June 17, 2011

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

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

An international team of researchers has developed a new DNA technology which makes it possible to perform reliable analyses on DNA quantities that are a thousand times smaller than was previously the case. The method can be used, for example, to study small quantities of stem cells, starting tumour tissue, parts of plant and animal tissue, and archaeological samples. The team, which includes a researcher from Plant Research International, part of Wageningen UR, is publishing the new method in Nature Methods under the name LinDA.

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.

9 pages of supplemental information






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