Transcriptome analysis of the roots of Arabidopsis Col-0 and root-type FNR-deficient mutants
Transcriptome analysis of the roots of Arabidopsis Col-0 and root-type FNR-deficient mutants
The excised roots from 200 seedlings were snap-frozen with liquid N2 as one biological replicate. Sampling was done three times independently. The seedlings were vertically grown for 4 days on a solid medium containing 50 mL of 1/2-MS salts without vitamins (Code M0221; Duchefa Biochemie) supplemented with 0.05% (w/v) MES-KOH (pH 5.7), 1% (w/v) sucrose, and 0.5% (w/v) gellan gum (Fujifilm Wako) under a PPFD of 25 µmol m−2 s−1 (constant light) at 22°C. Frozen samples were ground with a Multi-Beads Shocker (Yasui Kikai) using zirconia beads (diameter: 5 mm). Total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions with on-column DNase digestion (Qiagen). RNA quality was evaluated with a Qubit RNA IQ Assay Kit (ThermoFisher Scientific). RNA samples with RNA IQs 9.8–10.0 were used for library preparation. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit with Sample Purification Beads, a NEBNext Poly(A) mRNA Magnetic Isolation Module, and a NEBNext Multiplex Oligos for Illumina (New England Biolabs, Tokyo, Japan).