RNA-seq of Quercus douglasii: leaf of seedling under drought and well-watered treatments
We imposed two short periods of drought stress to 48 seedlings germinated from seven maternal trees (also called families) from a single natural site in California, before harvesting and sequencing transcriptomes of all seedlings. Leaf tissue from all seedlings was sampled at two time points for RNA extractions: pre- and post-drought stress. Raw sequence reads were de-multiplexed allowing one mismatch per barcode.  Reads that failed the Illumina quality filter were removed, and remaining reads were converted to fastq format.  Adapter sequence was trimmed with Scythe version 0.994 BETA (Buffalo, 2011), and Sickle version 1.33 (Joshi & Fass, 2011) was used to trim low quality sequence from read ends falling below an average Phred score of 30 in a sliding window, followed by removal of reads less than 20 bp.  Low complexity sequences were removed with the Fastx Toolkit (Hannon, 2010).