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555 protocols using dm6000b

1

Fluorescence Microscopy Protocol for Species Identification

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For microscopic analysis 7–10 replicas of each species have been used. Specimens were analysed under the fluorescent microscope Leica DM6000B equipped with a digital camera DC300F (Wetzlar, Leica Microsystems, Germany) and confocal laser scanning microscope Leica TCS SP5 (Wetzlar, Leica Microsystems, Germany) at the Optical Microscopy and Spectrophotometry Core Facilities of Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences” (Moscow Region, Russia). For Leica DM6000B microscopic analysis a fluorescent filter I3 (excitation spectrum of 450–490 nm, emission spectrum of 515 nm) was used for the identification of Alexa488 fluorophore, while TRITC fluorophore was detected with a N2.1 filter (excitation spectrum of 515–560 nm; emission spectrum of 590 nm). For CLSM Leica TCS SP5 analysis, the microphotographs presented are either a maximal projection of a total of 16 to 32 consequent optical sections reconstructed at maximum fluorescence intensity, or a single optical section (or a snapshot), obtained by scanning through 30–40 μm sample thickness.
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2

Automated Fluorescence Microscopy Imaging

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Imaging was done at 10×/0.40 NA (15506285 HCX PL APO 10×/0.40 CS, Leica Microsystems GmbH) on a fluorescent microscope (Leica DM6000B, Leica Microsystems GmbH) with motorized stage automatically controlled through µManager52 (link). Images were acquired by a Hamamatsu OrcaFLASH 4.0 digital camera (C11440-22CUORCA-Flash4.0 V2 Digital CMOS camera, Hamamatsu Photonics K.K.) at 16 bit depth resolution with 2048 × 2048 pixels. All widefield imaging except for rabies injections done in Camk2a-cre and Gad2-cre animals were done on the Leica DM6000B. For Camk2a-cre and Gad2-cre mice we used an IN Cell Analyzer 6000 with the 10×/0.45 NA objective (GE Healthcare Life Sciences, Chicago, US).
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Histological Analysis of Enucleated Eyes

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Enucleated eyes or eye cups free of cornea and lens were fixed in 4% paraformaldehyde before further processing to make paraffin sections or cryosections. Paraffin sections 4 μm thick were subject to hematoxylin and eosin (H&E) staining. The H&E-stained sections were observed and the images were recorded by a fluorescent microscope under bright field settings (DM6000B, Leica, Germany). IHC of rhodopsin (1:1000, Novusbio, USA) and opsin M (1:100, Millipore, USA) was performed on paraffin sections 4 μm thick as well. IHC of glial fibrillary acidic protein (GFAP) (1:500, Dako, Denmark), vimentin (1:50, Cell Signaling Technology, USA) and Iba1 (1:500, Wako, Japan) was performed on cryosections 12 um thick. Counterstaining of 4-6-Diamidino-2-phenylindole (DAPI) was performed for the indicated IHC assessment. The thickness of outer nuclear layer (ONL) was measured after H&E or DAPI staining. Images were recorded using a fluorescent microscope under fluorescent settings (DM6000B, Leica, Germany).
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4

Visualizing Protein Droplet Formation

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Droplet formation of protein samples was monitored by DIC microscopy. 15 μl of sample were loaded onto glass coverslips and DIC images were acquired on a DM6000B (Leica) microscope with a 63×-objective (water immersion). Alexa-488-labeled protein was prepared using Alexa Fluor 488 microscale protein labeling kit (Thermo Fisher Scientific). To confirm the presence of protein in the droplets, Alexa-488-labeled protein was mixed with unlabeled protein and the images were acquired on a DM6000B (Leica) microscope with a 63×-objective (water immersion) using a 488 nm argon laser line. Images were processed using ImageJ.
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5

Immunofluorescence Staining of EdU-Labeled Cells

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In this study, EdU was detected in all immunofluorescence experiments to allow identification of S phase cells. Cells were treated with 10 μM EdU for 30 min before fixation to label the S phase cells. At each time point after IR, the EdU-treated cells were washed once with phosphate-buffered saline (PBS) and fixed with 4% paraformaldehyde in PBS for 10 min at 4 °C, followed by permeabilization with 0.5% Triton X-100 in PBS for 5 min at 4 °C. Primary antibodies were then applied for 30 min at 37 °C, followed by reaction with Alexa 488- or 555-conjugated secondary antibodies (Life Technologies, USA) for 30 min at 37 °C. Nuclei were counterstained with 4′,6-diamidino-2-phenylindole (DAPI). All of the antibodies were diluted in 5% skim milk/Tris-buffered saline with 0.1% Tween 20.
After immunofluorescence staining, EdU was detected following the manufacturer’s protocol. Images were acquired using a fluorescence microscope (DM6000B, Leica, Germany) or a confocal fluorescence microscope (LSM800, Zeiss, Germany). For image acquisition using DM6000B (Leica), x63 or x100 objective lenses, CCD camera (Orca R2, Hamamatsu Photonics), and FW4000 software were used. For image acquisition using LSM800 (Zeiss), x63 or x100 objective lenses, GaAsP detector, and ZEN 2.1 image acquisition software were used.
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6

Histological and Molecular Analysis of Kidneys

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The removed kidneys were fixed with 4% paraformaldehyde, embedded in paraffin and then cut into 4-μm-thick sections. Periodic acid–Schiff (PAS, Sigma-Aldrich, USA) staining was performed on the sections for histologic analysis. Glomerulosclerosis scoring was assessed blindly on a minimum of 10 glomeruli per section using a light microscopy (Leica DM 6000B; Leica Microsystems, Wetzeler, Germany).
Immunohistochemical staining for METTL14 (HPA038002, Sigma), WT1 (sc-7385, Santa Cruz Biotechnology) and Sirt1(ab110304, Abcam) was performed. Briefly, after dewaxing, subjected to antigen retrieval and blocked, the sections were incubated with the primary antibodies overnight at 4 °C. The next day, positive staining was revealed by incubating with HRP-conjugated secondary antibodies, diaminobenzidine staining and counterstaining with hematoxylin. Slides were visualized by a light microscopy (Leica DM 6000B; Leica Microsystems, Wetzeler, Germany).
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7

Histological Evaluation of Bone Tunnel Graft

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Immediately after sacrifice, the specimens were fixed in 10% neutral-buffered formalin for 48 h, decalcified in formic acid, dehydrated through an alcohol gradient, cleared and then embedded in paraffin wax. The samples were cut into 5-µm slides perpendicular to the longitudinal axis of the bone tunnel. These sections were then stained with hematoxylin and eosin for histological evaluation. The graft-bone interface was visualized by inverted-light microscopy (Leica DM6000B; Leica Microsystems GmbH, Wetzlar, Germany), and digital images were captured using DP Manager (Leica DM6000B; Leica Microsystems GmbH).
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8

EpCAM Immunostaining of Adherent Cells

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Cells were smeared on climbing coverslips. After washing with PBS, cells were fixed with 4% formaldehyde for 30 min. Then, cells were incubated with primary EpCAM antibody (ab71916, Abcam) at 4°C overnight. Subsequently, cells were incubated with a 1:1000 dilution of the secondary goat anti-rabbit immunoglobulin G (A-11012, Invitrogen, USA) for 1 hour and counterstained with 4′,6-diamidino-2-phenylindole for 5 min to stain cell nuclei. The slides were scanned by Leica DM6000B (Leica, Germany).
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9

Evaluating Breast Cancer Cell Apoptosis

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Human breast cancer cells were seeded 2 ×  105 cells on 16 mm glass coverslips in 6 well plates with the culture medium for 24 h and then starved in serum-free DMEM-F12 for 16 h. hUCMSCs were seeded 1 ×  105 cells in 0.4 μm pore, 24 mm transwell inserts with the culture medium for 24 h and starved for 16 h in DMEM-LG medium with 1% FBS. Then breast cancer cells were pretreated with 50 μM embelin and hUCMSCs were pretreated with100 ng/ml IL-1β for 24 h. After pretreatment, the transwell inserts were moved into 6 well plates to co-culture breast cancer cells and hUCMSCs for 24 h in DMEM-LG with 1% FBS. The coverslips were removed and Annexin V-FITC Apoptosis Detection Kit (Strong Biotech Corporation, TPE, ROC) were used to detect apoptosis. Breast cancer cells were stained with 2% Annexin V-FITC (AV) and 2% Propidium Iodide (PI) in a binding buffer for 10 min in the dark. After staining, the images were immediately captured by using a Fluorescent Microscope (Leica DM6000B, Wentzler, Germany). The apoptotic rate in Fig. 5 was determined by calculating the proportion of cells that have undergone apoptosis (cell numbers of Annexin V+/PI−, Annexin V+/PI+ expressing cells) in relation to the total number of cells in five randomly selected fields of three independent experiments.
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10

Drosophila Eye Imaging and Histology

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For imaging of external eyes, adult 2–3d Drosophila females were anesthetized with ether, placed on microscope slide using double-sided tape, and imaged using Leica Z16 APOA (Leica Biosystems, Buffalo Grove, IL). For internal sections, fly heads were fixed in Bouin’s solution (Sigma-Aldrich, St. Louis, MO) for 96 hr. Heads were rinsed in leaching buffer (50mM Tris/150mM NaCl) overnight and processed with increasing concentrations of ethanol (70%, 80%, twice with 95%, twice with 100%) for 30 min each, twice in xylene for 30 min each and embedded in paraffin at 63°C twice for 1 hr each. Paraffin blocks were made using Shandon Histocentre2 (ThermoFisher Scientific, Grand Island, NY), and 8μm sections were cut using Leica RM2255. Sections were deparaffinized with Histoclear (National diagnostics, Atlanta, GA) and mounted on SuperFrost plus slides (ThermoFisher Scientific, Grand Island, NY) using Cytoseal XYL (ThermoFisher Scientific, Grand Island, NY). Images of endogenous autofluorescence were taken using Leica DMRA2 or Leica DM6000B fluorescence microscopes.
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