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18 protocols using axio observer 7 inverted microscope

1

Immunostaining for DNA Modifications

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Embryos were fixed in 4% PFA/Phosphate Buffer (PB) for 20 min at room temperature. The embryos or sections were washed in TBS with 0.5% Triton (TBS-T) and subsequently blocked with 5% FBS in TBS-T for 3 h at RT. The embryos or sections were incubated in primary antibody solution at 4°C fortwo days. The primary antibody used were mouse monoclonal anti-5mC (Abcam, ab10805, 1:500), rabbit polyclonal anti-5hmC (Active Motif, Cat Nº 39791, 1:500), goat polyclonal anti-hSOX2 (Santa Cruz Biotech; Y-17; 1:500, for Figure 2A), rabbit monoclonal anti-SOX2 (Abcam, ab92494, 1:1,000; for Figures 6C,F), and anti-PAX7 IgG1 (Developmental Studies Hybridoma Bank, 1:10). The secondary antibodies used were donkey anti-rabbit 594, donkey anti-mouse 488, donkey anti-goat 647, goat anti-rabbit 594, and goat anti-mouse IgG1 647 (all from Molecular Probes, 1:500). After several washes in TBS-T, the embryos and sections were mounted and imaged by using Carl ZEISS Axio observer 7 inverted microscope (Axio observer Colibri 7, Axiocam 305 color, Axiocam 503 mono) and Carl ZEISS ZEN2 (blue edition) software. The negative controls omitting the primary antibodies (anti-5mC and anti-5hmC) fails to detect any specific mark (see Supplementary Figure S1).
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2

Visualizing NF-κB Translocation in Macrophages

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To observe the location of NF‐κB, immunofluorescent staining was used on Raw 264.7 macrophages. Cells were seeded in 12‐well plates at a density of 3 × 105 every well. After 0.1% DMSO or oridonin (10 μM) pre‐treatment for 0.5 h, macrophages were treated with oxLDL (20 μg/mL) for two more hours at 37°C 5% CO2. Subsequently, macrophages were fixed with 4% paraformaldehyde for 10 min. 0.1% Triton X‐100 was used for permeabilization. After washed with PBS, macrophages were blocked with 1% goat serum for 30 min. Primary antibody against NF‐κB (ab16502, 1:200) was used to incubate cells at 4°C overnight. AlexaFluor 555 anti‐rabbit secondary antibody (#4413, 1/1000) was used to visualize NF‐κB staining. Nuclei were also co‐stained using DAPI staining. Images were obtained using a Zeiss Axio Observer 7 inverted microscope.
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3

Immunolabeling of Whole Embryos

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Whole embryos were fixed for 15 min in 4% PFA, washed in TBST (500 mM Tris-HCl, pH 7.4, 1.5 M NaCl, 10 mM CaCl2, and 0.5% Triton X-100) and blocked in 5% FBS in TBST for 1h at RT. Embryos were then incubated in mouse anti-Tuj1 (1:250; Covance) and/or mouse anti-HNK1 (1:10; supplied by the Developmental Studies Hybridoma Bank) overnight at 4°C diluted in TBST-FBS. Secondary antibodies were goat anti-mouse IgG2a Alexa Fluor 647 (1:500) and goat anti-mouse IgM Alexa Fluor 568 (1:500) for one hour at room temperature. After several washes in TBS-T, whole embryos or sections were mounted and imaged by using Carl ZEISS Axio observer 7 inverted microscope containing an Axiocam 503 camera and Carl ZEISS ZEN2.3 (blue edition) software.
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4

Axio Observer Confocal Imaging Protocol

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DIC images were acquired on a wide-field Axio Observer 7 Inverted Microscope (Zeiss) with a ×63/1.4–numerical aperture (NA) Plan-Apochromat (oil immersion) objective. Single-slice confocal images were acquired using a Marianas Spinning Disk confocal microscope (Intelligent Imaging Innovations) consisting of a spinning disk confocal head (CSU-X1; Yokagawa) on a Zeiss Axio Observer inverted microscope equipped with ×63/1.4-NA Plan-Apochromat (oil immersion). Images were acquired with a Prime sCMOS camera (Photometrics) controlled by SlideBook 6 (Intelligent Imaging Innovations). Temperature was stabilized to 23 °C using the microfluidic temperature stage (CherryTemp; CherryBiotech). For fluorescent samples, protein labeled with Alexa-488 was excited with a 488-nm line from a solid-state laser (LaserStack) and collected with a 440-/521-/607-/700-nm quad emission dichroic and 525-/30-nm emission filter.
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5

Visualizing Coacervate Fusion Dynamics

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Fusion events of coacervates were collected at a rate of 65 ms per frame using a wide-field Axio Observer 7 Inverted Microscope (Zeiss) with a ×63/1.4-NA Plan-Apochromat (oil immersion) objective. Cover glass bottoms were treated with 1% Pluronics F127 for 25 to 30 min and washed with deionized water prior to protein incubation. Images were acquired with an Axiocam 506 mono camera (Zeiss) controlled by the Zen software (Zeiss). ImageJ was used for further format and images processing, and MATLAB was used to analyze fusion events as previously described (57 (link)).
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6

Live-cell Imaging Setup for Quantitative Analysis

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Cells were imaged in culture media supplemented with 20 mM HEPES (SH3023701, HyClone) at 37°C, on a Marianas Imaging System (Intelligent Imaging Innovations) consisting of an Axio Observer 7 inverted microscope (Zeiss) attached to a W1 Confocal Spinning Disk (Yokogawa) with Mesa field flattening (Intelligent Imaging Innovations), a Phasor photomanipulation unit (Intelligent Imaging Innovations), a motorized X,Y stage (ASI), and a Prime 95B sCMOS (Photometrics) camera. Illumination was provided by a TTL triggered multifiber laser launch (Intelligent Imaging Innovations) consisting of 405, 488, 561, and 637 lasers, using a 63×1.4 NA Plan-Apochromat objective (Zeiss). Temperature and humidity were maintained using a Bold Line full enclosure incubator (Oko Labs). The microscope was controlled using Slidebook 6 Software (Intelligent Imaging Innovations).
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7

Widefield Microscopy of Membrane Fusion

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For fusion measurement, samples were prepared in Grace BioLabs CultureWells with coverslip bottom treated with 1% Pluronics F-127 (1 h). Timeseries of fusion events were collected at 49-ms time intervals on a widefield Axio Observer 7 Inverted Microscope (Zeiss) with a ×63/1.4 NA Plan-Apochromat (oil immersion) objective. FITC was excited with a 120-W metal halide lamp (X-cite 120) with 470/40 nm excitation and 525/50 nm emission filters. Images were acquired with a Axiocam 506 mono camera (Zeiss) controlled by the Zen software (Zeiss). ImageJ was used to further format and process images, and MATLAB was used to analyze fusion events as described previously69 (link).
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8

Immunofluorescence Imaging of Frizzled3 Receptor

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The specimens were fixed with 4% paraformaldehyde in Phosphate-Buffered Saline (PBS) at 4 °C overnight. The fixed samples were washed with PBS with 0.3% Triton X-100 (PBST), treated with 1.5% normal goat serum in PBST for 1 h, and incubated with rabbit anti-human Frizzled3 polyclonal antibody (CSB-PA882067ESR2HU; Cusabio) at 4 °C overnight. The primary antibody was used at a dilution of 1:50 in PBST containing 0.5% Bovine Serum Albumin (BSA). After a brief rinse with PBST, the samples were reacted at room temperature for 2 h with a secondary antibody, Alexa Fluor 488-conjugated goat anti-rabbit IgG (Invitrogen), diluted 1:1000 in PBST containing 0.5% BSA. After washing with PBS, the samples were placed with the apical surface downward in a thin-glass-bottomed Petri dish filled with PBS, gently pressed onto the bottom by metal weights, and examined under a Carl Zeiss LSM880 confocal laser-scanning microscope (Carl Zeiss).
The light source, an argon laser, was coupled to an Axio Observer7 inverted microscope (Carl Zeiss). Excitation wavelength was 488 nm. Laser power was reduced to 1.0% by a neutral density filter. An objective was Plan-Apochromat 40× with oil immersion. Emitted fluorescence was detected by a photomultiplier and displayed as a 512 × 512 pixel resolution image using Carl Zeiss ZEN 2 software.
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9

Fluorescent Probe Assay for LLP

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LLP was studied using a fluorescent probe, FOAM-LPO. FOAM-LPO was synthesized as previously described (26 (link)). Cells were cultured on an 8 Well μSlide (ibidi, 80807) and treated with inhibitors and with or without DC661. Cells were incubated with media containing FOAM-LPO (1 M) in an atmosphere of 5% CO2 and 95% air for 5 minutes at 37°C. The cells were washed twice with media, and then cells were observed under the microscope (Zeiss Axio Observer 7 inverted microscope) to detect fluorescence shifting from 586 to 512 nm in response to LLP.
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10

Imaging Actin Dynamics in Live Cells

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Cells were imaged in culture media supplemented with 20 mM HEPES (SH3023701, HyClone) at 37°C, with or without 1 µM SiR-Actin (CY-SC001, Cytoskeleton) or 2 nM Calyculin A (101932-71-2, Cayman), on a Marianas Imaging System (Intelligent Imaging Innovations) consisting of an Axio Observer 7 inverted microscope (Zeiss) attached to a W1 Confocal Spinning Disk (Yokogawa) with Mesa field flattening (Intelligent Imaging Innovations), a Phasor photomanipulation unit (Intelligent Imaging Innovations), a motorized X,Y stage (ASI), and a Prime 95B sCMOS (Photometrics) camera. Illumination was provided by a TTL triggered multifiber laser launch (Intelligent Imaging Innovations) consisting of 405, 488, 561, and 637 lasers, using a 63 × 1.4 NA Plan-Apochromat objective (Zeiss). Temperature and humidity were maintained using a Bold Line full enclosure incubator (Oko Labs). The microscope was controlled using Slidebook 6 Software (Intelligent Imaging Innovations).
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