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34 protocols using goat igg

1

Immunoprecipitation of CaMKII Complex

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Wt islets (∼1,000) were lysed in co-IP lysis buffer containing 20 mM Tris ·HCl (pH 8.0), 137 mM NaCl, 2 mM EDTA, 1% Nonidet P-40, and a mixture of protease and phosphatase inhibitors (Roche). After centrifugation (16,000g at 4 °C for 10 min), the supernatant was divided into two aliquots. Immunoprecipitation studies were performed as described68 (link). In brief, samples were incubated overnight at 4 °C with either an anti-CaMKIIδ antibody (goat IgG, Santa Cruz) or the same amount of goat IgG (Santa Cruz). After this step, reaction mixtures were incubated with protein A/G PLUS agarose beads (Santa Cruz) for 4 h at 4 °C. The immunoprecipitated proteins were washed three times with a buffer containing 10 mM Tris ·HCl (pH 7.4), 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, and 1% Triton X-100, followed by SDS-PAGE analysis.
Immunoblots were probed with anti-barr2, anti-CaMKII (pan), and anti-CaV1.2 (α1 (α1 subunit69 (link)) antibodies, using the Quick Western Kit (IRDye 680RD, LI-COR Biosciences). Western blots were scanned and validated with an infrared imaging system (Odyssey CLx; LI-COR Biosciences). The antibodies used are listed in the Supplementary Table 2 above.
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2

ChIP Assay for Sox10 and Olig2 in Mouse Spinal Cord

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ChIP assays were performed on pooled thoracic spinal cords from postnatal day 15 (P15) C57BL/6 mice using the following antibodies: goat IgG (Santa Cruz Biotechnology, sc-2028), Sox10 (R&D, AF2864), and Olig2 (Millipore, AB9610). ChIP-qPCR was performed as described previously17 (link), 18 on three independent experiments, and primers used will be provided on request. P-values were obtained from the Student’s two-tailed t test to compare percent recoveries in Sox10 or Olig2 ChIP assays compared with that in a control IP (goat IgG) (p < 0.05 is considered to be statistically significant).
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3

ChIP-seq analysis of transcription factors

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ChIP was carried out as described previously 25 (link), 57 (link) with the following antibodies: goat IgG (Santa Cruz Biotechnology, sc-2028), Sox10 (R&D, AF2864), and Tead1 (BD Biosciences, 610923). Primers used included the following:
Tekt3 +7.8kb (Forward: aataccagcagatccggaagac, Reverse: ttgactcgttctcccaggtttt),
Itga6 −22.8kb (Forward: tgcttctgataagccccaac, Reverse: aagtcccagacacgtccttg),
Itga6 −20.6kb (Forward: tggaggcagaaggagaaaaa, Reverse: aggggcctgttaggaacact),
Itga6 −16.2kb (Forward: gacttgagctgtctgcatgg, Reverse: tggactgactaggcttccaca),
Itga6 −8.5kb (Forward: aaaagccaaacaaacccaga, Reverse: ggctagggcaagctaaggat),
Itga6 −7.8kb (Forward: tgcttttggtcatgtggttg, Reverse: accactggctagctcagcat),
Itga6 −165bp (Forward: tcgataaaacgccggagagt, Reverse: gtagctagcagccgctcaat),
Dag1 +3kb (Forward: atgaacccctcttcctgacc, Reverse: ccttgctgagactgtgctca),
Dag1 −36kb (Forward: ggatggaagactgaaaggcc, Reverse: ccctttccctctggtgtgag).
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4

Blastocyst Hatching Modulation by OPN

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Mouse blastocysts were collected at 08:00 on day 4 of pregnancy, and the zona pellucida (ZP) was examined under a microscope before being transferred into single-step medium (Irvine, USA) under mineral oil (Sigma) and cultured at 37°C, 5% CO2 with BSA, different concentrations of recombinant mouse OPN protein (rOPN, R&D Systems, Minneapolis, USA, 0.1 µg/mL, 1.0 µg/mL and 10.0 µg/mL), goat IgG (Santa Cruz Biotechnology) or anti-OPN antibodies (Santa Cruz Biotechnology, Santa Cruz, CA, 0.01 µg/mL, 0.1 µg/mL and 1.00 µg/mL). Fourteen hours later, the hatching rate was examined by three independent persons, and the experiments were repeated three times.
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5

Molecular Mechanisms of Mitochondrial Regulation

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Antibodies against VDAC1 (B-6), IKKα/β (H-470), IKKβ (H-4), ΙΚΚγ (FL-419, B-3), HSP60 (K-19 and N-20), IκBα (C-21), Bcl-2, Bcl-xL, Cyclophilin D, c-Src, Enhanced green fluorescence protein (EGFP), MK2, p-MK2, and goat IgG were purchased from Santa Cruz Biotechnology (Dallas, TX, USA). Antibodies against p-IKKα/β, p-IκBα, ANT2 (E2B9D), Bax, p-Src (Y416), p-JNK (T183/Y185), JNK1/2, p38, and p-p38 were from Cell Signaling Technology (Danvers, MA, USA). Anti-cytochrome c antibody was from BD Bioscience (San Jose, CA, USA). Antibodies to Prx III and β-actin were obtained from AbFrontier (Seoul, Korea). Anti-MFF1 antibody was purchased from Proteintech (Rosemont, IL, USA). Recombinant GST-fused p38 enzyme was purchased from R&D systems (Minneapolis, MN, USA).
Mouse monoclonal antibody against α-tubulin, hydrogen peroxide, glucose oxidase, diamide, cyclosporine A, cycloheximide, coomassie brilliant blue R250, and DuoLink in situ fluorescence reagent were purchased from Sigma-Aldrich (St. Louis, MO, USA). SB203580, MG132, bongkrekic acid, lactacystin, bafilomycin A1, and 4,4’-diisothiocyanostilbene-2,2’-disulfonic acid) were purchased from Calbiochem (San Diego, CA, USA). Tetramethylrhodamine, ethyl ester (TMRE) was purchased from Invitrogen (Waltham, MA, USA). MK inhibitor IV was purchased from Cayman Chemical (Ann Arbor, MI, USA).
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6

ChIP-Seq and ChIP-qPCR Protocol for Epigenetic Analysis

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ChIP was performed largely as described previously (O’Geen et al., 2011 (link)). Briefly, cells were crosslinked with 1% formaldehyde, lysed, and sonicated to an average fragment length of 500 bp before being immunoprecipitated with selected antibodies. The resulting chromatin was used for qPCR or library preparation for ChIP-Seq. For each ChIP, 20–50 μg of sonicated chromatin was used, with magnetic Dynabeads (Invitrogen) for immunoprecipitation. For ChIP-qPCR experiments, enrichment was calculated relative to the IgG negative control and then further normalized to an intergenic negative control region. The following antibodies were used: Rabbit IgG (Santa Cruz sc-2027), Goat IgG (Santa Cruz sc2028), H3K27ac (Abcam ab4729), H3K4me3 (Millipore 04–745), Dppa4 (R&D Systems AF3730), OCT4 (Abcam ab19857). HDAC1 (Abcam ab31263), HDAC2 (Abcam ab12169). Primers are listed in Supplemental Table 1.
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7

Metastatic Potential of HCC Cell Lines

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Three human HCC cell lines with unique metastatic characteristics were investigated. Hep3B cell line with the lowest metastasis potential [19 (link)] was purchased from Cell Bank of the Chinese Academy of Sciences (Shanghai, China); MHCC97L cell line with the moderate metastasis potential and HCCLM3 cell line with the highest metastasis potential were kindly obtained from the Liver Cancer Institute of Fudan University (Shanghai, China) [20 (link), 21 (link)]. All cell lines were maintained in DMEM medium (Gibico), supplemented with 10 % fetal bovine serum (FBS, Gibico), penicillin (100 U/ml), and streptomycin (100 μg/ml). Cells were incubated at 37 °C with 5 % CO2, and were harvested with 0.25 % trypsin/EDTA (Gibico) in their logarithmic growth phase, washed with PBS, and resuspended in new media. The reagents used were as follows: Recombinant human HMGB1 (rhHMGB1) and recombinant human RAGE/Fc chimera, homologs to soluble form of RAGE (sRAGE), utilized as ex-RAGE were purchased from R&D systems (Inc., Minneapolis, MN, USA). The antibodies used were as follows: anti-HMGB1 neutralizing antibody, anti-RAGE neutralizing antibody (Abcam), anti-GAPDH (Cell Signal Technology), anti-NF-κB P50, anti-NF-κB P65, and goat IgG (Santa Cruz).
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8

Immunofluorescent Staining of Nervous System

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Sections were treated with 100mM glycine in PBS for 30 minutes, rinsed and immersed for 1 hour in SuperBlock buffer (ThermoScientific), and stained overnight with primary antisera to protein gene product 9.5 (PGP9.5, 1:800, rabbit IgG, AbD Serotec), calcitonin gene-related peptide (CGRP, 1:600, sheep IgG, Enzo Life Sciences), and langerin (1:800, goat IgG, Santa Cruz Biotechnology), which have been characterized previously [6 (link), 32 (link)]. After rinsing in PBST, sections were incubated for 1h with Cy2-conjugated donkey anti-goat (1:200), Cy3-conjugated donkey anti-rabbit (1:800), or Cy3-conjugated donkey anti-sheep (1:400) IgG secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.), rinsed in PBS and coverslipped with Fluoromount G. Three sections at 240μm intervals were analyzed per animal.
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9

Chromatin Immunoprecipitation of Telomeric DNA

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Cross-linking was carried out by treating HPFs or HeLa cells with 1% formaldehyde for 15 min; the reaction was stopped with 0.125 M glycine. Cells were then lysed, and chromatin was extracted according to Galati et al. [47 (link)]. Chromatin was then incubated overnight with 7.5 μg of mouse monoclonal anti-AKTIP (Sigma), 1μg of mouse IgG (Sigma), 7μg anti-TRF1 antibody (Santa Cruz), or 1μg of goat IgG (Santa Cruz) at 4°C, and ChIP was carried out as described [47 (link)]. DNA was slot-blotted onto a Hybond N+ and hybridized with a 650 bp telomeric probe from a plasmid containing a 1.6 Kb of TTAGGG repeats (a gift of E. Gilson), or with an ALU probe obtained by genomic DNA amplification with the 5’-CGCCTGTAATCCCAGCACTTTG-3’ and 5’-ACGCCATTCTCCTGCCTCAGC-3’ oligos. Signals were quantified using the ImageQuant Software.
For the BrdU-ChIP assay, before cell harvesting at each time point, the cells were incubated with 20 μM BrdU (Sigma) for 1 h. After dot-blotting and before hybridization with the telomeric probe, BrdU incorporation into telomeric DNA was evaluated by western blot analysis by incubating the membrane with the primary anti-BrdU antibody (Becton Dickinson).
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10

Dopamine Receptor Expression in Monocytes

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Day 0 and Day 3 monocytes (1x106) were stained with antibodies to D1R (Catalog number 324390), D3R (Catalog number 324402), D5R (Catalog number 324408) (1:5 dilution) (Calbiochem, Billerica, MA), D2R (Catalog numbers sc-9113 and sc-5303) (1:10 dilution), D4R (Catalog number sc-31480) (1:10 dilution) (Santa Cruz Biotechnology, Santa Cruz, CA) or negative control rabbit serum, rabbit IgG, mouse IgG2a (Sigma-Aldrich, St. Louis, MO) or goat IgG (Santa Cruz Biotechnology) in 50 μL on ice for 30 min. The dopamine receptor antibodies are specific for extracellular regions of each receptor and were titered to determine optimal staining conditions for monocytes. After two washes, cells were incubated with PE-conjugated anti-rabbit, mouse or goat IgG (1:5 or 1:10 dilution) (Sigma-Aldrich) on ice in the dark for 30 min., washed twice, and fixed in 2% paraformaldehyde. Fluorescence intensity was acquired using a BD FACSCanto-II flow cytometer (BD Biosciences, San Jose, CA). Any background reactivity with the appropriate isotype matched negative control antibody was subtracted from the dopamine receptor signal to determine the mean fluorescence intensity for each dopamine receptor.
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