design: High throughput transcription profiling of mature green fruits 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: 1) 8th leaf from the                     apex of 8 week old plants; 2) 8th leaf with 30% loss of fresh weight; 3) mature                     green fruits of S. lycopersicum, S. pennelli and Peri1 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).