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. Overall design: In total 5 samples were generated from the F9 teratocarcinoma cell system: mRXRa-RARg-LinDA;mRXRa_100xfold-diluted_LinDA; mRXRa(1) and two others previously described in GSE30538 (mRXRa(2): !Series_sample_id=GSM757796; mRARg : !Series_sample_id=GSM757803). In addition, 14 samples were generated from the H3396 breast cancer cell system. Those samples containing the label "LinDA" has been amplified following the Linear DNA amplification method developed by Pattabhiraman et al. ((2011), Nature Methods 8, 565-67) prior library preparation for Solexa sequencing.