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12 protocols using ecl plus western blotting reagent

1

EGF-induced EGFR activation and signaling

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After culturing under serum-starved conditions for 16–24 h, cells were treated with EGF (20 ng/ml) for 15 min, washed with PBS and homogenized and solubilized by sonication for 10 sec in cold lysis buffer [50mM HEPES (pH7.5), 150 mM NaCl, 1% Nonidet P40, 2 mM EDTA, 7.5 μg/mL aprotinin, 10 μg/mL leupeptin, 10 mM NaF, 2 mM orthovanadate, and 2 mM PMSF]. After clarification by centrifugation (12,000 x g for 15 min), cellular lysates were immunoprecipitated with anti-EGFR antibody overnight, and then with protein A/G Sepharose beads (GE Healthcare Life Sciences) for 3 h. The immunocomplexes were then washed with cold lysis buffer, resuspended in SDS sample buffer, and subjected to SDS-PAGE and immunoblotting with the respective antibodies using ECL Plus Western blotting reagent (Amersham Biosciences). For the EGFR or Src inhibition, the cells were treated with specific inhibitor, AG1478 or PP2 (Calbiochem), respectively.
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2

Histone H4 Acetylation Analysis

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11 million S2 cells per 10 cm dish were treated with 220 ug of the corresponding dsRNA (dsWhite or dsMtor) per plate for 72 hours. Samples were treated again with the same amounts of dsRNA for another 72 hours after the first round of KD (6 days total). Samples were collected and washed 2x in 1X PBS. Standard acid extraction of histones was then performed on this sample: 0.4 N H2SO4 was added for 3 hours, followed by TCA precipitation and resuspension in 100 uL H2O. Protein concentration was quantified using BCA protein assay kit (ThermoFisher) and equal amounts of protein were loaded (3 and 6 ug). and separated on 15% SDS-PAGE gels. Proteins were transferred to nitrocellulose membranes, probed with Ponceau then washed, and incubated overnight at 4C using primary antibodies at the following dilutions: rabbit anti-H4K16ac (sc-8662) 1:2000 and rabbit anti-Histone H3 (ab1791) 1:10,000 (which was probed for on same membrane, after membrane was stripped). Membranes were incubated with rabbit HRP secondary antibody at 1:5000 for 2 hr at room temperature and detected using ECL-Plus western blotting reagent (Amersham Biosciences).
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3

Immunohistochemical Profiling of Neuroinflammation

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NMDA, α-AA, the mouse monoclonal anti-glial fibrillary acidic protein (GFAP), and the biotin-conjugated isolectin B4 (IB4) from Bandeiraea simplicifolia were all purchased from Sigma (St. Louis, MO). The mouse monoclonal anti-NeuN was purchased from Chemicon (Temecula, CA), the mouse anti-rat CD11b antibody (clone MRC OX-42) was from Serotec Ltd. (Oxford, UK), and the rabbit polyclonal anti-S100B antibody was from DAKO (Dako Diagnostics, Barcelona, Spain). The goat polyclonal AMCase (M-19) antibody that specifically binds the transcription factor YM1 was from Santa Cruz Biotechnology (Santa Cruz, CA) as was the rabbit polyclonal anti-GR antibody. Secondary antibodies and immunohistochemical reagents were from Sigma.
[3H]PK-11195 was purchased from Perkin-Elmer (Boston, MA). [3H]Corticosterone was from Amersham Bioscience (Bucks, UK) and RU-28362 was purchased from Sigma. Dodecyl sulphate-polyacrylamide gel electrophoresis standards were purchased from Bio-Rad (Hercules CA), Immobilon-P membranes were from Millipore (Bedford, MA), and ECL Plus Western Blotting reagent was from Amersham Bioscience (Bucks, UK). The murine TNF-α ELISA development kit was purchased from PeproTech (Paris, France).
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4

Western Blot Protein Detection Protocol

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Western blotting was performed using standard protocols. Primary antibodies were diluted in 5% milk solution, according to manufacturer’s instructions. We used anti-FLAG (#F7425, Sigma-Aldrich), anti-CHD4 (#ab72418, Abcam), anti-BPTF # A300-973A, Fortis Life Sciences), anti-SMARCA5 (#A301-017A-T, Fortis Life Sciences), anti-KDM1 (#ab37165, Abcam), anti-HDAC2 (#ab12169, Abcam). Primary antibodies were incubated for 2 h at RT with the nitrocellulose membranes. Washing of the nitrocellulose membranes was done 3 times for 5 min, after which secondary antibodies (anti-mouse or anti-rabbit, Bio-Rad) were incubated for 1 h. After three more washes, membranes were developed using the ECL-Plus Western Blotting Reagent (Amersham Biosciences).
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5

Histone H4 Acetylation Analysis

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11 million S2 cells per 10 cm dish were treated with 220 ug of the corresponding dsRNA (dsWhite or dsMtor) per plate for 72 hours. Samples were treated again with the same amounts of dsRNA for another 72 hours after the first round of KD (6 days total). Samples were collected and washed 2x in 1X PBS. Standard acid extraction of histones was then performed on this sample: 0.4 N H2SO4 was added for 3 hours, followed by TCA precipitation and resuspension in 100 uL H2O. Protein concentration was quantified using BCA protein assay kit (ThermoFisher) and equal amounts of protein were loaded (3 and 6 ug). and separated on 15% SDS-PAGE gels. Proteins were transferred to nitrocellulose membranes, probed with Ponceau then washed, and incubated overnight at 4C using primary antibodies at the following dilutions: rabbit anti-H4K16ac (sc-8662) 1:2000 and rabbit anti-Histone H3 (ab1791) 1:10,000 (which was probed for on same membrane, after membrane was stripped). Membranes were incubated with rabbit HRP secondary antibody at 1:5000 for 2 hr at room temperature and detected using ECL-Plus western blotting reagent (Amersham Biosciences).
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6

Phosphotyrosine-mediated JMJD1a regulation

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Standard western blotting techniques and Amersham ECL Plus Western blotting reagent were used. Following antibodies were used: JMJD1a (12835-1-AP, Proteintech, USA, 1:1,000), YAP/TAZ (sc-101199, Santa Cruz Biotechnology, USA, 1:500), GAPDH (5G4, HyB test 1:5,000), Tubulin (12G10, Hybridoma bank, 1:5,000), Lamin A/C (sc-7292, Santa Cruz Biotechnology, 1:1,000), H3K9me2 (#7658, Cell Signaling, 1:1,000), Histone 3 (#4499, Cell Signaling, 1:1,000), actin (clone AC-74, Sigma, 1:1,000), alpha-SMA (A2547, Sigma, 1:1,000) and antiphosphotyrosine antibody (APY03, Cytoskeleton, 1:1,000). For the phosphotyrosine pull-downs, MDA-MB-231 cells co-transfected with GFP-JMJD1a and CA-Src or empty vector were lysed and subjected to pulldown with beads of APY03 covalently coupled to sepharose (Anti-Phosphotyrosine Affinity Beads # APY03-Beads (Cytoskeleton) according to the manufacturer's instructions. The pulldowns and cell lysate were resolved on SDS–PAGE and subjected to western blot analysis with anti-GFP antibody (Abcam #1218).
Uncropped scans of the most important blots are provided as Supplementary Fig. 10.
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7

Western Blot Analysis of RAS Pathway

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Fifty µg of total protein isolated from RASMC-miR483 cells was used for the Western blotting assay. Fractions were prepared as above. The membrane was incubated overnight in primary antibody specific for AGT (Cat. No. ab108334; Abcam, MA, USA), ACE-1 (Cat. No. ab134709; Abcam), ACE-2 (Cat. No.AF933 R & D Systems, MN, USA and Cat. No. ab108252; Abcam) or AGTR2 (Cat. No. AT21-A and AT22-A; Alpha Diagnostic International, TX, USA). The membrane was washed and then incubated in 1:5000 diluted IgG secondary antibody labeled with HRP for 1h. Using ECL Plus Western Blotting Reagent (Amersham Biosciences) specific bands were detected. The same blots were subsequently stripped and re-probed for actin (Cat. No. MAB1501; Millipore, MA, USA). Densitometry analysis was performed for each experiment. Mean band intensity values were determined using the Kodak® 1D Image Analysis Software (Eastman Kodak Company). Total protein values were normalized to actin and compared to the vector control samples.
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8

Western Blot Analysis of Cell Signaling

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The Western blot procedure was performed as described previously [10 (link)]. Proteins were resolved on SDS-PAGE and transferred to Immobilon polyvinyldifluoride (PVDF) membranes. The blots were blocked with 5% non-fat dry milk in Tris-buffered saline with 0.5% Tween-20 (TBST) for 1 h at room temperature and then probed with p-p38, p-ERK, p-JNK, p38, ERK, JNK (Cell signaling, USA), anti-c-fos, anti-NFATc1 (Santa Cruz Biotechnology, Dallas, TX) for 1 h at room temperature. After three washes, he blots were washed in TBST and developed with horseradish peroxidase conjugated in an anti-mouse antibody (Santa Cruz Biotechnology, Dallas, TX) (diluted in 1:5000) for 1 h in ambient temperature. After another wash, the membrane was subjected to film treated with a chemiluminescence reagent with ECL plus Western blotting reagents (Amersham). Every individual blot was then stripped and re-probed with anti-β actin antibodies to allow the standardization of expression amongst samples. This experiment was replicated three times to corroborate the results of this assay.
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9

Western Blot Analysis of Brain Proteins

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All antibodies with the exception of protein phosphatase 2A catalytic subunit (PP2A/c) (Calbiochem) and beta-actin (Sigma) were purchased from Cell Signaling Technology. Briefly, crushed frozen brains were added to a lysis buffer containing 2% SDS, 60 mM Tris-HCl buffer (pH 6.8), 50 mM EDTA, 2.5 mM sodium pyrophosphate, 1 mM β-glycerolphosphate, 1mM PMSF, 1 μM leupeptin and homogenized on ice. Homogenates were then sonicated for 10–15 seconds and boiled for 5 minutes at 95°C. Samples were then centrifuged at 15,000xg for 10 min at 4°C. 30 μg of protein were electrophoresed in a SDS–polyacrylamide gel and transferred onto a PVDF membrane (Invitrogen). The membrane was incubated with a blocking buffer (5% nonfat dried milk in PBS containing 0.05% Tween 20 (PBST)) for 1hr at room temperature, followed by incubation with a primary antibody for 1hr at room temperature or overnight at 4°C. The primary antibodies were used 1:1000 dilutions, unless stated otherwise. The membrane was then washed four times in PBST, probed with the secondary HRP-linked antibody (1:5000) in blocking buffer for 1hr at room temperature. Detection of the signal was performed using ECL Plus Western blotting reagents (Amersham Pharmacia Biotech) or Immobilon Western (Millipore). A t-test was used for statistical analysis and a p value of < 0.05 was considered significant.
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10

Celastrol-Induced Western Blot Analysis

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Cells were treated with celastrol (1 µM) or vehicle for 24 h, washed with PBS, and then lysed with lysis buffer (TrisHCl 50 mM pH 8.0, KCl 50 mM, EDTA 10 mM, NP40 1% supplemented with protease inhibitor cocktail, pH 7.4) for 30 min on ice. Thirty micrograms of each cell lysates (untreated and treated) was run on 15% sodium dodecyl sulfate-polyacrylamide gels (SDS-PAGE), transferred to nitrocellulose membranes (Roche, Mannheim, Germany), and probed with the indicated antibodies (Supplementary File S1). Detection was accomplished using the corresponding horseradish peroxidase (HRP)-conjugated secondary antibodies followed by development with ECL Plus Western Blotting Reagents (formerly Amersham Biosciences, Uppsala, Sweden).
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