NP-40 permeabilized cells were digested with DNase I for 3 minutes at 22oC as previously described (Bert et al). A range of DNase I concentrations was used to get the optimal digestion, the initial amounts varied depending on the cell type. Following DNA purification, samples were analyzed by qPCR comparing the amount of PCR product generated between regions expected to be DNase I hypersensitive (e.g. TBP promoter) and regions which should not be cleaved (e.g. a gene desert region of chromosome 1). Optimally digested samples gave a ratio of ~0.7. DNA fragments (80-300bp) were isolated from favorable samples by agarose gel extraction and further validated by qPCR analysis before library preparation. Libraries were prepared from approximately 10ng DNA from DNaseI samples, according to manufacturer's instructions (Illumina).  Samples were sequenced using 50bp single end reads
GEO Accession
GSM2091498