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8 protocols using hc pl apo 63x 1.40 oil cs2

1

Colocalization analysis of NPC1 and LAMP2

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For confocal microscopic co-localization studies, the cells were seeded onto BD Falcon Cultures Slides (Becton Dickinson). Next day the fibroblasts were washed, fixed with ice-cold methanol, blocked with 5% FBS in PBS and co-labelled rabbit monoclonal anti-NPC1 (1:100, ab134113, Abcam) and mouse monoclonal anti-LAMP2 (1:500, H4B4, Iowa Hybridoma Bank) antibodies at 4 °C overnight. Secondary antibodies were donkey anti-IgG anti-mouse alexafluor555 or anti-rabbit alexafluor488 conjugates (Pierce) diluted 1:1000. Leica SP8X laser scanning confocal system equipped with 470 nm–670 nm 80 MHz pulse continuum White Light Laser 2 and HC PL APO 63x/1.40 OIL CS2 (W.D. 0.14 mm) objective was used to image the samples. Image acquisition conditions were: excitation at 496 nm or 553 nm, one voxel 42.2 × 42.2 × 130 nm, 7 Z-steps (fulfilling Nyquist sampling theorem), Hybrid detectors at 503–553 nm or 566–650 nm. Acquired confocal images were deconvolved using theoretical point spread function in Huygens Professional software (Scientific Volume Imaging - SVI, Hilversum, The Netherlands). Overlay colocalization maps and Object Pearson’s coefficients were computed using Huscript (SVI), the grayscale maps were converted to colour coding look-up table (LUT) in Fiji/ImageJ software (NIH, Bethesda).
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2

High-resolution Cardiac Imaging Techniques

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Bright field and fluorescent whole mount images of full hearts were captured on a stereo-microscope (Leica, MZ10F), equipped with a color/fluorescence camera (Leica, DFC 450c). Scale bars were added and images processed using the LAS software v4.8. Immunofluorescence images were acquired using either an upright fluorescent microscope (Zeiss, Axio Imager.Z2), equipped with X-Cite 120LED excitation source (Excelitas Technologies), using a 20x objective (Zeiss, Plan-Apochromat” 20x/0.8), and the ZEN2 software (Zeiss, blue edition) for acquisition, or using confocal imaging (SP8-AOBS, Leica) with 40x (Leica, HC PL APO 40x/1.30 Oil CS2, FWD = 0.24 mm) or 63x (Leica, HC PL APO 63x/1.40 Oil CS2, FWD = 0.14) objectives, using very-high sensitivity HyD detectors for the emission of 488, 561 and 633 lasers, and the LASX software. At least 3 independent rounds of stainings were done and images were acquired keeping same setting across all time-points used in the comparison analysis. All quantification and image processing were performed using Fiji version 1.0 (Schindelin et al., 2012 (link)). Z stacks with 0.5 μm step size were converted by Z-projection of the average intensity for each channel. Individual channels were merged and pseudo-colored.
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3

Microscopic imaging methods for histology and immunofluorescence

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The brightfield images for histological stains were captured using the Olympus BX60 microscope with a digital camera (Olympus, DP70) and CellSens Entry Software (Olympus Corporation 2011; Version 1.5) with a 10X or 20X objective (Olympus UPIanFI 4/0.13). White balance was performed before the images were captured. The immunofluorescence images were captured on the Olympus BX60 wide-field microscope with Olympus DP70 camera or Leica STELLARIS 5 confocal microscope with a 63X oil immersion objective (Leica; HC PL APO 63x/1.40 OIL CS2) using Leica Application Suite X software (Leica; 4.1.1.232273). The exposure was held constant between controls and the experimental groups. Wholemount skeletal preparations were imaged with Leica MZ16F stereoscope and Leica DFC490 camera with Leica software. Images were processed using Adobe Photoshop and Fiji/ImageJ and page set in Adobe InDesign.
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4

Microscopy Imaging Protocol for Cell Studies

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All images were acquired at room temperature. Images in Fig. 3 a, b, j, k; Extended Data Fig. 2b,f; Extended Data Fig. 4d,g; Extended Data Fig. 6; Extended Data Fig. 6; and Extended Data Fig. 9f,e were acquired in an inverted confocal microscope (FluoView FV1000; Olympus), equipped with a digital camera (DP73; Olympus) and a 20x objective (UPLSAPO 20X/0.75 FWD= 0.6 mm, Olympus). Camera, filter wheels, and shutters were controlled by FluoView Software (Olympus). Confocal images in Extended Data Fig. 2k and Extended Data Fig. 3 were acquired using an upright confocal integrated microscope system (SP8vis, Leica) with a 63x objective (HC PL APO 63x/1.40 Oil CS2, FWD= 0.14 mm, Leica).
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5

Quantitative Immunofluorescence Imaging Analysis

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Immunofluorescence and confocal microscope observation were performed, as previously described [6 (link)]. Images were acquired using a TCS SP8 confocal laser scanning fluorescence microscope (Leica, Wetzlar, Germany) equipped with an objective lens (HC PL APO 63x/1.40 OIL CS2, Leica). The number of fluorescent punctae was determined using ImageJ based on the size threshold specified in each legend. For the analysis of green fluorescent protein (GFP)-TFEB, the fluorescence intensities of certain areas in cytoplasmic and nuclear regions were measured using ImageJ.
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6

Imaging Mitochondrial and Protein Localization

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Cells were seeded on coverslips. After treatment, the cells were fixed with 4% paraformaldehyde for 30 min at room temperature, washed with Tris-phosphate buffer and incubated overnight at room temperature with the following antibodies Anti-GPX4 (1:100), ani-3F3-FMA (1:100) and anti-Drp1 (1:100) or Anti-vimentin (1:100) overnight. For mitochondrial staining, mitotracker red CMXRos (100 nM 20 min, before fixation) was used. The next day, the cells were washed 3 times with Tris-phosphate buffer and incubated with the respective secondary antibodies (The Jackson Laboratory) for 2 h. Hoechst 33342 (1:1000) was used for nuclear staining. The images were acquired in the Leica SP8 microscope in confocal mode with HC PL APO 63x/1.40 OIL CS2 oil immersion objective and post-processed with the Lightning super resolution module. The images were exported in .lif format and processed in Imaris v 9.1 software (Bitplane Inc) for 3D reconstruction and mitochondrial volume analysis.
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7

Microscopy Imaging Protocol for Cell Studies

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All images were acquired at room temperature. Images in Fig. 3 a, b, j, k; Extended Data Fig. 2b,f; Extended Data Fig. 4d,g; Extended Data Fig. 6; Extended Data Fig. 6; and Extended Data Fig. 9f,e were acquired in an inverted confocal microscope (FluoView FV1000; Olympus), equipped with a digital camera (DP73; Olympus) and a 20x objective (UPLSAPO 20X/0.75 FWD= 0.6 mm, Olympus). Camera, filter wheels, and shutters were controlled by FluoView Software (Olympus). Confocal images in Extended Data Fig. 2k and Extended Data Fig. 3 were acquired using an upright confocal integrated microscope system (SP8vis, Leica) with a 63x objective (HC PL APO 63x/1.40 Oil CS2, FWD= 0.14 mm, Leica).
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8

Fluorescence Imaging of Redox State and Apoptosis

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Ratio-metric imaging of Grx1-rGFP was performed on an inverted microscope (DMI 6000; Leica) equipped with hybrid photon counting detectors (HyD; Leica). The sample was excited sequentially frame by frame with 408 nm and 488 nm with the detection set to 500-535 nm. Fluorescence was collected through a 63x 1.40 NA oil immersion objective (HC PL APO 63x/1.40 Oil CS2; Leica). Images were captured using the LAS X software (Leica). All imaging was performed at 37˚C in pre-warmed Leibovitz medium for maximum 90 min per sample.
For confocal microscopy of fixed BrU samples the imaging was performed using a Leica TCS SP8 inverted microscope equipped with 405-, 488-, 552-and 638-nm lasers and a Plan-Apochromat oil objective (×63, NA 1.4). The Lightning mode (Leica) to generate deconvolved images. Microscope acquisitions were controlled by LAS X (v. 3.5.2) software from Leica.
CLEM and Caspase 3/7 samples were imaged on a Zeiss LSM 700 inverted confocal microscope with equipped with a Plan-Apochromat oil objective (×63, NA 1.40) and 488-nm and 555-nm solid-state lasers and three photomultipliers. Acquisitions were controlled by the Zeiss Zen (v. 6.0.0) software.
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