design: High throughput transcription profiling of leaves under water                 defecit conditions from a periclinal chimera of S.lycopersicum and S.pennellii                 plants. Mapping of the transcriptomic reads to the S. lycopersicum genome sequence                 and their allele at the predicted polymorphic positions indicated to which species                 each read belongs and thus, the layer specific gene expression was                 defined.
library_construction_protocol: Total RNA was extracted from 8th leaf with 30% loss                     of fresh weight of periclinal chimera plants. PolyA RNA was isolated by                     homogenization of frozen ground tissue in RNA extraction buffer (8M guanidinium                     hydrochloride; 20mM MES; pH7) and phenol:chloroform:isoamyl alcohol (v/v                     50:48:2). After centrifugation the aqueous phase was re-extracted with                     phenol:chloroform: isoamyl alcohol and then subjected to three successive                     precipitations with ethanol/sodium acetate; 4M LiCl; and ethanol/sodium acetate.                     The final pellet was washed in 70% ethanol and re-suspended in                     diethylpyrocarbonate treated water. Highly purified poly(A)+ RNA was prepared                     using Magnetight Oligo(dT) Particles, Straight A’s TM mRNA Isolation System                     (Novagen, Inc.) following the manufacturer’s instructions. . Whole transcriptome                     libraries were prepared from each sample, following the procedures of the SOLiD                     Whole Transcriptome Analysis Kit (Life Technologies). Libraries were barcoded                     and pooled prior to ePCR amplification. One flowcell was loaded and 50bp                     fragments were sequenced with a SOLiD version 3 instrument (Life Technologies,                     Carlsbad, CA, USA).