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77 protocols using mini protean gel

1

Protein Quantification and Western Blot Analysis

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The protein concentration of samples was determined using the DC (detergent compatible) protein assay (Bio-Rad, #5000112). Samples were prepared in a total volume of 20 μL at 15 μg/μL in Laemmli loading buffer. Samples were run on 7.5% Mini-PROTEAN gels for cytoplasmic proteins and 12.5% Mini-PROTEAN gels for histones (Bio-Rad, #456025). Primary antibodies used: Rabbit anti-mH2A2 (Invitrogen, PA5-57437) at 1:250 dilution, mouse monoclonal anti-β-ACTIN (Sigma-Aldrich, A5441, lot # 127M4866V, clone AC-15) at 1:1000, rabbit anti-lamin A/C (Abcam, ab108595) at 1:1000, rabbit anti-OLIG2 (Millipore, AB9610) at 1:500, mouse anti-GFAP (Millipore, MAB360), rabbit anti-H3 (Cell Signaling Technology, #9715) at 1:500, rabbit anti-PDFGRA (Cell Signaling Technology, #3164) at 1:500, rabbit polyclonal anti-macroH2A1 (Millipore, ABE215) at 1:500. Secondary antibodies used: Goat anti-rabbit IgG H&L (HRP) (Abcam, #6721, lot # GR3192725-6) at 1:20,000 dilution, goat anti-mouse IgG H&L (HRP) (Abcam, #6789) at 1:2000 dilution.
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2

Immunoblotting Analysis of Neuronal Proteins

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Cell and brain lysates were resolved using SDS polyacrylamide gel electrophoresis (PAGE) on 4–20% Mini-Protean Gel (BioRad), followed by immunoblotting for NMNAT2 (1:100 anti-NMNAT2 (B-10) mouse monoclonal IgG1, sc-515206), STMN1 (1:1000 Anti-Stathmin 1 Rabbit Monoclonal Antibody, ab52630), STMN2 (1:1000 anti-SCG10, Shin et al., 2012 (link)), STMN3 (1:2000 Anti-STMN3 Rabbit Polyclonal Antibody, 11311-1-AP), STMN4 (1:1000 Anti-STMN4 Rabbit Polyclonal, 12027-1-AP), HSP90 (1:1000 Anti-HSP90 Rabbit IgG, C45G5), and TUJ1(anti-B3 tubulin, 1:10000 Sigma-Aldrich, T2200), and visualized using standard chemiluminescence. Band intensity was quantified using ImageJ. Blots were normalized to their respective loading controls and then normalized to the control sample.
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3

Western Blot Analysis of Circadian Clock Proteins

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Liver and brain tissue (5–10 mg) were collected at ZT16 and placed in 250–500 μL ice-cold RIPA lysis buffer (Thermo Fisher Scientific RIPA Lysis and Extraction Buffer, cOmplete Mini Protease Inhibitor Cocktail, 100 μM PMSF). Protein concentrations were determined via Bicinchoninic Acid Protein Assay (Thermo Fisher Scientific), and 30 μg protein was separated on 4%–20% Mini-PROTEAN gel (Bio-Rad) and transferred to a PVDF membrane (Millipore). Membranes were blocked with 5% nonfat milk in Tris-buffered saline (TBS) (20 mM Tris pH7.6, 150 mM NaCl) and incubated overnight at 4°C in 5% nonfat milk in TBS-Tween (TBS-T) (20 mM Tris pH7.6, 150 mM NaCl, 0.1% Tween-20) containing primary antibodies: anti-BMAL1 (1:1,000; Abcam, ab93806) or anti-GAPDH (1:100,000; Invitrogen, AM4300). Membranes were washed 6 times for 5 minutes in TBS-T and incubated for 1 hour at room temperature in TBS-T containing 5% nonfat milk and either anti-mouse or anti-rabbit secondary antibody (1:10,000; Abcam, 7076S and 7074S). Membranes were washed again, developed with SuperSignal West Pico PLUS Chemiluminescent Substrate (Thermo Fisher Scientific), and exposed using the Chemi-Doc MP Imaging System (Bio-Rad Laboratories).
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4

Western Blot Analysis of p-Syk and Syk

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Analysis of p-Syk and Syk levels were performed on 20 μg of total protein from samples processed in SDS-loading buffer and boiled for 10 min. Samples were loaded on a 4–20% Mini-PROTEAN gel (catalog no. 4561094; Bio-Rad) and transferred onto a polyvinylidene fluoride membrane. Membranes were blocked in 5% BSA–TBS with 0.02% Tween-20 for 1 h and incubated in primary antibody diluted (catalog no. 2710, 1:1,000; Cell Signaling; catalog no. 13198, 1:1,000; Cell Signaling) in 5% BSA–TBS with 0.02% Tween-20 overnight shaking at 4°C. The next day, after washing, secondary antibodies were applied for 1 h, shaking at RT. Membrane was washed three times for 5 min, developed using Pierce ECL Western Blotting Substrate (catalog no. 32106; Thermo Fisher Scientific), and imaged using a ChemiDoc imaging system. Blots were converted to grayscale and densitometry analysis was performed in ImageJ. Photoshop was used for post-quantification editing. Original unedited blots are available in the source data file for Fig. S3.
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5

Comprehensive Protein Analysis in Diverse Cellular Samples

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Cultured cells, and BS and SC tissue were lysed and homogenized in RIPA buffer (Sigma) using a Q125‐125‐watt Sonicator (MedSupply) at 50% amplitude for 10 s. Tissue and cell pellets were resuspended in RIPA buffer with phosphatase inhibitor (Sigma), protease inhibitor (Roche), 1 mM PMSF (Sigma), 50 mM NaF, 1 μM NaVO4 (Sigma), and 1 mM DTT (Sigma). Protein concentration was determined using BCA analysis (BIORAD). Lysates were run on 4−20% Mini‐PROTEAN gel (BIORAD) at 100 V and transferred using Trans‐Blot Turbo Transfer System (BIORAD) onto Immun‐Blot PVDF membranes (BIORAD). Membranes were blocked using Intercept (PBS) Protein‐Free Blocking Buffer (LI‐COR). The following primary antibodies were used: PDGFRA (CST, 3164S), 1:1000; myelin basic protein (MBP, CST, 78896), 1:1500; phospho‐Tyr762 PDGFRA (pPDGFRA, CST, 2992), 1:1000; ERK1/2 (CST, 9107), 1:1000; phospho‐Thr202/Tyr204 ERK1/2 (pERK1/2, CST, 9101), 1:1000; Akt (CST, 2920), 1:2000; phospho‐Ser473 Akt (pAkt, CST, 4060), 1:2000; and β‐actin (CST, 3700S), 1:5000. Polyclonal goat anti‐rabbit IgG (IRDye 800CW) and goat anti‐mouse IgM (IRDye 680RD) were used as secondary antibodies. Signal intensity was measured on the Odyssey imaging system (LI‐COR) per manufacturer's instructions, and densitometry analysis done using Image Studio (LI‐COR).
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6

Immunoblot analysis of GFP expression

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Whole cell lysates in 2x reducing sample buffer (125 mM Tris-HCl pH 6.8, 20% glycerol, 7.5% SDS, 5% 2-mercaptoethanol, 250 mM DTT, and 0.05% bromophenol blue) were denatured at 98° for 15 minutes, fractionated using SDS-PAGE (4–20% Mini-PROTEAN gel, Bio-Rad #4568093), and transferred to a polyvinylidene difluoride (PVDF) membrane (Millipore #IPVH00010). Immunoblots were probed with mouse anti-GFP (1:10,000 JL-8, Clontech #632380) and rabbit anti-β-actin (1:10,000 Cell Signaling #4967) followed by goat/sheep anti-mouse IgG IRDye 680 (1:10,000 LI-COR #926–68070) or goat anti-rabbit IgG-HRP (1:10,000 Jackson Labs # 111-035-144). HRP secondary antibody was visualized using the SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Fisher # PI34095). Images were acquired using the LI-COR Odyssey Fc imaging system.
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7

Western Blot Analysis of SEMA7A

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Suspended cells were collected, spun down, washed with cold PBS and lysed in 100 µl Novex Tris-Glycine SDS sample buffer (Thermo Fisher Scientific; LC2676). Adhered cells were washed with cold PBS, lysed in another 100 µl sample buffer, collected and combined with lysates from suspended cells. After sonication, samples were centrifuged at 20,000 g for 10 min at 4°C. Equal amounts of protein samples, measured with Nanodrop (Thermo Fisher Scientific), were denatured using DTT and heating at 95°C for 10 min followed by size separation on a 10% Mini-PROTEAN gel (Bio-Rad; 4561033). Proteins were transferred to PVDF membranes (Bio-Rad; 1074156) using the Trans-Blot Turbo system (Bio-Rad) after which membranes were blocked in TBST-5% milk. Membranes were incubated with human SEMA7A Ab (1:10,000, AF 2068; R&D systems) or GAPDH Ab (1:1000, 5174; Cell Signaling Technology) in blocking buffer overnight at 4°C. Thereafter, membranes were shortly washed and incubated with HRP-labelled secondary Abs (1:5000; Dako) for 1 h at room temperature. After thorough washing with TBST, protein bands were visualised using Western lightning ECL (PerkinElmer; NEL1030001EA) and the ChemiDoc Touch Imaging System (Bio-Rad).
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8

Protein Extraction and Western Blot Analysis

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Protein was prepared from iPSC-CMs by direct lysis in ice-cold radioimmunoprecipitation assay buffer containing phosphatase and protease inhibitors (Santa Cruz Biotechnology) followed by collecting of cells using a cell scraper and mechanical trituration. After centrifugation (14,000 g at 4°C) for 20 min, the supernatant was collected. Protein content was determine using the Pierce BCA Protein Assay (Thermo Fisher Scientific). Protein was buffered in 4× Laemmli sample buffer (Bio-Rad) and boiled at 100°C for 5 min before electrophoresis. 10 μg of protein were electrophoresed on a 10% Mini-PROTEAN Gel (Bio-Rad) and transferred to a prewetted polyvinylidene fluoride membrane. After blocking and probing with a primary antibody overnight, proteins bands were visualized using an IRDye secondary antibody and visualized using the IR Odyssey imaging system (LI-COR). Total protein loading was further measured for standardization using the REVERT Total Protein Stain Kit (LI-COR). For ERK visualization, rabbit polyclonal phospho-ERK1/2 (T202/Y204, IB 1:500, 9101; Cell Signaling Technology), and mouse monoclonal ERK (clone 3A7, IB 1:500, 9107; Cell Signaling Technology) were used along with LI-COR IRDye 800 goat anti-rabbit (1:10,000) and 680 goat anti-mouse (1:10,000) secondary antibodies.
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9

Pneumococcal Pilus Protein Detection

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Bacterial cultures were grown in Todd-Hewitt medium supplemented with 0.5% yeast extract to an O.D.600 of 0.8. Cultures were centrifuged and pellets were lysed in 100μL Pneumococcal lysis buffer (0.01% SDS, 0.1% DOC, and 0.015M Na Citrate). Equal amounts of protein were determined using a BCA Protein Assay (Pierce) loaded in Mini-Protean gel (BIO-RAD), transferred using a semi-dry transfer method (BIO-RAD Trans Blot SD), blocked with 5% non-fat milk, and probed with anti-Sp0463 (pilus) as the primary antibody, and goat-anti mouse conjugated to HRP as the secondary antibody. For western blot confirmation of AdcAII complementation, blotted lysates were probed with polyclonal rabbit antiserum against AdcAII (Rockland labs).
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10

SDS-PAGE Protein Separation and Visualization

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The supernatant was mixed at a ratio of 1:1 with 2× sample buffer [4% SDS, 20% glycerol, 10% DTT, 0.004% bromophenol blue and 0.125 M Tris–HCl pH 6.5] and boiled for 5 min. Twenty microlitres of the boiled sample was loaded onto a 12% or 15% polyacrylamide 12-well precast Mini Protean gel (Bio-Rad). Following electrophoresis at 120 V, the gel was removed and fixed for 30 min in 5 ml of 7% (v/v) glacial acetic acid in 40% (v/v) methanol. Later, the gel was stained with 150 ml of 0.25% (w/v) colloidal Coomassie brilliant blue G concentrate in 50% methanol, 10% acetic acid and 40% water for at least 4 h. After staining, the gel was rinsed with 10% acetic acid in 40% methanol for 1 min. Rinsing was repeated, and the gel was de-stained overnight in 25% methanol on a shaker at ambient temperature. The next day the gel was washed, scanned using a Bio-Rad gel imager (Gel Doc XR+ System) and recovered and fixed in 1% formic acid.
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