Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns,but require the integration of the latest genomic information.This study provides a comprehensive workflow impl...Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns,but require the integration of the latest genomic information.This study provides a comprehensive workflow implemented in an R package(rePROBE)to assign the entire probes and to annotate the probe sets based on up-to-date genomic and transcriptomic information.The rePROBE package can be applied to available gene expression microarray platforms and addresses both public and custom databases.The revised probe assignment and updated probe-set annotation are applied to commercial microarrays available for different livestock species,i.e.,chicken(Gallus gallus;ChiGene-1_0-st:443,579 probes and 18,530 probe sets),pig(Sus scrofa;PorGene-1_1-st:592,005 probes and 25,779 probe sets),and cattle(Bos Taurus;BovGene-1_0-st:530,717 probes and 24,759 probe sets),as well as available for human(Homo sapiens;HuGene-1_0-st)and mouse(Mus musculus HT_MG-430_PM).Using current species-specific transcriptomic information(RefSeq,Ensembl,and partially non-redundant nucleotide sequences)and genomic information,the applied workflow reveals 297,574 probes(15,689 probe sets)for chicken,384,715 probes(21,673 probe sets)for pig,363,077 probes(21,238 probe sets)for cattle,481,168 probes(23,495 probe sets)for human,and 324,942 probes(32,494 probe sets)for mouse.These are representative of 12,641,15,758,18,046,20,167,and 16,335 unique genes that are both annotated and positioned for chicken,pig,cattle,human,and mouse,respectively.Additionally,the workflow collects information on the number of single nucleotide polymorphisms(SNPs)within respective targeted genomic regions and thus provides a detailed basis for comprehensive analyses such as expression quantitative trait locus(eQTL)studies to identify quantitative and functional traits.The rePROBE R package is freely available at https://github.com/friederhadlich/rePROBE.展开更多
Parathyroid glands(PTG)are essential in maintaining mineral homeostasis,particularly in regulating blood calcium(Ca)and phosphorus(P)levels.The endocrine regulation via parathyroid hormone(PTH)is a prerequisite for th...Parathyroid glands(PTG)are essential in maintaining mineral homeostasis,particularly in regulating blood calcium(Ca)and phosphorus(P)levels.The endocrine regulation via parathyroid hormone(PTH)is a prerequisite for the efficient utilization of dietary P.The PTG contain lobules of PTH-producing chief cells surrounded by extracellular collagen.It is hypothesized that the areal proportions of chief cells and extracellular collagen in PTG are dependent on dietary P intake.Based on PTG gene expression patterns,a total of 18 crossbred pigs balanced for sex and litter were fed one of three long-term diets with low(n=6),medium(n=6),or high P levels(n=6)from weaning at d 28 until slaughter at d 120.Total dietary P levels of low,medium,and high P groups were 5.20,6.48 and 7.80 g/kg diet for grower,respectively,and 4.12,5.50 and 6.96 g/kg diet for fattener,respectively.The effects of P supply were analyzed for their impact on the microscopic structure of porcine PTG using microphotographs following Azan trichrome staining verified by immunohistochemistry of PTH,calcium-sensing receptor(CaSR),collagen type I(COL1),and collagen type III(COL3)and related to gene expression data.Histological stainings of PTG showed significantly reduced areas of PTG chief cells(P<0.001)and increased extracellular collagen(P<0.001)in animals fed low dietary P compared to control and high P diets.The long-term adaptation to a low P diet indicates a PTG reorganization and suggests that the lobular structure,along with the extracellular matrix,may play a role in the complex processes of mineral homeostasis.Mechanistically,this could be a component of a physiologic and possibly reversible response following long-term P intake,which has implications for PTG regulation and,consequently,PTH control.展开更多
基金partly funded by the Leibniz Science Campus Phosphorus Research Rostockfunding from the European Research Area Network on Sustainable Animal Production (ERA-NET Sus An) as part of the PEGa Sus project (Grant No. 2817ERA02D)The Research Institute for Farm Animal Biology (FBN) provided own matched funding
文摘Commercial and customized microarrays are valuable tools for the analysis of holistic expression patterns,but require the integration of the latest genomic information.This study provides a comprehensive workflow implemented in an R package(rePROBE)to assign the entire probes and to annotate the probe sets based on up-to-date genomic and transcriptomic information.The rePROBE package can be applied to available gene expression microarray platforms and addresses both public and custom databases.The revised probe assignment and updated probe-set annotation are applied to commercial microarrays available for different livestock species,i.e.,chicken(Gallus gallus;ChiGene-1_0-st:443,579 probes and 18,530 probe sets),pig(Sus scrofa;PorGene-1_1-st:592,005 probes and 25,779 probe sets),and cattle(Bos Taurus;BovGene-1_0-st:530,717 probes and 24,759 probe sets),as well as available for human(Homo sapiens;HuGene-1_0-st)and mouse(Mus musculus HT_MG-430_PM).Using current species-specific transcriptomic information(RefSeq,Ensembl,and partially non-redundant nucleotide sequences)and genomic information,the applied workflow reveals 297,574 probes(15,689 probe sets)for chicken,384,715 probes(21,673 probe sets)for pig,363,077 probes(21,238 probe sets)for cattle,481,168 probes(23,495 probe sets)for human,and 324,942 probes(32,494 probe sets)for mouse.These are representative of 12,641,15,758,18,046,20,167,and 16,335 unique genes that are both annotated and positioned for chicken,pig,cattle,human,and mouse,respectively.Additionally,the workflow collects information on the number of single nucleotide polymorphisms(SNPs)within respective targeted genomic regions and thus provides a detailed basis for comprehensive analyses such as expression quantitative trait locus(eQTL)studies to identify quantitative and functional traits.The rePROBE R package is freely available at https://github.com/friederhadlich/rePROBE.
文摘Parathyroid glands(PTG)are essential in maintaining mineral homeostasis,particularly in regulating blood calcium(Ca)and phosphorus(P)levels.The endocrine regulation via parathyroid hormone(PTH)is a prerequisite for the efficient utilization of dietary P.The PTG contain lobules of PTH-producing chief cells surrounded by extracellular collagen.It is hypothesized that the areal proportions of chief cells and extracellular collagen in PTG are dependent on dietary P intake.Based on PTG gene expression patterns,a total of 18 crossbred pigs balanced for sex and litter were fed one of three long-term diets with low(n=6),medium(n=6),or high P levels(n=6)from weaning at d 28 until slaughter at d 120.Total dietary P levels of low,medium,and high P groups were 5.20,6.48 and 7.80 g/kg diet for grower,respectively,and 4.12,5.50 and 6.96 g/kg diet for fattener,respectively.The effects of P supply were analyzed for their impact on the microscopic structure of porcine PTG using microphotographs following Azan trichrome staining verified by immunohistochemistry of PTH,calcium-sensing receptor(CaSR),collagen type I(COL1),and collagen type III(COL3)and related to gene expression data.Histological stainings of PTG showed significantly reduced areas of PTG chief cells(P<0.001)and increased extracellular collagen(P<0.001)in animals fed low dietary P compared to control and high P diets.The long-term adaptation to a low P diet indicates a PTG reorganization and suggests that the lobular structure,along with the extracellular matrix,may play a role in the complex processes of mineral homeostasis.Mechanistically,this could be a component of a physiologic and possibly reversible response following long-term P intake,which has implications for PTG regulation and,consequently,PTH control.
