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10 protocols using csu x 1 spinning disc

1

Confocal Imaging of Live Cells

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All confocal images were captured using a Nikon Ti microscope equipped with a Yokogawa CSU X-1 spinning disc and an Andor iXon897 EMCCD camera controlled by Andor IQ2 software. Epifluorescence was imaged using the same microscope in bright-field mode, and images were captured with an Andor Neo sCMOS camera, or at a FLoid benchtop imaging station (Invitrogen). TIRF images were captured using a TILL photonics iMIC microscope (FEI Munich) with an Andor iXon897 EMCCD camera. All live-imaging assays were performed in a humidified 5% CO2 incubation chamber.
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Confocal Microscopy for Live-Imaging

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All confocal images were captured using a Nikon Ti microscope equipped with a Yokogawa CSU X-1 spinning disc and an Andor iXon897 EMCCD camera controlled by Andor IQ3 software. Bright field movies of muscle contraction were acquired using the same microscope in wide field mode and images were captured with an Andor Neo sCMOS camera. All live-imaging assays were performed at 37 °C and in a 5% CO2 controlled and humidified environment.
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3

Imaging of Muscle Contraction

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Confocal images were captured using Nikon Ti microscope equipped with a Yokogawa CSU X-1 spinning disc and an Andor iXon897 EMCCD camera controlled by Andor IQ3 software. Phase-contrast movies of muscle contraction were acquired using the same microscope in Epi-mode and images were captured with an Andor Neo sCMOS camera. All live imaging experiments were performed with 5% CO2 and 37 °C humidified using in-situ microscope setup. Image analysis was performed using FIJI ImageJ V.2.0.0 and Bitplane Imaris 8.4.3 software.
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4

Confocal Imaging of Live Cells

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Confocal imaging was performed at the Nikon Imaging Center at the Whitehead Institute for Biomedical Research using a spinning disc system (Krakowiak et al., 2018 (link)) with the following parameters: Nikon Ti-E base, 1.49 NA, 100× objective, Yokogawa CSU-X1 spinning disc, Andor iXon 897E EM charge-coupled device camera, and MetaMorph acquisition software. Cells were grown and indicated fluorophores were imaged in SDC media, and heat shock was performed on live cells from 25°C to 39°C using an objective heater (Chowdhary et al., 2019 (link)). Images were autocontrasted using ImageJ, and single z-slices are shown.
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5

Immunostaining and Confocal Imaging of Insect Nervous System

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The ANSs were dissected as above and maintained in chilled locust saline until fixation (up to 60 min). For the purpose of immunostaining and histology, samples were prepared from a section of the dissected preparation (comprising the second abdominal ganglion and a section of the paired connectives), and thoroughly cleaned of all non-nervous tissue.
Samples were fixed in 4% PFA for 16 h at 4°C, then washed in PBS and permeabilized with ice-cold MeOH at −20 °C for 5 min, blocked, and further permeabilized with 10% fetal bovine serum and 1% Triton for 2h. Samples were agitated and actin was stained with Fluorescein Phalloidin (Invitrogen) at 10 μg/mL for 1h. Finally, samples were mounted with VectaShield (Vector Laboratories). Cover slides were sealed with nail polish until use.
Confocal images were captured using a Nikon Ti microscope equipped with a Yokogawa CSU X-1 spinning disc and an Andor iXon897 EMCCD camera controlled by Andor IQ3 software. Image analysis was performed using FIJI ImageJ V.2.0.0.
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6

Microscopy Protocols for Live-Cell Imaging

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Unless otherwise stated, all confocal, epifluorescence and brightfield images were captured using a Nikon Ti microscope equipped with Yokogawa CSU X-1 spinning disc, controlled by Andor IQ2 software. Epifluorescence was imaged using the same microscope in widefield mode. Confocal and widefield images were captured with Andor iXon897 EMCCD and Neo sCMOS cameras, respectively. In all live-imaging assays performed, imaging of myotube contractions, Fluo-3 transients, FM dye, axonal degeneration after H2O2 and axonal transport, living samples were maintained in a humidified incubation chamber at 37°C, 5% CO2. Details of fluorescent labels and excitation and emission parameters are given in supplementary material Table S1 below. Images were analyzed using ImageJ software, except for BTX-HB9::GFP colocalization, which was analyzed using Imaris (Bitplane) Coloc module and 3D rendering and surface modeling, which were performed using Imaris Surpass and Surface functions.
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7

Confocal Microscopy Imaging Protocol

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All confocal images were captured using a Nikon Ti microscope equipped with a Yokogawa CSU X-1 spinning disc and an Andor iXon897 EMCCD camera controlled by Andor IQ2 software. Images were analyzed using ImageJ software.
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8

Automated Microscopy and Single-Cell Analysis

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Images were acquired on a Yokogawa CellVoyager 7000 automated microscope equipped with a CSU‐X1 spinning disc, Neo sCMOS cameras (Andor) and UPLSAPO 20× (NA 0.75, Olympus) lens. CellProfiler software was used for image analysis, cell segmentation and single‐cell feature quantification as described in Stoeger et al (2015). We segmented the nuclear periphery by expanding and shrinking the nucleus segmentation by 5 pixels. We segmented the cytoplasm by masking the cell segmentation by the expanded nucleus. The CellProfiler pipeline is available as Dataset EV2. We employed CellClassifier (https://www.pelkmanslab.org/?page_id=63) for data clean up and classification of transfected cells and cells in S‐phase of the cell cycle. We excluded missegmented cells, mitotic cells and cells displaying staining artefacts from further analysis (Stoeger et al, 2015). Computations were performed on the Brutus computing cluster (ETH Zürich) using the task manager iBRAIN.
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9

Highly Versatile Microscopic Imaging

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Imaging experiments were performed using either a 1) Nikon TI inverted microscope with NIS Element Software (Nikon), equipped with a perfect focus system, a Yokagawa CSU-X1 spinning disc, an iXon Ultra 897 EM-CCD camera (Andor), or 2) a Nikon TI2 inverted microscope with NIS Element Software, equipped with a perfect focus system, a Yokagawa CSU-X1 spinning disc and an Prime 95B sCMOS camera (Photometrics). Both microscopes were equipped with a temperature-controlled hood. For experiments involving long-term time-lapse analysis (> 3 hr) a 60x 1.40 NA oil-immersion objective was used, while a 100x 1.49 NA oil-immersion objective was used for short-term analyses. A 100x 1.49 NA oil-immersion objective was used for experiments using 2D organoid cells. The siRNA screen (Figure 6B, 6C, S6B, S6H, S6J, and S6O) was performed using a 40x 0.95 NA air objective.
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10

Immunofluorescence Microscopy of IFITM3

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Cells were grown in µ-slide eight wells (Ibidi). Cells were fixed with 4% PFA and permeabilized with 0.5% Triton X-100 in PBS. Immunostaining was performed with primary antibodies for 1 h at room temperature for HA (1:1,000; BioLegend) or rabbit anti-IFITM3 (Cat. no. AP1153a, 1:500; Abcepta) and secondary antibodies conjugated to Alexa Fluor 488 and 647 (1:1,000; Invitrogen) for 1 h at room temperature. Nuclear DNA was stained with 2.5 µg/ml DAPI (Invitrogen) for 5 min at room temperature. Microscopic analysis was performed using a Nikon Ti-E microscope equipped with a Yokogawa CSU-X1 spinning-disc and an Andor DU-888 camera. ImageJ was used to prepare microscopy images and for quantification of signal intensity of the immunostaining.
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