Project description:Human iPSCs and NSCs were engineered by AAVS1 and/or C13 safe-harbor TALENs which mediated targeted integration of various reporter genes at single or dual safe-harbor loci. Multiple clones of targeted human iPSCs were used to compare with parental untargeted NCRM5 iPSCs. Polyclonal targeted human NSCs were used to compare with their parental untargeted NCRM1NSCs or H9NSCs. Total RNA obtained from targeted human iPSCs or NSCs compared to untargeted control iPSCs or NSCs.
Project description:Our previous studies identified an increase in the levels of the metabolite 1,5-anhydroglucitol (1,5-AG) in the plasma of patients with newly diagnosed B-ALL by untargeted metabolomics detection.Except for the direct influence of 1,5-AG on leukemia cells, the effect on macrophages is still unclear.We reported the application of RNA sequencing to determine the transcriptional response of murine macrophage Raw 264.7 cells in response to stimulate with 1,5-AG conditions.
Project description:A novel one-dimensional on-line pH gradient-eluted strong cation exchange (SCX)-nano-ESI-MS/MS method was developed for protein identification and tested with mixture of six standard proteins, total lysate of HuH7 and N2a cells, as well as membrane fraction of N2a cells. This method utilized an on-line nano-flow SCX column in a nano-LC system coupled with a nano-electrospray high-resolution mass spectrometer. Protein digests were separated on a nano-flow SCX column with a pH gradient and directly introduced into a mass spectrometer through nano-electrospray ionization. SCXLC-MS/MS showed identification capability for higher proportion of basic peptides compared to RPLC-MS/MS method, especially for histidine-containing peptides. Our SCXLC-MS/MS method is an excellent alternative method to the RPLC-MS/MS method for analysis of standard proteins, total cell and membrane proteomes.
Project description:Raw untargeted metabolomics profiled by Metabolon Inc. for 540 samples from healthy individuals. Files include sample names and run details which can be matched to their metagenomic sequencing samples from PRJEB11532 and PRJEB17643. Information regarding metabolite metadata is also available, including
Project description:The goal of this study is to compare the RNA expression profile of wild-type C. elegans nematodes to mutants defective in the synthesis of the biogenic amine neurotransmitters dopamine, serotonin, tyramine, and octopamine in day 2 adults.
Project description:Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell SPAtially resolved METabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet pipeline to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil and endometrium tissues, respectively. ScSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.