title: Transcriptome analysis of salt stress response of Thellungiella halophila root
design: Total RNA extraction, mRNA purification, and cDNA library construction were conducted by LC Sciences (Houston, TX, USA). In brief, total RNA was obtained from roots using the total RNA purification kit (LC Sciences, Houston, TX, USA) as instructed, treated with RNAase free DNAase and re-purified with the RNeasy kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol.   cDNA synthesis was performed by using SMART II™ cDNA Synthesis kit (Clontech Laboratories, Inc., Mountain View, CA, USA) following manufacturer’s recommendations. Double stranded cDNA was run on a 2% agarose gel, and the cDNA with a length no less than 100 bp was separated by gel extraction. The concentration of cDNA was determined using Bioanalyzer 2100 (Agilent Technologies, Inc. Waldbronn, Germany). Approximately 5 µg of cDNA sample was sheared via sonication into small fragments, and then Roche GS-FLX 454 pyrosequencing was conducted according to the manufacturer’s recommendations.