Glass bottomed dishes

Manufactured by MatTek

Sourced in United States

Glass-bottomed dishes are a type of laboratory equipment designed to facilitate microscopic observation and cell culture applications. These dishes feature a transparent glass bottom that allows for clear, unobstructed viewing of samples under a microscope. The glass-bottomed design enables researchers to observe cells, tissues, or other specimens with enhanced clarity and detail, supporting various research and experimental needs.

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Glass-bottomed 35 mm dish 35 mm glass-bottomed culture dish 35-mm glass-bottomed microwell dish Glass-bottomed Petri dish Glass-bottomed culture dish Glass cover slip-bottomed 50 mm petri dish with 30 mm glass diameter No. 1.5 glass-bottomed dish Glass coverslip-bottomed 50-mm Petri dish Glass-bottomed dish Glass-bottomed Petri dishes

99 protocols using glass bottomed dishes

Immunostaining Drosophila Tubule Tissues

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Unless stated adult flies were reared at 29°C and aged for 5 days prior to dissection in Schneider's Drosophila medium (Gibco, Thermo Fisher Scientific).
Immunocytochemistry staining as previously described (Halberg et al., 2015) .
Primary antibodies employed, mouse monoclonal anti-A5 Na + /K + vATPase asubunit (1:50), -43F discs-large 1 (1:500), -C594.9B Delta (1:200) all DSHB (Univ. of Iowa, IA, USA); rabbit polyclonal anti-Snakeskin and -Mesh (1:1000), Furuse Lab (Izumi et al., 2012; Yanagihashi et al., 2012) ; and rabbit polyclonal anti-Clc-A (1:50) (Cabrero et al., 2014) . Secondary antibodies, anti-rabbit Alexafluor 488 or 546 or anti-mouse Alexafluor 633 (Thermo Fisher Scientific)
(1:600). Tubules were also incubated in 500 ng/ml DAPI and Phalloidin TRITC (Sigma-Aldrich). Tissues were mounted on either Polysine slides (VWR International, Leuven) or glass bottomed dishes (MatTek Corporation, MA, USA) and analysed using Zeiss a LSM 880 confocal micro-system (Carl Zeiss Ltd., Cambridge UK). Confocal Z projection stacks used for cell counts, analyses, and presentation were opened in ImageJ (NIH, MA, USA) prior to transferal to Adobe Photoshop and Illustrator (CS6; CA, USA) for final presentation.

Dornan A.J., Halberg K.A., Beuter L., Davies S.A., & Dow J.A.T. (2020). The septate junction protein Snakeskin is critical for epithelial barrier function and tissue homeostasis in the Malpighian tubules of adult Drosophila.

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Knockdown of Dynein Heavy Chain in HEK293T Cells

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shRNA target sequences were obtained using the RNAi Consortium (TRC; Broad Institute). Oligonucleotides for shRNA against DHC (target sequence: 5′-CCCGTGATTGATGCAGATAAA-3′) were purchased from Integrated DNA Technologies, annealed and ligated into pLKO.1 - TRC viral plasmid. shRNA against LacZ in pLKO.1 - TRC (target sequence: 5′-CGCGCCTTTCGGCGGTGAAAT-3′) was a gift from Yasemin Sancak. One million HEK293T cells were seeded in 6-cm plates with 5 ml media. The next day, cells were transfected with 900 ng psPax2, 100 ng VSV-G, and 1,000 ng viral plasmid in JetPRIME Transfection Reagent with JetPRIME buffer for 48 h. Viral supernatant was collected, passed through a 0.45-μm PES membrane filter, and stored at −80°C. Flp-In TREx stable cell lines were seeded at 250,000 cells in a six-well dish. The next day, viral supernatant was thawed at room temperature was added to cells with 8 μg/ml polybrene and incubated for 48 h. Cells were moved to a 10-cm dish, and selection was added (1 μg/ml puromycin). ∼3 d later, cells were seeded onto no. 1.5 glass-bottomed dishes (MatTek) coated with 10 μg/ml fibronectin (Sigma-Aldrich) and were imaged 2 d later after incubation with 0.2 μg/ml tetracycline hydrochloride (Thermo Fisher Scientific) as described below.

Sloat S.R, & Hoppins S. (2022). A dominant negative mitofusin causes mitochondrial perinuclear clusters because of aberrant tethering. Life Science Alliance, 6(1), e202101305.

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Calcium Signaling in Mammalian Oocytes

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Human oocytes were loaded with 7.5 µM of Ca 2+ -sensitive dye Fura-2 acetoxymethyl (AM) ester (Invitrogen, Life Technologies) at 37°C in 6% CO2, 5% O2 for 30 min and subsequently extensively washed in Cook Cleavage medium. Oocytes were placed in glass-bottomed dishes (MatTek Corporation) and Ca 2+ imaging was performed on an inverted epi-fluorescence microscope (TH4-200, Olympus Soft Imaging Solutions GmbH) with a 20x objective. Fluorescence was recorded at an emission wavelength of ~510 nm every 5 s. The ratio of Ca 2+induced signal (340 nm/380 nm) was proportional to the concentration of free intracellular Ca 2+ (expressed in arbitrary units, AU).
For measuring spontaneous Ca 2+ oscillations in mouse oocytes, isolated GV oocytes were loaded with Fura-2 in KSOM-HEPES for 15 min. Oocytes were transferred to a drop of IVM medium and Ca 2+ signals were recorded every 30 s for a duration of 4 h. The strontiuminduced Ca 2+ oscillations were recorded every 5 s for a duration of 2 h, immediately after transferring the mouse oocytes to a drop of Ca 2+ -free KSOM with 10 mM strontium chloride, in the glass-bottomed dish.

Lu Y., Ferrer-Buitrago M., Popovic M., Neupane J., De Vos W.H., Lierman S., Van den Abbeel E., Van der Jeught M., Nikiforaki D., De Sutter P, & Heindryckx B. (2018). Patients with a high proportion of immature and meiotically resistant oocytes experience defective nuclear oocyte maturation patterns and impaired pregnancy outcomes. Reproductive biomedicine online, 36(4).

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Culturing Mouse Cortical Neurons for Neurodegenerative Studies

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Wild type primary neurons were obtained from cerebral cortex of CD1 mouse embryos, at embryonic day 15, as previously described [89 (link)]. Neurons were plated to a density 6×10⁵ viable cells/35-mm² on glass-bottomed dishes (MatTek Corporation, Ashland, MA, USA) previously coated with poly-D-lysine (10 μg/ml) for at least 1 h at 37°C. Cultures were maintained at 37°C with 5% CO₂, supplemented with neurobasal medium with 2% B27 nutrient, 2 mM L-glutamine, penicillin (100 units/ml) and streptomycin (100 μg/ml). At 12 days in vitro (DIV) neurons, transfected on day 7 with the plasmid peGFP-N1 (Clontech, Mountain View, CA) using lipofectamine 2000 (Invitrogen), were pre-treated with the Keap1 inhibitor, 22h (10 μM[22 (link)]), or 0.1% DMSO, for 16 h. Conditioned medium (CM) from Tg2576 transgenic, Aβ-enriched, or wild type mouse neurons, with and without 22h, was then added for a further 24h before analysis.

Kerr F., Sofola-Adesakin O., Ivanov D.K., Gatliff J., Gomez Perez-Nievas B., Bertrand H.C., Martinez P., Callard R., Snoeren I., Cochemé H.M., Adcott J., Khericha M., Castillo-Quan J.I., Wells G., Noble W., Thornton J, & Partridge L. (2017). Direct Keap1-Nrf2 disruption as a potential therapeutic target for Alzheimer’s disease. PLoS Genetics, 13(3), e1006593.

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Live Imaging of Medaka Embryos

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Embryos were prepared for live imaging as previously described (Seleit et al., 2017a (link); Seleit et al., 2017b (link)). 1× Tricaine (Sigma-Aldrich #A5040-25G) was used to anaesthetize dechorionated medaka embryos (20 mg/ml – 20× stock solution diluted in 1XERM). Anaesthetized embryos were then mounted in low melting agarose (0.6–1%) (Biozyme Plaque Agarose #840101). Imaging was done on glass-bottomed dishes (MatTek Corporation Ashland, MA, USA). For g3bp1-eGFP live imaging, temperature was changed from 21 to 34°C after 1 hr of imaging.

Seleit A., Aulehla A, & Paix A. (2021). Endogenous protein tagging in medaka using a simplified CRISPR/Cas9 knock-in approach. eLife, 10, e75050.

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Immunofluorescence Staining of Vero E6 Cells

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Vero E6 cells were cultured in glass-bottomed dishes (MatTek) or in six-well tissue culture plates. The cells were fixed with 4% paraformaldehyde for 30 min and permeabilized with 1% Triton X-100 for 15 min at room temperature for intracellular labeling. They were then incubated with the primary antibody for 2 h at room temperature. When a secondary antibody was required, the cells were incubated with the corresponding Alexa-Fluor-conjugated secondary antibody (Invitrogen) for 1 h at room temperature, and then counterstained with 4′,6-diamidino-2-phenylindole (DAPI; Sigma, USA) at room temperature for 15 min. Images were captured with an inverted fluorescent microscope (Zeiss, Munich, Germany) or LSM 800 confocal microscope (Zeiss) using oil immersion objective. The red-fluorescence-positive cells were quantified by averaging at least six fields of view.

Zhang J., Zhang L., Shi H., Feng S., Feng T., Chen J., Zhang X., Han Y., Liu J., Wang Y., Ji Z., Jing Z., Liu D., Shi D, & Feng L. (2021). Swine acute diarrhea syndrome coronavirus replication is reduced by inhibition of the extracellular signal-regulated kinase (ERK) signaling pathway. Virology, 565, 96-105.

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AKT PH Domain Localization Assay

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HEK 293 T cells were seeded in glass-bottomed dishes (MatTek, MA, USA), and treated with 10 μmol/L SC79 for 0.5 h or treated with CA (10, 1, and 0.1 μmol/L), CA4G (10, 1, and 0.1 μmol/L), FA (10, 1, and 0.1 μmol/L), or FA4G (10, 1, and 0.1 μmol/L) for 6 h. After washing once with PBS, cells were transfected with R25C or PH-GFP plasmid, which was used to indicate the cellular localization of the transfected fluorescent AKT PH domain protein with or without mutation, respectively, in a 37 °C incubator for 6 h. The cells were observed under a confocal microscope after incubation with 5 μmol/L Dil, a membrane dye, at 37 °C for 10 min. The excitation and emission wavelengths of GFP were 488 nm and 507 nm, respectively. The excitation and emission wavelengths of Dil were 549 nm and 565 nm, respectively.
The Pearson correlation coefficient was calculated by ImageJ software (Wayne Rasband, NIH, USA) with a Pearson correlation coefficient (PCC) colocalization plug.

Gao J., Zhang M., Zu X., Gu X., Hao E., Hou X, & Bai G. (2023). Glucuronic acid metabolites of phenolic acids target AKT-PH domain to improve glucose metabolism. Chinese Herbal Medicines, 15(3), 398-406.

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Cytochrome c Immunofluorescence Staining

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The expression of cytochrome c was analyzed by immunofluorescence staining. Cells grown on glass-bottomed dishes (MatTek, Ashland, MA, USA) were fixed with 4% formaldehyde solution (R&D Systems, Abingdon, UK) for 10 min and permeabilized with 0.5% TritonX-100 in phosphate-buffered saline (PBS) for 10 min. Slides were air-dried, washed with PBS, and incubated with anti-cytochrome c (1:25; Abcam, Cambridge, UK) in 3% bovine serum albumin in PBS. Further details on the protocol can be found in our previous article [68 (link)]. Images were observed under a confocal microscope (LSM Meta 700; Zeiss, Oberkochen, Germany) and were analyzed using Zeiss LSM Image Browser, version 4.2.0121.

Yun H.J., Kim M., Kim S.Y., Fang S., Kim Y., Chang H.S., Chang H.J, & Park K.C. (2022). Effects of Anti-Cancer Drug Sensitivity-Related Genetic Differences on Therapeutic Approaches in Refractory Papillary Thyroid Cancer. International Journal of Molecular Sciences, 23(2), 699.

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Automated Autophagy Quantification in MH-S Cells

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MH-S cells were respectively transfected with RFP-LC3 and RFP-GFP-LC3 plasmids, using LipofectAmine 2000 reagent (Invitrogen) in serum-free RPMI 1640 medium (Thermofisher Scientific, San Jose, CA) following the manufacturer’s instructions. Transfected MH-S cells were also starved (6 h) or treated with the autophagy inhibitor 3-MA (3 mM, 3 h) as a positive and negative control, respectively. For immunostaining, MH-S cells were grown in glass-bottomed dishes (MatTek, Ashland, MA) and fixed in 3.7% paraformaldehyde, permeabilized with 0.2% Triton X-100 in PBS and incubated with blocking buffer for 30 min [35 (link)]. Then the dishes were incubated with an HMGB1 antibody (Santa Cruz Biotechnology, Santa Cruz, CA) at 1/500 dilution in blocking buffer overnight and washed three times with wash buffer. Images were captured after incubation with an appropriate secondary antibody containing FITC using an LSM 510 Meta confocal microscope (Carl Zeiss MicroImaging, Thornwood, NY), and processed using the software provided by the manufacturer [22 (link)]. The confocal microscopy images were then used to semi-quantitatively measure the percentage of cells with significant LC3 punctation staining (100 cells/sample). The threshold for positive expression was set to 10 visible LC3 puncta.

Li Y., Gan C.P., Zhang S., Zhou X.K., Li X.F., Wei Y.Q., Yang J.L, & Wu M. (2014). FIP200 is Involved in Murine Pseudomonas Infection by Regulating HMGB1 Intracellular Translocation. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 33(6), 1733-1744.

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Automated Autophagy Quantification in MH-S Cells

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