Fast genomic μChIP-chip from 1,000 cells.docVIP

Open Access M d 2009DahletVoal.lumeetho10, Issue 2, Article R13 Fast genomic μChIP-chip from 1,000 cells John Arne Dahl, Andrew H Reiner and Philippe Collas Address: Institute of Basic Medical Sciences, Department of Biochemistry, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway. Correspondence: Philippe Collas. Email: philippe.collas@medisin.uio.no Published: 10 February 2009 Received: 14 November 2008 Revised: 16 January 2009 Accepted: 10 February 2009 Genome Biology 2009, 10:R13 (doi:10.1186/gb-2009-10-2-r13) The electronic version of this article is the complete one and can be found online at /2009/10/2/R13 ? 2009 Dahl et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. RapidpA nμeChIP-chipw met od for rapid genome-wide μChIP-chip from as few as 1,000 cells./p Abstract Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report here a fast microChIP (μChIP) assay for 1,000 cells in combination with microarrays to produce genome-scale surveys of histone modifications. μChIP-chip reliably reproduces data obtained by large-scale assays: H3K9ac and H3K9m3 enrichment profiles are conserved and nucleosome-free regions are revealed. Background tions, a few ChIP-PCR strategies have recently been reported. A carrier ChIP protocol [8] entails immunoprecipitation of chromatin from 100-1,000 mouse cells by mixing with mil- lions of Drosophila cells; however, the assay takes several days and is unsuitable for genom