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9 protocols using clone 9b11

1

Immunofluorescence Staining and Western Blotting

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Primary antibodies used at the indicated dilutions were rabbit α-DP (used at 1:200; A303-356A; Bethyl Laboratories); mouse α-Myc (used at 1:100 for immunostainings and 1:1000 for Western blottings; clone 9B11; Cell Signaling Technology); rabbit α-γ-catenin (PG; used at 1:200 for colocalization stainings and 1:1000 for proximity ligation assay (PLA); ab15153; Abcam); rabbit α-KIAA1217 (used at 1:500 for colocalization stainings and PLA; PA5-85468; Invitrogen; kindly provided by Tobias Zech, University of Liverpool); mouse α-Desmocollin 2/3 (used at 1:200 for colocalization stainings and PLA; clone 7G6; 32-6200; Invitrogen); mouse α-p120 catenin (used at 1:400 for colocalization stainings and 1:1000 for PLA; 612536; BD Transduction Laboratories), and mouse α-Lamin A/C (used at 1:200 for colocalization stainings and PLA; mab636; MA3-1000; Invitrogen). Secondary antibodies conjugated to Alexa Fluor 488 or 647 were from Jackson ImmunoResearch and used at 1:500 for immunostainings and α-mouse Alexa Fluor 680 from Thermo Fisher Scientific was used at 1:5000 from Western blotting. Alexa Flour 680–conjugated streptavidin was used at 1:500 dilution for immunostainings and Alexa Fluor 800 was used at 1:1000 for Western blotting (both from Thermo Fisher Scientific). 4′,6-diamidino-2-phenylindole readymade solution (Sigma) was used at a concentration of 1 μg/ml for immunostainings.
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2

Quantifying Pancreatic Beta Cells

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Pancreatic sections were stained with antibodies against insulin (1:400, polyclonal/A0564, Agilent), or myc-tag (1:200, clone 9B11, Cell Signaling) overnight at 4˚ C. After washing, slides were incubated with secondary antibody (5 μg/mL, Invitrogen) for 1 hour at room temperature, and imaged under a fluorescent microscope. For analysis of total pancreas sections, blocks were cut at two different depths to obtain unique sections of tissue, and were serially imaged using a Zeiss Axio Observer Z1 microscope and stitched together using ZenPro software (Carl Zeiss Microscopy). Regions of interest were drawn around the entire pancreas based on DAPI staining and beta cells based on insulin staining. % insulin+ area was calculated using ImageJ.
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3

Quantification of Surface GLUT4 Expression

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L6 myocytes were incubated in serum-free alpha-MEM for 3 hours, and then stimulated with 100 nM insulin for 20 minutes if necessary. Cells were placed on ice, washed twice with ice-cold phosphate-buffered saline (PBS: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4, pH 7.4) and fixed with 3% ice-cold paraformaldehyde (PFA) on ice for 10 minutes then at room temperature for a further 10 minutes. After removing the PFA, cells were washed twice with PBS and incubated with 100 mM glycine for 10 min to quench excess PFA. Cells were washed three times with PBS and blocked with 2% BSA in PBS for 15 min. To detect surface myc-GLUT4, cells were incubated with anti-myc primary antibody (mouse monoclonal, Cell Signaling Technologies clone 9B11, 1:1000 dilution in 2% BSA in PBS) at 4 °C for 1 hour with shaking. Following five PBS washes, cells were incubated with HRP-conjugated anti-mouse secondary antibody (1:1000 dilution in 2% BSA in PBS) at 4 °C for 45 minutes with shaking. For visualisation of HRP signal (surface GLUT4 expression), cells were washed five times in PBS then incubated with 3,3′,5,5′-Tetramethylbenzidine for three to five minutes. The reaction was quenched with 2 N HCl, and the absorbance at 450 nm recorded using a plate reader. Average background signal from cells in which the primary antibody step was omitted was subtracted from each well.
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4

Antibody Validation for Immunoblot and Immunohistochemistry

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For immunoblot experiments, the following antibodies were used: mouse anti-ATP5A (Abcam ab14748; RRID:AB_301447; 1:20000), rabbit anti-HA (Abcam ab9110; RRID:AB_307019; 1:1000), mouse anti-α-Tubulin (Sigma T9026, clone DM1A; RRID:AB_477593; 1:1500), rabbit anti-Porin (Millipore PC548; RRID:AB_2257155; 1:5000), mouse anti-V5 (Thermo Fisher Scientific R960-25; RRID:AB_2556564; 1:2000), mouse anti-Myc tag (Cell Signaling, clone 9B11; RRID:AB_331783; 1:800). Horseradish peroxidase-conjugated secondary antibodies: anti-mouse (Abcam ab6789-1; RRID:AB_955439; 1:5000-1:40000), anti-rabbit (Invitrogen G21234; RRID:AB_2536530; 1:3000 to 1:5000). Anti-MCU antiserum was raised in rabbits against a KLH-conjugated C-terminal peptide, RTQENTPPTLTEEKAERKY (Pepceuticals, 1:1000). For immunohistochemistry, tissues were incubated with mouse anti-ATP5A (Abcam ab14748; RRID:AB_301447; 1:500) and secondary antibody anti-mouse AF488 (Invitrogen: A11001; RRID:AB_2534069; 1:200).
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5

Nanobody Binding Assay for US28 Mutants

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Fifty micrograms of membrane extracts of HEK293T-iUS28 or HEK293T cells transfected with the different US28 ICL mutants were coated overnight in a 96 well MicroWell MaxiSorp flat bottom plate (Sigma-Aldrich, Saint Louis, Missouri, USA). The next day, plates were washed with 1× PBS and blocked with 2% (w/v) skimmed milk in PBS for 1 h at RT. Nanobodies were diluted in 2% (w/v) skimmed milk and incubated for 1 h at RT. Nanobodies were detected with mouse-anti-Myc antibody (1:1000, Clone 9B11, Cell Signaling Technology, Leiden, The Netherlands) and horseradish peroxidase (HRP)-conjugated goat-anti-mouse antibody (1:1000, Bio-Rad). Incubations with antibodies were done for 1 h at RT. Wells were washed three times with 1× PBS between all incubation steps. Binding was determined with 1-step Ultra TMB-ELISA substrate (Thermo Fisher Scientific) and the reaction was stopped with 1 M H2SO4. Optical density was measured at 450 nm with a PowerWave plate reader (BioTek). Data were analyzed using GraphPad Prism version 8.0 (GraphPad Software, Inc., La Jolla, CA, USA).
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6

Quantifying US28 Receptor Expression

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The experiments were performed
as described previously.27 (link) US28 expression
was detected using polyclonal rabbit-anti-US28 antibody (1:700, Covance),
while nanobody binding was detected using mouse-anti-Myc antibody
(1:500, 9B11 clone, Cell Signaling). MACH2 Universal HRP-Polymer detection
was used as secondary antibody (Biocare Medical, Pacheco, California,
USA).
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7

Immunofluorescence Analysis of Mitochondrial Dynamics

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Coronal brain sections (30 µm) from mice receiving rAAV2-eGFP and Drp1-K38A-eGFP were incubated in M.O.M™ mouse IgG blocking reagent (Vector Laboratories) overnight before incubation with polyclonal anti-GFP (1:500, Invitrogen) and monoclonal anti-TH (1:500; Sigma). For Fis1-myc, monoclonal anti-myc (1:2000, 9B11 clone, Cell Signaling) and polyclonal anti-TH (1:500, Calbiochem) were used. Corresponding secondary antibodies Alexa Fluor 488 and 594 (Invitrogen) were used. Nuclei were visualized with 4’,6-diamidino-2-phenylindole dihydrochloride (DAPI) (1:1000, Invitrogen). Images were scanned at 0.5 µm intervals throughout the whole section and analyzed using confocal microscopy (FV1000; Olympus).
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8

Visualizing GPCR Interactions in HEK293T and U251 Cells

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Transiently transfected
HEK293T or (US28-overexpressing) U251 cells were seeded in poly-l-lysine (Sigma-Aldrich) coated 96-well plates and were grown
at 37 °C and 5% CO2. Cells were prepared for immunofluorescence
microscopy as described previously.25 (link) Briefly,
cells were fixed with 4% paraformaldehyde (Sigma-Aldrich) for 10 min
at RT and subsequently permeabilized with 0.5% NP-40 (Sigma-Aldrich)
for 30 min at RT. Nanobodies were incubated for 1 h at RT and detected
using Mouse-anti-Myc antibody (1:1000, 9B11 clone, Cell Signaling).
US28 was visualized with the rabbit-anti-US28 antibody (1:1000, Covance41 (link)). Subsequently, cells were washed and incubated
with Goat-anti-Rabbit Alexa Fluor 546 (1:1000 in 1% (v/v) FBS/PBS,
Thermo Fisher Scientific) and Goat-anti-Mouse Alexa Fluor 488 (1:1000
in 1% (v/v) FBS/PBS, Thermo Fisher Scientific). When binding of VUN100
to CX3CR1 was assessed, receptor expression was detected using Rat-anti-HA
antibody (1:1000 in 1% (v/v) FBS/PBS, Clone 3F10, Roche) or Rabbit-anti-HA
antibody (1:1000 in 1% (v/v) FBS/PBS, H6908, Sigma-Aldrich) and Goat-anti-Rat
Alexa Fluor 546 (1:1000 in 1% (v/v) FBS/PBS, Thermo Fisher Scientific)
or Goat-anti-Rabbit Alexa Fluor 546 (1:1000 in 1% (v/v) FBS/PBS, Thermo
Fisher Scientific). Cells were visualized with an Olympus FSX-100
microscope.
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9

Immunohistochemical Analysis of Mitochondrial Dynamics

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Coronal brain sections (30 μm) from mice receiving rAAV2-eGFP and Drp1-K38A-eGFP were incubated in M.O.M mouse IgG blocking reagent (Vector Laboratories) overnight before incubation with polyclonal anti-GFP (1:500, Invitrogen) and monoclonal anti-TH (1:500; Sigma). For Fis1-myc, monoclonal anti-myc (1:2,000, 9B11 clone, Cell Signaling) and polyclonal anti-TH (1:500, Calbiochem) were used. Corresponding secondary antibodies Alexa Fluor 488 and 594 (Invitrogen) were used. Nuclei were visualized with 4′,6-diamidino-2-phenylindole dihydrochloride (1:1,000, Invitrogen). Images were scanned at 0.5 μm intervals throughout the whole section and analysed using confocal microscopy (FV1000; Olympus).
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