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6 protocols using non immune mouse igg

1

Immunoprecipitation Assay Protocol

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Cells were collected and lysed in 1 ml immunoprecipitation lysis buffer (50 mM Tris-HCl [pH 7.4], 150 mM NaCl, 0.5% NP-40) with complete protease inhibitor cocktail (Roche Diagnostics). The cell lysates were precleared and then incubated with the indicated antibodies for 1 h at 4 °C. The complexes were precipitated with Protein A/G-Sepharose beads (Santa Cruz Biotechnology Inc.), washed, and resuspended in 40 μl SDS loading buffer. Non-immune mouse IgG or non-immune rabbit IgG (Santa Cruz Biotechnology Inc.) served as a negative control.
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2

Immunohistochemical Analysis of Tumor Samples

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Tumor specimens were fixed in 10 % neutral buffered formalin and embedded in paraffin. Sections were stained with hematoxylin and eosin and immunostained with anti-Ki67 antibody (Santa Cruz Biotechnology) and anti-CD31 antibody (abcam, San Francisco, CA, USA). Deparaffinized sections were pretreated by autoclaving in 10 % citric acid buffer (pH 8.0) at 120 °C for 15 min. Following treatment with protein block serum (Dako Cytomation, Kyoto, Japan) for 10 min and incubation with 2 % skim milk for 30 min to block nonspecific reactions, sections were incubated with primary antibody at 4 °C overnight. The EnVision polymer solution (horseradish peroxidase; Dako Cytomation) was then applied for 1 h. Signals were developed in 0.02 % 3,3′-diaminobenzidinetetrahydrochloride solution containing 0.1 %. As negative controls, the sections were incubated with tris(hydroxymethyl)aminomethane-buffered saline with non-immune mouse IgG (Santa Cruz Biotechnology) or non-immune rabbit IgG (Santa Cruz Biotechnology). Sections were then lightly counterstained with hematoxylin and examined under a fluorescence microscope (Olympus, Tokyo, Japan). For endothelial cell counting in tumors, five vascularized areas in a visual field (×100) were chosen, and the number of CD31+ cells was then counted.
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3

Immunoprecipitation of GABA Receptor Subunits

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Microdissected DG was obtained as described above. Lysates were obtained by passing the tissue through a 21G needle (25X) followed by agitation at room temperature (15 min) and then at 4°C (90 min). Lysates were centrifuged at 15,000 × g for 20 min to remove cell debris and pre-cleared by shaking with 40 μl of sepharose beads (1 h at 4°C). 300–350 μg of protein were incubated with 5 μg of mouse monoclonal antibodies for α1 (NeuroMab, Davis, CA) or β2/3 (Millipore, Billerica, MA) subunits or with 5 μg of non-immune mouse IgG (Santa Cruz Biotech, Santa Cruz, CA). After overnight incubation at 4°C, immune complexes were mixed with 25 μl of protein G-sepharose beads (GE Health Care, Piscataway, NJ) and incubated for 2 h at 4°C. Beads were washed with RIPA buffer and proteins were released in 25 μl of 2X Laemmli buffer by boiling for 3 min.
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4

ChIP-PCR Analysis of RAE1 in Breast Cancer

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ChIP analysis was performed as previously described42 with minor modifications. Chromatin was prepared from stable RAE1-overexpressing and control breast cancer cell lines. Briefly, 1 × 106 cells were cross-linked with 1% formaldehyde for 15 min, followed by the addition of glycine at 125 mM. Chromatin was sheared by sonication to fragments averaging between 0.5 and 1 kb in buffer containing 1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate, 10 mM EDTA, 50 mM Tris-HCl (pH 8.0), and protease inhibitor cocktail (Roche Applied Science, Basel, Switzerland). Chromatin was pre-cleared with protein A/G beads containing 50% slurry (Santa Cruz Biotechnology, Dallas, TX, USA) and salmon sperm DNA, followed by immunoprecipitation with anti-RAE1 antibody (Abcam) coupled to protein A/G beads under each experimental condition. Nonimmune mouse IgG (Santa Cruz Biotechnology) was used as a control. ChIP-PCR data are shown as the percentage of input after normalization with IgG. Primers for ChIP-PCR are listed in Table 2.

Primer sequences used for ChIP-PCR assay.

Amplicon sitesSequence (5′ → 3′)
pZEB1 #1F- GGA TCC CAC GGT TCT ACG C
R- GCG ACC GGA GAG AGG CTA
pZEB1 #2F- CTC ATC AAG GGA ACT CCC CG
R- GAA TTG AGG GGC GAG GGA AA
pZEB1 #3F- CCC ACC ACA CCT GAG GAA AA
R- CAT GAT CCT CTC GCT TGT GTC
Gene desertF- TGG TGG TCT GCC TTC TGC CAG T
R- TCA CGT GGG AGG AAG AAG TAG GGC
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5

Immunoprecipitation and Western Blot Analysis of KRIT1

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Cells were treated with or without 1μM 8-pCPT-2′-O-Me-cAMP-AM (Tocris/R&D Biosystems) as indicated in the figure legends. Lysates were prepared as reported previously[12 (link)]. KRIT1 was immunoprecipitated using 2μg monoclonal anti-KRIT1 (EMD Millipore, Darmstadt, Germany). Lysates were probed with polyclonal rabbit anti-KRIT1 Δ6832 (Ginsberg Lab, UCSD) at a dilution of 1:1000. Control lysates were immunoprecipitated with mouse non-immune IgG (Santa Cruz, Dallas, TX). Antibodies used for Western blot were rabbit anti-actin (Sigma, St. Louis, MO), rabbit anti-GAPDH (Santa Cruz), rabbit anti-PLCε (Smrcka Lab, University of Rochester), and rabbit anti-VE cadherin (Cayman Chemical, Ann Arbor, MI). The secondary antibodies used were goat anti-rabbit Dylight-680 (Thermo Fisher Scientific) and goat-anti rabbit 800 (Fisher). An Odyssey Infrared Imaging System (LI-COR Biosciences, Lincoln, NE) was used to image membranes and for densitometry.
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6

Nox4 Protein Interaction Profiling

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Lysates were prepared as reported previously4 . Nox4 was immunoprecipitated using 2 µg monoclonal anti-Nox4 antibody (Millipore/Sigma). Lysates were probed with polyclonal rabbit anti-Nox4 (Novus Biologicals, Littleton CO) at a dilution of 1:1000. Control lysates were immunoprecipitated with mouse non-immune IgG (Santa Cruz, Dallas, TX). Goat anti-rabbit Dylight-680 and goat-anti rabbit 800 (ThermoFisher) were used as secondary antibodies and the membranes imaged using an Odyssey Infrared Imaging System. NF-κB p65 was detected using a rabbit polyclonal anti-p65 (C-20) antibody from Santa Cruz. Tubulin was detected as a loading control (monoclonal anti-α-tubulin, Sigma). Goat anti-rabbit and goat anti-mouse HRP were used as a secondary antibodies and the blot was developed using Luminata™ Forte Western HRP substrate reagent, then exposed to film.
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