title: Illumina HiSeq 2500 sequencing; Bisulfite-Seq and RNA-seq in rootstock of Arabidopsis thaliana grafts
design: Bisulfite-Seq and RNA-seq in rootstock of Arabidopsis thaliana grafts
library_construction_protocol: Plants of Arabidopsis thaliana accessions Col-0 and C24 were utilized in our experiments, as well as a previously described dcl2-1/dcl3-1/dcl4-2 triple mutant (Col-0 background). The C24 plants harbored a GFP transgene silenced by a partial GFP inverted-repeat, termed GxGF-IR. Arabidopsis plants were grown under 10 h supplemental fluorescent lighting at 20ºC, on vertical plates of 0.8% agar, 1⁄2 Murashige and Skoog media, pH 5.7. Micrografting was conducted seven days after germination.Plant tissue was harvested five weeks after grafting, taking care to separate root from scion and exclude tissue 0.3-0.5 cm surrounding the graft junction. RNA-seq libraries were prepared from total RNA extracted as previously described in Molnar et al (Science 2010, 328, 872–875). RNA-seq libraries were generated with the ScriptSeq RNA-seq Library Preparation Kit (Epicentre) according to the manufacturer's instructions.