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36 protocols using us4000 ccd camera

1

Baculovirus Reconstitution and COMPASS Complex Imaging

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Baculovirus reconstitution was performed as previously described (Takahashi et al. 2011 (link)). All COMPASS complexes were prepared for EM using the conventional negative-staining protocol (Ohi et al. 2004 (link)) and imaged at room temperature with a Tecnai T12 electron microscope operated at 120 kV using low-dose procedures. Images were recorded at a magnification of 71,138× and a defocus value of ∼1.5 μm on a Gatan US4000 CCD camera. All images were binned (2 × 2 pixels) to obtain a pixel size of 4.16 Å on the specimen level. All particles were manually excised using Boxer (part of the EMAN 1.9 software suite) (Ludtke et al. 1999 (link)).
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2

Cryo-EM Sample Preparation for PikAIII

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Sample quality and homogeneity were evaluated by conventional negative
stain EM52 (link). For cryo-EM, 3
μL of PikAIII preparations under different conditions (described above)
was adsorbed on glow-discharged Quantifoil R2/2 200 mesh grids followed by
blotting and vitrification with a Vitrobot (FEI, Mark IV). All specimens were
imaged on a Tecnai F20 transmission electron microscope (FEI) equipped with a
field emission gun operated at 120kV. Images were recorded at a magnification of
66,964x on a Gatan US4000 CCD camera and defocus values ranging from
−1.5 to −3.5 μm (Extended
Data Fig. 1c
). All images were acquired using low-dose procedures
with an estimated dose of ~20 electrons/Å2.
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3

Tilt-Series Cryo-Electron Tomography

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15-nm Colloidal gold particles (Aurion, The Netherlands) were adsorbed on both sides of the grids (and section) to serve as fiducial markers for the alignment of the tilt-series. Grids were placed into a Model 2040 high-tilt holder (Fischione Instruments, Pittsburgh, USA) or Single Tilt Holder for Ultra Twin (#FP 6596/05, FEI, Eindhoven, The Netherlands) and imaged using a 300 kV Tecnai F30 transmission electron microscope (FEI, Eindhoven, The Netherlands). Digital micrographs and tilt-series were recorded on a US4000 CCD camera (Gatan, USA) with a 1° increment over various tilt ranges at a pixel size of 0.9–1.32 nm. For the reconstruction of tomograms, the IMOD software package (version 4.3.1; (Kremer et al., 1996 (link))) was used. Sub-tomogram averaging was performed as previously described (Al-Amoudi et al., 2007 (link)).
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4

Cryo-EM Imaging of Exosome Morphology

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Cryo-EM was used to determine the shape of exosomes in culture media as described previously. Briefly, 3 μL of prepared exosome suspension was pipetted onto a copper grid with quantifoil support film (QUANTIFOIL, Großlöbichau, Germany). The grid was vitrified to preserve exosomes in their native state and placed in a Gatan 626 specimen holder (Gatan, Pleasanton, CA), within a JEOL 2100 microscope for TEM (JEOL, Osaka, Japan). The samples were imaged at 15,000–30,000 magnification with a 200 kV electron beam from a LaB6 emission source, and images were recorded on a Gatan US4000 CCD camera.
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5

Negative Staining of Bacterial Cells

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Bacterial cells or purified NCs were applied to glow-discharged carbon-coated Cu grids and stained with 2% uranyl acetate. Images were acquired with Digital Micrograph (Gatan Inc.) on a FEI Tecnai T12 electron microscope (120 kV) equipped with a US4000 CCD camera (Gatan Inc.).
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6

Transmission Electron Microscopy of DNA Origami

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3 μl of sample was applied to a freshly glow-discharged carbon-coated grid. Sample was incubated for 1 min at room temperature; excess sample was removed by blotting off with the filter paper and stained with 0.75% (w/v) of uranyl formate (UF). Grids were imaged using Tecnai T12 transmission electron microscope operated at a voltage of 120 kV. Images were recorded at a magnification of 50,000X and a defocus value of-1.0 μm on a Gatan US4000 CCD camera. All images were binned over 2 × 2 pixels to obtain a pixel size of 4.16 Å on specimen level.
For DNA origami, 1,421 particles were picked manually from the binned micrographs by using boxer of the EMAN 1.9 software suite [11 (link)]. Particles were then subjected to reference-free 2D classification using EMAN 1.9 image processing suite [11 (link)] and classified into 10 classes.
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7

TEM Tomography of Biological Samples

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250 nm thick sections were collected on Formvar-coated slot grids for TEM tomography. Next, 15 nm colloidal gold particles (Sigma-Aldrich, Saint-Louis, MO, USA) were applied on the supporting film to serve as fiducial markers for tomogram alignment. The tomographic data collection was performed using Tecnai F30 transmission electron microscope (Thermo Fisher Scientific, Waltham, MA, USA) equipped with a US4000 CCD camera (Gatan, Pleasanton, CA, USA). Regions of interests (ROIs) were pre-exposed at 3000 e/Å2 to minimize the section drift and warping [56 (link),57 (link)]. The dual-axis tomographic acquisition was done at 12,000× magnification (1.96 nm/pixel, camera binning 2) using Serial EM software (University of Colorado [55 (link)]) running a continuous tilt-scheme from −60° to +60° and a constant angular increment of 1.5°. Tilt series alignment and tomogram reconstruction were performed using ETOMO program of IMOD software package [58 (link)].
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8

Vitrification and Imaging of Exosomes

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To determine the shape of exosomes in maternal plasma, 3 μL of prepared exosome suspension was pipetted onto a copper grid with quantifoil support film (QUANTIFOIL, Germany). The support film was patterned with a regular array of circular holes. When the excess liquid was blotted away from the grid, a 60–120 nm-thick film of sample suspension remained in these holes. The grid was then plunged into a small crucible of liquid ethane that was cooled to its melting point by liquid nitrogen. In the liquid ethane, the sample suspension was cooled at over 10,000 degrees/s, solidifying the water in an amorphous state. This “vitrification” process preserves the exosomes in their native state without distorting their geometry by crystallization and density change41 (link). The vitrified sample on the grid was then placed in a Gatan 626 specimen holder (Gatan, Pleasanton, CA), which was placed in a JEOL 2100 TEM (JEOL, Osaka, Japan). The samples were imaged with a 200 kV electron beam from a LaB6 emission source, and images were recorded on a Gatan US4000 CCD camera. Images were captured at 15,000–30,000 magnification.
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9

Electron Microscopy Negative Staining Protocol

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Samples were prepared for electron microscopy using the conventional negative staining protocol (Peisley and Skiniotis, 2015 (link)). The negative stained samples were imaged at room temperature with a Tecnai T12 electron microscope operated at 120 kV using low-dose procedures. Images were recorded at a magnification of ×71,138 and a defocus value of ~1.4 μm on a Gatan US4000 CCD camera. All images were binned (2 × 2 pixels) to obtain a pixel size of 4.16 Å on the specimen level. Particles were excised using Boxer (part of the EMAN 2.1 software suite) (Ludtke et al., 1999 (link)). Two-dimensional reference-free alignment and classification of particle projections was performed using Stable Alignment and Classification (ISAC) (Yang et al., 2012 (link)). 13865 projections of GRK5-DC were subjected to ISAC, producing 274 classes accounting for 9352 particle projections. Similarly, 15292 projections of GRK5 ionic lock mutant were subjected to ISAC, producing 341 classes accounting for 13521 particle projections. Representative class averages are shown in Figure S3.
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10

Electron Microscopy Imaging of EntF

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EntF, purified as described above, was prepared for electron microscopy using the conventional negative staining protocol38 (link), and imaged at room temperature with a Tecnai T12 electron microscope operated at 120 kV using low-dose procedures. Images were recorded at a magnification of 71,138x and a defocus value of ~1.5μm on a Gatan US4000 CCD camera. All images were binned (2 × 2 pixels) to obtain a pixel size of 4.16 Å on the specimen level. Particles were manually excised using e2boxer [part of the EMAN 2 software suite]39 (link). 2D reference-free alignment and classification of particle projections was performed using ISAC40 (link). 17,431 projections of EntF were subjected to ISAC producing 133 classes consistent over two-way matching and accounting for 5,344 particle projections (Extended Data Fig. 8B).
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