Sample description:

S_001	whole seedlings, grown in LL for 7 days on 0.5 MS + 1% sucrose at 23 C, before transfer
S_002	1h after transfer to liquid MS (1h mock control)
S_003	12h after transfer to liquid MS (12h mock control)
S_004	1h after transfer to liquid MS supplemented with 150 mM NaCl (1h salt stress)
S_005	12h after transfer to liquid MS supplemented with 150 mM NaCl (12h salt stress)
S_006	1h after transfer to liquid MS supplemented with 300 mM mannitol (1h osmotic stress)
S_007	12h after transfer to liquid MS supplemented with 300 mM NaCl (12h osmotic stress)
S_008	1h after transfer to liquid MS supplemented with 100 µM ABA (1h ABA treatment)
S_009	12h after transfer to liquid MS supplemented with 100 µM ABA (12h ABA treatment)
S_010	1h after transfer to liquid MS at 8 C (1h cold stress)
S_011	12h after transfer to liquid MS at 8 C (12h cold stress)
S_010	1h after transfer to liquid MS at 30 C (1h heat stress)
S_011	12h after transfer to liquid MS at 30 C (12h heat stress)


Sample preparation:

After seedlings had been grown for 10 days on solid MS medium at 21 C,
they were transferred to liquid MS medium containing no additives
(mock control), 200 mM NaCl (salt stress), 300 mM mannitol (osmotic
stress) or 100 µM ABA. For cold and heat stress, seedlings were
transferred to pre-chilled or pre-warmed liquid MS medium and
incubated at 8 C and 30 C, respectively. Samples were taken after 1 h
and 12 h of continuous stress treatment (3 biological replicates). RNA
was extracted from whole seedlings. For synthesis of targets, 1 µg of
total RNA was used as template for generation of cRNA using the
MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We
followed the manufacturer's instruction with one exception: For tiling
arrays, biotinylated NTPs were replaced by unmodified NTPs (stock
solution 25 mM each). 7 µg unmodified cRNA (for tiling arrays) was
converted into dsDNA (GeneChip(R) WT Double-Stranded cDNA Synthesis
Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using
the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany). 7.5 µg
dsDNA was fragmented and labeled using the GeneChip(R) WT
Double-Stranded DNA Terminal Labeling Kit (Affymetrix). Targets were
hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42 C. Arrays
were washed using a Fluidics Station 450, wash protocol
FS450_0001. Tiling arrays were scanned using a GeneChip(R) Scanner
3000 7G.