GSM5903342: Leaf_rep1; Oryza sativa Japonica Group; OTHER
Genomic DNA was extracted using a DNeasy Plant Mini Kit (Qiagen) following the manufacturer's instruction, and 100 ng was used for ALE-seq following the previously described protocol (Cho et al., 2019). Libraries for ALEseq (https://doi.org/10.1038/s41477-018-0320-9) were prepared following the previously described protocol (Cho et al., 2019), with minor modifications. Briefly, an adapter, containing T7 promoter sequence at its 5' end, was ligated to the end of extrachromosomal DNA, following by in vitro transcription with T7 RNA polymerase. The synthesised RNA was then reversed transcribed using the primer binding the transcripts at the LTR-TE conserved PBS site. the obtqained cDNA was amplified following the standard ALE-seq procedure.