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13 protocols using orca flash 4

1

Isoproterenol-Induced Calcium Dynamics in iCMs

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iCMs at different days of culture were labeled with Fluo-4, a calcium-sensitive dye (Life Technologies), as instructed by the manufacturer. Videos were recorded using a fluorescence microscope (Zeiss, Hamamatsu ORCA flash 4.0) right before incubation with isoproterenol to determine the baseline for calcium transient and beat rate of the cells. Then medium of the cells was replaced with medium supplemented with 1 μM isoproterenol and incubated for 10 min at 37°C. Immediately after isoproterenol incubation the beat rate and calcium transient of iCMs were recorded using a fluorescence microscope (Zeiss, Hamamatsu ORCA flash 4.0). Videos from at least 3 different wells from different differentiation batches were recorded and from each well at least 2 field of views were captured. All data acquired for each culture day was averaged. From each well at least 3 field of views were captured and analyzed.
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2

Visualizing PrecA-mCherry Expression in S. venezuelae

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To visualize the expression of the PrecA-mcherry fusion in S. venezuelae (KS80), cells were grown in triplicate in liquid MYM with and without MMC, ciprofloxacin, and MMS as described. Cells obtained from each culture were immobilized on a 1% agarose pad and visualized using a Zeiss Axio Observer Z.1 inverted epifluorescence microscope fitted with an sCMOS camera (Hamamatsu Orca Flash 4), a Zeiss Colibri 7 LED light source, and a Hamamatsu Orca Flash 4.0v3 sCMOS camera. Images were acquired using a Zeiss Alpha Plan-Apo 100×/1.46 oil differential inference contrast (DIC) M27 objective with an excitation/emission bandwidth of 577 to 603 nm/614 to 659 nm to detect fluorescence emitted by the mCherry reporter fusion. Still images were collected using the Zen Blue software and further analyzed using the Fiji imaging software (63 (link)). To normalize the mCherry fluorescence intensity across different MMC treatments, images were corrected for background fluorescence.
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3

Automated Imaging of Stained Samples

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Stained samples were subjected to automated imaging using a Zeiss Axioscan. Z1 slide scanner (Zeiss, Oberkochen, Germany) equipped with a Hamamatsu Orca Flash 4 camera and a Zeiss 20× objective lens (Plan-Apochromat 20×/0.8 M27) with a resolution of 0.325 microns/pixel. Slides containing three specimens each were loaded onto the scanner to enable simultaneous image acquisition, leveraging its high capacity to accommodate up to 100 slides. Before initiating the acquisition, the region of interest was determined for each specimen. The acquisition process adhered to the predefined parameters outlined in the Scanning profile, encompassing the acquisition of 9 sections per specimen (z-stack) with intervals of 2.50 µm. The Extended Deep Focus technique used the “Variance” method to capture detailed images. The primary focus during image acquisition was directed toward βIII-tubuline-positive cells, with the secondary antibody conjugated to Alexa Fluor 555 Donkey (Life Technologies—Thermo Fisher Scientific, Geneva, Switzerland). To achieve this, a filter with excitation at 540 nm and emission at 561 nm was used. The light source intensity was 58.32%, and the exposure time was fixed at 100 ms (Figure 1A). Images presenting acquisition defects that could bias the computation were not included in the study.
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4

Cell Suspension Vortexing Protocol

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One millilitre of cells in culture medium at a density of 1 × 106/mL–1 × 107/mL was vortexed continuously for 30 s at max speed. Cells were observed, and images were captured on a Zeiss imager Z2 microscope with ORCA Flash4 camera and ×40 oil immersion objective.
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5

MuSCs Culturing and Imaging

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MuSCs were plated on a microscopy culture chamber (IBIDI, 80826) and cultured in growth media supplemented as above. The plate was incubated at 37 °C, 5% CO2 and 3% O2 in a Pecon incubation chamber. A Zeiss Observer.Z1 connected to a Plan-Apochromat 20x/0.8 M27 objective and Hamamatsu Orca Flash 4 camera piloted with Zen software (Carl Zeiss) was used.
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6

Live-cell imaging and analysis of cell migration

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Cells were transfected and seeded as indicated above. The plate was then incubated at 37 C, 5% CO 2 , and 3% O 2 (Zeiss, Pecon). A Zeiss Observer.Z1 connected to an LCI PlnN 10 3 /0.8 W objective and Hamamatsu Orca Flash 4 camera piloted with Zen (Zeiss) was used. Cells were imaged every 13 min for the time indicated. Distance and velocity plots were obtained using the Manual tracking plugin available in Fiji (Figure 3D) or automatic tracking (remaining experiments) provided by TrackMate (Tinevez et al., 2017) after contrast enhancement using a median filter followed by ''Detect Edges'' functions available in FIJI. Track parameters were kept within the same datasets; track segment splitting was allowed with a maximal distance between time frames of 50 mm. For the kymograph, cells were manually tracked and a fixed ROI of 150px by 150px containing the cell in its center was extracted for each time point. A line encompassing the cell nucleus was drawn and the Dynamic Reslice plugin in Fiji was used to obtain the corresponding kymograph.
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7

Vesicle Trafficking in Fly Wings

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Intact, injured or crushed wings (1 to 5 days old flies) were dissected and mounted in Halocarbon oil 27 beneath a coverslip and imaged immediately. Images of vesicle trafficking were acquired on a spinning disc microscopy (Zeiss Examiner Z1) with a 63X oil-immersion objective at the location indicated (Fig. 1A). Time-lapse images were acquired with CCD camera (Hamamatsu Orca Flash 4.0) using Zen software (Zeiss) for a 3 minutes window. The wings were sitting in halocarbon oil no longer than 15 min before imaging. All the wings were imaged including the those with only labeled severed neurons or intact neurons.
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8

High-throughput Timelapse Imaging of Cell Interactions

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We previously described a method called TIMING that allows high throughput, timelapse, and single-cell level imaging of thousands of nanowells, each containing 1 to 4 cells18 (link).50 (link) Effector (T cells) and target cells (mouse EL4 cells stably expressing human CD19), were labeled respectively with 1 µM PKH67 (PKH Green) and PKH26 (PKH Red) fluorescent dyes (Sigma-Aldrich) according to the manufacturer’s protocol and loaded on the array. Cell apoptosis was detected by immersing the array in phenol red-free cell-culture media containing a dilution of 1:60 annexin V - Alexa Fluor 647 (AF647) (Life Technologies). Arrays were imaged for 6 hours at an interval of 5 min using an Axio fluorescent microscope (Carl Zeiss) utilizing a 20×0.8 NA objective, a scientific CMOS camera (Orca Flash 4.0), a humidity/CO2 controlled chamber, and the tile function of the Zen software.
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9

Measuring Spindle Assembly Checkpoint Strength

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To measure SAC strength in live cells, cells were incubated in a 24‐well plate in full‐growth media in a heated chamber (37°C and 5% CO2) and imaged with brightfield microscopy using a 10×/0.5 NA objective and a Hamamatsu ORCA‐ER camera at 2 × 2 binning on a Zeiss Axiovert 200M, controlled by Micro‐manager software (open source: https://micro‐manager.org/) or a 20×/0.4 NA air objective and a CMOS Orca flash 4.0 camera at 4 × 4 binning on a Zeiss Axio Observer 7. Mitotic exit was defined by cells flattening down in the presence of nocodazole and MPS1 ± PLK1 or BUB1 inhibitors. MPS1 was inhibited with AZ‐3146 shortly prior to imaging, with or without PLK1 inhibition with BI‐2536 or BUB1 inhibition with BAY‐1816032. In Fig EV2G, cells entering mitosis in the presence of nocodazole were analysed. In Figs 2E, 3H, EV3J and 5A, cells entering in mitosis in the presence of AZ‐3146 were analysed. In Figs 5D and EV5C, cells arrested in mitosis at the time of AZ‐3146 ± BI‐2536 or BAY‐1816032 treatment were analysed.
To measure SAC strength in fixed cells, nocodazole and MG132 ± BI‐2536 or BAY‐1816032 were added first for 30 min to ensure complete inhibition, followed by a time course of AZ‐3146 ± BI‐2536 or BAY‐1816032 in media containing nocodazole and MG132. Cells were fixed and analysed by immunofluorescence, probing for KNL1‐pMELT or BUB1.
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10

Microscopy and Image Analysis Methods

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WISH, SISH, histological stainings and IHC on sections of all mouse experiments were documented with a Leica DM5000 microscope equipped with a Leica DFC300FX digital camera and the used software was Leica FireCam (Version 1.9.1). Immunofluorescence staining of mouse tissue sections were photographed with the Leica DMI6000 microscope equipped with a Leica DFC350FXR2 camera and the Leica Application Suite X software. Images were processed in Adobe Photoshop CS4 or CC, or FIJI ImageJ version 2.0.0, figures assembled using Adobe Illustrator CS4, CS6 or CC. Xenopus WISH was imaged with a Zeiss SteREO Discovery.V12 or if sections were made with a Zeiss Axioskop 2 mot plus each equipped with an AxioCam HRc in combination with AxioVision 4.7. Fluorescence imaging of Xenopus was performed on a Zeiss AxioObserver with a LSM700 and Zeiss ZEN black software. CBF was documented with a Zeiss Axioskop 2 mot plus equipped with a high-speed Hamamatsu video camera Orca flash 4.0 and Zeiss ZEN blue. CGF analysis was done with a Zeiss Axioskop 2 mot plus combined with a Zeiss AxioCam HSm camera and Zeiss AxioVision 4.7. CBF and CGF was assessed using the ImageJ plugin Particle Tracker56 (link). All trajectories were further analysed using a custom-made program written in RStudio which calculated the velocity of each particle track57 (link).
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