Project description:Raw sequence data and targetted loci from crocidurine and myosoricine shrews (Soricidae) and one outgroup eulipotyphlan (Hylomys suillus). Raw sequence reads
Project description:Deep sequencing of mRNA from Chinese tree shrew; Chinese tree shrew (Tupaia belangeri chinensis) is placed in Order Scandentia and embraces many unique features for a good experimental animal model. Currently, there are many attempts to employ tree shrew to establish model for a variety of human disorders such as social stress, myopia, HCV and HBV infection, and hepatocellular carcinoma .We present here a publicly available annotated genome sequence for Chinese tree shrew. Phylogenomic analysis of tree shrew and other mammalians highly supported its close affinity to primates. Characterization of key factors and signaling pathways of the nervous and immune systems in tree shrews showed that this animal had common and unique features, and had essential genetic basis for being a promising model for biomedical researches. Analysis of ploy(A)+ RNA of different specimens:kidney, pancreas, heart, liver, brain, testis and ovary form Chinese tree shrew
Project description:The increasing application of RNA-seq to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based tool for processing, analyzing, and interpreting RNA-seq data from any eukaryotic species. ExpressAnalyst contains a series of modules that enable raw data processing and annotation of FASTQ files, and statistical and functional analysis of counts tables and gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst enables researchers to obtain global expression profiles and gene-level insights from raw RNA-seq reads within 24 hours. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-seq data from multiple non-model salamander species, including two that do not have a reference transcriptome.
Project description:Acute respiratory distress syndrome (ARDS), a common cause of acute fatal respiratory, is characterized by severe inflammatory lung injury as well as hallmarks of increased pulmonary vascular permeability, neutrophil infiltration, and macrophage accumulation. Tree shrew, a squirrel-like small animal model, has been confirmed more similar traits to human ARDS with one-hit intratracheal instillation of LPS in our previous study. In this study, we characterized protein profile changes induced by intranasal LPS challenge in the tree shrew model through tandem mass tag (TMT)-based quantitative proteomics and type II alveolar epithelial cells through pathological analysis. In total, 4070 proteins (p < 0.05) were identified from lung tissues of the LPS-induced group and PBS group. Among the differential expression proteins (DEPs) detected by t-test (≥|1.5-fold|), 529 DEPs were identified, of which 304 were upregulated, and 225 were downregulated. The most important pathways involved in the process of ARDS had been identified by enrichment analysis: oxidative stress, apoptosis, inflammatory responses, and vascular endothelial injury. In addition, proteins have been reported in animal models or clinical patients also detail investigated for further analysis, such as ceruloplasmin (CP), hemopexin (HPX), sphingosine kinase 1 (SphK1), lactotransferrin (LTF), and myeloperoxidase (MPO) were upregulated in induced tissues and confirmed by western blot analysis. Overall, this study not only reveals a comprehensive proteomic analysis of the ARDS tree shrew model but also provides novel insights into multi-pathways responses induced by the LPS challenge of tree shrews. We highlight shared and unique proteomic changes in the lungs of ARDS tree shrews and identify novel pathways for acute lung injury, which may promote the model into basic research and translational research.
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.