Hypocotyl control and silicon, replicate 1
Frozen samples were ground to a fine powder using a mortar and a pestle. Total RNA was extracted from 100 mg of ground material using the RNeasy Plant Mini Kit according to the manufacturer's guidelines. An on-column DNase I treatment, were performed following the manufacturer's instructions. Total RNA integrity was evaluated using the RNA Nano 6000 assay and a 2100 Bioanalyzer, with quality parameters tailored for plant RNA profiles. Samples with RNA Integrity Numbers (RINs) below 8 were excluded from the study. RNA purity was assessed by measuring absorbance at 230 nm, 260 nm, and 280 nm with a Nanodrop ND1000 spectrophotometer. cDNA libraries were prepared from 1 g of purified, intact total RNA using the KAPA mRNA HyperPrep Kitt according to the manufacturer's instrucions. The libraries were analyzed and quantified as described in Legay et al. (2015). Pooled libraries were sequenced on an Illumina NextSeq2000 using the Illumina Mid Output Kit V2.5 (300 cycles) to generate 150 base-pair paired-end reads.