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24 protocols using aim software

1

3D Confocal Imaging and Analysis

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3D image z-stacks were collected on an inverted laser scanning confocal microscope (LSM5 Pascal, Carl Zeiss, Thornwood, NY, USA) using either a Plan-Neofluar 10×/0.3, Plan-Neofluar 40×/0.75 or C-Apochromat 40×/1.2 W objective (Carl Zeiss, Thornwood, NY, USA). The EGFP reporter was excited with the 488 nm laser line using the FITC filter and all other imaging parameters were as described in Kasemeier-Kulesa et al. (2005) (link). Images were collected, processed and analyzed using AIM software (Carl Zeiss, Thornwood, NY, USA). Statistical analysis was performed using the Student's t-test.
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2

Quantifying Protein Translocation Dynamics

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Two regions of 4 μm2 each were selected in each cell as follows: one in the cytoplasm, and one in the cell membrane. Mean intensities in the selected regions were calculated using the Zeiss AIM software at the different time points; the ratio of the intensities for membrane/cytoplasm was then calculated and normalized to the time 0 values. The increase in the membrane/cytoplasm ratio indicates translocation.
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3

Pulmonary Airway-Breast Cancer Cell Interactions

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Pulmonary airway cells in MCF‐7 medium were diluted to 1000, 500, 250, 100, or 50 SAEC per well of a 96‐well tissue culture plate in duplicate wells. SAEC were given 24 h at 37°C to attach. Following incubation, MCF‐7 medium in each well was removed and replaced with 2 × 103 MCF‐7 cells in 0.1 mL of medium. After 24 h at 37°C, cells were stained with 2% crystal violet and scattering was measured as described above.
For visualization of MCF‐7 interactions with pulmonary epithelium, SAEC were labeled with 1 μg/μL SNARF®‐1 carboxylic acid, acetate succinimidyl ester (Invitrogen, Thermo‐Fisher Scientific, Waltham, MA) for one hour, followed by transfer of the cells in SAGM onto glass chamber slides at approximately 50% confluency. After overnight incubation to allow the cells to adhere to the glass, GFP‐labeled MCF‐7 cells were added in 50% SAGM and MCF‐7 medium. The use of the vital dye and GFP allowed imaging of living cells. After another overnight incubation, cells were visualized and photographed with a Zeiss LSM510 fluorescent microscope, with AIM software (Carl Zeiss MicroImaging, Inc., Jena, Germany). Excitation and transmission settings for GFP were 488 and 505 nm, respectively, and settings for SNARF®‐1 carboxylic acid, acetate succinimidyl ester were 488 and 560 nm, respectively.
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4

Confocal Imaging of GapYFP in Cells

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Images were collected on an inverted laser scanning confocal microscope (LSM5 Pascal, Carl Zeiss, Thornwood, NY) using either a Plan-Neofluar 10X/0.3, Plan-Neofluar 40X/0.75 or C-Apochromat 40X/1.2W objective (Carl Zeiss, Thornwood, NY). The GapYFP was excited with the 488 nm laser line using the FITC filter and all other imaging parameters were as described in (36 ). Images were collected, processed and analyzed using AIM software (Carl Zeiss, Thornwood, NY).
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5

Detecting circASAP1 via FISH

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A cyanine 3–labeled specific probe for circASAP1 was designed and synthesized by RiboBio, and signals were detected with a fluorescence in situ hybridization (FISH) kit (RiboBio) according to the manufacturer’s instructions. Confocal images were captured using Zeiss AIM software and a Zeiss LSM 700 confocal microscope system.
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6

Embryo Explant Time-lapse Microscopy

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Three-dimensional image z-stacks were collected on an inverted laser scanning confocal microscope (LSM5 Pascal, Carl Zeiss) using either a Plan-Neofluar 10 × /0.3, Plan-Neofluar 40 × /0.75 or C-Apochromat 40 × /1.2 W objective (Carl Zeiss). For embryo explant time-lapse microscopy, the microscope was surrounded with a snug-fitting cardboard box and thermal insulation (Reflectix, BP24025, Markelville, IN) with a table-top incubator (Lyon Electric, 950-107, Chula Vista, CA) fed into one side of the box (Kulesa and Kasemeier-Kulesa, 2007). The EGFP plasmid was excited with the 488-nm laser line using the FITC filter. Time-lapse images were recorded every 5 min for an average of 12–16 h. Images were collected, processed and analysed using AIM software (Carl Zeiss) and ImageJ v1.30 software (developed at NIH and available on the Internet at http://rsb.info.nih.gov/ij/). Statistical analysis was performed using the Student's t-test.
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7

GFP-LC3 Transfection and Confocal Imaging

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H9C2 cardiac myoblast cells were transfected with a GFP-LC3 construct as shown previously [16 (link)] and treated 24 h after transfection. Images were sequentially acquired with Zeiss AIM software on a Zeiss LSM 510 confocal system and quantified blindly using Zen 2.3 sp1 software.
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8

Time-lapse Confocal Imaging of Embryo Explants

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3D image z-stacks were collected on an inverted laser scanning confocal microscope (LSM5 Pascal, Carl Zeiss) using either a Plan-Neofluar 10X/0.3, Plan-Neofluar 40X/0.75 or C-Apochromat 40X/1.2W objective (Carl Zeiss). For embryo explant time-lapse microscopy, the microscope was surrounded with a snug fitting cardboard box and thermal insulation (Reflectix, BP24025, Markelville, IN) with a table top incubator (Lyon Electric, 950-107, Chula Vista, CA) fed into one side of the box (Kulesa and Kasemeier-Kulesa, 2007). The EGFP plasmid was excited with the 488 nm laser line using the FITC filter. Time-lapse images were recorded every 5 minutes for an average of 12–16 hours. Images were collected, processed and analyzed using AIM software (Carl Zeiss) and ImageJ v1.30 software (developed at NIH and available on the Internet at http://rsb.info.nih.gov/ij/). Statistical analysis was performed using the Student’s t-test.
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9

Detecting circGLIS3 via FISH-IF

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Cy3-labeled probes specific for circGLIS3 were designed and synthesized by GenePharma, and the signals were detected by a FISH Kit (GenePharma) according to the manufacturer’s instructions. FISH + IF was performed with a FISH in situ hybridization immunofluorescence counterstaining kit (C009, Gefan, Shanghai). Confocal images were captured using Zeiss AIM software and a Zeiss LSM 880 with Airyscan confocal microscope system (Carl Zeiss Jena, Oberkochen, Germany).
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10

Confocal Microscopy for Fluorescence Quantification

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Confocal microscopy was performed on a Zeiss LSM 510 laser scanning confocal microscope (Oberkochen, Germany) as described previously (Wu et al., 2010a). Fluorescence intensities and nuclear areas were measured from the acquired image files using Zeiss AIM software. Identical microscope and detector settings were used whenever fluorescence measurements were compared (Figures 2 and 4).
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