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24 protocols using normal igg

1

ChIP-seq Analysis of Prostate Tissues

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ChIP-DNA prostate tissues of hHGFtg:H11hMET/+:PBCre4 and hHGFtg:H11hMET/+:Ctnnb1L(Ex3)/+:PBCre4 mice was obtained by ChIP assay. Briefly, mouse prostate tissues were minced, cross-linked with 1% formaldehyde for 25 min at room temperature (RT), and quenched with 150 mM glycine for 10 min. Samples were homogenized in cell lysis buffer (140 mM NaCl, 50 mM Tris-HCl [pH 8.0], 1 mM EDTA, 10% Glycerol, 0.5% NP-40, and 0.25% Triton X-100). The chromatin was resuspended in nuclear lysis buffer (0.2% SDS, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, and 0.5 mM EGTA) and fragmented to an average size of 200–500 bp with a Sonic Dismembrator Model 100 (Thermo Fisher Scientific) at 4 °C. After centrifugation, the cell sonicate was diluted with ChIP dilution buffer (0.01% SDS, 167 mM NaCl, 16.7 mM Tris-HCl [pH 8.1], 1.1% Triton X-100, and 1.2 mM EDTA), pre-cleared using Dynabead Protein G (10003D, Invitrogen) and then was subjected to immunoprecipitation with Dynabead Protein G conjugated with SP1 antibody (Novus, NB600-233) or normal IgG (Cell Signaling) for 4 h at 4 °C. Crosslinks were reversed, and then chromatin DNA fragments were analyzed by qRT-PCR with specific primers (Supplementary Table 1).
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2

Immunoprecipitation of β-Arrestin2 in Cultured Cells

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Lysates containing 4 mg of total protein were made using NP40 lysis buffer (Promotor, Wuhan, China) in TKPTS cells cultured on plates and were incubated with 4 μg of an anti-β-arrestin2 antibody at 4°C overnight. Normal IgG (2729S, Cell Signaling Technology) was used as a negative control. Then Protein A/G Plus Agarose (sc-2003, Santa Cruz Biotechnology) was put into the compound for 8 hours at 4°C. After the beads were washed 3 times, the lysates were resuspended and boiled. Immunoblotting was operated as a method of Western blot.
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3

Glucocorticoid Receptor Modulation Pathway

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Fluocinolone acetonide (FA), E2, DHT, RU0486 (Mifepristone), and ICI182,780 (Fulvestrant) were from Sigma-Aldrich (St. Louis, MO, USA). Croton oil (CO) was from Santa Cruz Biotechnology (Dallas, TX, USA). We used antibodies against GR (Santa Cruz Biotechnology), ER (EMD Millipore, Danvers MA, USA), REDD1 (Proteintech Group, Rosemont, IL, USA), GAPDH (Sigma-Aldrich), tubulin, and normal IgG (Cell Signaling, San Jose, CA, USA).
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4

Macrophage NF-κB Activation Assay

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Macrophages were cultured in control, 200 μg/mL MSU and 200 μg/mL MSU in conditioned medium from DRG. Total cell lysates were incubated overnight at 4 °C with P65 (Cell Signaling Technology, 8242, 5 μg) or normal IgG (Cell Signaling Technology, 2729, 5 μg) as a control. Antibody-antigen complexes were precleared with Crosslink Magnetic IP/Co-IP Kit (Thermo Fisher scientific, 88805). After several washes, samples were boiled and analyzed by immunoblot.
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5

Co-Immunoprecipitation Assay for Protein-Protein Interactions

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Co-IP assays were carried out as described [9 (link), 14 (link)]. The antibodies used are as follows: Ajuba (#4897, Cell Signaling Technology), SP1 (#sc-420, SCBT), Flag (Sigma-Aldrich, F7425), Myc (9B11, #2276, SCBT), normal IgG (#2729, Cell Signaling Technology). GST-tagged SP1 and His tagged Ajuba were expressed in BL21 respectively, and purified by Glutathione Sepharose beads (17–0756-01, GE Healthcare) or Ni-beads (17–5318-06, GE Healthcare). For the in vitro binding assays, the purified proteins of GST-SP1 were mixed with His-Ajuba was added into the mixture for 12 h.
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6

Immunoprecipitation of β-catenin and Ubiquitin

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Cell lysates were prepared by incubating cells in 1% Tris-Triton cell lysis buffer (Cell Signaling Technology, America) containing 1 mM phenylmethylsulfonyl fluoride (PMSF) and the protease inhibitor cocktail on ice for 30 min, following which, lysates were centrifuged at 12,000 × g for 10 min. The supernatants were incubated overnight with 30 μL Dynabeads Protein A (Life Technologies, America) precoated with anti-β-catenin (Abcam, Cambridge, UK), or anti-ubiquitin (Abcam, Cambridge, UK) antibodies. The immunocomplexes were analyzed by western blots. A normal IgG (Cell Signaling Technology, America) control was assayed simultaneously.
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7

Immunocytochemical Analysis of CCN2 Expression

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Rat NP cells were plated in 96-well flat-bottom plates (3 × 103 cells/well) and incubated for 24 h. The cells were treated with 1.0 μM BIO, fixed with 4% paraformaldehyde, permeabilized with 0.5% Triton X-100 (vol:vol) in phosphate-buffered saline (PBS) for 10 min, blocked with PBS containing 10% FBS, and incubated overnight at 4 °C with antibodies against CCN2 (1:100, Santa Cruz Biotechnology). The cells were washed and incubated with an anti-rabbit Alexa Fluor 488 (green) antibody (Thermo Scientific, IN, USA) at 1:200 and with 10 μM 4′,6-diamidino-2-phenylindole (DAPI) for 1 h at room temperature for nuclear staining. The samples were observed under a fluorescence microscope interfaced with a digital imaging system. Cells treated with normal IgG (Cell Signaling Technology) at equal protein concentrations were used as negative controls.
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8

m6A-seq Analysis of CSFV Infection

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PK-15 cells seeded in 6-well plates were transfected with siRNA targeting METTL14 and infected with CSFV (MOI = 1). At 48 hpi, the total RNA was extracted by using TRIzol reagent (TAKARA, Japan). 20–50 μg fragmented RNA was precleared with 40 μL protein A/G agarose beads (Santa Cruz, USA) supplemented with 40U RNase inhibitor overnight at 4°C. The mixture and 2 μg m6A antibody (A19841, ABclonal, China) were incubated overnight at 4°C. A negative control was included with normal IgG (Cell Signaling Technology, USA). protein A/G agarose beads were added to capture the immunoprecipitated complexes. RNA was eluted from the beads by incubation in 500 μL of elution buffer (5 mM Tris-HCl, pH 7.4; 1 mM EDTA, pH 8.0 and 0.05% sodium dodecyl sulfate) with 20 mg of proteinase K for 1 h at 60°C. Following ethanol precipitation, the input and m6A-enriched RNA were reversely transcribed with random primer, and the gene enrichment was determined by RT-qPCR. The primers of m6A-enriched gene mRNAs used in this study were shown in S2 Table.
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9

Chromatin Immunoprecipitation of SOX7 Targets

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Chromatin immunoprecipitation (ChIP) assays were performed as previously reported [50 (link)]. Samples immunoprecipitated by a normal IgG (Cat# 7074, Cell Signaling Inc., Beverly, MA, USA) and a SOX7 antibody (Cat# AF2766, R&D Systems) were analyzed with quantitative PCR using the FastStart Universal SYBR Green Master Mix (Roche Diagnostics GmbH, Mannheim, Germany) and the primer sets designed based on the promoter sequences of SPRY1, SLIT2, TRIB3 and MTHFD2 genes. The information of these primer sets is available in Table S1.
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10

ChIP-qPCR Analysis of MIR34 Promoters

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PBL-B were crosslinked, nuclear extracts sonicated, and mixed with 10 μg of antibodies H3 (Abcam ab791), H3K27me3 (Millipore 17-622) and 4 μg of antibody H3K4me3 (Active Motif 39159). Parallel preimmune control precipitation was performed by normal IgG (Cell Signaling 2729). DNA precipitated in the ChIP experiments was amplified by RT-qPCR at the promotors, transcription start sites (TSS) and genomic regions for MIR34A and MIR34B/C using the primers in Supplemental Table 1 a/b.
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