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31 protocols using ixon3 897

1

Rab37-Mediated SFRP1 Trafficking Dynamics

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EV, Rab37WT, Rab37Q89L and Rab37T43N cells were seeded on a 29 mm glass bottom dish. After 24 h, cells were transfected with GFP-SFRP1 for 16–18 h before image analysis. TIRF microscopy system was built on an inverted microscope (Olympus IX81, Tokyo, Japan). The system was equipped with a high sensitivity EMCCD Camera (iXOn3897, Andor technology, New York, NY, USA) and an UPON 100X oil objective lens (NA = 1.49, Olympus) to capture 100–200 nm images below the interface. GFP was excited with 491 nm solid laser and driven by Xcellenace software (Olympus imaging software). To observe the Rab37-mediated SFRP1 trafficking events, the images sequences were recorded in stream model for every 3 s.
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2

Super-Resolution Imaging of the DIB

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The DIB was imaged using an inverted microscope (Eclipse Ti-U, Nikon) equipped with a 60× oil immersion TIRF objective (numerical aperture = 1.49; Plan Apo, Nikon). The fluorescence was excited with a 473-nm diode-pumped solid-state laser (100 mW; Changchun New Industries Optoelectronics Technology). The image was acquired with an electron-multiplying charge-coupled device camera (iXon3 897, Andor). The exposure time was set to 3 to 30 ms. The maximum field of view was 135 μm by 135 μm.
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3

Multicolor Single-Molecule Imaging Protocol

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Imaging was performed through Olympus UPlanSApo 100x 1.4 NA oil-immersion objectives mounted on Olympus IX71 inverted microscopes with back optics arranged for oblique incident angle illumination. The microscope contained a custom pentaband dichroic and pentanotch filter (Chroma Technology Corp, Bellows Falls VT) and laser lines at 488/561/647/750 nm (detailed in the Supplemental Experimental Procedures) for excitation of Atto 488, Cy3B, Alexa Fluor 647 and DyLight 750, respectively. A 405-nm laser was used for reactivation of dyes. Images were acquired on an Andor iXon3 897 or 897Ultra EMCCD camera through a QV2 quadview image splitter (Photometrics; Tucson AZ). Each camera pixel corresponded to ∼158 nm in sample space and the total imaging field size was ∼40 μm × 40 μm. Axial focus during imaging was maintained in an automated manner as described previously (Dempsey et al., 2011 (link)).
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4

TIRF Imaging of C1-Ten Plasma Membrane Localization

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Plasma membrane localization of WT and 3KQ mutant forms of C1-Ten were imaged using an objective-type TIRF microscope built on an inverted microscope (IX-81, Olympus, Tokyo, Japan) equipped with an XY-axis automated stage (MS-2000, Applied Scientific Instrumentation, Eugene, OR, USA). A 488-nm laser (35-LAL-415–220R, Melles Griot, NY, USA) was aligned and collimated to focus on the back focal plane of an oil-immersion 60× objective lens (APON 60×OTIRF/1.49, Olympus). A dichroic mirror (ZTUV-405/488/561RPC, Chroma, Taoyuan City, Taiwan) and an emission filter (ZET405/488/561M, Chroma) were used. Images were collected with an electron multiplying charge-coupled device (EM-CCD) camera (iXon3 897, Andor Technology, Belfast, UK). For higher magnification, we used a 1.6× amplifier and inserted a 1.43× tube lens. The images were obtained before and after insulin treatment (2 min, 5 min, 7 min, and 9 min) at a frame rate of 20 Hz. At the indicated time point, the fluorescence intensity of each cell was subtracted from the background fluorescence measured outside the cell. Fluorescence intensity was determined for each condition by normalizing fluorescence intensity of the image in the NT condition.
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5

Super-resolution TIRF Imaging Protocol

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TIRF imaging was done using a Leica GSD/TIRFM ground state depletion superresolution microscope. Solid-state laser light (405, 488, 532, and 642 nm) was focused at the back focal plane of a 160× numerical aperture 1.43 objective. Signals were recorded by using an Andor iXon3 897 high-speed electron-multiplying charge-coupled device camera. For TIRF imaging, the stained cells were mounted in an open chamber filled with 1× PBS.
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6

Super-Resolution Microscopy System Setup

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The SD-SIM is a commercial system based on an inverted fluorescence microscope (IX81, Olympus) equipped with a widefield objective (×100/1.3 oil, Olympus) and a scanning confocal system (CSU-X1, Yokogawa). It used software MetaMorph (v7.8.1.0) to capture images. Four laser beams of 405 nm, 488 nm, 561 nm, and 647 nm were combined with the SD-SIM. The Live-SR module (GATACA systems) was equipped with the SD-SIM. The images were captured either by an sCMOS camera (C14440-20UP, Hamamatsu) or an EMCCD camera (iXon3 897, Andor).
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7

Live-cell and super-resolution imaging

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Imaging was performed with an inverted fluorescence microscope (TE2000-U; Nikon) equipped with an electron-multiplying charge-coupled device camera (Cascade II; Photometrics) and a Yokogawa spinning disc confocal system (CSU-Xm2; Nikon). Live-cell imaging was performed at 37°C. Images were captured with a 100x NA 1.4 oil objective and acquired using MetaMorph (version 7.0; MDS Analytical Technologies).
Super-resolution microscopy (SIM) was performed with an inverted fluorescence microscope (TI-E; Nikon) equipped with an electron-multiplying charge-coupled device camera (iXon3 897; Andor). Z-stack images were captured every 200 nm and reconstructed using NIS elements with SIM (Nikon).
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8

Multi-channel Fluorescence Microscopy Protocol

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Imaging was performed on a Nikon Eclipse Ti inverted epifluorescence microscope using a 100× objective (Plan Fluo, NA 1.40, oil immersion) with a 2.5× TV relay lens, using a mercury lamp as the light source (X-Cite 200DC, Excelitas Technologies), within a cage incubator (InVivo Scientific) at 30 °C, and acquired using a cooled EMCCD (electron multiplying charge-coupled device) camera (iXon3 897, Andor, Belfast, United Kingdom). The fluorescent filters used in the study were as follows (Xnm, Yex [bandwidth] excitation filter/dichroic beamsplitter wavelength/Xnm, Yem [bandwidth] emission filter/company): cyan (436 nm, 20ex/455 nm/480 nm, 40em/Nikon), yellow (500 nm, 20ex/515 nm/535 nm, 30em/Nikon), and red (560 nm, 40ex/585 nm/630 nm, 75em/Nikon). The images are acquired with these exposures: phase-contrast (100 ms), red (500 ms), yellow (100 ms), and cyan (200 ms). These color names correspond to the filters used for the colors shown in the images.
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9

Single-molecule BODIPY Fluorescence Imaging

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Fluorescence images were acquired on
an ECLIPSE Ti-E epifluoresence/TIRF microscope (NIKON, Japan) equipped
with 405, 488, 561, and 647 nm lasers (Coherent, California). All
lasers are individually shuttered and collected in a single fiber
to the sample through a 1.49 NA, ×100, apochromat TIRF oil objective
(NIKON, Japan). A dichroic mirror for the 488 nm laser (ZT491rdcxt,
CHROMA) was used. The excitation light was filtered using a laser
clean up filter (ZET 488/10x, CHROMA). The emitted light was filtered
using a band-pass filter (ET bandpass 532/50, CHROMA). Images were
recorded with an EM-CCD camera (iXon3 897, Andor). To keep the sample
in focus over time, we employed a perfect focusing system (NIKON,
Japan). Exposure time of the EM-CCD camera was set to 400 ms. We sampled
at various rates but did not observe different dynamics below a 400
ms exposure. Such an exposure time also allowed us to collect signals
of sufficient quality with the chosen laser excitation power density.
The laser power was optimized to achieve the best possible signal-to-noise
ratio and long enough bleaching time for the BODIPY fluorophore.
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10

Confocal Imaging of Ras and PIP3 Waves

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Confocal imaging was performed using an inverted microscope (ECLIPSE Ti; Nikon) equipped with a confocal unit (CSU-W1; Yokogawa). Laser sources for 488 nm and 561 nm excitation light were solid-state CW lasers (OBIS 488NM X 50MW and OBIS 561NM X 50MW, respectively; Coherent). Time-lapse images were acquired through a 60× oil immersion objective lens (CFI Apo TIRF 60X Oil, N.A. 1.49; Nikon) with an EM-CCD camera (iXon3 897; Andor). Cells were transferred to a 35 mm Glass Base Dish (Grass 12 φ, 0.15–0.18 thick; IWAKI) and suspended in 200 µl DB with 4 mM caffeine and 5 µM latrunculin A (Sigma). Caffeine was added to induce Ras and PIP3 waves and to inhibit cAMP relay (Shibata et al., 2012 (link)). Inhibitors were added after 15 min treatment with caffeine and latrunculin A. latrunculin A (2 mM), LY294002 (40 µM or 100 µM; Cayman), Torin2 (1 mM; TOCRIS) and BPB (10 mM; TCI Japan) in DMSO were diluted to the final concentration (DMSO≤1%). The effectiveness of LY294002 during the 60 min observation was confirmed by replacing the extracellular medium (Fig. S3I). Time-lapse images were obtained at 200 ms exposure for each channel at 2 s intervals (488 nm laser power was ∼50 µW, and 561 nm laser power was ∼150 µW).
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