Project description:aCGH performed to identify copy number variants in Quarter Horses and perform casec-control GWAS Two-condition experiment, All samples were compared to a single Quarter Horse reference to identify copy number variants to be used in the CNV GWAS
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:Investigating genome-wide characteristics of CNVs in 6 horses representing 6 distinct breeds by using the aCGH method and performed GO and KEGG analysis for the CNVs genes.This result is an important complement to the mapping of horse whole-genome CNVs and helpful to study plateau horses’ adaption to the plateau’s environment.
Project description:Complement proteins are deposited in the muscles of patients with myositis. However, the local expression and regulation of complement genes within myositis muscle have not been well characterized. In this study, bulk RNA sequencing (RNAseq) analyses of muscle biopsy specimens revealed that complement genes are locally overexpressed and correlate with markers of myositis disease activity, including the expression of interferon-gamma (IFN )-induced genes. Single cell and single nuclei RNAseq analyses showed that most local expression of complement genes occurs in macrophages, fibroblasts, and satellite cells, with each cell type expressing different sets of complement genes. Biopsies from immune-mediated necrotizing myopathy patients, who have the lowest levels of IFN -induced genes, also had the lowest complement gene expression levels. Furthermore, data from cultured human cells showed that IFN upregulates complement expression in macrophages, fibroblasts, and muscle cells. Taken together, our results suggest that in myositis muscle, IFN coordinates the local overexpression of complement genes that occurs in several cell types.
Project description:Immune cell infiltration in myositis were by examining microarray expression profiles in muscle biopsies from 31 myositis patients and 5 normal controls.
Project description:Immune cell infiltration in myositis were by examining microarray expression profiles in muscle biopsies from 31 myositis patients and 5 normal controls. Muscle samples from 36 subjects (5 normal controls, 5 NM, 8 DM, 8 PM and 10 IBM) were studied
Project description:The relative contribution of innate and adaptive immunity to idiopathic inflammatory myopathy is poorly defined. We therefore sought to clarify these components of disease pathogenesis using our novel murine model of histidyl-tRNA synthetase (HRS)-induced myositis. Myositis was induced in WT and various congenic strains of C57BL/6 mice through intramuscular immunization with recombinant HRS. Histopathological, immunohistochemical, flow cytometric, and transcriptomic assessments were used to characterize muscle-infiltrating cell populations in these congenic strains. RAG1 KO mice developed markedly reduced muscle inflammation relative to WT mice, demonstrating a key requirement for T cells in driving HRS-induced myositis. Diminished cellular infiltration in CD4-Cre.MyD88fl/fl conditional knockout and OT-II TCR transgenic mice highlighted roles for innate and TCR-mediated/adaptive immune signaling in T cells. Transcriptionally-based pathway analyses showed that disruption of T cell signaling alters the function of macrophages, fibroblasts, and other non-lymphoid cell populations. Overall, these findings demonstrate that HRS-induced myositis reflects complex cellular interactions requiring the activation of both innate and adaptive T cell-mediated signaling pathways.
Project description:Macrophages with innate immune memory are in a modified steady-status with altered responsiveness to stimulation featured by rewired epigenetic program. To better convey the concept of IGF-2-mediated innate immune memory and help understanding the anti-inflammatory responsiveness of macrophages, we analyzed histone modifications (H3K4me1, H3K4me3, and H3K27ac) by whole genome chip-sequencing analysis in control macrophages and IGF-2-preprogrammed macrophages. In the whole genome chip-sequencing analysis, we found that IGF-2 has limited effects on H3K4me1and H3K4me3, but mainly modulates H3K27ac status during macrophages maturation.
2019-09-23 | GSE123184 | GEO
Project description:Exome sequencing and association between identified variants and racing performance in Quarter Horses
