RNA-seq of Root and Shoot from Arabidopsis thaliana
As described in Oh et al. (2014), PMID:24563282.  In short: Schrenkiella parvula and Arabidopsis (Arabidopsis thaliana Col-0) plants were grown on root wash mix soil (Plant Care Facility, University of Illinois at  -Champaign) in a growth chamber with a 14-h-day/10-h-night cycle, 130 mmol m22 s21 light intensity, and 22°C to 24°C temperature. Plants were watered every other day, with a supplement of one-twentieth-strength Hoagland solution once every 6 d. For RNA-seq experiments, root and shoot tissues were pooled from 10 4-week-old plants. Plants grown in different batches were sampled for three biological repeats. Total RNAs extracted with the RNeasy Plant kit (Qiagen) were processed using TruSeq RNA Sample Prep Kits version 2 (Illumina) and sequenced by the HiSeq2000 system (Illumina). AtR1, AtR2, and AtR3 are derived from root tissue samples, and AtS1, AtS2, and AtS3 are from shoot (aerial part of the plants) samples.