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Pierce Agarose ChIP Kit


A simple chromatin IP kit with a quick, optimized protocol.

Pierce ChIP Assay Kit for chromatin immunoprecipitation assays.The Thermo Scientific Pierce Agarose ChIP Kit provides a complete set of reagents and a simple, fast and reproducible protocol to perform chromatin immunoprecipitation (ChIP) assays.

The Pierce Agarose ChIP Kit contains sufficient reagents to perform 30 ChIP assays with appropriate controls using an optimized protocol and a convenient spin-column format. ChIP-validated and quality-guaranteed antibodies are also available for use the the Pierce Agarose ChIP Kit. Because antibodies that work for Western blotting may not function in ChIP assays, have assembled our most popular ChIP-validated monoclonal and polyclonal antibodies here to help you move from experimental setup to results more quickly.

Highlights:

  • Simple and fast ChIP assay protocol (< 8 hours)
  • Highly efficient isolation and lysis of nuclei
  • Easy and reproducible enzymatic digestion
  • Low-background and high-binding capacity Protein A/G agarose resin
  • Highly specific positive controls included: RNA polymerase II antibody and GAPDH PCR primers
  • Fast and reproducible spin-column format
  • High-recovery DNA purification
  • Choose a complete ChIP assay kit or the separate chromatin preparation module
  • ChIP-validated antibodies available

Product Details:

The strength of the ChIP assay is its ability to capture a snapshot of specific protein-DNA interactions as they occur in living cells, and then quantitate the interactions using standard or quantitive PCR. A successful ChIP assays requires a number of critical steps to be carried out (crosslinking, chromatin preparation, immunoprecipitation) prior to detecting the target genomic DNA sequence. Individually, each step in the ChIP assay protocol can be time consuming to optimize. The Pierce Agarose ChIP Assay Kit simplifies the process, making accurate and reproducible results easier to obtain.

To perform ChIP assays with the Pierce Agarose ChIP Kit, protein-DNA complexes are stabilized and then extracted. In vivo crosslinking is traditionally achieved with formaldehyde. Crosslinking performed directly in cells locks-in the protein-DNA complexes, trapping these unstable and sometimes transient interactions. To lyse, extract and solubilize the crosslinked complexes, the ChIP assay kit includes the Thermo Scientific Chromatin Prep Module (also sold separately, Part No. 26158). Together, this complete ChIP assay kit provides a simple, reliable and convenient means for isolating chromatin-bound DNA and enriching samples for the proteins of interest with less than 15% contamination from other cellular compartments - without a Dounce homogenizer.

ChIP assay preparation of genomic DNA with MNase vs Sonication. Micrococcal nuclease digestion is more reproducible than sonication for shearing crosslinked chromatin. HeLa cells were cultured in EMEM containing 10% FBS. Crosslinking was achieved by adding formaldehyde directly to cells in growth media to a final concentration of 1% and incubating for 10 minutes. Nuclei were isolated using the Thermo Scientific Chromatin Prep Module (Part No. 26158) and divided into four equal samples. Samples 1 and 2 were processed using a Branson Sonifier™, and enzyme digestion was performed on samples 3 and 4. Following nuclei lysis, crosslinking was reversed and samples were electrophoresed on a 1.2% agarose gel containing SYBR green for 1 hour. Gels were imaged with a UV light. MNase treatment delivered uniform results while sonication yeilded variable average fragments sizes.

Pierce ChIP assay kit has higher signal to ratio. The Thermo Scientific Pierce Agarose ChIP Kit has greater specific signal and less background than other kits. A431 lung carcinoma cells were cultured in DMEM containing 10% FBS for 24 hours. Following a 24 hour serum withdrawal, half of the cultures plated were treated with 100ng/mL EGF for 10 minutes. Crosslinking was achieved using a final concentration of 1% formaldehyde in the media for 10 minutes. ChIP assays were performed according to the manufacturers' protocols. Quantitive real-time PCR data was obtained with a Bio-Rad iQ5™ Thermocycler, Abgene Absolute SYBR Green Fluorescein QPCR master mix, and primers designed to amplify a region of the human MYC promoter proximal to the transcription start site. The Pierce Agarose ChIP Kit exhibited the highest signal to noise ratio.

ChIP assay for C/EBP, NeuroD and RNA Pol II on the cFOS proximal promoter. The Thermo Scientific Pierce Agarose ChIP Kit demonstrates binding of NeuroD, C/EBPα and RNA polymerase II to the proximal cFos promoter. SH-SY5Y wild type cells and a stable clone over-expressing TrkB (SH-SY5Y[TRKB]) were cultured for 3 hours in 0.2% charcoal dextran-treated media. Cells were then treated with 100ng/mL of BDNF for 15 minutes. Chromatin-Immunoprecipitation of the three targets using the appropriate antibodies and the Pierce ChIP Kit reveal increased binding to the cFOS promoter with BDNF treatment.

Transcription factor profiling using the Pierce ChIP Assay Kit
The Thermo Scientific Pierce Agarose ChIP Kit is effective for profiling multiple transcription factors. A431 lung carcinoma cells were cultured in DMEM containing 10% FBS for 24 hours. Following a 24 hour serum withdrawal, half of the cultures plated were treated with 100ng/mL EGF for 10 minutes. Crosslinking was achieved using a final concentration of 1% formaldehyde in the media for 10 minutes. ChIP assays were performed with the Pierce ChIP Kit to determine binding of phosphorylated-STAT3, acetylated-CBP, CBP, trimethyl histone H3, acetylated-histone H3, histone H3, and RNA polymerase II to the proximal MYC promoter. Primary antibody amounts were determined empirically. Quantitive real-time PCR data was obtained with a Bio-Rad iQ5™ Thermocycler, Abgene Absolute SYBR Green Fluorescein QPCR master mix, and primers designed to amplify a region of the human MYC promoter proximal to the transcription start site.

References:

  1. Lee, D.Y., et al. (2005). Role of protein methylation in regulation of transcription. Endocr Rev 26(2):147-70.
  2. Zeng, P.Y., et al. (2006). In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation. Biotechniques 41:694-8.
  3. Aparicio, O., et al. (2004). Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Cell Biol UNIT 17.7: 17.7.1-17.7.23.
  4. Wells, J. and Farnham, P.J. (2002). Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 1:48-56.
  5. Das, P.M., et al. (2004). Chromatin immunoprecipitation assay. Biotechniques 6:961-9.
  6. Yuichi, Y. and Hughes, D.E. (2006). C/EBPα and HNF6 protein complex formation stimulates HNF6-dependent transcription by CBP coactivator recruitment in HepG2 cells. Hepatology 43(2):276-86.

Related Resources:

Review of chromatin IP (ChIP) assay procedure and essential tools

Related Products:

Pierce Magnetic ChIP Kit
ChIP Validated Antibodies
Halt Protease and Phosphatase Inhibitors
Subcellular Fractionation Kits


Ordering Information
 
Product # Description Pkg. Size Instructions MSDS CofA Price
26156 Pierce Agarose ChIP Kit
Formulation: Multi-component kit
Sufficient For: 30 complete chromatin IP assay experiments

Kit Contents:
ChIP Grade Protein A/G Plus Agarose, 0.65mL
IP Dilution/Wash Buffer (5X), 11mL
IP Wash Buffer 3 (5X), 4.5mL
IP Elution Buffer (2X), 4.5mL
Column Accessory Pack, 3 packs
Microcentrifuge Tubes (1.5mL), 75 tubes
DNA Clean-Up Column, 40 columns
DNA Column Binding Solution, 30mL
DNA Column Wash Solution, 6mL
pH Indicator, 0.8mL
DNA Column Elution Solution, 5mL
Anti-RNA Polymerase II Antibody, 25µL
Normal Rabbit IgG (1mg/mL), 10µL
ChIP Positive Control Primers (GAPDH promoter), 100µL
Pierce Chromatin Prep Module (Part No. 26158)
30-rxn kit Product Instructions for product #26156 Pierce Agarose ChIP Kit MSDS for product #26156 Pierce Agarose ChIP Kit Certificate of Analysis for product #26156 Pierce Agarose ChIP Kit $488.00

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26158 Pierce Chromatin Prep Module
Formulation: Multi-component kit
Sufficient For: 30 chromatin preparations for ChIP assays

Kit Contents:
Membrane Extraction Buffer, 10mL
Nuclear Extraction Buffer, 10mL
MNase Digestion Buffer, 5mL
MNase Stop Solution, 0.5mL
Halt Protease and Phosphatase Inhibitor Cocktail EDTA-free (100X), 4 x 90µL
Sodium Chloride (5M), 3mL
Glycine Solution (10X), 15mL
PBS (20X), 15mL
Micrococcal Nuclease (ChIP Grade) (10 U/µL)
Proteinase K (20mg/mL), 0.25mL
DTT, Lyophilized, 1 vial
30-rxn kit Product Instructions for product #26158 Pierce Chromatin Prep Module MSDS for product #26158 Pierce Chromatin Prep Module Certificate of Analysis for product #26158 Pierce Chromatin Prep Module $250.00

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26159 ChIP-Grade Protein A/G Plus Agarose
Formulation: Protein A/G on crosslinked 6% beaded agarose, slurried in water with sodium azide
Sufficient For: Use in approx. 30 typical ChIP assays
0.65mL MSDS for product #26159 ChIP-Grade Protein A/G Plus Agarose Certificate of Analysis for product #26159 ChIP-Grade Protein A/G Plus Agarose $105.00

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26161 ChIP-Grade Protein A/G Plus Agarose
Formulation: Protein A/G on crosslinked 6% beaded agarose, slurried in water with sodium azide
Sufficient For: Use in approx. 500 typical ChIP assays
10mL MSDS for product #26161 ChIP-Grade Protein A/G Plus Agarose Certificate of Analysis for product #26161 ChIP-Grade Protein A/G Plus Agarose $1,103.00

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26160 Proteinase K
Formulation: Proteinase K diluted to 20mg/mL from stock with an activity of ≥ 30U/mg at 35°C
Sufficient For: Use in approx. 30 typical ChIP assays
0.25mL MSDS for product #26160 Proteinase K $84.00

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Instructions | MSDS | CofA
Product Instructions | MSDS | CofA  

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