35 mm glass bottom dish

Manufactured by MatTek

Sourced in United States

The 35 mm glass bottom dish is a laboratory equipment item designed for cell culture and microscopy applications. It consists of a 35 mm diameter plastic petri dish with a glass coverslip bonded to the bottom, providing a transparent surface for imaging and observation.

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Lab products found in correlation

Lsm800 confocal microscope, by Zeiss (8 mentions) Hoechst 33342, by Thermo Fisher Scientific (3 mentions) Axio observer z1, by Zeiss (3 mentions) Lsm 710 confocal microscope, by Zeiss (3 mentions) Fluo 4 am, by Thermo Fisher Scientific (3 mentions) Hepes buffered physiological saline, by Thermo Fisher Scientific (2 mentions) Prolong gold antifade mountant with dapi, by Thermo Fisher Scientific (2 mentions) Lsm 780, by Zeiss (2 mentions) Uplsapo30xsir, by Olympus (2 mentions) Fluoview 1200 mpa, by Olympus (2 mentions) Dnase 1, by Merck Group (2 mentions) Papain, by Worthington (2 mentions) Stellaris dmi8, by Leica (2 mentions) Hepes, by Thermo Fisher Scientific (2 mentions) Live cell imaging solution, by Thermo Fisher Scientific (2 mentions) Csu x filter wheel, by Hamamatsu Photonics (2 mentions) Orca flash 4, by Hamamatsu Photonics (2 mentions) Zen software, by Zeiss (2 mentions) A1 confocal microscope, by Nikon (2 mentions) Lipofectamine 2000, by Thermo Fisher Scientific (2 mentions)

75 protocols using 35 mm glass bottom dish

Quantifying Mitochondrial Superoxide and Hydroxyl Radical

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For detection of superoxide, 10⁵ cells were plated and grown overnight in a glass-bottom 35mm dish (Mattek). Two fluorescent probes, MitoSox and HPF, are used according to the manufacturer’s protocol. For detection of superoxide in the mitochondria, MitoSox was added at a final concentration of 1µM and after 30 min cells were subjected to confocal microscopy. For detection of hydroxyl radical, the cells were prepared in the same way but incubated with 1µM of HPF for 30 min and subjected to confocal microscopy. Phosphorescent values of each cell were computed by measuring phosphorescence of a cell divided by an area of a whole cell using FV10-ASW 3.1 Viewer. Each sample has an average value of 10 cells and the indicated error bars were standard error of each sample. Student’s t-test was utilized to compare group means. Means with p-value below 0.05 were considered statistically different.

Wiese A.K., Prior S., Chambers T.C, & Higuchi M. (2017). Intracellular Oxygen Concentration Determined By Mitochondrial Respiration Regulates Production of Reactive Oxygen Species. Integrative cancer biology & research, 1(1), 006.

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Live Imaging of Microglial Dynamics in Zebrafish

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For live imaging, Tg(mpeg:EGFP-CAAX);Tg(NBT:dsRed) zebrafish larvae were anesthetized with 0.2 mg/ml of tricaine in embryo medium and mounted in 1.2% low-melting agarose gel on a glass bottom 35-mm dish (MatTek) and covered with embryo water containing 0.2 mg/ml tricaine. Time-lapse image was performed on a Nikon CSU-W1 spinning disk/high speed widefield microscope. We took time-lapse images from the optic tectum collecting 40–60 mm z-stacks (step size: 0.5 mm) at 5 min intervals for 30 min-1 hr. The images were processed by ImageJ software. For analysis, we calculated the number of dsRed(+) neurons in microglia for the first 30 min of each video. For the analysis of process motility, we carefully observed each microglia process for the first 30 min of each video and classified all processes into three categories: 1) ‘ramified’ were defined as processes with or without movement that have no phagocytic cup formation, 2) ‘cup formation’ denoted processes with or without movement that contained or formed phagocytic cups, and 3) ‘soma retraction’ - processes that enclosed dsRed+ cells that were subsequently trafficked toward the microglial soma). Statistical analyses were performed by Graphpad Prism software.

Escoubas C.C., Dorman L.C., Nguyen P.T., Lagares-Linares C., Nakajo H., Anderson S.R., Cuevas B., Vainchtein I.D., Silva N.J., Xiao Y., Lidsky P.V., Wang E.Y., Taloma S.E., Nakao-Inoue H., Schwer B., Andino R., Nowakowski T.J, & Molofsky A.V. (2023). Type I interferon responsive microglia shape cortical development and behavior. bioRxiv.

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Live-Cell Imaging of Apoptosis

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2 × 10⁵ cells were seeded in each glass-bottom, 35-mm dish (MatTek Corporation). Cells were incubated with Hoechst 33342 (Molecular Probes) for 20 min and imaged on a Zeiss LSM 780 or Leica DMi8 microscope with temperature and CO₂ control. Images were taken every 10 or 5 min as indicated in the figure legends. Medium change for treatment and recovery was performed between scans. To live-monitor caspase 3 activation during EtOH treatment, NucView 488 (Biotium) was added. NucView 488 binds irreversibly to DNA and thus inhibits anastasis.

Sun G., Guzman E., Balasanyan V., Conner C.M., Wong K., Zhou H.R., Kosik K.S, & Montell D.J. (2017). A molecular signature for anastasis, recovery from the brink of apoptotic cell death. The Journal of Cell Biology, 216(10), 3355-3368.

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Quantifying Protein Mobility via FRAP

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FRAP analyses were carried out as previously described (Snapp et al., 2003 (link)) using a resonant scanning confocal microscope (SP8; Leica) equipped with a Plan Apochromat 60×, NA 1.2 oil-immersion objective. Briefly, 2 × 10⁵ H4 mRuby PKR cells were grown on a glass-bottom 35-mm dish (MatTek) and transfected with poly I:C as described above 60 min before starting the experiment. Cells were imaged at 37°C and 5% CO₂ in phenol-free DMEM complete medium. ROIs for each mRuby-PKR cluster were identified, and two to three clusters per cell were bleached with a 561-nm laser. Because of the high concentration of mRuby-PKR in the clusters, a 15-s continuous bleaching pulse was used to achieve complete bleaching. For normalization, ROIs of similar areas were selected in the cytosol, and the mean intensity of cytosolic ROIs was subtracted from the mean intensity of each bleached cluster. The mobile fraction was calculated as follows:

M_{f} = \frac{I_{\infty} - I_{0}}{I_{i} - I_{0}},

where, I_∞ is the last fluorescence value collected, I₀ is the fluorescence value before photobleaching, and I_i is the first value after photobleaching. The immobile fraction was defined as 1 − M_f.

Zappa F., Muniozguren N.L., Wilson M.Z., Costello M.S., Ponce-Rojas J.C, & Acosta-Alvear D. (2022). Signaling by the integrated stress response kinase PKR is fine-tuned by dynamic clustering. The Journal of Cell Biology, 221(7), e202111100.

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Cultivation of Insulin-Producing Cell Lines

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MIN6⁶⁷ (link) and INS1⁵⁸ (link) cells were grown in DMEM with 25 mM glucose (Gibco), 0.071 mM β-mercaptoethanol (MilliporeSigma, St Louis, MO), 10% HI-FBS, and 100 U/mL penicillin-100 μg/mL streptomycin. Primary β-cells were harvested from dissociation of isolated islets (see later in discussion in the islet isolation and in the pseudoislet generation procedure) and culture in islet media [RPMI-1640 media with 11 mM glucose (Gibco, Dublin, Ireland) plus 10% HI-FBS and 100 U/mL penicillin-100 μg/mL streptomycin (Gibco)] in a glass-bottom 35-mm dish (MatTek, Ashland, MA) coated with human extracellular matrix [ECM] (Corning). Primary β-cells were cultured over one night before fixation for imaging.

Ho K.H., Jayathilake A., Mahircan Y., Nour A., Osipovich A.B., Magnuson M.A., Gu G, & Kaverina I. (2023). CAMSAP2 localizes to the Golgi in islet β-cells and facilitates Golgi-ER trafficking. iScience, 26(2), 105938.

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Scratch Assay for Cell Migration

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Example 11

Scratch Assay: LN-229 or U87MG cells were transfected with miR-3189-3p (SEQ ID NO: 2) and plated in a 35 mm glass bottom dish (MatTek Corporation, Ashland, Mass.) at a density of 1.8×10⁵cells/dish. The scratch assay was performed by moving a pipette tip across the cell monolayer. Migration into the cell-free area was monitored for up to 24 h using live cell time-lapse imaging (VivaView FL incubator fluorescent microscope, Olympus, Center Valley, Pa.).

US10308939B2. Use of an miRNA to reduce proliferation of a cancer cell (2019-06-04). Board of Supervisors of Louisiana State University and Agricultural and Mechanical College [US]. Inventors: Francesca Peruzzi [US], Duane Jeansonne [US].

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Extracellular pH Measurement in MCF10A Cells

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Cells were grown to confluence, washed with warm PBS, then cultured with a HEPES-buffered phenol-red free DMEM (Thermo Fisher Scientific) for 16 h. pH was assessed as described by Najy et al. [34 (link)] where conditioned media were collected, and the cell debris was removed by centrifugation at 2000 RPM for 5 min. The pH of the conditioned media was measured using a Beckman Ф300 Digital pH Meter, and pH readouts were subtracted from the pH at time zero to determine changes in extracellular pH, which were further normalized to the live cell numbers (10⁶ cells). Extracellular pH was also monitored using a fluorescent pH indicator [35 (link)]. Parental MCF10A cells were plated in a 35 mm glass bottom dish (MatTek, Ashland, MA, USA) and grown for 16 h then loaded with the 10 µM N-(Fluorescein-5-Thiocarbamoyl)-1,2-Dihexadecanoyl-sn-Glycero-3-Phosphoethanolamine (DF) dye for 10 min. Cells were then stimulated with the conditioned media from the respective MCF10A cell variants and imaged using a Zeiss Axiovert 200 at 40× magnification. Experiments were read in triplicates and performed in at least three separate experiments.

Najy A.J., Jung Y.S., Kim S., Fridman R, & Kim H.R. (2021). Regulation of Tumor Metabolism and Extracellular Acidosis by the TIMP-10–CD63 Axis in Breast Carcinoma. Cells, 10(10), 2721.

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RGCs Encapsulation in Thermosensitive Hydrogel

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RGCs (8 × 10³) were suspended in a solution of 5 wt % PSHU–PNIPAAm–RGD or 5 wt % PSHU–PNIPAAm in complete medium; 50 μL of the cell suspension in the polymer solutions was pipetted into each 35 mm glass bottom dish (MatTek, Ashland, MA) (Figure 1) and placed in a 37 °C incubator for 10 min to allow polymer gelation and RGC encapsulation. After incubation, 1 mL of warm, RGC medium was added to the culture dish, using a hot plate set at 37 °C to maintain gel stability when the dish is removed from the incubator. Cells were cultured for 3, 5, and 7 days, with daily changes of media.

Laughter M.R., Ammar D.A., Bardill J.R., Pena B., Kahook M.Y., Lee D.J, & Park D. (2016). A Self-Assembling Injectable Biomimetic Microenvironment Encourages Retinal Ganglion Cell Axon Extension in Vitro. ACS applied materials & interfaces, 8(32), 20540-20548.

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Quantifying Oligomeric Size of GFP-K-Ras

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Fluorescence measurements for N & B analysis were carried out with Nikon A1 confocal microscope using CFI Plan Apo IR 60× 1.27 NA water immersion objective at 22°C. Live cells were maintained at 37°C in DMEM, 10% bovine calf serum (Hyclone), and 5% (vol/vol) CO₂ in a 35-mm glass bottom dish (MatTek Corporation). The cells were imaged in live cell imaging solution containing Hepes buffered physiological saline at pH 7.4 (Life Technologies). Fluorescence images were acquired using a 488-nm laser power at 0.5% that corresponded to 1.75 mW at the measured samples. Rest of the measuring parameters and microscope settings were similar to what has been described in previous report (84 (link)). Briefly, for the N & B analysis, acquired images were scanned with 64 × 64 pixel box along the cell margins. Brightness values of the BHK cells expressing mem-EGFP (membrane-bound EGFP, a GFP containing an N terminally palmitoylated GAP-43 sequence cloned in a pEGFP-1 vector) have been used as brightness standards and for calibrating laser power and other microscope parameters. Our data have been analyzed following previous reports (84 (link)). Oligomeric size of GFP-K-Ras^G12V has been determined as the ratio of the measured brightness and the brightness of monomeric mem-EGFP after subtracting the apparent brightness of immobile molecules.

Liang H., Mu H., Jean-Francois F., Lakshman B., Sarkar-Banerjee S., Zhuang Y., Zeng Y., Gao W., Zaske A.M., Nissley D.V., Gorfe A.A., Zhao W, & Zhou Y. (2019). Membrane curvature sensing of the lipid-anchored K-Ras small GTPase. Life Science Alliance, 2(4), e201900343.

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Immunofluorescence Imaging of Tagged Proteins

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Cells were seeded and grown in 35 mm glass bottom dish (MatTek). After compound treatment, cells were rinsed twice with PBS and fixed in 1 mL of 4% paraformaldehyde (v/v in PBS) for 15 min at room temperature. The fixed cells were rinsed twice with PBS, permeabilized and blocked with 0.1% Triton X-100 (v/v in 5% BSA in PBS) for 30 min at room temperature. The cells were incubated overnight (14 h) at 4°C with FLAG or HA antibody at 1/100 dilution (in 0.1% Triton X-100/5% BSA in PBS). Cells were washed with 0.1% Triton X (in PBS) three times and incubated with Alexa Fluor 488-conjugated goat anti-mouse IgG (H+L) secondary antibody (for FLAG tag) or Alexa Fluor 568-conjugated goat anti-rabbit IgG (H+L) secondary antibody (for HA tag) at 1/1000 dilution (in 0.1% Triton X-100/5% BSA in PBS) at room temperature in dark for 1 h. Cells were washed with 0.1% Triton X (in PBS) three times and mounted with ProLong Gold Antifade Mountant with DAPI (P36931, Invitrogen). Cells were imaged with Zeiss LSM780 in The Core Microscopy Facility at Scripps Research. Images were processed in ImageJ software. To quantify the degree of nucleus-localized fluorescence signal, background was subtracted. The nuclear and whole cell area were selected and quantified for each cell examined. Relative nucleus with respect to whole cell fluorescence intensity was presented.

Zhang X., Crowley V.M., Wucherpfennig T.G., Dix M.M, & Cravatt B.F. (2019). Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16. Nature chemical biology, 15(7), 737-746.

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