title: RNA-seq of coffea canephora FRT02: bean during maturation
design: RNA extraction, libraries preparation and RNA-Seq Coffee fruits were collected at four maturation stages (small green fruit (SG), large green fruit (LG), yellow fruit (Y) and red fruit (R) as published by Privat et al. 2008 (New Phytologist, Volume178, Issue4, June 2008, Pages 781-797, https://doi.org/10.1111/j.1469-8137.2008.02425.xDigital Object Identifier (DOI).  The bean 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 libraries were prepared from 250ng total RNA using the TruSeq Stranded mRNA Kit (Illumina) and indexed adapters. During the process, the poly(A) RNA was purified using poly-T oligo attached magnetic beads and then fragmented to convert to double stranded cDNA followed by library construction. Libraries were then pooled at an equimolar ratio and clustered on a paired-end sequencing flow cell (Illumina). Sequencing was performed with an Illumina HiSeq 2500 system at 2x100-base pair (bp) paired-end sequencing using the SBS v3 chemistry (Sequencing by Synthesis).  Primary data quality control was performed during the sequencing run to ensure the optimal flow cell loading (cluster density) and check the quality metrics of the sequencing run (QC30). RNASeq data obtained were demultiplexed and processed using bcl2fastq software.
library_name: CAGATC_L006
identifiers.namespace: SUB16081812
identifiers.id: CAGATC_L006