Journal: PLoS ONE

Article Title: Differential Mitochondrial Toxicity Screening and Multi-Parametric Data Analysis

doi: 10.1371/journal.pone.0045226

Figure Lengend Snippet: Hoechst33342, TO-PRO-3, and TMRM were used to characterize the untreated HepG2 population and the cell toxicity response induced by different compounds. Cells were seeded at the same time and density, incubated for 24 h with 100 µM of different compounds, stained with a cell marker cocktail, and analyzed using an iCys imaging cytometer. A. Representative images (500×368 µm) demonstrate fluorescent signal distribution for individual channels. A merged color image representing a combination of channels (TMRM-red, Hoechst33342-blue, TO-PRO-3-magenta) is shown to demonstrate co-localization. A light-scatter image is shown to realize cell morphology. B. Cumulative probability functions demonstrate TMRM change induced by different treatments: FCCP - red line, chelerythrine – green line, nicardipine – blue line, and untreated (DMSO) - black line. C. Bar graph represents the fraction of viable (TO-PRO-3-negative) cells (black), and the fraction of dead (TO-PRO-3-positive) cells (shaded). D. The bar graph represents responses of two parameters, TMRM KS values (solid bars) and the fraction of viable cells (shaded), to various treatments. E. Color-coded representation of 2-parameter response for each of four compounds. Viability is rescaled from −1 (all dead) to +1 (all live) to match the range for KS values.

Article Snippet: Ninety-six well plates were analyzed using an iCys Imaging Cytometer (Compucyte, Corp.) configured with three excitation lasers and four emission detector PMTs for blue, green, orange, and near-infrared.

Techniques: Incubation, Staining, Marker, Imaging, Cytometry

Journal: Cells

Article Title: Spectral Algal Fingerprinting and Long Sequencing in Synthetic Algal–Microbial Communities

doi: 10.3390/cells13181552

Figure Lengend Snippet: List of algal cultures used for recordings during artificial mix experiment and library construction with ID7000 spectral cell analyzer.

Article Snippet: Samples were recorded in parallel on three instruments: 7-laser ID7000 spectral cell analyzer (Sony Biotechnology, San Jose, CA, USA), 5-laser BD FACSAria Special Order cell sorter (BD Biosciences, Franklin Lakes, NJ, USA), and 4-laser ImageStreamX MarkII (Amnis–Cytek, Fremont, CA, USA) imaging flow cytometer equipped with 40× and 60× objectives [ ].

Techniques:

Journal: Cells

Article Title: Spectral Algal Fingerprinting and Long Sequencing in Synthetic Algal–Microbial Communities

doi: 10.3390/cells13181552

Figure Lengend Snippet: Schematic overview of the proposed experimental workflow for the analysis combining full-spectrum cytometry and sequencing. The workflow involves parallel analysis of obtained samples using a MinION Mk1C-based sequencing platform (ONT) and ID7000 spectral cell analyzer (Sony Biotechnology). The first step in the analysis of spectral data requires ( a ) recording and isolation of single spectral signatures, for which the“Autofluorescence Finder” tool is utilized. During this step ( b ), a set of optimal virtual filters for discrimination autofluorescent populations is determined. As defined using the tool, AF-A corresponds to Microcystis sp. and AF-B to debris within the sample; ( c ) respective emission spectra of two defined autofluorescent populations displayed below (red line—AF-A, blue line—AF-B). ( d ) Single spectral signature is then extracted, and ( e ) a library containing unique spectral signatures corresponding to respective phytoplankton species is then constructed and utilized during subsequent analysis, including unsupervised clustering techniques (e.g., t-SNE).

Article Snippet: Samples were recorded in parallel on three instruments: 7-laser ID7000 spectral cell analyzer (Sony Biotechnology, San Jose, CA, USA), 5-laser BD FACSAria Special Order cell sorter (BD Biosciences, Franklin Lakes, NJ, USA), and 4-laser ImageStreamX MarkII (Amnis–Cytek, Fremont, CA, USA) imaging flow cytometer equipped with 40× and 60× objectives [ ].

Techniques: Cytometry, Sequencing, Isolation, Construct

Journal: Cells

Article Title: Spectral Algal Fingerprinting and Long Sequencing in Synthetic Algal–Microbial Communities

doi: 10.3390/cells13181552

Figure Lengend Snippet: Identification of artificial mix subpopulations compared between SONY ID700 spectral cell analyzer and BD FACSAria SORP cytometer. Subpopulations of interest were first gated on the plots (red region) to eliminate debris. The first column represents data recorded on SONY ID7000 using a set of VFs best optimized for artificial mix discrimination. Opt-SNE demonstrates successful discrimination of the 9 subpopulations within the mix based on VF data. The second column represents data recorded on SONY ID7000 using a set of VFs matching optical filters used on BD FACSAria. Similarly, all 9 subpopulations were discriminated. The last column represents data recorded on BD FACSAria. Based on the optical configuration of the instrument, only 8 subpopulations were identified using opt-SNE.

Article Snippet: Samples were recorded in parallel on three instruments: 7-laser ID7000 spectral cell analyzer (Sony Biotechnology, San Jose, CA, USA), 5-laser BD FACSAria Special Order cell sorter (BD Biosciences, Franklin Lakes, NJ, USA), and 4-laser ImageStreamX MarkII (Amnis–Cytek, Fremont, CA, USA) imaging flow cytometer equipped with 40× and 60× objectives [ ].

Techniques: Cytometry