Project description:As the most studied type of epigenetic modifications found in many taxa, DNA methylation has been confirmed to play a crucial role in transposon silencing, transcriptional regulation and thus phenotypic variation, as well as rapid adaption to changing environments. To fully understand the methylome variation in Trichinella, here, we report 12 single-base resolution methylomes of three life stages using WGBS. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparative epigenomics, we observe that the methylome variation in Trichinella is significantly divergent and host-related. By comparing DNA methylation patterns between different host classes of species, we found a fraction of parasitism-related genes under epigenetic regulation, such as G-protein-coupled receptor, DNaseII and ligand-gated chloride channel. Moreover, we also reveal associations between methylation divergence and genetic basis, including nucleotide variant and structural variation.
Project description:As DNA methylation can modulate gene expression, we then focused our analysis on changes of methylation at the host taxonomic level, that is between encapsulated and non-encapsulated clade, and within non-encapsulated clade, to reveal epigenetic regulation on transcriptomes from Ad and ML stages. By comparing DNA methylation patterns between different host classes of species, we found a fraction of parasitism-related genes under epigenetic regulation, such as G-protein-coupled receptor, DNaseII and ligand-gated chloride channel.
Project description:Spermathecal fluid was extracted from adult queens at two different life stages (virgins and mated 2 week old) and separated from sperm by centrifugation. Queens were all sourced from the same grafting event and mated on the same schedule. Virgin queens were 2 days old at sampling. Some mated 2 week old queens were then held in a queen bank for a further two weeks (final age = 4 weeks), creating three groups of queens. Unbanked mated 2 week old queens were actively ovipositing, whereas banked mated queens were not actively laying.
Project description:7 daphnia magna life stages from embryo development till adult were profiled using a new custom made microarray on a 4*160K platform
Project description:We compare the epigenomes of mouse intestinal epithelial cells at different intestinal regions and life stages of the mouse. We use a sequencing assay for transposase accessible chromatin (ATAC-seq) to determine highly accessible genomic regions. We determine regions that are differentially accessible between intestinal regions (duodenal crypt, duodenal villus, and colon) and between life stages (12-to-15-day-old/juvenile, 90-day-old/adult, and 21-month-old/geriatric).
Project description:To obtain the global gene expression trends during ovule development, we collected samples of the gynoecium in developmental stages 9–10, 11, and 12 with three biological replicates to perform microarray assay.
Project description:Using full-genome arrays, the expression of all XMEs was examined during fetal (gestation day (GD) 19), neonatal (postnatal day (PND) 7), prepubescent (PND30), middle age (12 mon), and old age (18 and 24 mon) in the C57Bl6/J mouse liver and compared to young adults. Fetal and neonatal life stages had a dramatic effect on XME expression compared to the relatively minor effects of old age. At all life stages except PND30 down-regulated genes outnumbered up-regulated genes. The altered XMEs included those in all of the major metabolic phases including phase I (alcohol and aldehyde dehydrogenase and Cyp genes), phase II (aldo-keto reductase, glutathione-S-transferases, sulfotransferases and UDP-glucuronosyl transferases) and phase III (transporters). We have generated a comprehensive catalog of XME hepatic gene changes through the life stages of the mouse that can be used to predict chemicals and chemical classes different life stages are more sensitive to. Some CEL files used in this study have been submitted through GSE21224. Keywords: gene expression/microarray