ChIP-Seq from Limited Starting Material of K562 Cells and Drosophila Neuroblasts Using Tagmentation Assisted Fragmentation Approach

Junaid Akhtar; Piyush More; Steffen Albrecht

doi:10.21769/BioProtoc.3520

ChIP-Seq from Limited Starting Material of K562 Cells and Drosophila Neuroblasts Using Tagmentation Assisted Fragmentation Approach

Bio Protoc. 2020 Feb 20;10(4):e3520. doi: 10.21769/BioProtoc.3520.

Authors

Junaid Akhtar¹, Piyush More², Steffen Albrecht³

Affiliations

¹ Institute of Developmental Biology and Neurobiology, University of Mainz, Hanns-Dieter-Hsch Weg 15, 55128 Mainz, Germany.
² Department of Pharmacology, University Medical Center, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany.
³ Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Hsch-Weg 15, 55128, Mainz, Germany.

Abstract

Chromatin immunoprecipitation is extensively used to investigate the epigenetic profile and transcription factor binding sites in the genome. However, when the starting material is limited, the conventional ChIP-Seq approach cannot be implemented. This protocol describes a method that can be used to generate the chromatin profiles from as low as 100 human or 1,000 Drosophila cells. The method employs tagmentation to fragment the chromatin with concomitant addition of sequencing adaptors. The method generates datasets with high signal to noise ratio and can be subjected to standard tools for ChIP-Seq analysis.

Keywords: Easy workflow; High Signal-to-Noise ratio; High reproducibility; Low Input ChIP-Seq; Tagmentation.