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Chromatin Isolation via RNA Precipitation (ChIRP) Probe Sets

ChIRP is a rapid technique to discover RNA-associated DNA sequences and map genomic binding sites of chromatin associated long noncoding RNAs (lncRNAs) with high sensitivity and low background. This method allows you to map which chromatin regions come together for coordinated expression, determine which genes are expressed together, and learn the role of lncRNA in chromatin regulation. Target lncRNAs are affinity captured using antisense-oligos, designed by our ChIRP probe designer, and the lncRNA-associated DNA chromatin is sequenced to create a sequencing library. With the DNA sequence data, it is possible to generate a genomic binding site map at a resolution of several hundred bases.

ChIRP Probe Designer


ChIRP oligo sets can be designed at LGC, Biosearch Technologies' dedicated web-based designer and ordered directly. The oligos are delivered in plates with 5 nmol of each individual oligo per well, so that they may be combined into suitable sets.  We recommend using between 8 and 48 oligos per set. The linker we use is C3(Biotin); 3’ modification which is different than the one used originally, but has been approved by the originators of this technology. Buffers and other reagents for the complete ChIRP method are provided by EMD/Millipore. Biosearch Technologies and EMD/Millipore are exclusively licensed to provide ChIRP probe sets.

A protocol from the inventors of ChIRP, practical considerations, and a video demonstrating the protocol can be found here. Specific experimental questions should be directed to the authors. More literature references can be found under the Literature Reference tab of this page.

ChIRP Technology

Chromatin Isolation by RNA Purification (ChIRP) as first described by Chu et al. (1), reviewed by Chu et al. (2), and shown by Chu et al. (3), is covered under US Patent (4). Results from the successful practice of the method also has been published here (5, 6) and elsewhere.

We do not, however, offer technical support for the use of ChIRP probes.  The user is referred to practical considerations well explained and shown by Chu et al. in reference 3.  Specific experimental questions should be directed to the authors.

References

  1. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions Mol. Cell 44(4), 667-78. doi: 10.1016/j.molcel.2011.08.027
  2. Chu C, Spitale RC, Chang HY (2015) Technologies for illuminating long noncoding RNA function and mechanism. Nat. Struct. Mol. Biol. 22(1), 29-35 doi: 10.1038/nsmb.2921.
  3. Chu C, Quinn J, Chang HY (2012) Chromatin isolation by RNA purification (ChIRP). J. Vis. Exp. (61), e3912. doi: 10.3791/3912
  4. Chang HY, Chu C (2014) RNA interactome analysis. US Patent 8,748,354
  5. Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, Vergara IA, Davicioni E, Erho N, Ghadessi M, Jenkins RB, Triche TJ, Malik R, Bedenis R, McGregor N, Ma T, Chen W, Han S, Jing X, Cao X, Wang X, Chandler B, Yan W, Siddiqui J, Kunju LP, Dhanasekaran SM, Pienta KJ, Feng FY, Chinnaiyan AM (2013) The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat. Genetics 45(11), 1392-8. doi: 10.1038/ng.277
  6. Quinn JJ, Ilik IA, Qu K, Georgiev P, Chu C, Akhtar A, Chang HY (2014) Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification.Nat. Biotechnol. 32(9), 933-40. doi: 10.1038/nbt.2943

FAQs

  • Product Documentation:

    • Where can I find usage information and chemical properties for Biosearch Technologies' products?

      Product information sheets contain important usage information and chemical properties. You may download the product information sheets, by clicking on the appropriate link located under the Technical Specs tab of individual product pages. If for any reason you are unable to find what you need on our website, please e-mail our Technical Support team.

    • Does LGC Biosearch Technologies make Safety Data Sheets (SDS) available?

      Safety Data Sheets (SDS), formerly referred to as Material Safety Data Sheets (MSDS), are available for download under the Technical Specs or Related Info tabs found on most product webpages. If you are unable to access this document or need additional information, please contact our Technical Support team.

  • Shipping & Handling:

    • How do freeze thaw cycles affect oligonucleotides?

      Oligonucleotides should be subjected to minimum number of freeze-thaw cycles. Therefore, we recommend that you prepare aliquots and store microvials each having sufficient material for a day’s set of experiments and freeze at -20 °C or -80 °C.

      “The repetitive freezing/thawing of an oligonucleotide strand can lead to the undesirable decomposition of a sample through the loss of a terminal phosphate group, a base or the entire oligonucleotide unit. This observation relates to the fact that during the freezing/thawing process the oligonucleotide and buffer components isolate from the solvent system. As a result this isolation increases the percentage of similar intermolecular attractions and bond breakages.”

      Analysis of the degradation of oligonucleotide strands during the freezing/thawing processes using MALDI-MS. (Analytical Chemistry, Volume 72, Number 20, pages 5092 - 5096, 2000)

    • I left my oligonucleotides sitting on the lab bench over the weekend. Are they still ok to use?

      Dry oligonucleotides are quite stable at room temperature and not likely to degrade over the short term. We recommend they be moved into cold storage upon delivery or as soon as possible. Oligonucleotides in solution at high concentration can be stored refrigerated for a few days or even one week. At lower concentrations, oligonucleotides are more susceptible to degradation. In all situations, Dual-labeled BHQ® probes should be protected from light to avoid photo-bleaching.

    • Why were my oligonucleotides shipped at room temperature?

      Unless otherwise requested, we will ship our oligonucleotide products in a dried state, at ambient temperature, by overnight delivery. Dried products are very stable at ambient temperature and are not likely to degrade should there be unavoidable delays, e.g. customs clearance. Products in solution are more susceptible to degradation than dried products and must be shipped frozen.

    • How should orders be placed for shipment to locations outside the United States?

      LGC Biosearch Technologies maintains distribution agreements with partners in countries listed on our Distributors webpage. For all other countries, LGC Biosearch will ship internationally subject to local customs restrictions. All payments must be in US dollars.