Project description:The Nucleosome Remodeling and Deacetylase (NuRD) complex is essential for development in complex animals but has been refractory to detailed analysis because of its low abundance and resistance to recombinant production. As part of a larger project, absolute quantification using isotopically-labelled AQUA peptides was performed on natively-purified NuRD and six recombinantly-expressed NuRD subcomplexes. This is the first time the NuRD complex has been quantified using the AQUA strategy.
Project description:Probing epigenomic marks such as histone modifications at a single cell level in thousands of cells has been recently enabled by technologies such as scCUT&Tag. Here we developed a multimodal and optimized iteration of scCUT&Tag called nano-CT (for nano-CUT&Tag) that allows simultaneous probing of three epigenomic modalities at single-cell resolution, using nanobody-Tn5 fusion proteins. nano-CT is compatible with starting materials as low as 25 000 cells and has significantly higher resolution than scCUT&Tag, with a 16-fold increase in the number of fragments per cells. We used nano-CT to simultaneously profile chromatin accessibility, H3K27ac and H3K27me3 in a complex tissue - juvenile mouse brain. The obtained multimodal dataset allowed for discrimination of more cell types/states that scCUT&Tag, and inference of chromatin velocity between ATAC and H3K27ac in the oligodendrocyte (OL) lineage. In addition, we used nano-CT to deconvolute H3K27me3 repressive states and infer two sequential waves of H3K27me3 repression at distinct gene modules during OL lineage progression. Thus, given its high resolution, versatility, and multimodal features, nano-CT allows unique insights in epigenetic landscapes in different biological systems at single cell level.
2022-09-20 | GSE198467 | GEO
Project description:microbial studies of biological aqua crust
Project description:Profiling miRNA expression in cells that directly contribute to human disease pathogenesis is likely to aid the discovery of novel drug targets and biomarkers. However, tissue heterogeneity and the limited amount of human diseased tissue available for research purposes present fundamental difficulties that often constrain the scope and potential of such studies. We established a flow cytometry-based method for isolating pure populations of pathogenic T cells from bronchial biopsy samples of asthma patients, and optimized a high-throughput nano-scale qRT-PCR method capable of accurately measuring 96 miRNAs in as little as 100 cells. Comparison of circulating and airway T cells from healthy and asthmatic subjects revealed asthma-associated and tissue-specific miRNA expression patterns. These results establish the feasibility and utility of investigating miRNA expression in small populations of cells involved in asthma pathogenesis, and set a precedent for application of our nano-scale approach in other human diseases. We analyzed the concordance in results obtained by nano-scale qPCR and miRNA microarrays. RNA extracted from human Th2 cells was used for parallel profiling by both nano-scale PCR and microarray method. Fifty nanograms (ng) of RNA was used for the microarray method and cDNA from 1 ng (~1000 cell equivalent) of RNA, pre-amplified by 18 cycle PCR reaction, was used for miRNA detection by the nano-scale qPCR method (G.Seumois et al. in submission). Out of the 92 miRNAs assayed, 51 were detected by nano-scale qPCR. Of these, 45 were detected by microarray analysis, including the 32 miRNAs with the strongest signal intensities on the nano-scale qPCR platform.
Project description:To deeply investigate the details of the nano-SiO2 effects, we examined the gene expression profile alterations after nano-SiO2 treatment in BMMCs. The difference analysis between the groups showed that 285 genes were significantly expressed after treatment with nano-SiO2. Compared with the blank group, both nano-SiO2 exposure and DNP-HSA stimulation increased the expression of genes related to the MAPK signaling pathway in mast cells to varying degrees.