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4 protocols using application suite imaging software

1

Paleontological Specimen Imaging and Archiving

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Specimens investigated for the study are housed at the Paläontologisches Museum Nierstein, Germany (SSN), the Museum für Naturkunde Berlin, Germany (MB), Institut für Geowissenschaften Johannes Gutenberg Universität Mainz (N), and the Staatliches Museum für Naturkunde Stuttgart, Germany (SMNS) under the collections numbers indicated. Specimens were investigated and photographed using a Leica MZ12 stereomicroscope and Leica DFC 420 camera set-up in combination with the Leica Application Suite Imaging Software. A thin layer of 70% ethanol was applied to fossils prior to photography to enhance visibility of bony elements.
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2

Validated Antibody-based Assays for Protein Analysis

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The following antibodies were used for immuno-analyses: anti-RND3 (Cocalico Biologicals), anti-Snail1 (Santa Cruz, sc-28199), anti-E-cadherin (CST, 3195S), anti-claudin (Bioword, BS1063), anti-c-myc (9E10, Santa Cruz, sc-40), and anti-HA (Santa Cruz, SC-7392, SC-805). Even protein loading in the immunoblotting analysis was verified by the intensity of the GAPDH blot (Santa Cruz, sc-20357). The immunostaining, immunoblotting, and immunoprecipitation were conducted as described previously [8 , 20 (link)]. The immunoblotting densitometry was quantified by the Gel Logic 6000 PRO Imaging System (Carestream Health, Inc. Rochester, NY, USA), and the immunofluorescent and immunohistochemical image quantifications were conducted by Leica Application Suite Imaging Software (Version 4.0, Biberach, Germany).
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3

Imaging Fixed Whole Cells and Cytoskeletons

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Phase-contrast, fluorescence, and IF images of fixed whole cells and cytoskeletons were acquired at room temperature using a microscope (DM5500B; Leica) with either a 40×, NA 1.25 HCX Plan Apochromat oil immersion objective (Leica) or a 100×, NA 1.4 HCX Plan Apochromat oil immersion objective (Leica), and a digital camera (Orca-ER; Hamamatsu Photonics) or a scientific complementary metal–oxide semiconductor camera (Neo 5.5; Andor Technology). The images were acquired in Application Suite Imaging Software (Leica). Morphometric measurements and quantification of IF signals were performed using ImageJ software (National Institutes of Health; Schneider et al., 2012 (link)).
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4

Antibody Validation and Quantification

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The following antibodies were used for immunoanalyses: anti-RND3 (Cocalico Biologicals, Reamstown, PA, USA), anti-NOTCH1 (Abcam, Boston, MA, USA ab27526), anti-HES1 (Abcam, ab71559), anti-pHis3 (Santa Cruz, Dallas, TX, USA sc-8656), anti-c-Myc (9E10, Santa Cruz, sc-40), anti-Flag (sigma, St. Louis, MO, USA F7425), anti-Histone H3 (Rabbit, abcam, ab1791), anti-GFP (Rabbit, Santa Cruz, sc-5385), anti-LaminB (Rabbit, Santa Cruz, sc-20682), APC-conjugated anti-BrdU antibody (BD, 552598). The specificity and sensitivity of the anti-RND3 antibody was validated in our previous study 14 (link). Even protein loading for immunoblotting analysis was verified by the intensity of the GAPDH blot (Santa Cruz, sc-20357). The immunoblotting densitometry was quantified by the Gel Logic 6000 PRO Imaging System (Carestream Health, Inc. Rochester, NY, USA), and the immunofluorescent and immunohistochemical image quantifications were conducted by Leica Application Suite Imaging Software (Version 4.0, Biberach, Germany).
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