Determining how proteins interact with DNA to regulate gene expression is essential for full understanding of many biological processes and disease states. Specific DNA-protein interaction sites can be isolated by chromatin immunoprecipitation (ChIP). Illumina combines whole-genome ChIP with massively parallel DNA sequencing to identify and quantify binding sites for DNA-associated proteins. The TruSeq ChIP protocol enables researchers to cost-effectively and reliably identify binding sites for a broad range of targets across the entire genome with high resolution and without constraints.

The streamlined TruSeq workflow reduces the number of purification, sample transfer, pipetting and clean-up steps, with TruSeq universal adapters further improving efficiency and enabling robust multiplex sequencing. The TruSeq ChIP process begins with the enrichment of specific cross-linked DNA-protein complexes using an antibody against a protein of interest (A-B). The stretches of DNA bound to the target protein are then isolated and used as input DNA for library generation. DNA fragments are end-repaired and an 'A'-base added to the blunt ends of each strand, preparing them for ligation to the sequencing adapters (C-D). Each TruSeq adapter contains a 'T'-base overhang on the 3'-end providing a complementary overhang for ligating the adapter to the A-tailed fragmented DNA (E). Final product is created (F) and after size selection, all of the ChIP DNA fragments can be simultaneously sequenced (single-read or paired-end) on all Illumina sequencer, including the MiSeq or any instrument in the HiSeq system family. 

TruSeq ChIP Highlights

• Proven TruSeq Data Quality: Most complete and accurate profile of target protein:DNA interactions
• Low DNA Input Requirement: Robust results from just 5 ng DNA for a range of sample sources
• Simple, Streamlined Workflow: Enhanced scalability with an easy-to-use, simplified workflow
• Multiplexed Sequencing with 24 Available Indexes: Optimize sequencing output distribution across samples, reducing cost per sample