RNA-Seq of Cucumis sativus: White Dadagi flesh
For RNA isolation, fresh cucumber samples were homogenized in liquid nitrogen using a mortar and pestle. The homogenized sample was transferred into Eppendorf-tubes filled with TRI reagent solution and stored at 80 C until RNA purification. Library preparation and RNA sequencing were performed using the Illumina Hiseq4000 platform by Macrogen (Seoul, Korea) (http://www.macrogen.com; accessed December 25, 2021). Prior to RNA sequencing, a 2100 Bioanalyzer (Agilent, Bblingen, Germany) was used to determine the total RNA quality and amount separated from the samples. For library preparation, we confirmed that all samples had RNA integrity  7.5. Library construction was performed by using the TruSeq Stranded mRNA LT sample prep Kit (Illumina, San Diego, CA, USA) by Macrogen (Seoul, Korea). Raw data were trimmed by filtering according to the following criteria: unpaired reads, empty nucleotides, adaptor-only nucleotides, short reads (< 36 bp), and low-quality nucleotides (Q-value: Phred quality value  20). Processed reads were aligned to Cucumis sativus (GCF_000004075.3_Cucumber_9930_V3) using HISAT2 (version 2.1.0). After alignment, aligned reads were assembled into transcripts using StringTie (version 2.1.3b).