Project description:Fluorescence-activated cell sorting (FACS) is a specialized technique to isolate cell subpopulations with a high level of recovery and accuracy. However, the cell sorting procedure can impact the viability and metabolic state of cells. Here, we performed a comparative study and evaluated the impact of traditional high-pressure charged droplet-based and a microfluidic chip-based sorting approach on the metabolic and phosphoproteomic profile of different cell types. While microfluidic chip-based sorted cells more closely resembled the unsorted control group for most cell types tested, the droplet-based sorted cells showed significant metabolic and phosphoproteomic alterations. In particular, greater changes in redox and energy status were present in cells sorted with the droplet-based cell sorter along with higher transcriptional and spliceosomal regulation and mechanical stress signaling. These results indicate microfluidic chip-based sorting is less disruptive compared to droplet-based sorting.

2023-11-09 | MSV000093348 | MassIVE

Nitrifiers Bedford Basin

Project description:Nitrifiers Bedford Basin Targeted loci environmental

| PRJNA715654 | ENA

Cell type purification by single-cell transcriptome-trained sorting

Project description:Traditional cell type enrichment using fluorescence activated cell sorting (FACS) relies on methods that specifically label the cell type of interest. Here we propose GateID, a computational method that combines single-cell transcriptomics, for unbiased cell type identification, with FACS index sorting, to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without resorting to specific antibodies or transgenes.

2019-10-07 | GSE112438 | GEO

High-throughput, Microscope-based Sorting to Dissect Cellular Heterogeneity

Project description:Microscopy is a powerful tool for characterizing complex cellular phenotypes, but linking these phenotypes to genotype or RNA expression at scale remains challenging. Here, we present Visual Cell Sorting, a method that physically separates hundreds of thousands of live cells based on their visual phenotype. Automated imaging and phenotypic analysis directs selective illumination of Dendra2, a photoconvertible fluorescent protein expressed in live cells; these photoactivated cells are then isolated using fluorescence-activated cell sorting. First, we use Visual Cell Sorting to assess hundreds of nuclear localization sequence variants in a pooled format, identifying variants that improve nuclear localization and enabling annotation of nuclear localization sequences in thousands of human proteins. Second, we recover cells that retain normal nuclear morphologies after paclitaxel treatment, then derive their single cell transcriptomes to identify pathways associated with paclitaxel resistance in cancers. Unlike alternative methods, Visual Cell Sorting depends on inexpensive reagents and commercially available hardware. As such, it can be readily deployed to uncover the relationships between visual cellular phenotypes and internal states, including genotypes and gene expression programs.

2020-04-01 | GSE141030 | GEO

Sorting nexin 10 sustains platelet-derived growth factor receptor signaling in glioblastoma stem cells via endosomal protein sorting

Project description:Glioblastoma is the most malignant primary brain tumor for which the prognosis is still dismal despite aggressive surgical, medical, and radiation therapies. Glioblastoma stem cells (GSCs) promote therapeutic resistance and cellular heterogeneity due to their self-renewal properties and capacity for plasticity. To understand the molecular processes essential for maintaining GSCs, we performed an integrative analysis comparing active enhancer landscapes, transcriptional profiles, and functional genomics profiles of GSCs and non-neoplastic neural stem cells (NSCs). We identified sorting nexin 10 (SNX10), an endosomal protein sorting factor, as selectively expressed in GSCs compared to NSCs and essential for GSC survival. Targeting SNX10 impaired GSC viability and proliferation, induced apoptosis, and reduced self-renewal capacity. Mechanistically, GSCs utilized endosomal protein sorting to promote platelet-derived growth factor receptor β (PDGFRβ) proliferative and stem cell signaling pathways via post-transcriptional regulation of the PDGF receptor tyrosine kinase. Targeting SNX10 expression extended survival of orthotopic xenograft-bearing mice, and high SNX10 expression correlated with poor glioblastoma patient prognosis, suggesting its potential clinical importance. Thus, our study reveals an essential connection between endosomal protein sorting and oncogenic receptor tyrosine kinase signaling and suggests that targeting endosomal sorting may represent a promising therapeutic approach for glioblastoma treatment.

2023-03-31 | GSE221714 | GEO

Repli-seq sample preparation using cell sorting with cell-permeant dyes

Project description:Repli-seq sample preparation using cell sorting with cell-permeant dyes

| PRJNA1033555 | ENA

Eph-ephrin signaling couples endothelial cell sorting and arterial specification

Project description:Eph-ephrin signaling couples endothelial cell sorting and arterial specification

| PRJNA928081 | ENA