ChIP-Seq (Chromatin Immunoprecipitation Sequencing)

By combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing, ChIP-Seq can be used to accurately survey interactions between protein, DNA, and RNA, enabling the interpretation of regulation events central to many biological processes and disease states.

Leveraging Illumina’s industry-leading sequencing technology, ChIP-Seq can identify a broad range of protein/nucleic acid interactions with confidence, generating millions of counts across multiple, indexed samples per lane for cost-effective and precise analysis.


TruSeq ChIP Library Preparation Data Sheet
TruSeq ChIP Library Prep Guide
TruSeq ChIP Library Prep Experienced User Card
TruSeq ChIP Library Prep Lab Tracking Form
TruSeq ChIP Sequencing Data Sheet
ChIP Sequencing Library Prep Guide


There are a number of third party software solutions available for ChIP-Seq data analysis, including MACS, an open-source solution available through Galaxy, as well as Avadis.

Avadis NGS

Avadis NGS

Avadis NGS is an integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports extensive workflows for RNA-Seq, small RNA-Seq, DNA-Seq, and ChIP-Seq experiments. The platform includes a number of biological interpretation and discovery tools that drive data analysis from raw reads to publishable results.
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ChIP-Seq Kits

Library Preparation Kits
TruSeq ChIP Library Prep Kit
SBS / Cluster Kits
A full list of kits compatible with your instrument may be found on the Systems page. For TruSeq ChIP sequencing, Illumina recommends using single reads of at least 50 bp.

Key Publications

Marban C, Su T, Ferrari R, Li B, Vatakis D, et al. (2011) Genome-wide binding map of the HIV-1 Tat protein to the human genome. PLoS One 6: e26894.

Fujiki R, Hashiba W, Sekine H, Yokoyama A, Chikanishi T, et al. (2011) GlcNAcylation of histone H2B facilitates its monoubiquitination. Nature 480: 557–560.

Botti E, Spallone G, Moretti F, Marinari B, Pinetti V, et al. (2011) Developmental factor IRF6 exhibits tumor suppressor activity in squamous cell carcinomas. Proc Natl Acad Sci U S A 108: 13710–13715.

Bernt KM, Zhu N, Sinha AU, Vempati S, Faber J, et al.  (2011) MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. Cancer Cell 20: 66–78.

de Almeida SF, Grosso AR, Koch F, Fenouil R, Carvalho S, et al. (2011) Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol 18: 977–983.

Wu H, D'Alessio AC, Ito S, Xia K, Wang Z, et al. (2011) Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473: 389–393.

View a complete, searchable list of Illumina publications.

FAQs (Frequently Asked Questions) and Support

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