title: Transcription in roots of tomato near-isogenic lines in response to rapid-onset water       stress 
design: For each sample: ~1/4 of the root mass was ground in liquid nitrogen to a fine powder with a mortar and pestle 100 mg of each sample was processed using the Qiagen RNeasy mini kit Isolated RNA was quantified using Life Technologies Qubit RNA Broad Range Assay kit, and quality control was performed with the Agilent Bioanalyzer RNA 6000 Nano kit 10 µg of total RNA was used as input for the Bioo Scientific NEXTflex Poly(A) Beads isolation kit Isolated mRNA was quantified using the Life Technologies Qubit RNA High Sensitivity Assay kit Libraries were prepared using the Bioo Scientific NEXTflex Rapid RNA-Seq kit with NEXTflex RNA-Seq barcodes  Library quality control was performed on the Agilent Bioanalyzer with the DNA High Sensitivity DNA kit, and quantified via qPCR at the UC Berkeley Vincent J. Coates Genomics Sequencing Laboratory (GSL) All barcoded libraries were pooled and sequenced at the GSL on 12 lanes of single-end 50 sequencing on the Illumina Hi-Seq 2000 Reads from each sequencing lane were sorted with CASSAVA v1.8.2 