Glass bottom dish

Manufactured by Ibidi

Sourced in Germany

The Glass-bottom dish is a laboratory equipment designed to provide a transparent surface for cell culture and imaging applications. It features a glass bottom that allows for high-quality optical observation and imaging of cells and other biological samples.

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Lab products found in correlation

Pluronic f 127, by Merck Group (2 mentions) Inverted sp8 confocal microscope, by Leica Microsystems (2 mentions) Lsm710nlo two photon microscope, by Zeiss (2 mentions) Lumox dish, by Sarstedt (2 mentions) Matrigel, by Corning (2 mentions) Mitotracker green, by Thermo Fisher Scientific (2 mentions) Fluo 4 am, by Thermo Fisher Scientific (2 mentions) Non essential amino acids (neaa), by PAN Biotech (1 mentions) Penicillin streptomycin, by PAN Biotech (1 mentions) Fetal calf serum (fcs), by PAN Biotech (1 mentions) Nucspot live 488, by Biotium (1 mentions) Mitoview fix 640, by Biotium (1 mentions) Elyra 7 lattice sim super resolution microscope, by Zeiss (1 mentions) Plan apochromat 63 na1, by Zeiss (1 mentions) Hoechst, by Thermo Fisher Scientific (1 mentions) Plan apochromat 40 objective, by Zeiss (1 mentions) Lsm 800, by Zeiss (1 mentions) Vt1200, by Leica camera (1 mentions) Lsm780 confocal laser scanning microscope, by Zeiss (1 mentions) Fibronectin, by Ibidi (1 mentions)

9 protocols using glass bottom dish

Neuronal Cell Culture Protocols

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N2A cells were cultured in MEM Eagle with EBSS, supplemented with 10% FCS, 1% Penicillin-Streptomycin and 1% non-essential amino acids (all Pan Biotech, Germany), and incubated at 37 °C, 5% CO₂. Prior to the experiments, 70,000 cells were seeded in a glass bottom dish (diameter 35 mm, ibidi, Germany). Cells were allowed to attach to the dish and subsequently cultured in serum-free medium for two to three days to promote neurite outgrowth and neuronal differentiation^{17 (link)} (Fig. 1a,b).Figure 1

Cell types used in this study. a, b: N2A cells before (a) and three days after serum deprivation (b). (c,d) Primary mouse cortical neurons, 7 (c) and 14 (d) days after start of culture. Mature cells formed dense clusters that did not allow for single cell stimulation. Therefore, neurons were used at the earlier time point. Scale bar corresponds to all panels.

Mouse cortical neurons (MCN) were obtained from Thermo Fisher Scientific (USA) and cultured according to the supplier’s protocol in 35 mm glass bottom dishes. Neurobasal® Medium supplemented with 0.5 mM Glutamax^TM-I and 2% B-27® was used as culture medium and refreshed every third day. After one week in culture, the neurons had developed multiple long neurites. Experiments were performed after 7–10 days in culture (Fig. 1c,d).

Johannsmeier S., Heeger P., Terakawa M., Kalies S., Heisterkamp A., Ripken T, & Heinemann D. (2018). Gold nanoparticle-mediated laser stimulation induces a complex stress response in neuronal cells. Scientific Reports, 8, 6533.

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Imaging Mitochondrial Dynamics in SH-SY5Y Cells and Macrophages

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SH‐SY5Y were plated on a 35 mm Ibidi Glass Bottom dish at a concentration of 2 × 10⁵ cells per dish. 48 h after seeding, cells were incubated with 1× NucSpot® Live 488 (Biotium Inc., USA) and 1× MitoView® Fix 640 (Biotium Inc., USA) for 30 min at 37°C prior to imaging. TNF was added immediately before starting the image acquisition. Imaging was carried out using an Elyra 7 Lattice‐SIM Super‐Resolution microscope (Zeiss, Oberkochen, Germany) every 2 min for 30 min with a 63× oil objective (Plan‐Apochromat 63×/NA1.4). Image analysis was performed with Imaris 9.9.1 (Bitplane AG, Switzerland) using the Spot (mitochondria) and surface (nucleus) functions. Mitochondrial shortest distance to the nucleus is color‐coded.
Macrophages were plated on at 50,000 cells/well in μ‐Slide 8‐well chambers (80826, Ibidi, Martinsried, Germany) and incubated with 0.5 μM MitoTracker Green (Thermo Fisher Scientific) for 15 min at 37°C prior to imaging. The nuclei were stained using 2 μM Hoechst (Thermo Fisher Scientific). TNF was added immediately before staring video recording. Imaging was carried out using a confocal microscope (LSM800, Carl Zeiss, Oberkochen, Germany) and LD Plan‐Apochromat 40× objective.

Wu Z., Berlemann L.A., Bader V., Sehr D.A., Dawin E., Covallero A., Meschede J., Angersbach L., Showkat C., Michaelis J.B., Münch C., Rieger B., Namgaladze D., Herrera M.G., Fiesel F.C., Springer W., Mendes M., Stepien J., Barkovits K., Marcus K., Sickmann A., Dittmar G., Busch K.B., Riedel D., Brini M., Tatzelt J., Cali T, & Winklhofer K.F. (2022). LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF‐κB to the nucleus. The EMBO Journal, 41(24), e112006.

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Evaluating Platelet Activation and Reactivity

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The release of platelets’ calcium ions provides a sensitive tool to evaluate platelets’ activation and reactivity [72 (link)]. Isolated platelets (read above for platelets isolation) were resuspended in 1 mL of Tyrode’s buffer at the concentration of 1 × 10⁶ platelets/mL. Platelets were seeded in a glass bottom dish (Ibidi, Gräfelfing, Germany) and incubated with 10 µM Fluo-4 AM (Thermo Fisher, Monza, Italy), 0.1% (w/v) Pluronic F-127 (Sigma Aldrich, Milan, Italy). Platelets without and with the addition of 400 ng/mL of PFOA were activated with 10 µM TRAP-6. Platelets were analyzed in time-lapse, with DMI6000CS fluorescence microscope and 40×/0.60 dry objective magnification (Leica Microsystem, Wetzlar, Germany) for 30 min at 37 °C. Images were analyzed in real time using a differential interference contrast (DIC) and fluorescence objectives. Samples were acquired using a DFC365FX camera and processed using the Leica Application Suite (LAS-AF, Wetzlar, Germany) 3.1.1. software (Leica Microsystem, Wetzlar, Germany).

De Toni L., Radu C.M., Sabovic I., Di Nisio A., Dall’Acqua S., Guidolin D., Spampinato S., Campello E., Simioni P, & Foresta C. (2020). Increased Cardiovascular Risk Associated with Chemical Sensitivity to Perfluoro–Octanoic Acid: Role of Impaired Platelet Aggregation. International Journal of Molecular Sciences, 21(2), 399.

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In Vivo Brain Imaging Procedure

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Lycopersicon lectin (DL-1178, vector Laboratories) was injected i.v. 30 min prior to humane euthanasia of the mice. Brains from mice were harvested and immersed in cold PBS to be sectioned at 200 µm thickness using a vibratome (Leica VT 1200 s). The tissues were placed in a µ-Dish 35 mm, high Glass Bottom dish (81158, ibidi) and subjected to high-resolution confocal microscopy (Zeiss LSM780 laser scanning confocal microscope).

Spinelli C., Adnani L., Meehan B., Montermini L., Huang S., Kim M., Nishimura T., Croul S.E., Nakano I., Riazalhosseini Y, & Rak J. (2024). Mesenchymal glioma stem cells trigger vasectasia—distinct neovascularization process stimulated by extracellular vesicles carrying EGFR. Nature Communications, 15, 2865.

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Stamping Fibronectin Patterns for Cell Confinement

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The protocol for stamping circular fibronectin patterns for cell confinement experiments was adapted from Doxzen et al. (2013) (link). Briefly, PDMS stamps bearing circular features of 100 μm diameter were prepared using a silanized wafer generated using soft lithography techniques. Stamps were then incubated with a mixture of fibronectin (Sigma-Aldrich) and cyanine 5 (Cy5)-conjugated fibronectin for 1 h, followed by three washes with phosphate-buffered saline (PBS) and air drying. Dried and labeled fibronectin stamps were then gently pressed against a glass-bottom dish (Ibidi, Martinsried, Germany 81151) to replicate the patterns on the dish. The area outside the patterns was then blocked by treatment with 0.2% Pluronic F-127 (Sigma-Aldrich) for 1 h, followed by two washes with PBS before cells were seeded.

Rao M.V, & Zaidel-Bar R. (2016). Formin-mediated actin polymerization at cell–cell junctions stabilizes E-cadherin and maintains monolayer integrity during wound repair. Molecular Biology of the Cell, 27(18), 2844-2856.

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Tracking Osteosome Uptake by Prostate Cancer Cells

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Osteosomes and control liposomes were labeled with the red fluorescent lipophilic dye PKH26 (InVitrogen)^{23 (link)}. Next, PKH26-labeled osteosomes or liposomes (3×10⁵ particles) were added to prostate cancer cells (1×10⁴ cells), C4-2b or PC3-mm2, in RPMI1640 containing exosome-depleted 0.1% FBS, and cells were plated on a glass-bottom dish (ibidi). Exosome or liposome uptake into cells was observed by live-cell imaging on a BioStation (Nikon), in which images were captured every 30 min over 30 h using both bright-field and red fluorescence channels^{24 (link)}. For antibody blocking, PKH26-labeled osteosomes were preincubated with anti-Cad11 monoclonal antibody 1A5^{25 (link)} at a final antibody concentration of 3 μg/ml before the osteosome-antibody mixture was added to prostate cancer cells for live-cell imaging analysis. PBS buffer alone and an unrelated antibody with similar IgG isotype were used as negative controls.

Bilen M.A., Pan T., Lee Y.C., Lin S.C., Yu G., Pan J., Hawke D., Pan B.F., Vykoukal J., Gray K., Satcher R.L., Gallick G.E., Yu-Lee L.Y, & Lin S.H. (2017). Proteomics profiling of exosomes from primary mouse osteoblasts under proliferation versus mineralization conditions and characterization of their uptake into prostate cancer cells. Journal of proteome research, 16(8), 2709-2728.

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Visualizing Mitochondrial Dynamics in HeLa Cells

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The penicillin-streptomycin 100x solution, 0.25% Trypsin-EDTA, and Phosphate-Buffered Saline (PBS) were supplied from Corning Cellgro. HyClone Fetal Clone III serum was obtained from GE Healthcare and Modified Eagle’s Medium (MEM) was purchased from Biowest. Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) and wt-GFP solution in PBS was purchased from Sigma. Celllight BacMam 2.0 Mito-GFP was provided by Thermofischer.
HeLa cell line was purchased from ECACC (Cat. No. 93021013), grown under standard culture conditions and seeded inside of two silicone inserts wells on a 35 mm glass-bottom dish (Ibidi) in MEM culture media supplemented with 10% serum, 1% of penicillin-streptomycin, incubated under 5% of CO₂ at 37 °C. CellLight Mitochondria-GFP BacMam 2.0 was added to the cells in appropriate proportion following the supplier’s protocol and incubated overnight.

Savchuk O.A., Silvestre O.F., Adão R.M, & Nieder J.B. (2019). GFP fluorescence peak fraction analysis based nanothermometer for the assessment of exothermal mitochondria activity in live cells. Scientific Reports, 9, 7535.

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Imaging Skin Explant Dynamics

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Lateral skin explants were taken from E13.5 embryos (H2B-EGFP^tg/wt) and transferred to media (advanced DMEM + 2 mM L-glutamine + 0.1 mg/ml penicillin/streptomycin + 10% FBS) at 37 °C where they formed rolls. The rolls were embedded in 1% low-melting agarose or Matrigel (Corning) in media at 37 °C, where the cutting edge was touching the membrane-bottom of a Lumox® dish (Sarstedt) or a glass-bottom dish (ibidi). The dishes were covered with media and incubated at 37 °C and 5% CO₂ until imaging. Time-lapse imaging was carried out between E13.5 and E14.5 using an inverted SP8 confocal microscope (Leica microsystems), an inverted Dragonfly Spinning disc confocal microscope (Andor), or an inverted LSM710NLO Two-Photon microscope (Zeiss) with 20× air objective or 40× water or oil immersion objective and incubation at 37 °C and 5% CO₂.

Damen M., Wirtz L., Soroka E., Khatif H., Kukat C., Simons B.D, & Bazzi H. (2021). High proliferation and delamination during skin epidermal stratification. Nature Communications, 12, 3227.

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Imaging Embryonic Skin Explant Dynamics

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Lateral skin explants were taken from E13.5 embryos (H2B-EGFP tg/wt ) and transferred to media (advanced DMEM + 2 mM L-Glutamine + 0.1 mg/ml Penicillin/Streptomycin + 10% FBS) at 37 °C where they formed rolls. The rolls were embedded in 1 % low-melting agarose or Matrigel (Corning) in media at 37 °C, where the cutting edge was touching the membrane-bottom of a Lumox® dish (Sarstedt) or a glass-bottom dish (ibidi). The dishes were covered with media and incubated at 37 °C and 5 % CO2 until imaging. Time-lapse imaging was carried out between E13.5 and E14.5 using an inverted SP8 confocal microscope (Leica microsystems), an inverted Dragonfly Spinning disc confocal microscope (Andor) or an inverted LSM710NLO Two-Photon microscope (Zeiss) with 20x air objective or 40x water or oil immersion objective and incubation at 37 °C and 5 % CO2.

Damen M., Wirtz L., Soroka E., Khatif H., Kukat C., Simons B.D., & Bazzi H. (2020). A two-phase model of skin epidermal stratification: lessons from centrosomes.

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