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92 protocols using image lab software 5

1

Protein Extraction and Analysis Protocol

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Cells were washed with ice-cold PBS and lysed on ice for 30 min with cell lysis buffer containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, supplemented freshly with a protease and phosphatase inhibitor cocktail (5872, Cell Signaling Technology), 10nM Calyculin A (Cell Signaling Technology, 9902) and 1 mM DTT (ThermoFisher, R0861). Lysates were subjected to centrifugation at 12,000g for 10 min at 4°C and protein concentrations were determined usin g the Bradford assay (Bio-Rad, 5000006). Protein lysates were boiled for 10 min and subjected to SDS-PAGE electrophoresis. Densitometry was calculated using the Image Lab Software 5.2.1 (Bio-Rad).
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2

Subcellular Fractionation and Analysis

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Fibroblast cells grown on a 100‐mm dish were harvested with 0.05% trypsin‐EDTA when they reached 70% confluence and rinsed with ice‐cold PBS twice. Nuclei were separated from cytoplasm following the manual of NE‐PER Nuclear and Cytoplasmic Extraction Reagents (#78835; Thermo Scientific). After centrifuging, the cytoplasm supernatant was removed. The pellets containing nuclei were resuspended well in lysis buffer (50 mm Tris–HCl, pH 7.4, 150 mm NaCl, 1% Triton X‐100, 0.1% deoxycholate, complete mini protease inhibitor cocktail tablet) and subjected to slight sonication at 20% amplitude for 30 s. (FB120; Fisher Scientific). The whole nuclei lysate was further centrifuged at 16 000 g for 5 min at cold. The supernatant was saved as the soluble fraction of the nuclei while the pellet was saved as the insoluble fraction of the nuclei. Both fractions of nuclei were prepared for Western blot assay by adding Laemmli sample buffer (Bio‐Rad). A one‐fifth portion of either soluble or insoluble fraction sample was loaded onto 10% SDS–PAGE gel and then proceeded for Western blot analysis. Images were taken with ChemiDoc Touch Imaging System (Bio‐Rad), and band intensity analysis was carried out with Image Lab software 5.2.1 (Bio‐Rad).
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3

P2Y1 Receptor Modulation of Islet Signaling

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Mouse islets were preincubated for 1 h in 1 mmol/L glucose Krebs‐Ringer Bicarbonate (KRB) and subsequently treated for 20 min with P2Y1 agonists, ATP (10 μmol/L) and MRS2365 (100 nmol/L; EC50 0.4 nmol), or 30‐mmol KCl ± P2Y1 antagonist, MRS2500 (1 μmol/L; EC50 0.78 nmol). Following treatment, cells were lysed in buffer containing (in mmol/L): 20 Tris‐HCl (pH = 7.5); 150 NaCl, 1 EDTA, 1 EGTA, 2.5 sodium pyrophosphate, 1 EDTA, 1 b‐glycerophosphate, 25 N‐ethylmaleimide, 1% Triton X‐100, and 1X protease inhibitor cocktail. Protein lysates were separated using sodium dodecyl sulfate‐polyacrylamide gel electrophoresis (SDS‐PAGE), transferred to nitrocellulose membranes, incubated overnight at 4°C with primary antibodies (phospho‐PKD/PKCmu (serine 916) Rabbit A [Cell signalling] and anti‐β‐actin; sc‐4778 [Santa Cruz Biotechnology]), and visualized with horseradish peroxidase‐labeled anti‐rabbit IgG as secondary antibodies (Amersham, Baie d’Urfe, PQ). Images were acquired using a ChemiDoc MP System (Bio‐Rad) and analyzed using the densitometry analysis function in Image Lab Software 5.2.1 (Bio‐Rad) and normalized to actin as a loading control and expressed as a fold increase from baseline.
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4

Western Blot Analysis of MAML3 Protein

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Total proteins were obtained by extraction with a cell lysis buffer containing 0.125 M Tris-HCl, pH 6.8, 4% SDS, 20% glycerol, and quantified by BCA assay (ThermoFisher Scientific, Waltham, MA, USA). Equal amounts of proteins per sample were separated by SDS-PAGE (ThermoFisher Scientific, Waltham, MA, USA) and subsequently blotted to a PVDF membrane (Biorad, Hercules, CA, USA). Membranes were incubated with specific primary antibodies and the corresponding HRP-conjugated secondary antibodies. Immunoreactive proteins were visualized by enhanced chemiluminescence (ECL) system and acquired using a ChemiDoc Touch Gel Imaging System (Biorad, Hercules, CA, USA). Images were analyzed with Image Lab software 5.2.1 (Biorad, Hercules, CA, USA). Antibodies used were anti-MAML3 (cat # PA5-13678, ThermoFisher Scientific, Waltham, MA, USA) and anti- beta I Tubulin [EPR16778] (cat # ab179511, Abcam).
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5

Western Blot Analysis of Protein Expression

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Whole-cell lysates for western blot analysis were prepared using standard radioimmunoprecipitation assay buffer. In brief, 30 μg protein were separated on 10% acrylamide/bis-acrylamide gels before transfer to polyvinylidene difluoride membranes (Bio-Rad, Hercules, CA, USA) using CAPS buffer (10 mM 3-[cyclohexylamino]-1-propane sulfonic acid, pH 11; 10% methanol). The following primary antibodies were diluted in 5% w/v BSA (Sigma) in TBS-T: 1:1000 anti-Bcl-2 (Dako), 1:1000 anti-cleaved caspase 3 (Cell Signaling Technologies, Danvers, MA, USA), 1:30 000 anti-tubulin (Promega, Madison, WI, USA), 1:1000 anti-VEGFA (vascular endothelial growth factor, Abcam) and 1:1000 anti-NMYC (Abcam). Horseradish peroxidase-labeled secondary antibodies were used (Dako) and detection was carried out with Lumi-Light POD-substrate (Roche, Basel, Switzerland). Quantification of band intensities was performed using Image Lab Software 5.2.1 (Bio-Rad) and adapted to the corresponding loading control.
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6

Western Blot Analysis of Intestinal Proteins

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Proteins were extracted from mouse ileum by homogenizing in T-PER Tissue Protein Extraction Reagent (Thermo Fischer, 78510) supplemented with a protease inhibitor cocktail (cOmplete ULTRA Tablets, Sigma-Aldrich; 5892953001) and a phosphatase inhibitor (PhosSTOP, Sigma-Aldrich; 4906845001). 40 μg of total protein was loaded onto 4–20% gradient SDS-PAGE and transferred to a PVDF membrane. Membranes were blocked with 5% nonfat dry milk in PBS with 0.1% Tween-20. For detection with anti-STAT3 antibodies, membranes were blocked with 5% BSA in PBS with 0.1% Tween-20. Membranes were incubated at room temperature for one hour with the following primary antibodies: anti-REG3G antiserum raised against recombinant REG3G (Cash et al., 2006 (link)) and anti-succinate dehydrogenase (Abcam; ab14715), and at 4°C overnight with the following antibodies: anti-STAT3 (Cell Signaling; 4904S), anti-phospho-STAT3 (Tyr705) (Abcam; ab76315), and anti-lipocalin-2 (R&D systems; AF1857). After washing with PBS with 0.1% Tween, membranes were incubated with HRP-conjugated secondary antibodies. Membranes were visualized using a Bio-Rad ChemiDoc Touch system, and band density was quantified using Bio-Rad Image Lab Software 5.2.1.
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7

Insulin Signaling Pathway Analysis

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INS 832/13 cells were grown to 100% confluence in 6-well plates. Cells were treated with wortmannin (100 nM) or equivolume DMSO (0.1%) in KRB at the beginning of the 2.8 mM glucose 2-hr pre-incubation at 37 °C; these compounds were present for the duration of the experiment. Cells were treated with insulin (200 nM) or forskolin (1 μM) for 15 min in 16.7 mM KRB. Cells were then washed once with PBS, and then lysed using a standard RIPA lysis buffer supplemented with phosphodiesterase and protease inhibitor cocktails (Millipore, Etobicoke, ON).
Cell lysates were subjected to SDS-PAGE on Mini-PROTEAN TGX Stain-Free gels (Bio-Rad, Mississauga, ON) transferred to polyvinylidene difluoride membranes (Millipore, Billerica, MA), and probed with primary antibodies: anti-phospho-(Ser/Thr) AKT substrate; #9611, anti-phospho-(Ser/Thr) PKA substrate; #9621, anti-AKT; #9272, anti-PKA C-α; #4782 (Cell Signaling Technology, Beverly, MA) and anti-β-actin; sc-4778 (Santa Cruz Biotechnology). Detection was with peroxidase-conjugated secondary anti-rabbit (NA934V) and anti-mouse antibodies (NA931V) (GE Healthcare), and visualization by chemiluminescence with ECL-Plus (GE Healthcare). Images were acquired using a ChemiDoc MP System (Bio-Rad) and analyzed using Image Lab Software 5.2.1 (Bio-Rad).
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8

Protein Expression Analysis in Cells

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SDS-PAGE and immunoblot were performed as previously described [23 (link)]. The following primary antibodies were used SERCA2 (1:1000, SantaCruz Biotecnology, Dallas, TX, USA, sc-376235), Acetylated-Tubulin (1:1000, Sigma-Aldrich, St. Louis, MO, USA # T7451), Tubulin (1:2000, Abcam, Cambridge, UK, # ab59680), Ryanodine Receptor (C3-33) (1:1000, Abcam # ab2827), CACNA1c (1:500, Abcam # ab81095), NCX-1 (1:250, SantaCruz Biotecnology, Dallas, TX, USA #sc-32881), Phospho-Phospholamban (Ser16) (1:5000, Merck Millipore, Burlington, MA, USA # 07-052), Phospholamban (1:8000, Abcam #ab2865). The band density was evaluated using the Image Lab software 5.2.1 (BioRad, Hercules, CA, USA) and quantifications were normalized either to total protein concentration (Ponceau red staining) or Tubulin.
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9

Frataxin Protein Expression Analysis

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Frozen brain tissues were lysed using cell lysis buffer (Cell Signaling Technology, MA, United States) supplemented with 400 μM PMSF protease inhibitor (Cell Signaling Technology, MA, United States) and incubated on ice for 30 min. Lysates were subjected to centrifugation at 12,000 × g for 30 min at 4°C and protein concentrations were determined by Pierce BCA assay (Thermo Fisher Scientific, MA, United States). A total of 50 μg of protein lysates were boiled for 10 min and subjected to SDS-PAGE electrophoresis using 4–15% precast gels (Bio-Rad). Densitometry was calculated using the Image Lab Software 5.2.1 (Bio-Rad Laboratories, CA, United States). Antibodies used in this study are as follows: anti-Frataxin (1:250) (Abcam Cat# ab113691, RRID:AB_10862125), anti-Tubulin (1:10,000) (Abcam Cat# ab6160, RRID:AB_305328), rabbit anti-Rat HRP (1:5000) (Abcam Cat# ab6734, RRID:AB_955450), and goat anti-Mouse HRP (1:300) (Agilent Cat# P0447, RRID:AB_2617137). Non-relevant gel lanes and unspecific bands were excised by digital treatment using Power Point. Original uncropped images are presented as Supplementary material.
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10

Western Blot Analysis of Protein Samples

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Cells were washed twice with PBS and lysed in 10 mM Tris-HCl (pH 8.0) with 1% SDS buffer heated to 95 °C. Lysates were sonicated for 10 min (Branson SLP), and protein concentration was measured by Pierce BCA assay (Thermo Fisher Scientific). A total of 10–30 µg of lysate was resolved by SDS-PAGE and transferred to PVDF membranes with a Trans Blot Turbo System (Bio-Rad). The membranes were dried at RT, rehydrated in TBS 0.1% Tween, immunostained with primary antibody overnight at 4 °C, washed, incubated with secondary antibody for 1 h at RT, washed and developed with ECL substrate (Bio-Rad). Images were acquired with a ChemiDoc Touch Imaging System (Bio‐Rad) and analyzed with Image Lab software 5.2.1 (Bio‐Rad). At least three independent replicates for an experiment were used. Uncropped membrane scans are provided in Source data.
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