DNA methylation profiling of the jejunum mucosa of two laying hen strains (Lohmann Brown-Classic (LB) and Lohmann LSL-Classic (LSL)) at 5 different ages
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ABSTRACT: Genome-wide DNA methylation of jejunum mucosa was studied using Reduced Representation Bisulfite Sequencing (RRBS) in two laying hen strains, Lohmann Brown-Classic (LB) and Lohmann LSL-Classic (LSL) collected at 10, 16, 24, 30 and 60 weeks of age.
Project description:Calcium (Ca) and phosphorus (P) are essential micronutrients that are linked to a wide set of biological processes. In laying hens there is still uncertainty about the optimal Ca/P ratio in feed and further strategies for the reliable mineral restriction in poultry diets are required. The dataset is based on Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) laying hens sampled at peak performance. The experimental design comprises four dietary groups differed in Ca (recommended vs. 15 % reduction) and mineral P (adequate vs. 20 % reduction) levels; 1) control diet (Con; Ca=34.4g/kg, P=5.3 g/kg and Ca/P ratio=7.45), 2) Low Ca and P diet (LCaP), 3) low Ca diet (LCa), and low P diet (LP). Jejunal transcriptome profiles were assessed by mRNA sequencing in a total of 80 animals (10 hens per experimental group for each laying line) at sampling age of 31 weeks) to approximate the consequences of variable Ca and P supply.
Project description:Calcium (Ca) and phosphorus (P) are essential micronutrients linked to arrays of biological processes and physiological conditions. In laying hens, the optimal Ca/P ratio in feed is inconsistent but necessary for reliable schemes of mineral restriction in poultry diets. This study investigates the effects of dietary treatments varying in the Ca and P levels in two laying hen strains (Lohmann Brown-Classic and Lohmann LSL-Classic) at the peak of egg production (31 weeks of age). Four dietary treatment groups were differed in Ca (recommended vs. 15 % reduction) and mineral P (adequate vs. 20 % reduction) levels; 1) control diet (Con; Ca=34.4g/kg, P=5.3 g/kg and Ca/P ratio=7.45), 2) Low Ca and P diet (LCaP), 3) low Ca diet (LCa), and 4) low P diet (LP). microRNA expression of the jejunum mucosa were profiled by microRNA sequencing in a total of 80 animals (10 hens per experimental diet group for each of the two laying line) at sampling age of 31 weeks. RNA-seq data of matched samples are also available (E-MTAB-9109).
Project description:This study investigated changes in gut transcriptome in response to the removal and reduction P (0 and 1 g P/kg feed) during the transition to egg production (at 19 and 24 weeks, before and after the onset of laying) in Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) chickens. A total of 80 LB and LSL hens were sampled in a 2x2x2 factorial design, encompassing two strains, age groups, and dietary.
Project description:We wished to investigate the role of E-cadherin loss in our mouse parietal cell/pre-parietal cell E-cadherin knock-out, p53 knock-out, oncogenic Kras induced model of gastric cancer. As such, we isolated RNA from stomach tissue from our E-cadherin knock-out model (Atp4b-Cre;Cdh1(fl/fl);Kras(LSL-G12D/+);Trp53(fl/fl);Rosa26(LSL-YFP/LSL-YFP)) and our E-cadherin heterozygous model (Atp4b-Cre;Cdh1(fl/+);Kras(LSL-G12D/+);Trp53(fl/fl);Rosa26(LSL-YFP/LSL-YFP)). We then performed a microarray on this stomach tissue from four independent mice of each genotype. Differentially expressed genes were identified and gene set overlap analysis was used to identify pathways enriched in one model over the other.
Project description:Three brain regions of the limbic system, the amygdala, hippocampus and hypothalamus, are responsible for survival behaviors such as feeding and physical challenging. Hypothalamus works together with pituitary and adrenal gland (HPA-axis) to adjust homeostatic state by modulating stress-response hormones. Unraveling molecular signatures such as DNA methylation of these tissues may provide deeper insights into a link between epigenetic regulation and phenotypic plasticity of behavioral responses of animals. We examined the DNA methylation profile of amygdala (n = 20), hippocampus (n = 20), hypothalamus (n = 19) as well as a non-brain tissue, adrenal gland (n=19) of German Landrace pigs using a cost effective method, Reduced Representation Bisulfite Sequencing (RRBS).
Project description:To investigate the role of SHP2 (Ptpn11) in pancreatic carcinogenesis, murine pancreatic whole tissue RNA samples of 9 week old mice with the genotypes Ptf1a-Cre;LSL-KrasG12D (ID-labels Kxxx) and Ptf1a-Cre;LSL-KrasG12D;Ptpn11fl/fl (ID-labels Mxxxx) were analyzed by microarray.
Project description:Lactating cows experience transient metabolic stresses during postpartum which results in abnormal concentrations of non-esterified fatty acids and beta-hydroxybutyrate that can impact oocyte maturation and ultimately reproductive success. We hypothesize that metabolic challenges in lactating cows influence DNA methylation changes of the oocyte affecting genes involved in oocyte developmental competency. Therefore, we compared whole genome bisultfite sequencing (wgbs) of the oocytes collected from 5-6 week (early) or 9-10 week (mid) post-partum against that of oocytes from nulliparous heifers as metabolically unchallenged condition control. Bisulfite-Seq DNA libraries were generated from pooled oocytes using an EZ DNA methylation-direct kit and Pico-Methyl seq library preparation kit (Zymo Research), and parallel sequenced using the illumina HiSeq2500 system.
Project description:Lactating cows experience transient metabolic stresses during postpartum which results in abnormal concentrations of non-esterified fatty acids and beta-hydroxybutyrate that can affect embryo-maternal communication and ultimately reproductive success. We hypothesize that metabolic challenges in lactating cows influence DNA methylation changes of the embryos prior to implantation affecting genes involved in embryo developmental competency. Therefore, we compared whole genome bisulfite sequencing (wgbs) of morulas derived from in vitro produced 2-4 cell embryos and transferred in the oviduct of metabolically profiled lactating cows until day 7. Similar stage of in vitro production (IVP) embryos were transferred to the oviduct of nulliparous heifers as a metabolically unchallenged control. Bisulfite-Seq DNA libraries were generated from groups of five morulas using an EZ DNA methylation-direct kit and Pico-Methyl seq library preparation kit (Zymo Research), and parallel sequenced using the illumine HiSeq2500 system at the institute of Genome Biology, Leibniz-Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
Project description:DNA methylation is an epigenetic mechanism that plays roles in gene regulation and expression. This study aims to profile DNA methylation at genome-wide scale and single base resolution using reduced representation bisulfite sequencing (RRBS) of the muscle of pigs differing in muscle metabolism and genetic background. Pietrain homozygous- positive (PiPP) and negative (PiNN) for the ryanodine receptor mutation and malignant hyperthermia-susceptible (MHS), Duroc and F2 crossbred Duroc-Pietrain homozygous-negative (DuPi) pigs were investigated to identify differentially methylated CpG sites/ regions and to integrate the results with gene expression data.