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Single-tube linear DNA amplification (LinDA) for robust ChIP-seq


Genome-wide profiling of transcription factors based on massive parallel sequencing of immunoprecipitated chromatin (ChIP-seq) requires nanogram amounts of DNA. Here we describe a high-fidelity, single-tube linear DNA amplification method (LinDA) for ChIP-seq and reChIP-seq with picogram DNA amounts obtained from a few thousand cells. This amplification technology will facilitate global analyses of transcription-factor binding and chromatin with very small cell populations, such as stem or cancer-initiating cells.

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Figure 1: Linear amplification of DNA.
Figure 2: ReChIP of RARγ-RXRα heterodimer using LinDA.

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We thank B. Jost, S. Vicaire and S. Le Gras for Illumina sequencing and mapping to the genomes, W. van Gool for help in the data analysis, A. Krebs for help with seqMINER and D. Ceschin advice on statistics and for critical reading of the manuscript. P.S. is a postdoc at the Ligue Nationale Contre le Cancer; M.W. is supported by fellowships of the Association pour le Recherche sur le Cancer and the Fondation pour la Recherche Médicale. This work was supported by funds from the Ligue Nationale Contre le Cancer (laboratoire labelisé) and European Community contracts LSHC-CT-2005-518417 'EPITRON', LSHG-CT2005-018882 'X-TRA-NET', LSHM-CT2005-018652 'CRESCENDO' and HEALTH-F4-2009-221952 'ATLAS'.

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P.S., L.M.T. and H.G. designed and optimized LinDA. M.-A.M.-P. performed the F9-cell experiments and did the bioinformatics analysis with P.S., and M.W. did the H3396-cell experiments. N.L. and L.W. performed the Illumina HiSeq 2000 sequencing and mapping to hg19 human genome assembly. H.G. and P.S. wrote the main text of the manuscript, which M.-A.M.-P. and L.M.T. corrected and improved; P.S. and L.M.T. wrote the Online Methods section.

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Correspondence to Hinrich Gronemeyer.

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Competing interests

H.G., P.S. and L.M.T. filed a patent application describing the methods presented here (European patent EP11305531.3).

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Supplementary Figures 1–6 and Supplementary Tables 1–2 (PDF 880 kb)

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Shankaranarayanan, P., Mendoza-Parra, MA., Walia, M. et al. Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nat Methods 8, 565–567 (2011).

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