design: High throughput transcription profiling of leaves from S.                 pennellii plants. Transcriptomic reads were mapped to the S. lycopersicum genome                 sequence enabling the identification of polymorphisms and quantification of the                 allele specific gene expression.
library_construction_protocol: Total RNA was extracted from: 1) 8th leaf from the                     apex of 8 week old plants of S. pennelli 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).