6533b82afe1ef96bd128c22d

RESEARCH PRODUCT

MOESM1 of Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning

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Additional file 1. Overview of the method. A) A diagram with the main protocol steps is shown. The fragments to be sequenced were isolated from an ethidium bromide-stained gel (see the example in the figure). The naked DNA samples were visually matched to the chromatin samples by choosing those with a similar maximum fragment size (arrow). Then, the mononucleosome-sized fragments (squares) were isolated. B) The chromatin (blue and red) and naked DNA signals (green) over the STL1 gene are shown as examples of the results, analyzed by qPCR. The chromatin data are presented before (blue) and after (red) the naked DNA correction. C) The naked DNA signal in the STL1 gene from different Saccharomyces cerevisiae strains. The qPCR results from each naked DNA digestion were standardized and represented as z-scores. D) Some examples of the results analyzed by massively parallel sequencing. The profiles represent the density of nucleosomes dyad axes calculated by DANPOS.