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RESEARCH PRODUCT

TAF-ChIP: An ultra-low input approach for genome wide chromatin immunoprecipitation assay

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Chromatin immunoprecipitation (ChIP) followed by next generation sequencing is an invaluable and powerful technique to understand transcriptional regulation. However, ChIP is currently limited by the requirement of large amount of starting material. This renders studying rare cell populations very challenging, or even impossible. Here, we present a tagmentation-assisted fragmentation ChIP (TAF-ChIP) and sequencing method to generate high-quality datasets from low cell numbers. The method relies on Tn5 transposon activity to fragment the chromatin that is immunoprecipitated, thus circumventing the need for sonication or MNAse digestion to fragment. Furthermore, Tn5 adds the sequencing adaptors while fragmenting the chromatin resulting in one-step generation of PCR ready library, which makes it an extremely simple approach with minimum hands-on time. The method can be directly implemented on sorted cells, and does not require de-multiplexing strategies to generate the profile from limited cell numbers. This can be very useful when the access to the starting material is restricted. Using our approach we generated the H3K4Me3 and H3K9Me3 profiles from 100 K562 cells and 1000 sorted neural stem cells (NSC) from Drosophila. We benchmarked our TAF-ChIP datasets from K562 cells against the ENCODE datasets. For validating the TAF-ChIP datasets obtained from Drosophila NSCs we performed conventional ChIP-Seq experiments in identical cell types. The epigenetic profiles obtained from both conventional ChIP-Seq and TAF-ChIP showed high degree of agreement, thereby underlining the utility of this approach for generating ChIP-Seq profiles from very low cell numbers.