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8 protocols using no 1.5 glass bottomed dishes

1

Quantifying HER4 Receptor Binding in CHO and MCF7 Cells

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Chinese Hamster Ovary (CHO) cells (STR profiled and mycoplasma tested) were seeded at a density of 0.75 × 105 cells dish on uncoated 35 mm no. 1.5 glass-bottomed dishes (MatTek Corporation, USA). Cells were transfected with HER4-CYT-eGFP the next day and were serum starved overnight the second day after transfection. MCF7 were seeded and grown for two days, before being starved overnight.
Cells were rinsed and cooled to 4°C for 10 min, then labelled with HER4 Affimer labelled with CF640R (Biotium) in concentrations ranging from 1 to 100 nM (CHO/HER4-CYT-eGFP) or from 10 to 500 nM (MCF7). Labelling was carried out at 4°C for 1 hr. Cells were rinsed and fixed with 3% paraformaldehyde plus 0.5% glutaraldehyde for 15 min at 4°C then 15 min at room temperature. Imaging was carried out in PBS using the standard confocal mode in a Leica TCS sp8 (see Data analysis of binding curves below).
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2

Single-Cell Growth Dynamics of B. subtilis

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Cultures grown to an OD600 below 0.3 were concentrated by
centrifugation at 6,000 × g for 30 sec. The cell pellet
was resuspended in growth medium, and applied to No. 1.5 glass-bottomed dishes
(MatTek Corp., MA). All cells were imaged under a 2% agarose pad containing
growth medium, with the top surface exposed to air, in a chamber heated to
37°C. Phase-contrast microscopy was performed using a Nikon Eclipse Ti
equipped with a Nikon Plan Apo λ 100×/1.4NA objective and an Andor
camera. We used a custom-built package in MATLAB to perform segmentation on
phase-contrast time-lapse movies, then calculated the growth rate of the surface
area of single B. subtilis chains. Each data point for the
single-cell growth rates (Figure 2d) is the
result of a single experiment; for each, >50 cells from multiple fields
of view across different areas of the agarose pad were imaged and analyzed.
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3

Mitochondrial Morphology Imaging in MEFs

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All cells were plated in No. 1.5 glass-bottomed dishes (MatTek). MEFs were incubated with 0.1 μg/ml MitoTracker Red CMXRos (Invitrogen) for 15 min at 37°C with 5% CO2, washed, and incubated with complete media for at least 45 min before imaging. For analysis of mitochondrial morphology under oxidative stress conditions, 100 μM diamide was added to the culture media for 1 h before imaging. MEFs were imaged at 37°C with 5% CO2. A Z-series with a step size of 0.3 μm was collected with a Nikon Ti-E widefield microscope with a 63× NA 1.4 oil objective (Nikon), a solid-state light source (Spectra X; Lumencor), and an sCMOS camera (Zyla 5.5 Megapixel). Each cell line was imaged by a blinded researcher on at least three separate occasions (n > 100 cells per experiment).
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4

Mitochondrial Dynamics Imaging Protocol

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Cells transduced with mito-PAGFP (#23348; Addgene) were plated in No. 1.5 glass-bottomed dishes (MatTek). MEFs were incubated with 0.1 μg/ml MitoTracker Red CMXRos (Invitrogen) for 15 min at 37°C with 5% CO2, washed, and incubated with complete media for at least 45 min before imaging. MEFs were imaged at 37°C with 5% CO2. A region that was ∼1 µm2 was activated using a 405-nm laser, and the same cell was imaged after 50 min. Images were collected with a Nikon Ti-E widefield microscope with a 63× NA 1.4 oil objective (Nikon), a solid-state light source (Spectra X; Lumencor), and an sCMOS camera (Zyla 5.5 Megapixel).
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5

Mitochondrial Imaging in Mouse Embryonic Fibroblasts

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All cells were plated in no. 1.5 glass-bottomed dishes (MatTek). MEFs were incubated with 0.1 μg/ml Mitotracker Red CMX Ros for 15 min at 37°C with 5% CO2, then washed and incubated with complete media for at least 45 min before imaging. A Z-series with a step size of 0.3 μm was collected with a Nikon Ti-E wide-field microscope with a 63× NA (numerical aperture) 1.4 oil objective (Nikon), a solid-state light source (Spectra X; Lumencor), and an sCMOS camera (Zyla 5.5 megapixel). Each cell line was imaged on at least three separate occasions (n > 100 cells per experiment).
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6

Mitochondrial Dynamics Imaging Protocol

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Cells transduced with mito-paGFP (#23348; Addgene) and either Mfn1-FLAG pBabe-hygro or Mfn2-FLAG-P2A-blasticidin pBabe were plated in No. 1.5 glass-bottomed dishes (MatTek). MEFs were incubated with 0.1 μg/ml MitoTracker Red CMXRos for 15 min at 37°C with 5% CO2, washed, and incubated with complete media for at least 45 min before imaging. MEFs were imaged at 37°C with 5% CO2. A region that was ∼1 μm2 was activated using a 405-nm laser, and the same cell was imaged every 10 min for 50 min. Images were collected with a Nikon Ti-E widefield microscope with a 63× NA 1.4 oil objective (Nikon), a solid-state light source (SPECTRA X; Lumencor), and an sCMOS camera (Zyla 5.5 Megapixel). Images were cropped and deconvolved using 15 iterations of 3D Landweber deconvolution on Offline Deconvolution software (Nikon). Data were then analyzed using Nikon NIS-Elements Analysis software. Background was removed, and maximum intensity projections were created. Each channel was thresholded separately for each cell, and the number of pixels that were both mCherry positive and GFP positive were recorded. Spread of paGFP was calculated as the number of pixels that were both GFP and mCherry positive divided by total number of mCherry pixels after 50 min divided by the same variable at 0 min (immediately after activation). Graphs were created in Prism (GraphPad).
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7

Single-Cell Growth Dynamics of B. subtilis

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Cultures grown to an OD600 below 0.3 were concentrated by
centrifugation at 6,000 × g for 30 sec. The cell pellet
was resuspended in growth medium, and applied to No. 1.5 glass-bottomed dishes
(MatTek Corp., MA). All cells were imaged under a 2% agarose pad containing
growth medium, with the top surface exposed to air, in a chamber heated to
37°C. Phase-contrast microscopy was performed using a Nikon Eclipse Ti
equipped with a Nikon Plan Apo λ 100×/1.4NA objective and an Andor
camera. We used a custom-built package in MATLAB to perform segmentation on
phase-contrast time-lapse movies, then calculated the growth rate of the surface
area of single B. subtilis chains. Each data point for the
single-cell growth rates (Figure 2d) is the
result of a single experiment; for each, >50 cells from multiple fields
of view across different areas of the agarose pad were imaged and analyzed.
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8

Mitochondrial Imaging with MitoTracker and NucBlue

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All cells were plated ingrown on no. 1.5 glass-bottomed dishes (MatTek) for ∼48 h before imaging. Cells were incubated with 0.1 μg/ml MitoTracker Red CMXRos with or without three drops NucBlue (Molecular Probes) for 15 min at 37°C with 5% CO2. After this, MEF cells were rinsed into complete media for at least 45 min before imaging, and the Flp-In TREx cells were incubated with 0.2 μg/ml tetracycline hydrochloride (Thermo Fisher Scientific) for 4 h. A Z-series with a step size of 0.3 μm was collected with a Nikon Ti-E wide-field microscope with a 60 × NA (numerical aperture) 1.4 oil objective (Nikon), a solid-state light source (Spectra X; Lumencor), and an sCMOS camera (Zyla 5.5 megapixel). Each cell line was imaged on at least three separate occasions by a blinded experimenter (n > 100 cells per experiment).
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