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Novex 4 20 tris glycine gel

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Novex 4–20% Tris-Glycine gels are precast polyacrylamide gels used for protein electrophoresis. They are designed for the separation and resolution of a wide range of protein molecular weights.

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38 protocols using novex 4 20 tris glycine gel

1

Pancreatic Tissue Protein Extraction and Western Blot

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Pancreatic frozen tissues were homogenized using a sonicator in ice-cold RIPA buffer including protease/phosphatase inhibitors (Roche Diagnosis, Indianapolis, IN). Samples were pre-boiled for 5 min and diluted to the same concentration using Laemmli buffer 2x and then separated using Novex 4–20% Tris-Glycine Gels (Invitrogen, Carlsbad, CA). Transfers were done onto a PVDF membrane (Millipore, Temecula, CA). Membranes were pre-blocked with TBST—5% Non-fat dry milk and then incubated with primary antibodies: Vimentin (ab92547, Abcam, Cambridge, MA), Col1a1 (sc-8784-R, Santa Cruz Biotechnology, Santa Cruz, CA) and Beta-actin (sc-47778, Santa Cruz Biotechnology, Santa Cruz, CA). After washing with TBS-0.1% tween-20, secondary antibodies (Cell signaling, Danvers, MA) were added and membranes incubated for 1 hour.
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2

Protein Analysis of CD4+ Cell Fractions

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Cytoplasmic and nuclear fractions of purified CD4+ cells were extracted using Nuclear Extract Kit (Active Motif). For preparation of total lysates, RIPA buffer was used. Lysates were resolved on Novex 4–20% Tris-Glycine gels (Invitrogen) and immunoblotted with antibodies to phospho-AKT, AKT, phospho-p42-44, phospho-p38, p38, NFAT1, NFAT2, cJun, NF-κB, CBLB, p27kip1, PARP1 (all from Cell Signaling), and β-actin (Sigma).
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3

Protein Expression Analysis Pipeline

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Protein extracts from cells were collected in RIPA buffer (Pierce, Rockford, IL). Tissue from the corpus was homogenized in RIPA buffer. Western blots were performed by re-suspending proteins in sample buffer, then resolving on Novex 4–20% Tris-Glycine gels (Invitrogen) using Tris running buffer, and then transferred to PVDF membrane using the iBlot Dry Blotting System (Invitrogen) according to the manufacturer’s instructions. The membranes were blocked in 5% non-fat milk for 1 h at room temperature and then sequentially probed overnight at 4°C with primary antibodies to SLFN4 peptides (custom made by GenScript), NOS2 (Abcam, #ab283655), CHOP (Abcam, #ab11419), cleaved Caspase-3 (Cell Signaling, #9661), β-Tubulin (Cell signaling, #5346S), GAPDH (MA5-15738, ThermoFisher).
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4

Non-Denaturing PAGE Analysis of Lipoproteins

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For non-denaturing polyacrylamide gel electrophoresis (PAGE), Novex™ 4–20% Tris-glycine gels (Invitrogen) were loaded with 5 μg protein per lane and run to termination at 1500 V h under non-denaturing conditions in Tris-glycine buffer. The gels were stained with EZ-Run protein gel staining solution (Fisher Bioreagents). Lipoprotein size was assessed by comparison with molecular standards from the HMW Native Marker Kit (GE Healthcare Life Sciences): thryoglobin (Mw = 669 kDa), ferritin (440 kDa), catalase (232 kDa), lactate dehydrogenase (140 kDa), and albumin (66 kDa). Stokes diameters of these folded globular proteins were indicated on the gels. SEC was performed with a Superose 6 10/300 GL column controlled by an AKTA UPC 10 FPLC system (GE Healthcare). Samples were eluted in phosphate buffer saline at pH 7.5 at a flow rate of 0.5 ml/min.
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5

Non-denaturing and Denaturing Protein Gel Electrophoresis

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For non-denaturing PAGE, Novex 4–20% Tris-glycine gels (Invitrogen) were loaded with 6 μg protein per lane and run to termination at 1500 V·h under non-denaturing conditions in Tris-glycine buffer. For SDS PAGE, Novex 16% or 18% Tris-glycine gels were loaded with 5 μg protein per lane and run at 200 V for 1 hr under denaturing conditions in SDS-Tris-glycine buffer. The gels were stained with Denville Blue protein stain (Denville Scientific).
SEC was performed with a Superose 6 10/300 GL column controlled by an ÄKTA UPC 10 FPLC system (GE Healthcare). Elution by 10 mM PBS at pH 7.5 was carried out at a flow rate of 0.5 ml/min.
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6

Western Blot Analysis of Gastric Proteins

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Gastric tissue was homogenized in RIPA buffer (Pierce, Rockford, IL). Western blots were performed using the SDS-PAGE System. Briefly, 20 μg of protein were resuspended in sample buffer, then electrophoresed on Novex 4–20% Tris-Glycine gels (Invitrogen) with Tris running buffer; transferred to PVDF membrane using the iBlot Dry Blotting System (Invitrogen) according to the manufacturer's instructions. The membranes were incubated in 5% nonfat milk for 1 hour at room temperature and then sequentially probed with primary antibodies to GLI2 (#sc271786, Santa Cruz Biotechnology, Dallas, TX), KIF3A (Abcam, #11256), or GAPDH (Thermo Fisher, #MA5-15738) overnight at 4°C.
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7

Protein Extraction and Analysis Protocol

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Cell lysates were prepared in RIPA buffer (50 mM Tris-HCl [pH 8.0], 150 mM NaCl, 0.1% sodium dodecyl sulfate [SDS], 0.5% SDC, 1% NP-40 with addition of cOmplete Mini EDTA-free protease inhibitor tablet [Millipore/Sigma: 11836170001]) and incubated on ice for 30 min with frequent vortexing and then clarified at 14,000 x g for 20 min at 4°C. Protein concentration was determined by bicinchoninic (BCA) protein assay (Pierce BCA Protein Assay Kit, ThermoFisher Scientific: 23227) and samples were resolved on NuPAGE 4%–12% Bis-Tris gels and Novex 4%–20% Tris-Glycine gels (Invitrogen) followed by transfer onto polyvinylidene fluoride (PVDF) membrane (Millipore/Sigma: IPVH00010). Membranes were blocked with 5% milk in PBS-T and incubated with primary antibody at 4°C overnight in 5% milk PBST. Membranes were washed 3x with PBST and incubated with secondary antibodies. For chemiluminescent readout, the membranes were incubated with HRP-conjugated secondary antibody and exposed using SuperSignal West Pico PLUS Chemiluminescent Substrate or SuperSignal West Femto Maximum Sensitivity Substrate (ThermoFisher Scientific: 34577 and 34095) by film in a dark room.
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8

Protein Extraction and Western Blot Analysis

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Protein extracts were prepared from the snap-frozen prostate tumors using RIPA buffer with HALT protease and phosphatase inhibitors (Thermo Scientific, Rockford, IL, USA). SDS-gel electrophoresis was performed on Novex 4–20% Tris-Glycine Gels (Invitrogen, Camarillo, CA, USA) and the proteins were transferred onto Immobilon-P PVDF membranes (MilliporeSigma, Burlington, MA, USA). Membranes were blocked with 3% BSA-TBST (50 mM Tris-HCl, 150 mM NaCl, Tween-20) and probed with the primary antibodies listed in Supplementary Table S1. Blots were then developed in ECL Prime solution (GE Healthcare, Piscataway, NJ, USA) and images were captured using the LAS-4010 ImageQuant imaging system (GE Healthcare, Piscataway, NJ, USA). Membrane stripping was achieved by subjecting them to SDS/β-mercaptoethanol solution (62.5 mM tris (pH 6.8), 2% SDS, and 100 mM β-mercaptoethanol) at 50 °C for 30 min. Stripped membranes were washed in TBST buffer, blocked and re-probed with additional primary antibodies as needed. Semi-quantitative densitometric analyses were made with ImageJ analysis software (https://imagej.nih.gov/ij/, accessed on 17 May 2020) using GAPDH as a loading control [38 ].
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9

Western Blot Analysis of Cleaved IL-1β and GsdmD

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The excised tumors were weighed and equal size tissue was homogenized in tissue lysis buffer (TPER, Thermo Scientific, 78510) supplemented with EDTA free protease inhibitor cocktail (Thermo Scientific, 87785), with ratio of ∼0.1g of tissue to 1 mL T-PER lysis buffer. The cell debris was separated by centrifugation at 10,000g for 10 min. After discarding the pellet, the protein concentration was determined using the BCA protein assay (Pierce). 10–50 μg of cell protein samples were resolved on Novex 4–20% Tris-Glycine Gels (Invitrogen) and transferred onto polyvinylidene fluoride membranes (Invitrogen). Blots were incubated with 1:1000 rabbit polyclonal antibody against cleaved IL-1β (Cell Signaling #63124), cleaved GsdmD (Cell Signaling #50928), or β-actin (Cell Signaling #8457 for 4h at RT or for 16 h at 4°C. The membranes were washed with PBST for 5 min × 3 times and incubated with 1:15000 horseradish peroxidase-conjugated goat anti-rabbit secondary antibody (Biorad) for 2h. The signal was detected with an enhanced chemiluminescent substrate (Pierce) and membranes were imaged using iBright CL750 Imaging System (Life Technologies, A44116). The western blot bands were quantified via densitometry using the iBright Analysis Software.
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10

Quantification of mRNA and Protein Expression

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For determination of changes in mRNA expression as measured by qRT-PCR, the ΔΔCT method was used.. Expression was normalized to internal control β-actin and gene knockdown was determined by comparing to control-treated cells.
Whole cell lysates were subjected to SDS-PAGE using Novex 4–20% Tris-glycine gels (Life technologies) and western blotting was performed as described (19 ). Since CD24 protein is heavily glycosylated, it runs differently on SDS-PAGE for individual cell lines as shown in Supplementary Fig. S1A.
For immunoprecipitations (IPs), cells were suspended in a lysis buffer containing 50mM Tris-HCl, pH 8.0, 120mM NaCl, 0.5% Nonidet P-40, phosphatase and protease inhibitor mixture (Roche Applied Sciences). Lysates were incubated with either Flag-conjugated agarose beads (F2426, Sigma-aldrich), or antibodies conjugated to protein A/G agarose beads (sc-2003, Santa Cruz Biotechnology) at 4°C overnight. Antibodies used for IP were anti-HA (MMS-101P, Covance), anti-AR (sc-7305), and anti-YY1 (sc-1703) from Santa Cruz Biotechnology. A matched isotype antibody was used as a negative control.
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