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18 protocols using plan apochromat 20x

1

Phagocytosis Assay of Apoptotic Jurkat Cells

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Jurkat cells were labelled using CellTracker™ Orange CMRA (ThermoFisher Scientific) according to the manufacturer’s recommendations. Mφ were seeded onto 8-well chambered coverslips (µ-slide, ibidi GmbH), stained with CFSE Cell Division Tracker Kit (Biolegend) and incubated with labelled apoptotic Jurkat cells at a 1:3 ratio. Upon removal of the non-phagocytosed cells, Mφ were analyzed by fluorescence imaging using a Plan-Apochromat 20x long range objective on a Zeiss LSM800 confocal microscope driven by the Zen 2009 software (Carl Zeiss) or by flow cytometry with a LSRII/Fortessa flow cytometer (BD Biosciences).
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2

Multimodal Histological Imaging of Nervous Tissue

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All the slides for each histological method were stained or immnostained at the same time. Then, they were imaged using a Pannoramic MIDI digital slide scanner (3DHistech, Budapest, Hungary; Plan-Apochromat 20x, 0.274 μm/pixel) on the same day.
The LFB-stained sections were examined under a light microscope (Axioplan 2, Carl Zeiss, Jena, Germany) (5x, NA 0.15) while the NF/Tub/MBP-stained sections and the NeuN/Fluoro Nisslstained sections were examined under a fluorescence microscope (AxioObserver Z1 inverted confocal, Carl Zeiss) (myelinated axons: Plan-Apochromat 63x, NA 1.4, dorsal horn cells: Plan-Apochromat 20x, NA 0.8, ventral horn cells: Plan-Apochromat 10x, NA 0.45).
The imaging settings were fixed for each histological method. The images were viewed using Case Viewer software (3DHistech).
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3

Imaging of GFP/RFP-labeled Cells

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We used an upright microscope set-up (Olympus FV1000MPE multi-photon laser scanning microscope or Zeiss 880, both with Spectra-Physics Mai Tai DeepSee 2-photon lasers) with water-immersion lens (Olympus XLPLN 25X WMP2 or Zeiss Plan-Apochromat 20X). The objective was immersed directly in the culture medium for imaging. The fluorophores used were all GFP or RFP derivatives, therefore the excitation wavelength was tuned between 925 and 935 nm. Laser power never exceeded 15%. Zen Blue (Zeiss) and ImageJ software was used to analyze movies. The Bleach Correction and Manual Tracking plugins were used to correct photobleaching and to track cells. The Correct 3D Drift plugin was used to correct for movements caused by tissue contraction. Adobe Photoshop (v21.1.3) and Adobe Premiere Pro (v14.2) were used to annotate and edit movies. Figures were generated using Adobe Illustrator (v24.1.3).
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4

Neomycin-induced Hair Cell Damage

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neomycin sulfate (Sigma) was dissolved in zebrafish embryo water to a stock concentration of 6 mM and then diluted to a working concentration of 50 μM [43 (link)]. Transgenic embryos were generated and screened for heart expression as above, then 5-day post fertilization larvae were incubated in neomycin for 1 h at 29 °C, rinsed in embryo water, and allowed to recover for approximately 0.5 h before initial imaging, then imaged at 24-h post injury on a Zeiss LSM 7 microscope with the Plan-Apochromat 20x (numerical aperture 0.8) objective. neomycin injury was confirmed by equivalently treating wild type larva and observing loss of DASPEI (2-[4-(dimethylamino)styryl]-l-ethyl-pyridinium iodide) staining [43 (link)].
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5

Quantifying Breast Cancer Organoid Formation

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Cells constitutively expressing S100A10 shRNA, S100A10, or corresponding control lentivirus constructs were seeded on Matrigel (Corning) in 96‐well plates (3 × 103 cells/well) and cultured at 37°C with 5% CO2, as previously described.27 The cells were fixed 8‐10 days after seeding with 4% paraformaldehyde for 10 min at room temperature, and then the number of organoids larger than 100 μm (breast cancer PDX cells) or 150 μm (breast cancer cell lines) in diameter was counted under an inverted fluorescent microscope (Axiovert 200, Carl Zeiss) with Plan‐Apochromat 20x NA = 0.8. Phase contrast and ZsGreen images were taken by AxioCam under the control of AxioVision. The ZsGreen images were used to measure the diameter.
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6

Fluorescence Microscopy for Salivary Gland Analysis

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SMG morphological evaluation was performed using a digital inverted fluorescence microscope (Nikon, Tokyo, Japan; Ti) equipped with a digital camera (Nikon, DS-Ri2) and a CFI Plan Fluor 4x objective (Nikon) or JuLI Br live cell movie analyzer (NanoEnTek, Seoul, Republic of Korea). Immunofluorescence images were taken by confocal laser scanning microscope (Carl Zeiss, Oberkochen, Germany;LSM700) equipped with Plan-Apochromat 10x, Plan-Apochromat 20x, and C-Apochromat 40x objectives (Carl Zeiss) and with 405, 488, and 555 nm wavelength excitation lasers. Live imaging of epithelial rudiments of SMG and SMG-C6 cells were conducted through a confocal microscope (Carl Zeiss) with a customized live cell chamber (Live Cell Instruments, Seoul, Republic of Korea) that maintained 5% CO2 and 37 °C conditions. To visualize peripheral cell movement (Fig. 4I,J), the epithelial rudiments of SMGs were briefly stained with 1 μg/ml Hoechst 33342 (Thermo Fisher Scientific, Waltham, MA; H3570) –culture media solution for 1 h. After staining, cells were washed with culture medium two times.
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7

Visualizing Mitochondrial Dynamics in hMDMs

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hMDMs at 900000 cells/well in 27 mm Nunc glass bottom dishes (Thermofisher) were washed twice with imaging media (HBSS containing 5mM glucose, 20 mM HEPES and 1% BSA) and stained with 500 nM MitoTracker Red CMXRos for 15 min. Cells were washed twice and visualized on a Zeiss LSM880 confocal microscope before data capture. Cells were then treated with sublytic MAC, anti-C7 control or 5 μM ionomycin for 15 min in imaging media without BSA, and visualized on the above system with a Zeiss Plan-Apochromat 20x or 63x objective. For 20X, 9 images were taken for each condition and donor (3 x 3 tile), for 63X, 5 images per condition and donor were taken. Mitochondrial dynamics were quantified using the Yen threshold in the semi-automated analysis macro tool MiNA, used with Fiji/ImageJ software (46 (link)) (4 cells per condition per donor analyzed). The mitochondrial branch length mean values were exported, averaged and used as a measure for mitochondrial network morphology.
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8

Imaging Drosophila Follicle Development

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Microscope images of fixed Drosophila follicles were obtained using LAS AS SPE Core software on a Leica TCS SPE mounted on a Leica DM2500 using an ACS APO 20 x/0.60 IMM CORR -/D objective (Leica Microsystems, Buffalo Grove, IL) or using Zen software on a Zeiss 700 LSM mounted on an Axio Observer.Z1 using a Plan‐Apochromat 20 x/0.8 working distance (WD) = 0.55 M27 or a EC-Plan-Neo-Fluar 40 x/1.3 oil objective (Carl Zeiss Microscopy, Thornwood, NY). Maximum projections (two to four confocal slices), merged images, rotations, and cropping were performed using ImageJ software (Abramoff et al., 2004 ). S9 follicles were identified during fixed imaging by the size of the follicle (~150–250 μm), the position and morphology of the outer follicle cells, and presence of a border cell cluster. The beginning of S10 was defined as when the anterior most outer follicle cells reached the nurse cell-oocyte boundary and flattened.
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9

Calmodulin-Binding MLCK-FRET Biosensor

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MLCK-FRET plasmid is a kind gift from Dr. James T. Stull (University of Texas Southwestern Medical Center). The MLCK-FRET plasmid is a calmodulin-binding based sensor, where calmodulin binding sequence is flanked with eCFP and eYFP and exhibits decreased FRET upon binding with calmodulin19 (link),38 (link). Cells expressing MLCK-FRET were imaged using Zeiss LSM 880 (Carl Zeiss, Jena, Germany), at 37 °C incubator, fitted with Plan-Apochromat 20 x, equipped with 458 nm and 514 nm Argon ion laser lines for excitation of eCFP and eYFP respectively. Incident excitation light was split using an MBS 458 nm/514 nm beam splitter and collected on a 32-spectral array GaAsp detector. The fluorescence emission was collected from 463–520 nm (ECFP), 544–620 nm (FRET channel and eYFP channel). Intensity based ratiometric FRET were obtained using custom-written scripts in ImageJ and MATLAB. Since MLCK-FRET is a single-chain construct, decrease in FRET, and increase in MLCK binding to calmodulin, was expressed as the ratio of emission intensity at 520 nm/emission intensity at 510 nm normalized at the basal levels.
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10

Immunohistochemical Analysis of Adult Drosophila Brains

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Day 1 adult brains were dissected in Schneider’s media (Sigma) then immediately transferred to cold 1% PFA (Electron Microscopy Sciences) and fixed overnight at 4°C. Following overnight incubation samples were washed in PAT3 Buffer (0.5% BSA/0.5% Triton/1X PBS pH 7.4) 3 times. Brains were blocked in 3% Normal Goat Serum for 90 minutes at RT. Primary antibodies 1:2000 rabbit anti-DAMB (Figure S7B) (a gift from Ronald Davis) (Feng et al., 1996 (link)), 1:20 guinea pig anti-DopR (Figure S7B) (Lebestky et al., 2009 (link)), 1:1000 chicken anti-GFP (Abcam ab13970) (Figure 1A) and 1:50 mouse anti-brp (Developmental Studies Hybridoma Bank nc82) (Figure 1A) were incubated 3 hours at RT then 2–3 days at 4°C. Brains were washed extensively in PAT3 Buffer. Secondary Alexa Fluor antibodies (Life Technologies) were incubated 3 hours at RT then 2–3 days at 4°C. Brains were washed 3 times in PAT3 Buffer then once in 1X PBS. Samples were mounted in Vectashield (Vector Laboratories). Images were captured on a Zeiss LSM 880 using a Plan-Apochromat 20X (0.8 NA) objective.
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