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7 protocols using 35 mm collagen coated glass bottom dish

1

Live Imaging of TMEV-Infected Cochlear Cells

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TMEV-infected cochleae were cultivated on a collagen-coated 35-mm glass-bottom dish (MatTek) for live imaging. For visualizing activated SCs and GERCs as macrophages, a Leica SP8 confocal laser-scanning microscope equipped with a HC PL APO 63×/1.40 CS2 oil objective was used. Images were captured every 5 min, from 8 to 25 h after TMEV infection, using a 488-nm argon laser with 10% intensity. While capturing images, the explant was maintained in a CO2 (5%) stage-top incubator (INUBG2F-GSI2, Tokai Hit) at 37 °C. The movies were constructed using Leica LAS AF software (9–14 h and 14–21 h, respectively).
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2

Live Imaging of EB1-EGFP in Cells

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For live imaging of EB1-EGFP, cells were collected by standard trypsinization and 1.4 x 106 cells were plated on a collagen-coated 35 mm glass-bottom dish (MatTek Corporation). After recovering overnight, the spent media was replaced with fresh media containing diluted DMSO/nocodazole. Each dish was treated and imaged separately at room temperature using an Eclipse TE2000 confocal microscope (Nikon). After imaging up to 15 min, treated plates were incubated in 5% CO2 at 37°C for an additional 1.75 hours. Adhesion activation was then analyzed via brightfield microscopy with images collected using a IX-71 microscope (Olympus), the same as similar assays in this paper. Cells were then fixed in -20°C methanol for 10 min, washed twice with PBS, then blocked for 30 min in 5% milk/PBST before overnight incubation with mouse anti-α-tubulin DM1A monoclonal antibody (Pierce, #62204) [1:2,500] at 4°C. Cells were then washed twice with PBS before incubation with rabbit anti-mouse IgG (H+L) 546 [1:500] in the dark for 2 hours at room temperature. Cells were washed twice and left in a third wash of PBS for imaging on an Eclipse TE2000 confocal microscope (Nikon).
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3

Insulin Sensitivity in Obese Myotubes

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Previously isolated human skeletal muscle cells (HSkMCs) from severely obese, insulin‐resistant women (BMI ≥40 kg/m2, HOMA‐IR ≥2.5, n = 6) and lean insulin‐sensitive women (BMI < 25 kg/m2, HOMA‐IR < 2.5, n = 6) were used in this study (Kugler et al., 2020). In brief, human skeletal muscle cells (Passage 3) were thawed, pooled together, and grown in a humidified environment with 5% CO2 at 37°C on a type‐I collagen‐coated flask (Greiner Bio‐one). At a confluence of ~80%–90%, myoblasts were subcultured onto type I collagen‐coated plates (Corning), 35 mm collagen‐coated glass‐bottom dish (MatTek), Seahorse XFp cell culture miniplate (Agilent Technologies), or 96 well clear bottom black polystyrene microplate (Corning) depending on experimental purposes. Upon reaching ~80%–90% confluency, myoblasts were switched to low‐serum (2% horse serum) media to induce differentiation into myotubes. On day 6 of differentiation, myotubes were treated with either Mdivi‐1 (20 μM) or vehicle (1% DMSO in PBS) for 12 h. For insulin signaling and glucose uptake measurements, myotubes were serum‐starved for 3 h, incubated with or without 100 nM of insulin for 10 min, and cell lysates were collected for further analysis as previously described (Bikman et al., 2010). All experimental procedures were repeated in three independent experiments.
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4

Tracking Amoebae Motility Dynamics

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Amebae grown and harvested in logarithmic growth phase were labelled with 10 μM CellTracker Green (Thermo Fisher Scientific) in BI medium for 40 min at 35.5°C. After washing with PBS, approximately 2 × 105 cells resuspended in 1.5 mL BI medium were transferred to a 35 mm collagen‐coated glass‐bottom dish (MatTek) and incubated in an anaerobic chamber at 35.5°C for 30 min. After the medium was removed, approximately 200 μl of warm BI was added to the center of the dish and covered with a cover glass. Time lapse images were captured on an LSM780 confocal laser scanning‐microscope (Carl Zeiss) using a 20× objective in every 30 s for 15 min. The motility of amebae was calculated as the total length of movement divided by duration of measurement by Imaris X64 software.
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5

Primary Myoblast Isolation and Characterization

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Previously isolated HSkMCs from severely obese, insulin-resistant, and lean insulin-sensitive humans were used in this study [14 ,18 (link),34 (link)]. In brief, HSkMCs were thawed (n = 6 per group), pooled together, and grown in growth media as previously described [18 (link)]. At a confluence of ∼80%, myoblasts were subcultured onto a 6-well type I collagen plate (Corning, Glendale, AZ), 35 mm collagen-coated glass-bottom dish (MatTek, Ashland, MA), Seahorse XFp cell culture miniplate (Agilent Technologies, Santa Clara, CA), or 96 well transparent bottom black polystyrene microplate (Corning, Glendale, AZ) depending on experimental purposes. Upon reaching ∼80% confluency, myoblasts were switched to low-serum (2% horse serum) media to induce differentiation. All experiments were performed on day 7 of differentiation. The experimental protocol was approved by the Internal Review Board for Human Research at the University of Massachusetts Boston.
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6

Muscle Cell Differentiation Protocol

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Immediately following the procedure, primary muscle cells were isolated
and cultured into myoblast, as previously described (26 (link)). After isolation, myoblasts (Passage 3) were
thawed and grown in a humidified environment with 5% CO2 at
37°C on a collagen I TC flask (Greiner Bio-one, Monroe, NC). At a
confluence of ~80–90%, myoblasts were subcultured onto either a
6-well type I collagen-coated plate (Corning, Corning, NY) or a 35 mm
collagen-coated glass-bottom dish (MatTek, Ashland, MA) for immunoblot and
fluorescence microscopy, respectively. At ~80–90% confluency,
myoblasts were switched to low-serum (2% horse serum) media to induce
differentiation into myotubes.
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7

Immunofluorescent Staining of DNA Damage and Senescence Markers

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Cells were seeded on a 35-mm collagen-coated glass-bottom dish (MatTek) one day before starting the cell treatments. For the staining, cells were fixed with 4% formaldehyde for 10 minutes at room temperature, permeabilized with 0.2% Triton X-100 (Sigma-Aldrich) for 15 minutes at 4°C, and then blocked with 3% BSA in PBS. Then, the cells were incubated with primary antibodies overnight at 4°C, washed twice with PBS, and then incubated with conjugated Alexa Fluor 647 goat-anti-mouse (Invitrogen, A32728) and Alexa Fluor 488 goat-anti-rabbit (Invitrogen, A32731) secondary antibodies at 1:1000 for 1 hour at room temperature. The cells were washed twice with PBS, incubated with 300 nM DAPI for 5 minutes at room temperature, and then imaged using a Zeiss Axio Observer Z1 microscope with an A-plan 10x/0.25NA objective. γ-H2AX and 53BP1 loci were quantified from microscopy images using standard tools implemented in FIJI software. The primary antibodies used for immunofluorescent staining were rabbit anti-53BP1 (Novus Biologicals, NB100304, 1:2000 dilution), mouse anti-γ-H2AX (Sigma Millipore, 05–636-I, 1:200), rabbit anti-p16 (Abcam, ab108349, 1:250), rabbit anti-p21 (Abcam, ab109199, 1:200), mouse anti-Lamin B1 (CST #68591, 1:200).
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