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12 protocols using ha hrp

1

Immunoblotting of Tagged Proteins

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Protein samples were incubated at 70°C for 10 min after adding 3× SDS sample buffer (stock concentration 30% glycerol, 3% SDS, 93.75 mM Tris‐Cl pH 6.8, 0.06% bromophenol blue). These samples were loaded on SDS–PAGE gels (8 or 12%) and run at 90 V. After dye front reached the end, these gels were transferred with TransBlot (Biorad) at conditions of 1.0 mA for 30 min onto PVDF membranes. Transferred membranes were blocked with 5% skim milk in TBST, and antibodies were added subsequently and incubated overnight at 4°C. The following antibodies were used; Flag‐HRP (Sigma, A8592), Myc‐HRP (Sigma, 16‐213), V5‐HRP (Sigma, V2260), HA‐HRP (Roche, 12013819001), MPK6 (Agrisera, AS12 2633), H+‐ATPase (Agrisera, AS07 260), and GFP‐HRP (Abcam, ab6663). Signals were detected using ECL substrates (Thermo Fisher, 34580). After detection, membranes were stained with Ponceau S solution (Sigma, P7170) to use as loading control. PageRuler™ Prestained Protein Ladder (Thermo Scientific, 26616) was used as molecular weight markers.
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2

Comprehensive Protein Detection Techniques

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For immunoblotting and co-immunoprecipitation: Actin (Santa Cruz, ♯sc-47778; 1:5000), ATF6 (Cell Signaling Technology, ♯65880; 1:1000), BCL-2 (AbCam, ♯ab182858; 1:500), BCL-XL (Cell Signaling Technology, ♯2764; 1:1000), Cleaved-Caspase-8 (Cell Signaling Technology, ♯8592; 1:1000), Caspase-3 (Cell Signaling Technology, ♯9665; 1:1000), Caspase-9 (Cell Signaling Technology, ♯9508; 1:1000), CHOP (Cell Signaling Technology, ♯2895; 1:250), GFP (AbCam, ♯ab13970; 1:2000), GRP78 (Cell Signaling Technology, ♯3177; 1:1000), FLAG-HRP (Sigma Aldrich, ♯A8592; 1:4000), HA-HRP (Roche, ♯11867423001; 1:2000), IP3R1 (Thermo Fischer, ♯PA1-901; 1:1000), IP3R1 & IP3R2 [previously described77 ; 1:1000], IP3R3 (BD Biosciences, ♯610312; 1:1000), KDEL (AbCam, ♯ab12223; 1:2000), MCL-1 (Cell Signaling Technology, ♯5453; 1:1000), Nicastrin (BD Biosciences, ♯612290; 1:1000), PARP (Cell Signaling Technology, ♯9542; 1:1000), SERCA2 (Cell Signaling Technology, ♯4388; 1:1000), STIM1 (Cell Signaling Technology, ♯5668; 1:1000).
For immunofluorescence: DAPI (Thermo Fischer, ♯D1306; 1 µg/ml), HA (Cell Signaling Technology, ♯3724; 1:500), BAP31 (Enzo Life Sciences, ♯ALX-804-601-C100; 1:250).
For proximity ligation assay: HA (Cell Signaling Technology, ♯3724; 1:500), HA (Enzo Life Sciences, ♯ENZ-ABS118-0200; 1:200), IP3R1 (Thermo Fischer, ♯PA1-901; 1:200), IP3R3 (BD Biosciences, ♯610312; 1:200).
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3

Western Blot Analysis of Chromatin Remodelers

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All proteins were resolved by SDS-PAGE and transferred to PVDF membrane (PerkinElmer) and blocked in 5% milk in TBS-T (50 mM Tris, pH 7.5, 150 mM NaCl, 0.1% Tween-20). The following antibodies were used in this study: T7 antibody (EMD Millipore, 69522–3), T7-HRP (EMD Millipore, 69048), Flag-HRP (Sigma, A8592 and Cell Signaling, 86861), SNF5 (Bethyl Laboratories, A301-087A, Abcam, ab12167, and Cell Signaling, 91735), BAF155 (Cell Signaling, 11956), GAPDH-HRP (Cell Signaling, 8884S), BAF170 (Bethyl Laboratories, A301-039A), BRG1 (Cell Signaling, 49360) HA-epitope tag (Cell Signaling, C29F4), HA-HRP (Roche, 12013819001), MYC (Abcam, ab32072), and BRD9 (Active Motif, 61537). Bands were visualized using Supersignal West Pico (Pierce) and traditional film development or using Clarity Western ECL substrate (Bio-Rad) in which a ChemiDoc MP (Bio-Rad) was used for development.
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4

Quantitative Western Blot Analysis of Protein Extracts

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Western blot analysis was performed in accordance with standard protocols [96 ]. For whole-cell protein extract preparation, 1.5 × 106 cells were pelleted by centrifugation at 1250g and lysed in 100 μl of Laemmli sample buffer (Bio-Rad). Protein concentrations were determined using the Bio-Rad DC protein assay reagent in accordance with the manufacturer’s protocol. 15–20 μg of whole-cell protein extracts, 10 μl of nuclear extracts, or entire eluate from immunoprecipitated samples were separated on an 8 % SDS–polyacrylamide gel and transferred to a polyvinylidene difluoride (PVDF) membrane (Thermo Scientific) and subjected to western blot analysis. Membranes were probed with various rabbit primary antibodies followed by incubation with donkey anti-rabbit HRP-conjugated IgG (1:3000; GE Healthcare, NA9340) secondary antibody where applicable. The antibody signals were detected using the ECL+ or ECL prime western blot detection system (GE Healthcare). Primary antibodies used: HA-HRP (1:6000; Roche, 2013189), SIN3 (1:2000; [21 (link)]), RPD3 (1:3000; [21 (link)]), dKDM5/LID (1:5000; kindly provided by Dr. Julie Secombe [32 (link)]), beta-actin (1:1000; Cell Signaling, 4967).
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5

Western Blot Antibody Reagents

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HRP conjugated rabbit and mouse secondary antibodies were purchased from GE Healthcare (Waukesha, WI), while goat-HRP and actin antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). Antibodies against Akt, pAktS473, pAktT308, GSK3β, pGSK3β, MTOR and pMTORS2481, and pMTORS2488 were purchased from Cell Signaling (Beverly, MA). HA-HRP was purchased from Roche (Indianapolis, IN), while anti-TRAF6 and BAFF-R FITC antibodies were purchased from Abcam (Cambridge, UK). IgG1 FITC was purchased from Becton Dickinson (Franklin Lakes, NJ), while IgG1 PE and TACI PE were purchased from R&D Systems (Minneapolis, MN).
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6

Western Blot Analysis of Protein Expression

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Aliquots of cell lysates were separated on 4–20% Tris-glycine gels (BioRad) and transferred to nitrocellulose membranes. Expression of GFP reporter and FLAG-aaRS was confirmed by immunoblotting with antibodies against GFP (Santa Cruz, RRID:AB_627695), HA-HRP (Roche, RRID:AB_390917), FLAG-HRP (Sigma, RRID:AB_439702), GAPDH (Millipore, RRID:AB_10615768), and corresponding secondary HRP-conjugated antibodies when needed (BioRad, RRID:AB_11125936 and Invitrogen, RRID:AB_2534727). Quantitative analysis of gel lanes was performed using ImageJ software.
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7

Western Blot Analysis of Protein Expression

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Sample cell lysate (30 μg) was loaded onto precast 4–20% Mini-Protean TGX gels (Bio-Rad, Hercules, CA, USA) and subjected to SDS-PAGE prior to iBlot (Invitrogen, Waltham, MA, USA) transfer to nitrocellulose membrane. The following antibodies were used: beta-Actin/ACTB (Abcam, Cambridge, UK, cat.no ab8227); SRC-2 (BD Biosciences, San Jose, CA, USA, cat. no 610985); HA-HRP (Roche, cat. no 12013819001); HRP goat-anti mouse IgG (BD Biosciences, cat. no 554002); HRP goat-anti rabbit IgG (Thermo Scientific, Waltham, MA, USA, cat. no 31460). Immunoblotted membranes were developed using Femto substrate (Thermo Scientific) and analyzed on a ChemiDoc XRS imager (Bio-Rad) equipped with QuantityOne densitometry software. For densitometry analyses, volumetric protein band intensity was normalized to that of ACTB in the same gel lane.
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8

Western Blot Analysis of Chromatin Remodelers

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All proteins were resolved by SDS-PAGE and transferred to PVDF membrane (PerkinElmer) and blocked in 5% milk in TBS-T (50 mM Tris, pH 7.5, 150 mM NaCl, 0.1% Tween-20). The following antibodies were used in this study: T7 antibody (EMD Millipore, 69522–3), T7-HRP (EMD Millipore, 69048), Flag-HRP (Sigma, A8592 and Cell Signaling, 86861), SNF5 (Bethyl Laboratories, A301-087A, Abcam, ab12167, and Cell Signaling, 91735), BAF155 (Cell Signaling, 11956), GAPDH-HRP (Cell Signaling, 8884S), BAF170 (Bethyl Laboratories, A301-039A), BRG1 (Cell Signaling, 49360) HA-epitope tag (Cell Signaling, C29F4), HA-HRP (Roche, 12013819001), MYC (Abcam, ab32072), and BRD9 (Active Motif, 61537). Bands were visualized using Supersignal West Pico (Pierce) and traditional film development or using Clarity Western ECL substrate (Bio-Rad) in which a ChemiDoc MP (Bio-Rad) was used for development.
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9

SDS-PAGE Protein Detection via Western Blot

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Whole cell lysates or RNA pull-down samples were separated by 10% SDS-PAGE, transferred to a PVDF membrane (BioRad), and probed with the appropriate antibody. Primary antibodies used in western blots included HA-HRP (Roche Applied Science), hnRNPM (OriGene). GAPDH (GE) and β-actin (Sigma-Aldrich) were used as loading controls. After incubation with HRP-tagged secondary antibodies, if appropriate, blots were visualized via chemiluminescence (Thermo Fisher).
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10

Immunoblot Analysis of Plant Photoreceptors

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Proteins were resolved on Bis-Tris Gels using MOPS running buffer (Invitrogen). Immunoblots were performed as described (Pedmale and Liscum, 2007 (link)). Antibodies used for the immunoblots as follows: CRY1 and CRY2 (C. Lin), phyA and phyB (A. Nagatani), Flag M2 (Sigma,MO), Flag M2-peroxidase (Sigma), c-Myc 9E10 (Covance, NJ), c-Myc-HRP and GFP-HRP (Miltenyi Biotec, CA), GFP-HRP (Abcam, MA), HA (3F10 clone) and HA-HRP (Roche, IN). Appropriate goat secondary antibodies conjugated to HRP were used (Bio-Rad, CA).
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