RNA-seq of Phaseolus vulgaris roots under conventional farming
Roots from line A25 managed under conventional farming were manually collected during early flowering. After carefully removing the soil, the roots were excised and stored in tubes for RNA extraction. Frozen common bean roots were mechanically homogenized using a TissueLyser II (Qiagen) equipped with a pre-chilled tube holder. The resulting powder was used for total RNA extraction with the NZY Total RNA Isolation Kit (NZYTech), following the manufacturers instructions. RNA concentration and integrity were assessed using an Agilent 2100 Bioanalyzer and the Agilent RNA 6000 Nano Kit. RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). mRNA was enriched by poly-A selection using the NEBNext Poly(A) mRNA Magnetic Isolation Module. The isolated mRNA was reverse transcribed into cDNA, and sequencing adapters were ligated to the fragments. Libraries were sequenced using paired-end 150 bp reads on an Illumina NovaSeq 6000 platform at Macrogen (Seoul, South Korea).