Project description:We use ChIP-seq targeting histone 3 lysine 27-acetylation (H3K27ac) to identify putative enhancer sites genome-wide in the ventral pallidum cortex of adult prairie voles
Project description:With the technological advances of the last decade, it is now feasible to analyze environmental samples of vast complexity, such as human stool specimen, using meta-omics techniques like metaproteomics. Still the most sophisticated, sensitive instruments can only extract information that a sample contains in the first place. This highlights the need for initial sample preparation to preserve as much unaltered information as possible. Yet little is known about the effects different processing approaches have on the final analysis results. This study analyzes human stool samples applying metaproteomics and shows that the initial sample storage has a massive effect on the taxonomic composition of proteins identified. The findings are backed up by the results of the metagenomics analysis of the same samples. This suggests, that great care should be taken in choosing storage conditions for (omics) studies, as well as in comparing the results of experiments with different initial processing.
Project description:Proteomic measurements from cyanobacteria colonies picked from the Gulf of Aqaba (Red Sea); analyzed to reveal interaction of cyanobacteria Trichodesmium and its taxonomically diverse microbial community partners. Samples were digested with trypsin, fractionated, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS processing pipeline against a metagenomics FASTA file sequenced at JGI.
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from several tissues from prairie voles (Microtus ochrogaster). Ear, liver, and brain samples from the Cornell University prairie vole colony were collected from 48 male and female prairie voles at various life stages: neonatal (<1 month old), sub-adult (2-4 months old), mature adult (4-10 months old), and middle aged/old adult (>10 months old). The pair bonded male and female prairie voles used in our study cohabitated with their partners for several months and produced at least three generations of litters. Animals were euthanized via rapid decapitation, their tissues rapidly extracted and frozen on dry ice before being stored at -80C until further processing for genomic DNA extraction. Brains were coronally sectioned and brain regions from the pair bonding circuit (PBC) were micro-dissected and pooled for each animal. The PBC brain regions included the prefrontal cortex, nucleus accumbens, lateral septum, ventral pallidum, and medial amygdala, and ventral tegmental area. Genomic DNA was isolated and purified using the phenol-chloroform extraction and ethanol precipitation method. A total of 144 tissue samples were collected and processed for DNA methylation analysis. Tissues: Brain, Ear, Liver
2023-08-07 | GSE174758 | GEO
Project description:Transcriptome of Brandt's voles