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6 protocols using isotype igg

1

Immunoprecipitation and Western Blot Analysis

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SKOV-3 cells were harvested and lysed in lysis buffer (150 mM NaCl, 50 mM Tris-HCl, 1 mM EDTA [pH 7.5] and 1% NP-40) containing protease inhibitor (Roche, CA, U.S.A.). Whole cell lysates were incubated with an anti-FBP1 antibody, anti-EZH2 antibody or isotype IgG (Abcam, Cambridge, U.K.) at 4°C for 2 h followed by incubation with prepared Protein A+G agarose beads (Santa Cruz, CA, U.S.A.) at 4°C overnight with rotation. After washing with lysis buffer, the precipitates were eluted in SDS-PAGE loading buffer by boiling for 5 min. The supernatants were then resolved by SDS-PAGE and transferred to PVDF membranes. Immunoblotting using appropriate antibodies was conducted using a standard Western blot protocol [47 (link)].
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2

Frozen Section Preparation of Undecalcified Hard Tissues

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For the preparation of frozen sections from non-fixed and undecalcified hard tissues, Kawamoto’s film methods were used. Samples were freeze-embedded with super cryoembedding medium (SECTION-LAB Co. Ltd., Hiroshima, Japan) and cut in thickness of 5 μm after mounting the adhesive film onto the sample surface. Samples were then immediately fixed with 4% paraformaldehyde (PFA) for 20 min and stained with hematoxylin and eosin. For immunohistological analysis, the specimens were incubated with the anti-CD146 antibody (Abcam, San Francisco, CA, USA), or the isotype IgG (Abcam) at 4 °C overnight after blocking with 5% goat serum (Life Technologies, Gaithersburg, MD, USA). After washing, the specimens were incubated with secondary antibody Alexa Fluor 488 donkey anti-rabbit IgG (Life Technologies) for 60 min at room temperature. All images were taken by fluorescence microscope (Biozero BZ-X700, Keyence, Osaka, Japan).
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3

Iodination of Anti-AT1R Monoclonal Antibody

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50 µg anti-AT1R mAb (Abcam, Cambridge, UK) or isotype IgG (Abcam) was iodinated with 15 µL Na131I (185 MBq) (China Institute of Atomic Energy, Beijing, China) using the Iodogen method as described previously [13] . Radioiodinated anti-AT1R mAb and isotype IgG were separated from free iodine using size exclusion columns (Sephadex G-25, Amersham Pharmacia Biotech, Uppsala, Sweden).
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4

ChIP Assay of FOXF2-Regulated Genes

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Chromatin immunoprecipitation (ChIP) assay was performed using a ChIP assay kit (EMD Millipore, Billerica, MA, USA) according to the manufacturer’s instructions. Anti-HA antibody (Abcam) was used for immunoprecipitation to enrich the promoter fragments containing putative FOXF2 binding site of target genes in MCF-10A cells constitutively expressing HA-tagged FOXF2 (MCF-10A-FOXF2). The isotype IgG (Abcam) was used as a negative control. The primers for the amplification of the TWIST1 promoter region containing a putative FOXF2 binding site from −2120 to −2113 relative to the transcription start site (TSS) were 5′-AGATTTCCTTTACACTTTACCC-3′ (forward) and 5′-GCGAGTGTTATTTCTCCAGCGA-3′ (reverse). The primers for the amplification of TWIST1 exon 1 (+408 to +841), which served as a negative control, were 5′-CAGCGAGGAAGAGCCAGACCG-3′ (forward) and 5′-GGAGGACCTGGTAGAGGAAGT-3′ (reverse).
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5

CDCA7 Chromatin Immunoprecipitation Assay

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KYSE150 cells were transfected with the V5-tagged CDCA7 plasmid for the chromatin immunoprecipitation (ChIP) assay. The assay was performed according to the instructions of the manufacturer (Millipore, Burlington, MA, USA). The DNA fragments were enriched by anti-V5 antibody (Abcam, Cambridge, UK), and the isotype IgG (Abcam, Cambridge, UK) was used as a negative control. CHIP-seq was performed by Novogene (Beijing, China). Screening and quality control of the CHIP-seq were based on standard protocol. The sequences of primers used for the amplification of CCNA2 genome regions containing a putative CDCA7 binding site are listed in Table S1.
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6

CTCF Binding Assay at rs2395304

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Raji cells were (>90% viability) were cross-linked in 1% formaldehyde for 10 min and ChIP assay was performed with the Chip-IT Express kit (Active Motif; Cat# 53009, Carlsbad, CA, USA) on the MNase-digested chromatin, as per the standard protocol. 5 µg of anti-CTCF (Millipore; cat# 07-729; Billerica, MA, USA); or, isotype IgG (Abcam; cat# ab46540, Cambridge, MA, USA) antibody was used. ChIP-qPCR primers for the rs2395304 site (chr6:32,982,837–32,982,952; 116 bp) were designed and custom-made by Life Technologies (Assay ID: 6457700_CCMSG0D, Grand Island, NY, USA). MNase digested chromatin was divided into three aliquots. Two of three chromatin aliquots were immunoprecipitated with rabbit anti-CTCF antibody or its IgG isotype antibody. The third aliquot was used as total Input DNA control to quantify the CTCF bound to the rs2395304 site. The candidate locus in ChIP samples was then analyzed by real-time PCR. The CTCF-bound to rs2395304 site was expressed as a percentage of input DNA, as described previously (24 ). ChIP experiments were performed three times from independent preparations of chromatin. The data were averaged with respect to the input chromatin.
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