Supplemental Table S2.Details of studies from which the expression data shown in the figures and other supplemental tables were obtained. All data were extracted from (Hruz et al. 2008). Where data relate to a specific original publication, the reference is cited.

ReferenceTreatment

Pandey et al. 2013 (drought 1)Rosette leaf samples of Col-0 grown for 21 day on soil without water limitation, then subjected to drought stress by withholding water for 9 days (soil moisture dropped to 30%). Other growth conditions: 16h light (120µmol photons m-2 s-1) / 8h dark cycles; 22°C.

Bhaskara et al. 2012 (drought 2)Seedling samples of Col-0 grown for 7 days on vertically oriented plates with solid 1/2 strength Murashige and Skoog medium pH 5.7 (medium water potential = -0.25MPa), then transferred to PEG-infused plates (medium water potential = -1.2MPa) for 4 days. Other growth conditions: continuous light (80-100μmol photons m-2 s−1), 25°C.

Pandey et al. 2010 (ABA)Arabidopsis plants were grown in growth chambers with an 8 hr light/16hr dark. Samples were treated with ABA (50 μM) or EtOH (solvent control) for 3 hrs. For each type of sample three independent biological replicates were performed.

Kinoshita et al. 2012 (osmotic)Shoot samples of Col-0 grown hydroponically for 30 days in basal MGRL medium, then subjected to osmotic stress for 3h by adding 0.3M mannitol to the medium. Other plant growth conditions: 12h light (150µmol photons m-2 s-1) / 12h dark cycles; 22°C.

Jung et al. 2007 (salt)Rosette leaf samples from 5-weeks-old Col-0 plants, treated with 250 mM NaCl for 24h.

Davletova et al. 2005 (external H2O2)Col-0 seedlings (5-day-old) were treated with 20 mM H2O2 for1 hour and compared with untreated controls.

Col-0 plants were grown for 2 weeks (16h light (120 μmol m−2 s−1) / 8h dark cycles, 23°C, 65–70% relative humidity) and then removed from soil and floated with adaxial surfaces facing the light source in 50μM MV, 0.01 % (v/v) Tween 20 solution for 2h at 120 μmol m−2 s−1 illumination, 23°C. After MV treatment aerial parts were separated from roots. The controls were treated with 0.01 % (v/v) Tween 20 solution for 2h.

Laloi et al. 2007 (flu mutant)Col-0 and the flu mutant were grown in long days for 3 weeks and harvested after and re-illuminated for 120 min following the dark period.

Queval et al. 2012 (cat2 mutant)Plants were grown for 5 weeks at high CO2) and then transferred to air for 2 days in either a short day growth regime (8h light/16h dark) or a long day regime (16h light/8h dark), both at 200 μmol m−2 s−1)

Bhaskara GB, Nguyen TT, Verslues PE (2012) Unique drought resistance functions of the highly ABA-induced clade A protein phosphatase 2Cs. Plant Physiol 160: 379-395

Davletova S, Schlauch K, Coutu J, Mittler R (2005)The zinc-finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol139: 847-856

Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W,Zimmermann P (2008)Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Advances in Bioinformatics 420747

Jung C, Seo JS, Han SW, Koo YJ, Kim CH, Song SI, Nahm BH, Choi YD, Cheong JJ (2008) Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis.Plant Physiol 146: 623-635

Kinoshita N, Wang H, Kasahara H, Liu J, MacPherson C, Machida Y, Kamiya Y, Hannah MA, Chua N (2012) IAA-Ala Resistant3, an evolutionarily conserved target of miR167, mediates Arabidopsis root architecture changes during high osmotic stress. Plant Cell24: 3590-602

LaloiC, Stachowiak M, Pers-Kamczyc E, Warzych E, Murgia I,Apel K (2007) Cross-talk between singlet oxygen- and

hydrogen peroxide-dependent signaling of stress responses in Arabidopsis thaliana. Proc Natl Acad Sci USA104: 672-677

Pandey S, Wang RS, Wilson L, Li S, Zao Z, GookinTE, Assmann SM, Albert R (2010) Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action. Mol Syst Biol 6:372

Pandey N, Ranjan A, Pant P, Tripathi RV, Ateek F, Pandey HP, Patre UV, Sawant SV (2013) CAMTA 1 regulates drought responses in Arabidopsis thaliana. BMC Genomics14: 216

Queval G, Neukermans J, Vanderauwera S, Van Breusegem F, Noctor G (2012)Day length is a key regulator of transcriptomic responses to both CO2 and H2O2 in Arabidopsis. Plant Cell Environ 35: 374-387