Growth Protocol:	Briefly, plants were grown in a controlled environment growth chamber. Seedlings were transplanted into the pots filled with Turface (Profile Products, LLC) and were grown in tap water for two days after transplanting. For the remainder of the experiment the plants were supplemented with half strength Yoshida solution (pH 5.8). Temperatures were maintained at 28 °C and 25 °C in day and night respectively, relative humidity was maintained at 60% in both day and night. Lighting was maintained at 800 μmoles·m−2·s−1 using high pressure sodium lights.
Treatment Protocol:	Salinity stress (6:1 molar ratio, NaCl:CaCl2) was increased to 6 dS·m-1 gradually in two 3 dS·m-1 intervals over a period of 24h. After 24h of 6 dS·m-1, aerial parts of the seedlings were excised from the roots and frozen immediately in liquid nitrogen.
Extract Protocol:	The samples were ground with Tissuelyser II (Invitrogen) and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
Library Construction Protocol:	96 libraries were prepared using TruSeq RNA v2 library preparation reagents. Eighteen samples were sequenced per lane.

Molecule Type:	poly(A)+ RNA
Library Source:
Library Layout:	SINGLE
Library Strand:	-
Platform:	ILLUMINA
Instrument Model:	Illumina HiSeq 2500
Strand-Specific:	Unspecific