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6 protocols using normal rabbit immunoglobulin g

1

Transcription Factor Regulation of Lipid Genes

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MKP5‐overexpressed mouse hepatocytes FL83B and control cells were stimulated with PA for 9 hours and crosslinked with formaldehyde at a final concentration of 1% for 10 minutes, followed by quenching with glycine. Cell lysates were fragmented by sonication and precleared with protein G Dynabeads and subsequently precipitated with anti‐phosphor activating transcription factor 2 (pATF2) antibody (Santa Cruz) or normal rabbit immunoglobulin G (Santa Cruz) overnight at 4°C. After washing and elution, crosslink reversal was done by incubating at 65°C for 8 hours. The eluted DNA was purified and analyzed by real‐time polymerase chain reaction (RT‐PCR) with primers specific to Cidea and Fsp27 promoters.
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2

Chromatin Immunoprecipitation of PPARγ in MIN6 Cells

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MIN6 cells were cultured with or without 10 μmol/L PIO for 48 h in a 10‐cm dish. We carried out the chromatin immunoprecipitation (ChIP) assay using an EZ‐ChIP chromatin immunoprecipitation kit (Merck Millipore, Billerica, MA, USA). After fixing with 1% formaldehyde, cells were lysed, briefly sonicated and immunoprecipitated at 4°C overnight. The following antibodies were used in the ChIP reactions: normal rabbit immunoglobulin G (Santa Cruz Biotechnology, Dallas, TX, USA), anti‐acetyl histone H3 (Merck Millipore) and anti‐peroxisome‐proliferator activated receptor (PPAR; Santa Cruz Biotechnology). We washed the ChIP reactions, and eluted chromatin based on the manufacturer’s protocol. Chromatin was purified with PCR clean up columns (Qiagen), and PCRs were carried out with AmpliTaq Gold PCR Master Mix (Thermofisher).
The following primers, designed for mouse genes, were used.
ADM‐P1 forward: 5′‐ CAAACTTGGCAAGCACTCAG‐3′
ADM‐P1 reverse: 5′‐ AATGGGCTAGGACACACTCC‐3′
ADM‐P2 forward: 5′‐ CAAACTTGGCAAGCACTCAG‐3′
ADM‐P2 reverse: 5′‐ ACGGGTACTCCAAATGAAGG‐3′
ADM‐P3 forward: 5′‐ AAACCCCAATTTCCAATTCAG‐3′
ADM‐P3 reverse: 5′‐ GAAGGGGAACCAGAACAACTC‐3′
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3

GATA-3 ChIP-qPCR Protocol

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Cells were subjected to ChIP based on the ChIP-IT® High Sensitivity kit protocol (Active Motif). Chromatin was immunoprecipitated with rabbit anti-GATA-3 mAb or normal rabbit immunoglobulin G (Santa Cruz). qPCR analysis was performed to determine the relative abundance of target DNA. DNA immunoprecipitated by GATA-3 antibody was normalized to the total DNA input.
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4

ChIP-based Analysis of Fgf21 Promoter

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ChIP assays were performed according to the manufacturer's protocol (Millipore, CA, USA) with anti-c-Jun antibody (Cell Signaling Technology, MA, USA) or normal rabbit immunoglobulin G (Santa Cruz Biotechnology, CA, USA) for negative control. Immunoprecipitated Fgf21 promoter was quantified using PCR with primers designed to amplify the 130-bp region encompassing the AP-1 site (forward, 5′-GCCCTTTTCATTCAGACCCC-3’; reverse, 5-TGCCCT CCCCACTCCTG -3′) or a 135-bp upstream region not involved in c-Jun response (forward, 5′- CCTCCCTCAGACCCAAGAGC-3’; reverse, 5′-GTGGCTGGGCTCTGCAGTT-3′).
The annealing temperature of PCR was 52 °C and PCR products were amplified with TaKaRa Ex Taq® DNA polymerase (Takara Bio Inc., Shiga, Japan).
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5

Chromatin Immunoprecipitation Assay in AtT20 Cells

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The chromatin immunoprecipitation assay was performed using AtT20 cells as previously described (30 (link)). Cells were fixed in 1% formaldehyde, 4.5 mM HEPES (pH 8.0), 9 mM NaCl, 0.09 mM EDTA, and 0.045 mM EGTA for 10 minutes at room temperature, and sonicated using a Bioruptor (Diagenode) in lysis buffer (1% sodium dodecyl sulfate, 10 mM EDTA, and 50 mM Tris-HCl pH 8.0) with proteinase inhibitor (Sigma-Aldrich, catalog No. P8340). Precleared lysates were incubated overnight at 4 °C with 2 µg of anti-STAT3 (Santa Cruz Biotechnology, catalog No. sc-482); anti-STAT5 (Santa Cruz Biotechnology, catalog No. sc-836); anti-CREB (Santa Cruz Biotechnology, catalog No. sc-186); or normal rabbit immunoglobulin G (Santa Cruz Biotechnology; catalog No. sc-2027). DNA fragments were isolated from immunoprecipitated chromatin and analyzed by quantitative PCR with SYBR Green PCR Master Mix (Applied Biosystems). PCR primers used were mPomc 5′-GCCGAGACTCCCATGTT, 5′-GTGGCCCATGACGTACT.
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6

Immunohistochemical Analysis of RUNX2 Expression

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Sections were deparaffinized using Hemo-Clear (Falma Co., Ltd., Tokyo, Japan) and subjected to antigen retrieval in 10 mM sodium citrate buffer, pH 6.0, at 95°C for 5 min. After endogenous peroxidase activity was blocked with 0.3% hydrogen peroxidase in methanol, sections were incubated overnight with a 1:100 dilution of an anti-RUNX2 antibody (rabbit anti-PEBP2αA [M70] polyclonal antibody, Santa Cruz Biotechnology, Inc., Santa Cruz, CA, USA) and then with an anti-rabbit peroxidase-conjugated secondary antibody (EnVision + Dual Link System Peroxidase, DakoCytomation, Denmark A/S, Glostrup, Denmark) at room temperature in humidified chambers. Antigen-antibody complexes were visualized using 3'3-diaminobenzidine tetrahydrochloride (Wako, Osaka, Japan), and the sections were counterstained with methyl green. Normal rabbit immunoglobulin G (Santa Cruz Biotechnology, Inc.) diluted to an equivalent protein concentration served as a negative control in place of the primary antibody.
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