Project description:Purpose:The goal of this study was to evalute gene expression patterns of equine chorioallantoic membrane during different stages of the pregnancy Method: mRNA profile of equine chorioallantoic membrane (CAM) from 45days, 4months, 6months and 10months (4 samples for each time points) generated by RNA-sequencing,using a Illumina HiSeq 4000 ( HiSeq 4000 sequencing kit version 1). The sequence reads were trimmed for adapters and quality using TrimGalore Version 0.4.4,and then mapped to EquCab2.0 using STAR-2.5.2b. Final quantification at the gen level was performed by analyzing the BAM files in cufflinks using the Equus_caballus_ENSEMBL_88 gtf file as Guide.
Project description:Genetic variations in drug metabolising enzymes play a role in how individuals respond to drugs. Pharmacogene variation data in the Ghanaian population is limited and this study looks at exploring common variations that exist in our population for commonly used drugs. Samples were validated with PCR-RFLP for accuracy
Project description:Genetic variations in drug metabolising enzymes play a role in how individuals respond to drugs. Pharmacogene variation data in the Ghanaian population is limited and this study looks at exploring common variations that exist in our population for commonly used drugs. In addition, the study also looks at the how variations in cytokines and HLA play a role in HBV pathogenesis. Samples were validated with PCR-RFLP for accuracy
Project description:Transcriptional profiling of HMB-treated (24h) differentiating equine satellite cells (3rd day of differentiation) exposed to hydrogen peroxide (1h; last hour of pre-incubation with HMB) compared to control HMB-untreated cells. Goal was to determine the effects of HMB pre-incubation on miRNA expression in equine satellite cells exposed to hydrogen peroxide.
Project description:Transcriptional profiling of GO-treated (24h) differentiating equine satellite cells (3rd day of differentiation) exposed to hydrogen peroxide (1h; last hour of pre-incubation with GO) compared to control GO-untreated cells. Goal was to determine the effects of GO pre-incubation on miRNA expression in equine satellite cells exposed to hydrogen peroxide.
Project description:Transcriptional profiling of gamma-oryzanol-treated (24h) differentiating equine satellite cells (3rd day of differentiation) compared to control GO-untreated cells. Goal was to determine the effects of gamma-oryzanol influence on gene expression in equine satellite cells during in vitro myogenesis Two-condition experiment, GO-treated (24h) differentiating equine satellite cells (3rd day of differentiation) vs. differentiating equine satellite cells without GO treatment (control). Biological replicates: 4 reps of examined condition (Cy5), 4 control replicates (Cy3)
Project description:To fully interrogate location-specific variations of microRNAs of the hair follicle in AGA and normal persons, we sought to perform a thorough and comprehensive microRNA profiling of different locations of hair follicles (bulb portions, bugle portions)
Project description:Emerging and neglected pathogens pose challenges as their biology is frequently poorly understood, and genetic tools often do not exist to manipulate them. Organism agnostic sequencing technologies offer a promising approach to understand the molecular processes underlying these diseases. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), the obligate intracellular causative agent of the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning, we investigated the transcriptional architecture of Ot, including operon structure and non-coding RNAs, and found evidence for wide-spread post-transcriptional antisense regulation. We compared the host response to two clinical isolates and identified distinct immune response networks that are up-regulated in response to each strain, leading to predictions of relative virulence which were confirmed in a mouse infection model. Thus, dual RNA-seq can reveal the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.
Project description:Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state, are not packaged by histones, and contain genes organized into polycistronic arrays, with minimal transcriptional regulation. We analyze the 3D genome of {Breviolum minutum}, and find large topological domains without chromatin loops, demarcated by convergent gene array boundaries (``dinoTADs’’). Transcriptional inhibition degrades dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.
