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 oligo sets can be designed at LGC Biosearch's 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. LGC 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.