ ) protein in mice , 2008 .

[41]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[42]  Béatrice Desvergne,et al.  From molecular action to physiological outputs: peroxisome proliferator-activated receptors are nuclear receptors at the crossroads of key cellular functions. , 2006, Progress in lipid research.

[43]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[44]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[45]  D. Ramji,et al.  Lipoprotein lipase: structure, function, regulation, and role in disease , 2002, Journal of Molecular Medicine.

[46]  K. Beauchemin,et al.  Effects of particle size of alfalfa-based dairy cow diets on site and extent of digestion. , 2002, Journal of dairy science.

[47]  C. McMaster,et al.  PC and PE synthesis: Mixed micellar analysis of the cholinephosphotransferase and ethanolaminephosphotransferase activities of human choline/ethanolamine phosphotransferase 1 (CEPT1) , 2002, Lipids.

[48]  J. Berger,et al.  The mechanisms of action of PPARs. , 2002, Annual review of medicine.

[49]  B. Hull,et al.  Site of nutrient digestion by dairy cows fed corn of different particle sizes or steam-rolled. , 2001, Journal of dairy science.

[50]  P. Siroka,et al.  In vitro study of the rumen and hindgut fermentation of fibrous materials (meadow hay, beech sawdust, wheat straw) in sheep. , 2000 .

[51]  J. Claverie,et al.  The significance of digital gene expression profiles. , 1997, Genome research.

[52]  J. Auwerx,et al.  The Organization, Promoter Analysis, and Expression of the Human PPARγ Gene* , 1997, The Journal of Biological Chemistry.

[53]  M. Vernay,et al.  Avoparcin and monensin effects on the digestion of nutrients in dairy cows fed a mixed diet , 1995 .

[54]  A. Vanhatalo,et al.  The role of the large intestine in post-ruminal digestion of feeds as measured by the mobile-bag method in cattle , 1995, British Journal of Nutrition.

[55]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[56]  E. N. Bergman Energy contributions of volatile fatty acids from the gastrointestinal tract in various species. , 1990, Physiological reviews.

[57]  N. Mcneil Nutritional implications of human and mammalian large intestinal function. , 1988, World review of nutrition and dietetics.

[58]  James W. Anderson,et al.  Short-Chain Fatty Acid Fermentation Products of Plant Fiber Affect Glucose Metabolism of Isolated Rat Hepatocytes , 1984, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[59]  G. E. Mitchell,et al.  Acetate and propionate production in the cecum and proximal colon of lambs. , 1984, Journal of animal science.

[60]  J. Nolan,et al.  Studies of the large intestine of sheep , 1982, British Journal of Nutrition.

[61]  W. Hoover Digestion and absorption in the hindgut of ruminants. , 1978, Journal of animal science.

[62]  J. Prescott,et al.  The effect in sheep of physical form and stage of growth on the sites of digestion of a dried grass , 1972, British Journal of Nutrition.

[63]  J. Hecker Ammonia in the large intestine of herbivores , 1971, British Journal of Nutrition.

[64]  G. Faichney Production of volatile fatty acids in the sheep caecum. , 1969 .

[65]  V. Williams Microbial metabolism in the forestomachs and the large intertine of sheep , 1965 .