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79 protocols using coolsnap hq

1

Confocal Imaging of Peripheral Nerves and Synapses

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Confocal imaging for peripheral nerves and synapses was performed on a Yokagawa CSU22 spinning disk confocal with a 60x/1.4 plan Apochromat objective. Z-stacks of peripheral nerves or NMJ on muscle 6/7 were acquired and maximum projections were used for analysis. Confocol images for the ventral nerve cords were acquired using an Andor Zyla sCMOS camera mounted to a Nikon Ti Microscope with an Andor Borealis CSU-W1 spinning disc confocal with a Nikon Plan Apo 20x/0.75. Deconvolution imaging for synapse morphology was performed using a Plan Apo objective 60x/1.4 (Carl Zeiss) on an Axiovert 200 inverted microscope (Carl Zeiss) equipped with a cooled CCD camera (CoolSNAP HQ; Roper Scientific). Image acquisitions were performed in SlideBook software (Intelligent Imaging Innovation).
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2

Immunofluorescent Imaging and Quantification

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Immunofluorescent image acquisition and analysis were as described by Meijer et al.17 In brief, slides were scanned at 100x magnification using a high‐resolution 12‐bit CCD camera (Coolsnap HQ, Roper Scientific Inc., Trenton, NJ, USA) on a fluorescence microscope (Axioskop, Zeiss, Göttingen, Germany). This resulted in grayscale images which were converted to binary images for further analysis. The tumor area was marked on the stained sections. Marker fractions were defined as the tumor area positive for the marker (binary images), divided by the total tumor area. Vascular density was calculated as the number of vascular structures per square millimeter.
For SLC1A5 and GLS2 staining, background intensity level hampered segmentation for binarizing the images. Therefore, these stainings required visual scoring. Fraction of tumor cells of the total tumor area stained for SLC1A5 and GLS2 were scored as <5%, 5%–20% and >20%. Slides were indivually scored by TM and JL. In case of disagreement, slides were discussed until agreement was reached.
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3

Immunostaining of Drosophila Larval Neurons

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Third-instar larvae were dissected, fixed in Bouin’s fixative or 4% PFA in PBS, and immunostained as previously described (Eaton et al., 2002 (link); Harris et al., 2015 (link)). Dissected third instar larvae were fixed with PFA (4%) and incubated overnight at 4 C with primary antibodies (mouse anti Flag 1:50; rabbit anti-RFP 1:100; rabbit anti-Dlg, 1:1000; anti-Syt1 1:1000, anti-Brp 1:100, Life Technologies). Alexa-conjugated secondary antibodies and goat anti-HRP were used (Jackson Laboratories 1:500). Images were acquired with either a Zeiss LSM700 confocal microscope equipped with Zen software using a 63X 1.6 NA oil immersion objective or an upright epifluorescence deconvolution confocal microscope (Axiovert 200, Zeiss) equipped with a 100X objective (N.A. 1.4), cooled CCD camera (CoolSnap HQ, Roper Scientific). Slidebook 5.0 (3I, Intelligent Imaging) was used for capturing, deconvolving and analyzing images. Structured illumination microscopy (Nikon LSM 710 equipped with 63X objective and Andor Ixon EMCCD camera) was used to perform Brp-GFP and MCTP-Flag colocalization experiments. Bouton numbers and Brp numbers and densities were quantified as described previously (Harris et al., 2015 (link)).
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4

Immunohistochemical Analysis of Bat and Mouse Spleens

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Spleens harvested from E. fuscus bats or BALB/c mice were embedded in OCT compound (Sakura, Torrence, CA). The tissues were frozen in slurry of dry ice and isopentane, and 8 μm cryosections were generated. For immunohistochemical analysis, cryosections were stained with biotin-conjugated mAb BT1-4F10 (bats) plus HRP-Streptavidin or biotin-conjugated anti-mouse K chain (mAb 187.1 (Yelton et al., 1981 (link))) plus HRP-Streptavidin. Immunohistochemistry was performed by the Wadsworth Center Histopathology Core. For fluorescence microscopy the cryosections were fixed in 100% ice-cold ethanol, blocked in Fc blocking solution (for mouse sections) or rabbit IgG (for bats), and stained with either Alexa 488-conjugated mAb BT1-4F10 (bats) or Alexa 488-conjugated anti-CD19 (mAb ID3; BD Biosciences. Stained sections were mounted with ProLong Gold with DAPI (Life Technologies). Images were captured with a 20 × objective on a Nikon TE2000 equipped with a CoolSNAP HQ charge-coupled device camera (Roper Scientific, Martinsried, Germany), and ImagePro software (Media Cybernetics, Rockville, MD), and Adobe Photoshop was used to process the images for display.
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5

Ultrastructural Analysis of Mouse Eyes

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Embryos or enucleated mouse eyes were fixed overnight in either 0.08 M (fish) or 0.10 M (mouse) cacodylate buffer containing 2% glutaraldehyde and 2% paraformaldehyde. Embryos were post-fixed in 1% osmium tetroxide followed by dehydration in a graded methanol series and infusion with epon (Embed 812; Electron Microscopy Systems). 0.5-μm sections were cut on a microtome (Ultracut E, Reichert-Jung) and stained with toluidine blue for light microscopy. Images were acquired on a Nikon Eclipse TE300 microscope operating NIS-Elements (Nikon Instruments) and a CCD camera (CoolSNAP HQ; Roper Scientific). Cryosection analysis was performed as previously described (Insinna et al., 2008 (link)). Nuclei were stained with TO-PRO-3 (Invitrogen). Images were acquired on a Nikon C1 Plus-EX3 AOM Confocal System using the Nikon EZ-C1 software with a 60x, 1.4-NA objective (Nikon Instruments). For TEM, 70 nm sections were cut on a microtome (RMC PowerTome MT-XL). Sections were collected on 200 Mesh hexagonal grids (EMS), and subsequently stained with uranyl acetate and lead citrate. Imaging was performed on a Hitachi H-600 transmission electron microscope.
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6

Drosophila Neuromuscular Junction Immunostaining

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Third-instar larvae were dissected, fixed in Bouin’s fixative or 4% PFA in PBS, and immunostained with previously described methods (Eaton et al., 2002 (link); Harris et al., 2015 (link)). Third instar larvae were dissected with cold HL3 and immediately fixed with PFA (4%) and incubated overnight at 4 C with primary antibodies (rabbit anti-Dlg, 1:1000; anti-Brp 1:100, Life Technologies). Alexa-conjugated secondary antibodies were used for secondary staining (Jackson Laboratories 1:500). An inverted epifluorescence deconvolution confocal microscope (Axiovert 200, Zeiss) equipped with a 100X objective (N.A. 1.4), cooled CCD camera (CoolSnap HQ, Roper Scientific) was used to acquire images. All acquisition, deconvolution and analysis were done by Slidebook 5.0 software (3I, Intelligent Imaging). Structured illumination microscopy (Nikon LSM 710 equipped with 63X objective and Andor Ixon EMCCD camera) was used to perform Brp puncta and Dlg labeling experiments. Bouton numbers were quantified as described previously (Harris et al., 2015 (link)).
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7

Live Imaging of EB3-GFP Dynamics in SH-SY5Y Cells

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SH-SY5Y cells plated on collagen type I-coated dishes 35 mm MatTek dishes (MatTek Corp, Ashland, MA) at 2 × 105 cells / dish and incubated with 10 μM all-trans-retinoic acid (Sigma) for 6 days in standard culture medium containing 1% FBS and then for an additional 2 days in serum free medium containing 2 nM brain-derived neurotrophic factor (BDNF, Sigma) as previously described [6 (link), 24 (link)]. The cells were co-transfected with 0.5μg of each plasmid (EB3-GFP and TTBK1 or EB3-GFP and pcDNA3.1+) and pretreated with 10 μm freshly prepared Aβ42 oligomer or vehicle as described [21 (link), 25 (link)]. The live imaging of comet movement of EB3-GFP homodimer was captured 24 h after the transfection using following setting: 100× oil objective (NA = 1.45), 488 nm excitation (100–300 ms exposure/frame, single plane), 0.53 fps for 40 frames, using the Nikon TE-2000 U inverted fluorescent microscope (Nikon Instruments, Melville, NY) output port and cooled charge-coupled device camera (Coolsnap HQ, Roper Scientific, Duluth, GA) as described [21 (link), 25 (link), 26 (link)].
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8

Neutrophil Migration Assay Protocol

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Cell migration assays were performed as described previously (45 (link)), with modifications. Briefly, Millicell EZ SLIDE 8-well glass (Millipore) or 35-mm glass-bottom dishes were coated with mouse ICAM-1 (1 or 5 μg per well, respectively; Sino Biological) and incubated for 2 hours at 37°C. Naïve mouse neutrophils were isolated and placed on the slide in L-15 medium containing glucose (2 mg/ml; CellGro). Cells were allowed to adhere to the bottom of the slide, and nonadherent cells were washed off. Cells were preincubated with inhibitors for 15 to 20 min, treated with the compounds of interest, and then imaged every 10 s for 25 min. Image acquisition was conducted on a DIC-enabled microscope (Nikon or Olympus) coupled to a Hamamatsu or CoolSNAP HQ (Roper Scientific) camera. Themagnification used was ×10, ×20, or ×60. The cells were tracked with the manual tracking functionality in ImageJ software, and the tracked cells were analyzed with the Chemotaxis tool (ibidi). All cells that appeared healthy were tracked, and no thresholding criteria were applied. Velocity for each cell was calculated by dividing the total distance moved by the total migration time.
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9

Time-lapse Imaging of Electroporated Rat Brain Slices

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Coronal slices of embryonic rat brains were prepared 48 hours after electroporation. Slices were placed on Millicell-CM inserts (Millipore) and incubated at 37 °C with 5% CO2 in culture medium that containing 25% Hanks balanced salt solution, 47% basal MEM (Invitrogen), 25% normal horse serum, 100 units/ml penicillin, and 100 μg/ml streptomycin (Invitrogen), and 0.66% glucose. Multiple GFP-positive cells were imaged on an inverted microscope. Time-lapse images were captured by using camera (CoolSNAP HQ; Roper Scientific) at intervals of six minutes for 5 hours and data were analyzed by using MetaMorph software (Molecular Devices).
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10

Fixation and Imaging of Cells

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Samples for imaging were fixed with 10% formalin added directly to growth media containing cells (final concentration of 1%), incubated for 10 minutes at room temperature, washed with 0.1M KH2PO4 pH 8.5, washed with 1.2M Sorbitol+0.1M KH2PO4 pH 8.5, resuspended in 1.2M Sorbitol+0.1M KH2PO4 pH 8.5, and stored at 4°C. Images were acquired at room temperature (25°C) using a Nikon Eclipse Ti-E inverted microscope with a 60× Plan Apo VC, 1.4 NA oil objective lens with a Photometrics CoolSNAP HQ camera (Roper Scientific). Metamorph 7.7 (Molecular Devices) was used to acquire images. Fixed samples were imaged in 1.2M Sorbitol+0.1M KH2PO4 pH 8.5 buffer on Concanavalin A-coated coverslips (VWR) adhered to glass slides (Corning). Exposure times were 10 ms for differential interference contrast and 300 ms for fluorescence.
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