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9 protocols using facs sortware

1

Optimized Cell Sorting Workflow

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All cell sorting experiments were performed on a BD Influx cell sorter running BD FACS Sortware. Laser alignment was performed using eight-peak rainbow beads (Spherotech), and drop delay was determined using BD Accudrop beads.
The plate holder apparatus on a BD Influx does not hold a nonskirted 96-well PCR plate tightly. To create a fitting holder, a 96-well polycarbonate rack typically used to hold individual 1.4-mL polypropylene round-bottom tubes was used. By removing the legs of the rack and shaving the bottom surface to be flat, we were able to create a rigid fit in the sort tray of the Influx sorter. Standard 96-well PCR plates were able to fit easily into the rack and were secured using individual portions of a pressure-sensitive adhesive (e.g., Blu-Tack) in several locations within the rack. To establish the alignment of the sort plate on the sort stage we performed sorts of 10 beads onto the lid of a 96-well plate. Cells were then index sorted into wells of a 96-well plate and analyzed further. To determine the precision of the cell sorter, cells were index sorted into 96-well PCR plates to perform Fluidigm real-time PCR analysis (Fig. 1C).
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2

Sorting and Profiling VGlut2-Cre Neurons

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The cell suspensions derived from VGlut2-CretdTomato animals were sorted on the BD Influx system using the BD FACS Sortware. A nozzle diameter of 140um and sheath pressure of 4.30 PSI were used with enrichment sort objective. The gating strategy, a high fluorescence intensity (85/29 [561]-tdTomato high FSC value) produced a single cloud of TdTomato+ events. A total of around 50,000 events per sorting session yielded ∼2000 TdTomato+ sorted cells. The full sorted cell populations were loaded to the 10x Chromium chip without delay.
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3

Rare Event Identification and Sorting

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For each experiment, index sort files were exported using BD FACS Sortware. These files were analyzed to assess the rare events in which no cell had been sorted (Fig. 1C). These wells were then manually entered into the Sortware index sort layout, and cells were sorted into these cells. A second index sort file was exported afterward. For all experiments, fcs-files and CSV-files were exported for comparison with the index sort files using Microsoft Excel and R.
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4

Generating ACE2-Expressing HEK-293T Cells

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To obtain HEK-293T cells with stable expression of ACE2 protein, a lentiviral system bearing ACE2 (Genbank ID: BAJ21180.1) gene was constructed. In brief, HEK-293T cells (ATCC) with 70%–80% confluence in a 10 cm dish were co-transfected with 12 μg of plasmid pHIV-puro encoding RRE and ACE2 genes, 8 μg of plasmid psPAX2 encoding gag and pol, and 4 μg of plasmid VSV-G encoding G glycoprotein of vesicular stomatitis virus(VSVG) using Lipofectamine 3000 Reagent (Invitrogen). Twelve hours later, the medium was changed to fresh DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) for another 48 h culturing. Medium containing virus particles was harvested and concentrated using a Lentivirus Concentration Kit (Genomeditech). The concentrated virus particles were used to infect HEK-293T cells under selection pressure of 10 μg/mL puromycin (Beyotime Biotechnology). The transfection efficiency was examined by flow cytometry using S1-mFc recombinant protein (Sino Biological) as primary antibody and FITC-AffiniPure Goat Anti-Mouse IgG (Jackson) as secondary antibody. The resulting bulk transfected population was sorted on a BD FACSJazz Cell Sorter (BD) with the BD FACS™ Sortware. Cells with top 1% fluorescence intensity were retained and expanded for subsequent use.
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5

Flow Cytometric Analysis of Fluorescent Proteins

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The assays were carried out as described previously (31 (link)). Culture samples were diluted 1:1000 in 1 ml of PBS. Fluorescence intensity of mNeonGreen and mCherry in cells was monitored by flow cytometry analysis on a BD FACSJazz (BD Biosciences), and data were acquired with the BD FACS Sortware. mNeonGreen and mCherry were excited with 488 and 561 nm solid-state lasers, and their emission was detected using 513/17 and 610/20 nm emission filters, respectively. For each sample, fluorescence of 20 000 cells was captured, and the data was analysed using FCS Express 7 (De Novo Software).
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6

Multiparametric Flow Cytometry Analysis

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Samples were run and 1,000,000-10,000,000 events were collected using either BD FACS Diva or BD FACS Sortware with a BD Aria II or BD Influx cell sorter respectively (BD Biosciences, Franklin Lakes, NJ). The BD Aria II was equipped with a 50 mW 405 nm laser, 20 mW 488 nm laser, and 18 mW 633 nm laser while the BD Influx was equipped with a 100 mW 355 nm laser, 200 mW 488 nm laser, and 120 mW 640 nm laser. Hoechst 33342 was excited using the 355 nm laser and detected through a 460/50 filter. Hoechst 34580 was excited using the 405 nm laser and detected through a 460/50 filter. JC-1, anti-CD71 PerCP eFluor 710 and Streptavidin PE-Cy7 were excited using the 488 nm laser and detected through 530/40, 692/40, and 750LP filters respectively. Atto633 and anti-CD45 APC eFluor 780 were excited using the 633 nm laser and detected through 670/30, 750LP filters respectively. The RBC and leukocyte population was selected based on FSC/SSC properties and single cells were gated based on either trigger pulse width or by using the FSC peak area to height ratio. Cell sorting was performed on the BD Influx into collection tubes and slides prepared as described earlier. Compensation and further analysis was performed using FlowJo v10.0.6 (Tree Star, Ashland, Oregon, USA).
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7

EGFR-Positive Cell Binding Assay

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Example 4

Cell Binding Experiments

Cell lines. EBC-1 and CHO-K1 cells were cultured in DMEM with 4 mM L-glutamine (Sigma-Aldrich) and DMEM-F12+GlutaMax™ (Gibco®), respectively, both supplemented with 10% fetal bovine (Sigma-Aldrich) at 37° C. and 5% CO2.

Cell binding experiments. Cell binding experiments were performed by using EGFR-overexpressing EBC-1[3] and EGFR-negative CHO-K1 cells in combination with confocal fluorescence microscopy and flow cytometry, respectively. Washing and incubation steps were performed at 4° C. using PBS with 1% BSA. For microscopy based experiments, cells were grown on glass coverslips followed by consecutive labelling with 100 nM of respective antibody-conjugates and 1:200 diluted Streptavidin Alexa Fluor® 488 conjugate (Life Technologies). Then, cells were fixed with 4% paraformaldehyde, mounted with ProLong® Diamond Antifade Mountant with DAPI (Life Technologies) and scanned using a Leica TCS SP5 confocal microscope equipped with a 100× objective (Leica Microsystems). For flow cytometry, 2×105 cells were incubated with 100 nM of respective antibody-conjugates and in a consecutive step with 1:200 diluted Streptavidin Alexa Fluor® 488 conjugate (Life Technologies). Cell fluorescence was determined using a BD Influx cell sorter and BD FACS Sortware with detection of 2×104 events.

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8

Flow Cytometry Analysis of Fluorescent Proteins

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Culture samples were diluted 1:1,000 in 500 μl of PBS. Fluorescence intensity of NeonGreen and mCherry in cells was monitored by flow cytometry analysis on a BD FACSJazz (BD Biosciences), and data were acquired with the BD FACS Sortware. mNeonGreen and mCherry were excited with 488 and 561 nm solid-state lasers, and their emission was detected using 513/17 and 610/20 nm emission filters, respectively. For each sample, fluorescence of 20,000 cells was captured, and the data was analyzed using FCS Express 7 (De Novo Software).
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9

Flow Cytometry Analysis of Fluorescent Proteins

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The assays were carried out as described previously (30) . Culture samples were diluted 1:1,000 in 1 mL of PBS. Fluorescence intensity of NeonGreen and mCherry in cells was monitored by flow cytometry analysis on a BD FACSJazz (BD Biosciences), and data were acquired with the BD FACS Sortware. mNeonGreen and mCherry were excited with 488 and 561 nm solid-state lasers, and their emission was detected using 513/17 and 610/20 nm emission filters, respectively. For each sample, fluorescence of 20,000 cells was captured, and the data was analysed using FCS Express 7 (De Novo Software).
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