Supplementary Information for sample sources: Global analysis of cytosine and adenine DNA modifications across the tree of life
Description
All the tissues, cell lines, yeast, and bacteria samples, unless differently stated, were extracted using Genomic Tip-20 kit (Qiagen) following the manufacturer's instructions. References 1. Allen, G. C., M. A. Flores-Vergara, S. Krasynanski, S. Kumar, and W. F. Thompson. 2006. “A Modified Protocol for Rapid DNA Isolation from Plant Tissues Using Cetyltrimethylammonium Bromide.” Nature Protocols 1 (5): 2320–25. 2. Gossmann, Toni I., Achchuthan Shanmugasundram, Stefan Börno, Ludovic Duvaux, Christophe Lemaire, Heiner Kuhl, Sven Klages, et al. 2019. “Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.” Current Biology: CB 29 (10): 1712–20.e7.
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DNA extracts were treated with RNase A (VWR, Cat.No. E866-5ML) at 37 °C for 45 min and DNA purification was performed according to the manufacturer’s instructions. Purified DNA was precipitated with isopropanol, washed with 70% ethanol, and resuspended in 10 mM Tris-HCl, pH 8.0. Quantification was done using a dsDNA BR Assay Kit (Qubit). The DNA sample was then digested into corresponding nucleosides using DNA Degradase Plus (Zymo Research, E2020). One µg of DNA was treated with 5 U of DNA Degradase at 37 °C for 2 h in a final volume of 25 μl and the reaction was inactivated, incubating the samples for 20 min at 70 °C as described by the manufacturer.