Rice cultivar, Koshihikari, was used as WT plant in the current study. After sterilisation, seeds were sown on ½ MS solid medium in a square petri dish and grown vertically in a growth cabinet under long day condition (16h light / 8h dark) at constant 30℃. After 3 days of growth, the root cap was excised and collected under a dissecting microscope for nuclei isolation. The crude extract was purified by FACS. The sorted nuclei were then loaded onto microfluidic chip (10X Genomics) to isolate and capture single nucleus. The sequencing library was constructed with reagent from a 3’ Gene Expression kit (10X Genomics) according to manufacture’s instructions. Sequencing was performed with an Illumina NovaSeq 6000 instrument to produce 150bp paired end reads to obtain the raw "fastq" files.The data contains all raw files in fastq format and processed gene-cell/nuclei matrix ("filtered-feature-bc-matrix"). The raw data was mapped to the Oryza sativa japonica rice reference genome by Cellranger-6.0.2 (10x Genomics) available from Ensembl in "igenome" of Illumina.