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10 protocols using tryple select 10

1

Measuring Intracellular pH in CEC SPs

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The pHi of CEC SPs was measured by using the cell-permeable probe 3′-O-acetyl-2′,7′-bis(carboxyethyl)-5,6-carboxyfluoresceinacetoxymethylester (BCECF-AM special packaging; Dojindo Laboratories. Kumamoto, Japan). Cells were detached with TrypLE Select 10 × (Thermo Fisher Scientific) for 15 min at 37 °C, washed twice with the HEPES buffer (152-mM NaCl, 5-mM KCl, 5-mM glucose, 20-mM HEPES), and then incubated with BCECF-AM for 30 min at 37 °C in full humidity with 5% CO2. Cells were washed twice with the HEPES buffer, and 150 µL/well of the cell suspension solution was poured into a 96-well plate. The fluorescence intensity was determined using a fluorescent plate reader with an excitation wavelength of 488 nm (GloMax Explorer; Promega Corporation, Madison, WI, USA). In this study, we used Dojindo’s assay kit (Dojindo Laboratories). The procedures for calibrating the BCECF fluorescence were described previously12 (link).
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2

Evaluating Exosome Uptake in RPE Cells

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EVs were isolated in aseptic conditions in PBS using size exclusion chromatography as described in Section 2.2. The assay design was to ensure that the levels of exogenous EVs per treatment were close to the RPE physiological levels of EVs (modelling co‐culture conditions and 1:1 ratio of donor:recipient cells). The volumes of CCM, cell numbers that the CCM was collected from (donor RPE) and the amounts of exogenous EVs per treatment were therefore determined considering the cell counts of RPE subjected to the treatment with exogenous EVs (host RPE). Cells were grown on either 0.3 or 1.1 cm2 Matrigel coated 0.4 μm PET hanging cell culture inserts (Merck) at a density of 450,000 cells/cm2. Exogenous EVs or an equivalent amount of PBS for controls were supplemented to the exosome depleted RPE cell media in 12 treatments over the course of 32 days in three biological replicates. A quarter of a transwell insert for each treatment category was collected and fixed immediately in 2% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.4 for TEM ultrastructural analysis. The remaining cells were either fixed in 4% paraformaldehyde (Santa Cruz Biotechnology) for 60 min, washed in PBS and stored at 4°C until use or dissociated with TrypLE Select 10× (ThermoFisher) and collected for western blotting.
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3

Quantifying Tumor Sphere Formation

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StemCO and diffCO were dissociated into single cells with TrypLE Select (10×) (Thermo Fisher Scientific) and cell aggregates were removed with a 20 μm cell strainer (pluriSelect Life Science). The cells were then suspended in SCM with 0.4% agar (CytoSelect 96-Well Cell Transformation Assay, Cell Biolabs) and 10,000 cells/well were seeded into 96-well culture plates according to the manufacturer. The wells were applied with 100 μL of SCM and incubated at 37 °C under 5% CO2 for 7 days. The cells were counted by CyQuant GR Dye according to the manufacturer.
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4

Efficient Cell Lysis and PCR Amplification

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The goal of this step was to continue to allow the processing of the clones in an efficient manner without having to perform DNA extraction for each well.
Phire Tissue Direct PCR Master Mix (Thermo Scientific) was used according to our optimized protocol. Briefly, after media removal cells were detached by adding 20 μl TrypLE™ Select 10× (LifeTechnologies) for 10 minutes at room temperature. The reaction was quenched by 40μl 20% FBS containing RPMI-1640 media. Samples were mixed well and 30 μl of cell suspension transferred into a 384 well PCR plate. Cells were pelleted by centrifugation for 10 minutes at 3000g, and the supernatant removed. Cells were then suspended in 20 μl lysis buffer (950 μl lysis buffer + 50 μl DNA release solution) and denatured for 5 min at 99°C.
A premix sufficient for 192 reactions in 6 μl final volume and 500 nM final primer concentration per each was prepared allowing for a 1× reaction mix after added DNA template. Five μl premix was dispensed into each well and 1 μl cell lysate was added. The amplification was performed under the following thermal profile: ([98 °C, 2 min], [98 °C, 10 s; 65–60 °C, −0.5 °C/cycle, 10 s; 72 °C, 20 s]10 cycles, [98 °C, 10 s; 62 °C, −1 °C/cycle, 10 s; 72 °C, 20 s]25 cycles, [72 °C, 2 min]). PCR products were used for either T7E1 assay or sequencing.
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5

Hepatocyte Detachment Protocol

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Untransduced or RFP-transduced mpPHH cultures were maintained from days to weeks before a detachment protocol was applied. Specifically, after multiple washes with WEM, the cultures were incubated for 30 min with HBSS (catalog no. 14175–095; Life Technologies) with 10-min interval washes to loosen hepatocyte tight junctions. Then, the cells were incubated with TrypLE Select (10×; catalog no. A12177-01; Life Technologies) for 4 to 5 min, and the cells were gently resuspended in W10 medium. After a 5-min spin at 50 × g, the cells were resuspended in W10, counted, and replated or retransplanted into FNRG mice.
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6

Efficient Cell Lysis and PCR Amplification

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The goal of this step was to continue to allow the processing of the clones in an efficient manner without having to perform DNA extraction for each well.
Phire Tissue Direct PCR Master Mix (Thermo Scientific) was used according to our optimized protocol. Briefly, after media removal cells were detached by adding 20 μl TrypLE™ Select 10× (LifeTechnologies) for 10 minutes at room temperature. The reaction was quenched by 40μl 20% FBS containing RPMI-1640 media. Samples were mixed well and 30 μl of cell suspension transferred into a 384 well PCR plate. Cells were pelleted by centrifugation for 10 minutes at 3000g, and the supernatant removed. Cells were then suspended in 20 μl lysis buffer (950 μl lysis buffer + 50 μl DNA release solution) and denatured for 5 min at 99°C.
A premix sufficient for 192 reactions in 6 μl final volume and 500 nM final primer concentration per each was prepared allowing for a 1× reaction mix after added DNA template. Five μl premix was dispensed into each well and 1 μl cell lysate was added. The amplification was performed under the following thermal profile: ([98 °C, 2 min], [98 °C, 10 s; 65–60 °C, −0.5 °C/cycle, 10 s; 72 °C, 20 s]10 cycles, [98 °C, 10 s; 62 °C, −1 °C/cycle, 10 s; 72 °C, 20 s]25 cycles, [72 °C, 2 min]). PCR products were used for either T7E1 assay or sequencing.
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7

Neuroblastoma Spheroid Generation and Assay

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A number of 129x1/SvJ-Tg TH-MYCN mice were originally obtained by Dr. William Weiss (University of California, San Francisco) [17 (link)]. Naturally occurring neuroblastomas in a male MYCN homozygote (Tg/Tg) mouse at 45 days of age were used for generation of neuroblastoma spheroids [34 (link)]. After culturing by cancer-tissue-originated spheroid (CTOS) methods [18 (link)], the spheroids were dissociated into single cells by treating with TrypLE Select (×10) (Life Technologies, Carlsbad, CA, USA) for 30 min at 37 °C, and used for cell viability assay in vitro.
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8

Isolation and FACS of Bone Cells

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Bones were collected in PBS on ice. The growth plate region was dissected under a stereomicroscope (Leica Microsystems) and cut into several small pieces. Digestion medium (2.5 mL/sample) containing 3 U/mL collagenase P (Roche, 11213865001) and 0.1% TrypLE Select (10×) (Gibco, A12177-01) in HBSS (MilliporeSigma, H6648) was added, and the tissue was shaken at 150 rpm in a 37°C water bath under a 60° angle for 30 minutes. Every 4–6 minutes the suspension was triturated with a 1 mL pipette. Then 2.5 mL ice-cold HBSS supplemented with 2% FBS was added. Cells were strained (Corning) and washed. Supernatant was removed by centrifuging at 300g for 10 minutes. Cells were counted and 1 μL Alexa Fluor 647 anti-mouse CD73 antibody (BioLegend, 127208) was added per million cells. Viability dye 7-aminoactinomycin D (eBioscience, 00-6993-50) was added 5 minutes before FACS. Cells were sorted with a BD FACSAria Fusion sorter and collected in RLT buffer supplemented with β-mercaptoethanol. Gating strategy was determined via incorporating negative controls and single-color positive controls. RNA was extracted with QIAGEN RNeasy Micro Kit and prepared for next-generation sequencing.
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9

Evaluating CNOT Complex in hiPSC-CMs

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At day 25 of differentiation, hiPSC-CMs were dissociated with TrypLE Select 10× (Gibco) for 12 min and neutralized with RPMI+10% FBS. Cells were resuspended in RPMI with 2% KnockOut Serum Replacement (KOSR; Gibco) and 2% B27 50× with vitamin A (Life Technologies) supplemented with 2 µM thiazovivin and plated at a density of 5000 cells/well in a Matrigel-coated 384-well plate. hiPSC-CMs were transfected with siRNA (Dharmacon) targeting siCNOT1 (L-015369-01), siCNOT2 (L020313-02), siCNOT3 (L-020319-00), siCNOT4 (L-020323-00), siNOT6 (L-019101-00), siNOT6L (L-016411-00), siCNOT7 (L-012897-00) and siCNOT8 (L-018791-00), using lipofectamine RNAiMax (Thermo Fisher Scientific). Each siRNA was tested in quadruplicate. Cells were labeled with 10 µM EdU (Thermo Fisher Scientific) 48 h post-transfection. After 24 h of EdU incubation, cells were fixed with 4% paraformaldehyde for 30 min. EdU was detected according to protocol and cells were stained with the cardiac-specific marker ACTN2 (Sigma-Aldrich, dilution 1/800) and DAPI. Cells were imaged with an ImageXpress Micro XLS microscope (Molecular Devices) and custom algorithms were used to quantify EdU-labeled hiPSC-CMs.
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10

Pluripotency and Hematopoietic Characterization

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At DD0, human iPSCs were analyzed by flow cytometry for investigating the expression of the pluripotency markers SSEA4 and TRA-1-60 (BD Biosciences). iPSCs were dissociated using Gentle Cell Dissociation Reagent (Gibco, Thermo Scientific) and aliquots of 1 × 105 cells/200 μL (0.5 M EDTA, pH 8.0, 1:90 DPBS) were prepared. Conjugated antibodies (10 μL/105 cells) were added to the cells and incubated on ice for 30 min in the dark. Unbound antibodies were removed by washing the cells with 900 μL of DPBS, centrifugation at 160×g for 5 min, and decanting the supernatant. Cells were resuspended in 400 μL of 4% paraformaldehyde (Tech & Innovation) for preservation up to 3 days.
At DD4, 11, 18, and 24, cells were analyzed by flow cytometry to evaluate their hematopoietic and erythroid characteristics. TrypleSelect × 10 (Gibco, Thermo Scientific) was used to dissociate the cells, if they were not evenly dissociated. Preparation procedures were identical to those used for DD0.
All antibodies used for flow cytometry have been listed in Table 2. The BD FACSVerse Flow Cytometer (BD Biosciences) and FlowJo (version 10.2, FlowJo, LLC, Ashland, OR, USA) were used for the analysis. Nonspecific immunoglobulin isotype controls of the corresponding class served as negative controls. Compensation beads were used to modify compensation matrixes.
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