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36 protocols using axioplan 2 microscope

1

Meiotic Chromosome Synapsis Assay

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Surface spreading of meiotic nuclei was performed as described by Grubb et al., 2015 (link). During spheroplasting, 20 μl of dithiothreitol (DTT) was used instead of the published 40 μl. Fixation was achieved with 4% PFA/sucrose solution. Spreads from Figure 3J,M were stained with anti-Zip1 guinea pig polyclonal antibody (a gift from Scott Keeney, 1:500 dilution), and then with goat anti-guinea pig polyclonal secondary antibody (Alexa Fluor 555; ThermoFisher; A-21435, 1:200 dilution). Spreads from Figure 3—figure supplement 2J were stained with anti Zip1 goat polyclonal antibody (Santa Cruz Biotechnology; y-N16, 1:50 dilution), and then with donkey anti-goat polyclonal secondary antibody (Alexa Fluor 555; ThermoFisher; A-21432, 1:1000 dilution). Slides were mounted in antifade with added DAPI (Prolong Gold, Invitrogen; P36930) and images were captured using a Zeiss AxioPlan II microscope, Hamamatsu ORCA-ER CCD camera and Volocity software. Synapsis was quantified by characterizing four classes of Zip1 staining pattern: no Zip1, foci only, a mixture of foci and lines, and lines only (as previously described by Chen et al., 2015 (link)).
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2

Immunofluorescence Imaging of DNA Repair Factors

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Previously published procedures were followed for IF and IF-FISH12 (link). IF for myc-tagged RPA32 or Ctc1 (mouse monoclonal, 9B11 or rabbit monoclonal, 71D10, Cell Signaling Technology), HA-tagged Stn1 (3724, Cell Signaling Technology), endogenous Polα (sc-137021, Santa Cruz), and 53BP1 (612522, BD Biosciences) was carried out using the cytoskeleton extraction protocol14 (link). Intensity measurements of RPA32-myc IF were performed in FIJI as follows: nuclei were identified using thresholding, segmented, and identified as regions of interest. The average image background was then subtracted from the image, and the total raw pixel intensity within each area of interest in the channel of interest was calculated. Rad51 (70-001, Bioacademia), and γH2AX (05636, Millipore) were detected in cells fixed in 3% PFA, and foci showing co-localization of Rad51 with γH2AX were quantified. IF imaging was performed on a Zeiss Axioplan II microscope equipped with a Hamamatsu C4742-95 camera using Volocity software or on a DeltaVision (Applied Precision) equipped with a cooled charge-coupled device camera (DV Elite CMOS Camera), a PlanApo 60× 1.42 NA objective or 100× 1.40 NA objective (Olympus America, Inc.), and SoftWoRx software.
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3

Combined Telomeric DNA FISH and IF

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Cells were grown on coverslips and fixed with 2% paraformaldehyde (PFA) in PBS for 10 min. Telomeric DNA FISH was combined with IF as described previously (Denchi and de Lange 2007 (link)) using the following antibodies: polyclonal rabbit anti-mTIN2 (#1447), polyclonal rabbit anti-human 53BP1 antibody NB 100-304 (Novus), and anti-HA antibody (12CA5, Roche). Secondary antibodies were Alexa Fluor 555 goat anti-rabbit IgG (Molecular Probe) or RRX-conjugated donkey anti-mouse IgG (Jackson Laboratories). A FITC-TelC (FITC-OO-CCCTAACCCTAACCCTAA; Applied Biosystems) probe was used to detect telomeric DNA using the protocol developed by Sedivy and colleagues (Herbig et al. 2004 (link)). DNA was stained with 4,6-diamino-2-phenylindole (DAPI). Where noted, nucleoplasmic proteins were removed using Triton X-100 buffer (0.5% Triton X-100, 20 mM Hepes-KOH at pH7.9, 50 mM NaCl, 3 mM MgCl2, 300 mM sucrose) for 2 min on ice prior to fixation with 2% PFA in PBS. Digital images were captured with a Zeiss Axioplan II microscope with a Hamamatsu C4742-95 camera using Improvision OpenLab software.
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4

Immunofluorescence Imaging of DNA Repair Factors

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Previously published procedures were followed for IF and IF-FISH12 (link). IF for myc-tagged RPA32 or Ctc1 (mouse monoclonal, 9B11 or rabbit monoclonal, 71D10, Cell Signaling Technology), HA-tagged Stn1 (3724, Cell Signaling Technology), endogenous Polα (sc-137021, Santa Cruz), and 53BP1 (612522, BD Biosciences) was carried out using the cytoskeleton extraction protocol14 (link). Intensity measurements of RPA32-myc IF were performed in FIJI as follows: nuclei were identified using thresholding, segmented, and identified as regions of interest. The average image background was then subtracted from the image, and the total raw pixel intensity within each area of interest in the channel of interest was calculated. Rad51 (70-001, Bioacademia), and γH2AX (05636, Millipore) were detected in cells fixed in 3% PFA, and foci showing co-localization of Rad51 with γH2AX were quantified. IF imaging was performed on a Zeiss Axioplan II microscope equipped with a Hamamatsu C4742-95 camera using Volocity software or on a DeltaVision (Applied Precision) equipped with a cooled charge-coupled device camera (DV Elite CMOS Camera), a PlanApo 60× 1.42 NA objective or 100× 1.40 NA objective (Olympus America, Inc.), and SoftWoRx software.
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5

Analysis of Mitotic Chromosome Spreads

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Mitotic cells were washed with warm media by centrifuging at 300 × g for 3 min. Cells were suspended in 500 µl of warmed swelling buffer (40% complete media + 60% deionized water). Samples were incubated in a 37°C water bath for 15–18 min. Swollen cells were fixed by adding 1 ml 3:1 methanol: acetic acid and then incubated for 10 min. The cells were pelleted for 5 min at 250 × g and then washed with 1 ml fixative and pelleted once more. The cell pellets were resuspended in 100–200 µl fixative, and then 40–50 µl of cell suspension was dropped from a height of 60 cm onto a 22-mm2 coverslip that was cleaned with 95% ethanol and wiped with acetic acid. The coverslips were immediately placed inside a 150-mm plastic culture dish on top of wet filter paper. The lid was left off, and the coverslips were allowed to dry in the humidified chamber. Once dried, coverslips were stained with 4′,6-diamidino-2-phenylindole (DAPI) (100 ng/ml) and SYBERGold nucleic acid dye (1:20,000). Slides were imaged with a Zeiss Axioplan II microscope using a 100× objective, Hamamatsu Orca II camera, and Metamorph software. At least 200 mitotic spreads were scored for each sample. If an individual cell spread had more than 10 single chromatids, then the cell was scored as fatigued.
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6

Immunostaining of Meiotic Chromosome Spreads

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Meiotic cells were collected at indicated time points and fixation and chromosome spread was performed essentially as described using 4% paraformaldehyde42 (link). Immunostaining was performed as described42 (link). Primary antibodies were anti-PCNA (Abcam; ab70472, 1:100), anti-Zip3 antibody (a gift from Dr. Akira Shinohara, 1:400) and anti-Zip1 (a gift from Dr. Scott Keeney, 1:400); all incubated overnight at room temperature in 100 ul TBS/BSA buffer (10 mM Tris PH7.5, 150 mM NaCl, 1% BSA) Secondary antibodies were anti-rabbit 568 (A11036 Molecular Probes, 1:1000), anti-mouse 488 (A11029 Molecular Probes, 1:1000), anti-rabbit 647 (A21245 Invitrogen), and anti-guinea pig 555 (A21435 Life Technologies); all for 1 hr at 37˚C. Coverslips were mounted with Prolong Gold antifade reagent (Invitrogen, P36930). Digital images were captured using a Zeiss Airyscan LSM800 with Axiocam and analyzed using Zen (blue edition); or a Zeiss Axioplan II microscope, Hamamatsu ORCA-ER CCD camera and analyzed using Volocity software. Co-localization of protein foci was assigned to overlapping foci. Random colocalization (levels of colocalization by chance) were estimated by rotating the PCNA and Zip3 channels by 90° relative to one another and requantifying focus colocalization. Scatterplots were generated using the GraphPad program in Prism.
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7

Immunostaining of Chromosome Spreads

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Chromosome spreads were processed for immunostaining as described previously (Grubb et al., 2015 (link); Loidl and Lorenz, 2009 (link)) using the following antibodies: mouse anti-HA antibody (Millipore Sigma; 11583816001, 1:200) and rabbit anti-Zip1 antibody (a gift from Dr. Akira Shinohara, 1:200). Goat secondary antibodies (anti-rabbit 568, A11036; and anti-mouse 488, A11029) were conjugated to Alexa 568 and Alexa 488 (Molecular Probes, 1:1000). Coverslips were mounted with Prolong Gold antifade reagent (Invitrogen P36930). Digital images were acquired using a Zeiss AxioPlan II microscope, Hamamatsu ORCA-ER CCD camera and analyzed using Volocity software. Scatterplots were generated using the Graphpad program in Prism.
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8

Meiotic Division and Sporulation Assay

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To analyze of meiotic divisions and sporulation, cells were fixed in 40% ethanol 0.1 M sorbitol, stained with DAPI, and ~200 cells were categorized for each time point. DAPI-stained cells were mounted in antifade (Prolong, Invitrogen) and images captured using a Zeiss AxioPlan II microscope, Hamamatsu ORCA-ER CCD camera and Volocity software.
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9

Immunostaining of Meiotic Chromosome Spreads

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Meiotic cells were collected at indicated time points and fixation and chromosome spread was performed essentially as described using 4% paraformaldehyde42 (link). Immunostaining was performed as described42 (link). Primary antibodies were anti-PCNA (Abcam; ab70472, 1:100), anti-Zip3 antibody (a gift from Dr. Akira Shinohara, 1:400) and anti-Zip1 (a gift from Dr. Scott Keeney, 1:400); all incubated overnight at room temperature in 100 ul TBS/BSA buffer (10 mM Tris PH7.5, 150 mM NaCl, 1% BSA) Secondary antibodies were anti-rabbit 568 (A11036 Molecular Probes, 1:1000), anti-mouse 488 (A11029 Molecular Probes, 1:1000), anti-rabbit 647 (A21245 Invitrogen), and anti-guinea pig 555 (A21435 Life Technologies); all for 1 hr at 37˚C. Coverslips were mounted with Prolong Gold antifade reagent (Invitrogen, P36930). Digital images were captured using a Zeiss Airyscan LSM800 with Axiocam and analyzed using Zen (blue edition); or a Zeiss Axioplan II microscope, Hamamatsu ORCA-ER CCD camera and analyzed using Volocity software. Co-localization of protein foci was assigned to overlapping foci. Random colocalization (levels of colocalization by chance) were estimated by rotating the PCNA and Zip3 channels by 90° relative to one another and requantifying focus colocalization. Scatterplots were generated using the GraphPad program in Prism.
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10

Immunofluorescence Microscopy Protocols

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Immunofluorescence was performed according to standard procedures67 . Samples were imaged with a Zeiss Axioplan 2 microscope using a Plan-Apochromatic 40× objective and a Hamamatsu ORCA II digital camera (Bridgewater, NJ) under the control of MetaMorph software (Molecular Devices, Sunnyvale, CA) or by spinning disk confocal microscopy. Immunofluorescence staining using the anti-PI(4,5)P2 antibody was performed according to Hammond et al.68 .
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