title: enome-Wide DNA methylation Analysis in response to salinity stress in Caliph medic: Control
design: DNA samples were separately extracted from roots of 10 saline-treated and untreated roots. Methyl-MaxiSeq™ libraries were prepared from 500 ng of genomic DNA digested with two units of Zymo Research’s (ZR) dsDNA Shearase™ Plus. The fragments produced were end-blunted and 3’-terminal-A extended, then purified using the Zymo Research (ZR) DNA Clean & Concentrator™ – 5 kit. The A-tailed fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine and the adapter-ligated fragments were filled in. Bisulfite treatment of the fragments was done using the EZ DNA methylation – Lightning kit. PCR was carried out with Illumina TruSeq indices and the size and concentration of the fragments were confirmed on the Agilent 2200 TapeStation, then sequenced on an Illumina Hiseq instrument.