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8 protocols using control goat igg

1

Co-Immunoprecipitation of Aire Nuclear Proteins

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Extraction of nuclear proteins and coimmunopreciptation were performed using the Universal Magnetic Co-IP Kit (Active Motif). Briefly, Aire-transfected HEK293 cells were lysed with hypotonic buffer and incubated on ice for 15 min. Cell lysates were centrifuged for 30 s at 14,000 x g, then the nuclei pellets were digested with an enzymatic shearing cocktail for 10 min at 37°C. After centrifugation of the nuclear lysates, the supernatants containing the nuclear proteins were first incubated with specific antibodies for 4 hr, then with Protein-G magnetic beads for 1 hr at 4°C with rotation. After four washes, bound proteins were eluted in laemmli/DTT buffer, separated by SDS/PAGE for 40 min at 200 V, transferred to PVDF membranes using the TurboTransfer System for 7 min at 25 V (BioRad) and blocked for 1 hr with TBS, 0.05% Tween, 3% milk. The western blot detection was done after incubation with primary (2 hr) and secondary antibodies (1 hr). Detection was performed by enhanced chemiluminiscence (ECL). Antibodies used for immunoprecipitation or revelation were: CLP1 (sc-243005, Santa Cruz), Flag-tag M2 (F1804, Sigma), goat IgG control (sc-2028, Santa Cruz), mouse IgG1 control (ab18443, Abcam), and horseradish peroxidase-conjugated anti-mouse IgG light chain specific (115-035-174, Jackson ImmunoResearch).
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2

Immunoprecipitation of FADD and ATG5 in Casp9-/- MEFs

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Casp9−/− MEFs were seeded at the 3 x 104 cells/cm2 density 24 h prior to the treatment. Boc‐D‐FMK at 20 μM (Cambridge Bioscience, Cambridge, UK, 1160–5) was added 24 h after stress induction to inhibit caspases. Cells were harvested 72 h after stress induction and lysed in 0.5 ml of ice‐cold NP‐40 lysis buffer (150 mM NaCl, 1% NP‐40, 10% glycerol, 10 mM Tris pH 8.0) supplemented with cOmplete™ Mini Protease Inhibitor Cocktail (Roche, Basel, Switzerland, 11836153001). The protein complex was immunoprecipitated using Dynabeads® M‐270 Epoxy (Invitrogen, Carlsbad, CA, USA, Kit number 143.21D) according to the manufacturer's instructions. Briefly, 1 mg of Dynabeads was conjugated to anti‐FADD (Santa Cruz, sc‐6036), anti‐ATG5 (CST, 8540) antibody, goat IgG control (Santa Cruz, sc‐2028) or rabbit IgG (Jackson ImmunoResearch, Ely, UK, 011‐000‐003) overnight at 4 °C. Dynabeads were washed in ice‐cold NP‐40 lysis buffer and combined with cell lysates on a rotor at 4 °C for 4 h. Following the incubation, the beads were washed and 50 μl of elution buffer was added. Beads were rotated at 4 °C for 5 min and precipitated on a magnet. The supernatants were transferred to fresh microfuge tubes and diluted in 50 μl of 2X sample buffer (4% (w/v) SDS, 120 mM Tris‐HCl, 10% (v/v) glycerol, 100 mM DTT and bromophenol blue).
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3

Intrathecal Injections for Hyperalgesia Assessment

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Intrathecal injection of morphine (in groups BM, BM+Ab and BM+IgG) or antibodies (in groups BM+Ab and B+Ab on day 15 after inoculation of Walker 256 cells) was performed as described previously (26 (link)), in order to determine whether MCP-1 was associated with hyperalgesia in MTBP rats. Briefly, rats were anesthetized with an intraperitoneal injection of pentobarbital sodium (40 mg/kg), and an intrathecal catheter (PE-10 tube) was inserted into the L4 and L5 intervertebral space. Subsequently, morphine (20 µg/kg, twice a day), anti-MCP-1 neutralizing antibody (10 µg; R&D Systems, Inc.) or control goat IgG (10 µg; Santa Cruz Biotechnology, Inc.) was injected intrathecally at a total volume of 10 µl. The MCP-1 association with hyperalgesia was then investigated with the paw withdrawal threshold (PWT) and thermal withdrawal latency (TWL) tests.
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4

Eosinophil STX17 Antibody Detection

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Antibodies for STX17 detection in eosinophils were an affinity-purified goat polyclonal antibody raised against a peptide mapping within a cytoplasmic domain of STX17 of human origin (Santa Cruz Biotechnology, TX, USA, sc-107095) used in parallel with control goat IgG (Santa Cruz Biotechnology) at concentrations of 5 μg/mL (immunoEM) or 10 μg/mL (flow cytometry). Secondary antibody for immunoEM studies was an affinity-purified rabbit anti-goat Fab fragment conjugated to 1.4-nm gold particles (1:100, Nanogold®, cat. # 2006, Nanoprobes; Stony Brook, NY). Secondary antibodies for flow cytometry were anti-goat antibodies conjugated to FITC (10 μg/mL, Jackson ImmunoResearch laboratories Inc., West Grove, PL, USA).
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5

Coimmunoprecipitation of STC Proteins

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Ten micrograms of control goat IgG (Santa Cruz), STC1 (R&D Systems), or STC2 (Santa Cruz) antibodies was incubated for 1 h at 4°C with 25ul prewashed protein A agarose beads (Santa Cruz) in 200 μl DTT‐free NP‐40 (reaction buffer) with 200 μg/ml BSA. Beads were washed three times in reaction buffer and mixed with 300 μg of protein extract in reaction buffer (100 μl). The reaction was incubated for 2 h at 4°C. For immunodepletion, the samples were spun down and supernatant was collected for subsequent experiments. One‐third of the supernatant fraction was taken for the PAPP‐A protease assay (100 μg extract/assay), one‐third for assessing STC1 or STC2 protein levels, and one‐third for assessing PAPP‐A protein levels by ELISA following manufacturer's protocol (R&D systems, Cat#DPPA00).
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6

Immunohistochemistry Protocol for Feline COX-1, COX-2, and CD147

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Immunohistochemistry protocols (IHC) were designed for the detection of cyclooxygenase-1 (COX-1), COX-2, and CD147. The COX-1 antibody was a polyclonal rabbit anti-ovine COX-1 antiserum (Cayman Chemical Company, Ann Arbor, MI, USA). The other antibodies were polyclonal rabbit anti-mouse COX-2 IgG (Cayman Chemical) and polyclonal goat anti-human CD147 IgG (Santa Cruz Biotechnology Inc., Dallas, TX, USA). Comparison of epitope sequence and predicted feline amino acid sequences available in NCBI databases revealed that the COX-2 antibody recognized an epitope that was 83% identical to feline COX-2, and the COX-1 antiserum recognized an epitope that was 91% identical to feline COX-1. The epitope sequence for the CD147 antibody was proprietary, but personal communication with the manufacturer (Santa Cruz) indicated 79% homology to feline CD147. Feline intestinal goblet cells were selected as a positive control for COX-1 [29 (link)], feline kidney (macula densa) was selected as a positive control tissue for COX-2 [30 (link)], and feline small intestine was selected as a positive control for CD147 expression [31 (link)]. For negative control purposes, primary antibodies and antiserum were replaced with control rabbit IgG (Millipore Sigma Company, Etobicoke, ON, Canada), control goat IgG, and control rabbit serum (Santa Cruz).
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7

Antibody Sources for Protein Localization

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Rabbit anti-IRBIT antibody was described previously [2 (link)]. Mouse anti-myc (9E10), goat anti-PIPKIα (C-17), anti-PIPKIβ (D-19), anti-PIPKIγ (M-19), anti-PIPKIIα (N-19), anti-PIPKIIβ (A-15), and control goat IgG were obtained from Santa Cruz Biotechnology. Rat anti-HA (3F10) and mouse anti-myc antibody conjugated with peroxidase were obtained from Roche Applied Science. Donkey anti-rabbit IgG conjugated with horseradish peroxidase (HRP) and goat anti-rat IgG conjugated with HRP were obtained from GE healthcare. Rabbit anti-goat IgG conjugated with HRP was obtained from Medical & Biological Laboratories. Rabbit anti-HA, Alexa Fluor 594-conjugated goat anti-rabbit IgG, and Alexa Fluor 488 or Alexa Fluor 647-conjugated goat anti-mouse IgG were obtained from Invitrogen.
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8

Enrichment and Activation of Plasmacytoid Dendritic Cells

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All human studies were performed according to the investigator's protocol approved by the Institutional Review Board of Columbia University. PBMC were isolated from healthy adult volunteers by Histopaque density gradient centrifugation; where indicated, pDCs were enriched using the Diamond pDC isolation kit (Miltenyi Biotec) to >95% purity. Human PBMC subsets for expression analysis were purchased from Allcells.
For pDC activation, PBMCs were plated at 5 × 3 105 /well of flat-bottom 96 well plates in RPMI medium with 10% FCS in the presence of affinity-purified polyclonal goat IgG antibody to the extracellular domain of human PTPRS (R&D Systems) or of control goat IgG (Santa Cruz Biotechnology). In titration experiments, antibody concentrations >0.01 μg/mL were found to have the same effect. CpG type A (ODN 2216, Invivogen) was added 1 hr later at 5 mM concentration. After 6 hr, protein transport inhibitor (BD Golgi Plug™, BD Biosciences) was added and cells were incubated for additional 10 hr. For the analysis by immunofluorescence, purified pDC were pre-incubated with anti-PTPRS or control IgG and then activated with CpG for 3 hr.
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