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6 protocols using six well tissue culture plates

1

Electroporation of KRas Constructs

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Electroporation of full-length KRas constructs (KRasWT, KRasG13C, KRasG13C-edaGDP, KRasG13C:acetyledaGDP and KRasG13C-edaGppCp) was performed based on the protocol described by Alex et al., 2019 (link) using the Neon Transfection System Kit (Thermo Fisher). For electroporation, 3 million cells per experiment were harvested by trypsinization, washed with PBS, and resuspended in 85 µL of the electroporation buffer R (Thermo Fisher). Increasing amounts of recombinant protein samples for each construct (0, 50, 100, 200 and 300 µg) were diluted 1:1 in buffer R followed by the addition of 30 µL of this protein master mix to the cell suspension. This cellular slurry was loaded into a 100 mL Neon Pipette Tip (Thermo Fisher) and electroporated with 2x35 ms pulses at 1000 V. After electroporation, the cells were washed twice with PBS (15 mL) to remove non-internalized extracellular protein and the cell pellet was resuspended in 2 mL complete growth media. Cells were transferred into six-well tissue culture plates (Sarstedt) and incubated for 24 hr at 37 °C and 5% CO2 in a humidified incubator for recovery before being processed for western blotting analysis.
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2

Adipogenesis Induction in Mouse Embryonic Fibroblasts

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MEFs were seeded at 1 × 105 cells per well in six-well tissue culture plates (Sarstedt). At confluency, cells were induced into adipogenesis by incubating with differentiation media (DM) containing DMEM and 10% FBS supplemented with 0.5 mM 3-isobutyl-1-methylxanthine (Sigma-Aldrich), insulin (10 μg/ml; Sigma-Aldrich), 1 μM dexamethasone (Sigma-Aldrich), and 10 μM rosiglitazone (Sigma-Aldrich). Cells were treated for 3 days (D3), followed by replacement of DM with DMEM, and 10% FBS, and incubation for another 6 days (D9). MEFs were washed with 1 ml of 1× PBS (Sigma-Aldrich) once before fixing for 5 min with 4% paraformaldehyde in PBS at room temperature. After fixation, MEFs were washed three times with PBS and once with 60% isopropanol and were completely air-dried. Triglyceride accumulation was unveiled by staining with Oil Red O (ORO; Sigma-Aldrich) for 10 min at room temperature. Excess stain residue was removed with four ddH2O washes. Approximately 1 ml of PBS was then added for microscopic visualization. Images were processed using a 4× objective lens, with transmitted bright-field light. For quantification, ORO stain particles were eluted with 100% isopropanol and analyzed using Thermo Fisher Scientific Varioskan Flash for spectrophotometry readings at 514 nm. Images were taken using light microscopy (×4 magnification, Leica).
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3

Chorioallantoic Membrane (CAM) Assay in Quail

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The chorioallantoic membrane (CAM) of fertilized Japanese quail (Coturnix japonica) eggs (a breeding colony of IABG SAS) was used as a pre-clinical model system. The eggs were incubated in a forced draught incubator (MIDI BIOS, Sedlcany, Czech Republic) at 37.5 °C and 50–60% relative humidity. The ex ovo cultures were prepared as follows: The surface of the eggs was disinfected with a 70% ethanolic solution at embryonic day 3 (ED3) in a sterile laminar flow hood. Subsequently, the eggs were opened with scissors, and the embryos were transferred into the six-well tissue culture plates (Sarstedt, Germany) and kept in a 37 °C humidified incubator (Memmert, Buchenbach, Germany) until ED11.
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4

Differentiation of iPSCs into Hematopoietic Cells

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Undifferentiated iPSCs were maintained on Matrigel® (Corning) with StemMACS iPS Brew XF (Miltenyi Biotec). For EB formation, colonies (>23 passages) were detached with collagenase IV. Cell clumps were seeded on low-binding suspension plates (Nunclon Sphera; Thermo Fisher Scientific) and cultivated for 5 days in human embryonic stem cell (hESC) medium without bFGF [17 (link)]. Thereafter, 10–15 spherical EBs were transferred to six-well tissue culture plates (Sarstedt) with STEMdiff APEL2 Medium (STEMCELL Technologies), 5% PFHM-II Protein-Free Hybridoma Medium (Thermo Fisher Scientific), 5 ng/mL interleukin 3 (IL-3; PeproTech), 100 ng/mL stem cell factor (SCF; PeproTech), and 3 U/mL erythropoietin (EPO; Erypo; Janssen Biologics B.V.). The medium was changed weekly (Fig. 1).
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5

Immunofluorescence Analysis of RGFP966 Treatment

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The 1.2 × 105 SVG-A cells were seeded in six-well tissue culture plates (Sarstedt) containing sterile glass coverslips (Fisher) and 2 mL of complete Dulbecco's modified Eagle media and incubated overnight at 37 °C and 5% CO2. After ∼16 h, cells were treated with either DMSO or RGFP966 at a final concentration of 10 μM for 24 h. Cells were briefly washed with warm 1× PBS, then fixed with warm 4% vol/vol paraformaldehyde (Sigma) for 10 min at 37 °C. After fixation, coverslips were washed again with 1× PBS and air dried. A total of 10 μL of SlowFade Gold plus DAPI (Thermo Fisher) was used to mount each coverslip. Z-stack images were acquired using an Olympus Delta Vision microscope at either 100× or 60× magnification with a 0.5-μm limit per image. Images were processed using Fiji ImageJ software.
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6

Trout Hepatocyte Isolation and Stress Response

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Trout hepatocytes were isolated as described previously using in situ collagenase perfusion (Boone & Vijayan 2002) (link). Hepatocyte viability was >95%. Cells were suspended in L15 (Gibco, Life Technology) medium and plated in six-well tissue culture plates (Sarstedt, Inc., Newton, MA, USA) at a density of 1.5 million cells/well (0.75 million cells/mL). Cells were allowed to recover for at least an hour, and then treated with either a vehicle (0.01% ethanol) or cortisol (100 and 1000 ng/mL). Treated cells were maintained at 11°C for 24 h at which time the L15 media was replaced and cells were again treated as previously. The cells either remained at 11°C or were subjected to a 1 h heat shock (+15°C above ambient) and allowed to recover for 24 h. This experimental protocol was previously used in Boone & Vijayan (2002) (link) to assess the effect of cortisol on Hsp70 expression in trout hepatocytes. Cells were collected and media was removed and fractionated as described below to obtain exosomes. Experiments were repeated with hepatocytes from five independent fish.
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