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4 protocols using multi gauge software version 2

1

Quantification of Exon 20 Inclusion Levels

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cDNA was synthesized from total RNA extracted from HEK-293 cells, patient fibroblasts (GM04899), and transgenic mice tissues, as described (29 (link)). The cDNA from human cells or mouse tissues was amplified using either vector-specific (pcDNA3.1) or human-specific primers (Supplementary Table S3), respectively, as described (29 (link)).
To calculate exon 20 inclusion levels, the 32P-labeled radioactive reverse transcription PCR (RT-PCR) amplicons were separated by native PAGE, followed by phosphorimage analysis on a FUJIFILM FLA-5100 instrument (Fuji Medical Systems USA, Inc.). We quantified the band intensities using Multi Gauge software Version 2.3 (FUJIFILM), and normalized the values for the G+C content according to the DNA sequence.
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2

Quantitative Western Blot Analysis of ESC Proteins

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Total proteins from ESCs were homogenized in a cell lysis buffer (Cell Signaling Technology, Danvers, MA, USA) containing a protease inhibitor cocktail (complete mini tablet, Roche, Indianapolis, IN, USA). Protein samples (50 μg) were loaded and electroblotted onto polyvinylidene fluoride membranes (MilliporeSigma, Burlington, MA, USA). The membranes were blocked at room temperature (25 °C) and incubated overnight with primary antibodies raised against proliferating cell nuclear antigen (PCNA), p21-activated kinase 4 (Pak4), protein kinase B (AKT), extracellular-signal-regulated kinase (ERK), and β-actin at 4 °C. After three washes with distilled water, the membranes were incubated with a horseradish peroxidase-conjugated anti-immunoglobulin G secondary antibody (Invitrogen, Carlsbad, CA, USA) and visualized using an enhanced chemiluminescent substrate (Life Technologies, Carlsbad, CA, USA). Densitometric quantification of the protein bands was analyzed using the Multi Gauge Software (Version 2.3, Fujifilm, Tokyo, Japan).
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Immunoblotting Analysis of Apoptosis Signaling

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Cells were collected and lysed for protein extraction and the followed immunoblotting as previously described [12 (link)]. Phosphorylation and level of protein was demonstrated by using antibodies against human cellular proteins, including caspase-3, caspase-9, caspase-8, cytochrome c, Poly (ADP-ribose) polymerase (PARP), Bcl-2, Bak, Bax, Fas, FasL, phosphorylated P38 (p-P38), total P38, phosphorylated JNK (p-JNK), total JNK, phosphorylated glycogen synthase kinase 3beta (GSK3β) (Ser9), cellular FLICE inhibitory protein (c-FLIP), and α-tubulin (Cell signaling, Beverly, MA). Detection of antigen–antibody complex was performed by using ECL reagent (Millipore, Bedford, MA, USA) and luminescence image system (LAS-4000 mini; Fujifilm, Tokyo, Japan). Semi-quantitation of reacted signals was determined using Multi Gauge software version 2.2 (FujiFilm, Tokyo, Japan). Three independent analyses were performed for statistical analysis.
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4

Immunoblotting of Microsomal Proteins

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Microsomal proteins (12–50 μg) were resolved by electrophoresis on a 7.5% (for UGT) or 10% (for P450) (w/v) polyacrylamide gel (sodium dodecyl sulfate-polyacrylamide gel electrophoresis, 14 × 20 × 0.15 cm3) and electrotransferred from the slab gel to a nitrocellulose membrane, as described previously [4 (link)]. Immunoblot analysis of microsomal Cyp1a1/2 was performed using Mab 1-7-1 [15 (link)]. Immunoblot analyses of microsomal Cyp2b9/10 and CPR were performed using rabbit polyclonal antibodies against rat CYP2B1 and CPR, respectively. Cytosolic proteins (20 μg) were resolved by electrophoresis on a 12% (w/v) polyacrylamide gel. Immunoreactive proteins were detected using a goat antirabbit IgG conjugated with horseradish peroxidase and visualized using an enhanced chemiluminescence detection kit (PerkinElmer Life and Analytical Sciences, Inc., Shelton, CA, USA). Relative band intensity was analyzed with the Multi Gauge software (version 2.2; Fujifilm Co., Tokyo, Japan).
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