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8 protocols using eight well chambers

1

FLIM-FRET Analysis of H2B Dynamics

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Stable FLIM cells were generated using lentivirus that expresses PGK-H2B-GFP and PGK-H2B-mCherry, and FACS sorted to produce populations with homogenous expression. For FLIM-FRET experiments, cells were seeded into eight-well chambers (ibidi) and treated with DMSO, 750 nM A23817, or 0.4 U/ml Thrombin for 15 min, before being fixed in 4% PFA for 10 min. Lifetime measurements were taken on a Leica TCS SP8 system, using a white light laser with a repetition rate of 80 MHz and an excitation wavelength of 488 nm. H2B-GFP emission was detected over an emission range of 495–530 nm. Data were fitted using the FLIMfit software tool developed at Imperial College London.
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2

Mesothelial Clearance Assay for Ovarian Cancer

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The mesothelial clearance assays were performed based on a protocol previously described [44 (link)] with minor alterations. MeT5A cells stably expressing EGFP protein were seeded in eight-well chambers (Ibidi) coated with 10 µg/mL of collagen type I (Millipore, Burlington, MA, USA) and 5 µg/mL of fibronectin (Sigma) and incubated for 24 h to form confluent monolayers. In parallel, aggregates of ovarian cancer cells were generated by seeding 350 cells per well in 96-well plates with a round bottom preciously coated with polyHEMA. After incubating for 24 h, the OVCA aggregates were transferred to the wells containing the mesothelial monolayers. Using the inverted motorized epifluorescence microscope Leica DMI 6000-time lapse, live cell imaging was performed for 24 h. To quantify the mesothelial clearance area, the non-fluorescent surface created by the invading ovarian cancer aggregate in the EGFP mesothelial monolayer was measured at 18 h of co-culture and divided by the initial two-dimensional area of the aggregate at the initial seeding time. All measurements were taken using the Fiji software. More than eight multicellular aggregates were imaged by each cell line in each experiment in a total of three biological experiments.
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3

Real-time Ferroptosis Monitoring in Cells

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Cells were seeded in DMEM in IBIDI eight-well chambers (Ibidi, Germany) 24 h before the experiment. The day after, cells were washed with PBS to replace the media by phenol red-free DMEM (Sigma-Aldrich, Germany) supplemented with FBS and antibiotics. Cells were loaded with 1-µM Fluo-4 AM, 2-µg/mL PI, or 1 µM of C11 BODIPY 581/591 for 30 min at 37 °C. All images were acquired with a Zeiss LSM 710 ConfoCor3 microscope (Carl Zeiss, Jena, Germany) or a gSTED Leica confocal microscopy equipped with incubator at 37 °C and 5% CO2. Time-lapse imaging with z-stack acquisition was carried out before and after ferroptosis induction. Transmitted light and fluorescence images were acquired through a Zeiss C-Apochromat 40X, NA = 1.2 water immersion objective or a 63X, NA = 1.2 oil immersion objective onto the sample. Excitation light came from Argon ion (488 nm) or HeNe (561 nm) lasers. All images were processed in Fiji. The percentage of Fluo-4 AM-positive cells was calculated at each time point. For this, individual cells were automatically detected based on the fluorescence of the Fluo-4 AM. To define cells as positive, we arbitrarily set a fluorescence threshold in which the percentage of Fluo-4 AM-positive cells did not exceed 5% in the negative control. The total number of cells in each condition was determined in the transmitted light images.
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4

Immunofluorescence Staining of Drosophila S2R+ Cells

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For staining of Drosophila S2R+ cells, cells were transferred to the polylysine-pretreated eight-well chambers (Ibidi) at a density of 2 × 105 cells per well. After 30 min, cells were washed with 1× DPBS (Gibco), fixed with 4% formaldehyde for 10 min, and permeabilized with PBST (0.2% Triton X-100 in PBS) for 15 min. Cells were incubated with mouse anti-Myc (1:2000; Enzo, 9E10) in PBST supplemented with 10% donkey serum overnight at 4°C. Cells were washed three times for 15 min in PBST and then incubated with secondary antibody and 1× DAPI solution in PBST supplemented with 10% donkey serum for 2 h at 4°C. After three 15-min washes in PBST, cells were imaged with a Leica SP5 confocal microscope using a 63× oil immersion objective.
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5

SARS-CoV-2 Infection of Primary Nasal Epithelial Cells

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HNEpCs were collected from healthy adult volunteers. Nasal cavities were anaesthetized using lidocaine, and nasal epithelial cells were collected by repeatedly scraping turbinates with a disposable bronchial cytology brush (CONMED). The tissue was resuspended in DMEM supplemented with 10% FBS and centrifuged at 300g for 5 min. The pellet was digested in a solution containing 1,000 U of Accutase (Sigma, A6964), 5,000 U of Dispase (Corning, 354235) and 1 mg ml−1 DNAse II (Sigma, D8764) for 8 min at 37 °C. The digestion was stopped by adding an equal volume of Pneumacult medium (Stem Cell Technologies, 5050) supplemented with 10% FBS and filtered through a 100 µm cell strainer. The cell suspension was centrifuged at 300g for 5 min, and the pellet was resuspended in red blood cell lysis solution (150 mM NH4Cl and 10 mM KHCO3) for 2 min. Cells were centrifuged at 300g for 5 min, resuspended in medium and seeded on eight-well chambers (Ibidi) at a concentration of 5 × 105 cells per well. After 48 h, cells were infected with SARS-CoV-2 (ref. 86 (link)) at 1 MOI as described above. Cells were cultured for 48 or 72 h and fixed in 4% paraformaldehyde for 15 min at room temperature for staining.
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6

FUCCI and Bright-field Time-lapse Imaging

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For FUCCI time‐lapse imaging, cells were plated at low density (approximately 15,000 cells per well) and imaged in 24‐well plates in DMEM inside a heated 37°C chamber with 5% CO2. Images were taken every 10 min with a 10×/0.5 NA air objective using a Zeiss Axio Observer 7 with a CMOS ORCA flash 4.0 camera at 4 × 4 binning. GFP‐53BP1/H2B‐RFP RPE1 cell lines were imaged on a DeltaVision Elite system in eight‐well chambers (Ibidi) in L15 media within a heated 37°C chamber. Images were taken every 4 min with a 40×/1.3 NA oil objective using a DV Elite system equipped with Photometrics CascadeII: 1024 EMCCD camera at 4 × 4 binning. For bright‐field imaging, cells were imaged in a 24‐well plate in DMEM in a heated chamber (37°C and 5% CO2) with a 10×/0.5 NA air objective using a Hamamatsu ORCA‐ER camera at 2 × 2 binning on a Zeiss Axiovert 200 M, controlled by Micro‐manager software (open source; https://micro‐manager.org/) or with a 20×/0.4 NA air objective using a Zeiss Axio Observer 7 (details above). For the time lapse shown in Fig 7A, cells were plated into Essen Imagelock 96‐well plates and imaged using a Sartorius IncuCyte ZOOM using a 10× objective and 15‐min imaging intervals.
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7

Quantifying Mitochondrial Dynamics in Drp1 Knockdown

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For Drp1 knockdown experiments, 24 h after siRNA transfection as described above, cells were seeded in eight-well chambers (Ibidi). After cell cycle synchronization, cells were released in phenol red free DMEM (Sigma-Aldrich) supplemented with FBS and P/S containing different drugs. MitoTracker Red CMXRos (Thermo Fisher Scientific) and DAPI (Thermo Fischer Scientific) were directly added to the wells and incubated for 30 min at 37 °C. Images were acquired with a Zeiss LSM 710 ConfoCor3 microscope (Carl Zeiss) equipped with incubator at 37 °C and 5% CO2. Transmitted light and fluorescence images were acquired through a Zeiss C-Apochromat 40×, numerical aperture (NA) = 1.2 water immersion objective onto the sample. For experiments testing the role of mitochondrial shape, cells were incubated for 30 min in DMEM containing 200 nM TMRE. Cells were then washed once with PBS and incubated in phenol red free L15 Medium (Invitrogen). Images were taken with a Leica DMi8 microscope with a 63× water objective (NA = 1.2) and a Hamamatsu OrcaFlash 4.0 camera.
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8

Organoid Dissociation and Wholemount Staining

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Organoids were single-cell dissociated using TrypLE Express Enzyme (Thermo Fisher Scientific, 12605010), and 15,000 cells were seeded per well in eight-well chambers (ibidi, 80826) suitable for confocal imaging. Wholemount staining was performed 7 days post single-cell dissociation using a standard immunofluorescence wholemount protocol.
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