title: RNA-Seq of Coffea arabica: Globule callus
design: RNA extraction  Frozen tissues were ground to a fine powder in liquid nitrogen and total RNA were extracted using RNeasy plant Mini Kit (QIAGEN, Germantown, MD - USA) and treated with RNase free DNaseI (QIAGEN) according to manufacturers instructions. The quality and quantity of total RNA were analyzed by using Agilent 2100 Bioanalyzer RNA chip (Agilent Technologies Inc., Santa Clara, CA - USA). The RNA samples with a RNA integrity number (RIN) higher than 7.0 were selected and used for the subsequent analysis.   Illumina sequencing  RNA sequencing was carried out by Nestl Research (Lausanne, Switzerland). The cDNA libraries were generated using the TruSeq Stranded mRNA Kit (Illumina) followed by PCR amplification for sequencing on Illumina HiSeq 2500. Paired-end cDNA libraries were generated from all samples and sequencing was performed to generate the ~125bp paired-end reads. Quality control and assessment of raw Illumina reads in FASTQ format were done by FastQC software (v0.11.5) to obtain per base quality, Guanine-Cytosine content, and sequence length distribution. Clean reads were obtained by removing the low-quality reads, adapters, and poly-N-containing reads from raw data. Approximately 95% of high quality reads were obtained in each library from generated data. An average of 90 million paired-end reads was obtained for each library.