cDNA libraries were constructed from 18 leaf and two floret samples using a TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, CA, USA) following the manufacturer’s instructions. Library quality was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and quantified via quantitative real-time PCR (qPCR) (Illumina protocol SY-930-10-10). Clustering was performed using a TruSeq Paired-End Cluster Kit on a cBot (Illumina Inc.). Paired-end sequencing was performed on an Illumina Genome Analyzer IIx Platform with TruSeq SBS 36-Cycle kits (Illumina Inc.) following the manufacturer’s specifications. RNA-seq was performed with floret libraries in two separate lanes without biological replicates. The remaining 18 leaf libraries from six different accessions (Table 1 ), each with three biological replicates, were distributed randomly in the flow cell with three libraries per lane.
The raw data was converted to FastQ files containing 72-bp reads. Quality control was performed using the NGS QC Toolkit v2.3.3 [52 (link)]. Initially, high-quality reads (Phred quality score ≥ 20 in at least 75% of bases) and reads with more than 60 bases were selected. Subsequently, reads were trimmed at the 3′ end for the removal of barcodes.
The raw data was converted to FastQ files containing 72-bp reads. Quality control was performed using the NGS QC Toolkit v2.3.3 [52 (link)]. Initially, high-quality reads (Phred quality score ≥ 20 in at least 75% of bases) and reads with more than 60 bases were selected. Subsequently, reads were trimmed at the 3′ end for the removal of barcodes.
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