Analytical dataset of short-term heat stress induced reshuffling of metabolism and transcriptomes in maize grown under elevated CO2

This data article describes the analysis of sudden heat stress (SHS) induced transcriptomes and metabolism in SQ maize cultivar (Zea mays L. cv. Silver Queen). Plants were grown under elevated CO2 in both field based open top chambers (OTCs) and indoor growth chamber conditions [1]. After 20 days after radicle emergence, intact leaf section of maize was exposed for 2 hours to SHS treatment. Samples were stored in liquid nitrogen immediately and used thereafter for metabolism and transcriptomes determinations. Metabolism consisting of 37 targeted metabolites together with corresponding reference standard were determined by gas chromatography coupled to mass spectrometry (GC-MS). Total RNA was extracted using TRIzol® reagent according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). RNA integrity was assessed using RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Transcriptomes were determined by Illumina Hiseq 4000 platform. Further interpretation and discussion on these datasets can be found in the related article entitled “Elevated CO2 concentrations may alleviate the detrimental effects of sudden heat stress on photosynthetic carbon metabolism in maize” [1].

may alleviate the detrimental effects of sudden heat stress on photosynthetic carbon metabolism in maize" [1].
© 2019 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data
The data collected for SQ maize cultivar exposed to combined effects of elevated CO 2 and sudden heat stress is presented in five segments of data: A) The relatedness of biological samples in four combination of CO 2 and SHS regarding to transcriptomes and metabolism in field OTCs conditions as shown in Fig. 1; B) Statistical analysis on sequencing quality across all bases from transcriptomes analysis in field OTCs (Figs. 2 and 3; Table 1); C) GO and KEGG analysis on enriched biological pathway involved in SHS and CO 2 response (Tables 2e3); D) Abundance of heat shock protein based on transcriptomes in different SHS and CO 2 treatments in growth chamber (Table 4); E) Photosynthetic carbon metabolites and the gene expression of their catalysing enzymes induced by SHS and CO 2 effects ( Fig. 4; Tables 5e6). The data included herein are based on the experimental results provided in a previous publication by present authors [1].
Specifications Table   Subject Agricultural and Biological Sciences (General) Specific subject area Heat stress induced modulation in metabolism and transcriptomes in maize Type of data Tables

Value of the Data
The experimental data presented herein as well as in Ref. [1] can be used to better understand the response of global gene expression in maize under multiple stress conditions. The generated datasets specifically provide information on the beneficial effect of elevated CO 2 on photosynthetic carbon metabolites in response to sudden heat stress treatments. The expression of heat shock protein in response to CO 2 treatments can be also learned from this study. Positive relationship regarding the photosynthetic carbon metabolites between field-based open top chambers (OTCs) and indoor growth chamber was investigated herein. The data can be used for reference of metabolite quantification and allow other researchers to extend the statistical analysis.

Materials and growth condition
SQ Corn seeds were supplied by the maize germplasm information resources from the United States of America, USA (GRIN: http://www.ars-grin.gov/). Experiments were conducted in both fields-based open top chambers (OTCs), and indoor conditions. The location of field is at Beltsville Agricultural Research Center (BARC), USDA-ARS (39e00 0 N, 76e56 0 W). The designed 4/4 random blocks for the experiment are as displayed in Fig. 5A. After germination, Corn seedlings were sown in 16 OTCs. The dimension for each OTC is: 2 m long, 2 m width and 2 m height (Fig. 5B). The interval between chambers is uniformly spaced by 2 m, to minimize shading effect. Maize seedlings for 7 days after radicle emergence were transplanted and spaced by 15 cm between each other as well. The soil in each OTC keeps moist by watering once a week. Plants in OTC are exposed to ambient air or ambient air plus 180 ppm CO 2 , as described elsewhere [2].
For indoor chambers, plants were grown under either ambient CO 2 (380 mmol mol À1 ) or high CO 2 (560 mmol mol À1 ) concentrations, as described earlier [3]. Day and night temperatures were 29/17 C,     Note: Metabolic responses of maize leaves to CO 2 and heat stress treatments were presented as: ambient CO 2 with non-heat stress (Amb_noSHS), elevated CO 2 with non-heat stress (Elv_noSHS), ambient CO 2 with heat stress (Amb_SHS), elevated CO 2 with heat stress (Elv-SHS). One-way ANOVA was used to estimate the significant effects of CO 2 and heat stress on each metabolite in maize leaves, while different alphabet letters represent significant difference at P < 0.05.
with soil temperature average of 25.7 ± 0.33 C/14.8 ± 0.41 C day/night. The light intensity and photoperiod were 1000 mmol m À2 s À1 and 12/12 h, respectively. Local air humidity was 60% during the day time.

Experimental design
SQ corn variety grown in fields OTCs and growth chambers for 20 days under ambient and high concentrations of CO 2 as mentioned above. The marked part of the whole intact leaves is placed in a water jacketed leaf chamber (Fig. 5C), with the internal radiator and fan for 2 hours of SHS treatment as described earlier [4]. By circulating heated water from the temperature control tank to the leaf cuvettes  ( Fig. 5C), the air temperature in the cuvette could increase to approximately 45 C. Air from the OTCs is constantly flushed through each leaf cuvette. Untreated or heat-treated leaves were immediately stored in liquid nitrogen for transcription and metabolic analysis.

Metabolism measurements
Leaves from six different plants around 20-day old were used ( Fig. 5D) for metabolic measurements.
30 mg leaf tissue with frozen dried is squashed by adding 3.2 mm ceramic beads and 100 ml fine pomegranate powder in 2.0 mL Eppendorf tube, followed by homogeniztion with a Tissue Lyzer ball mill at 30 cycles s À1 as previously described [4]. The squashed samples were subsequently dissolved using 50 ml mixture consisting of 2.5 mM alpha-aminobutyric acid, 2.0 mg ribitol and 1.4 mL cold 70% methanol and vortexed. Then the mixture was incubated in a water bath at 45 C for 15 min. After centrifugation for 5 min at 12,000 g, super-fluid was gently transferred to a 15 mL fresh conical plastic centrifuge tube. The particles are washed once with 70% methanol, and the supernatants were combined with prevoius step. Finally, the mixed supernatants were air-dried overnight and used for determination of starch as previously described [5]. Organic acids, amino acids and soluble carbohydrates were measured by gas chromatography coupled to mass spectrometry (GC-MS) as described elsewhere [6]. Derived samples are performed by GC-MS equipped with mass selective detection (7890 GC system, 7693 automatic sampler, 5975C idle XL MSD). Total ion chromatograms obtained were quantified using Agilent MSD Chemstation software program. Independent standard curves were prepared for each set of extractions with known mixtures of organic acids, amino acids and soluble carbohydrates. Ribitol added during extraction process as internal standard. Compounds in organic acid fraction: 2-oxoglutaric, quinic acid, adipic acid, shikimate, pyruvate, citrate, aconitate, maleic acid, malate, oxalic acid, malonic acid, glyoxylate, fumarate and succinate. Compounds in soluble carbohydrate fraction were: ribose, fructose, glucose, myo-inositol, sucrose, maltose, mannose, trehalose, raffinose and starch. The compounds present in amino acids fraction: leucine, Isoleucine, alanine, glycine, serine, valine, threonine, proline, putrescine, aspartate, glutamate and phenylalaine. Five biological replicates, with three technique replicates for each biological one, were conducted for metabolic measurements. Values of standard error (SE) were calculated based on data from three technique and five biological replicates. One-way analysis of variance (ANOVA) via software SPSS 10.0 (SPSS Inc., USA) was applied to identify significant differences between heat stress and CO 2 treatments for specific metabolite in SQ maize cultivar leaves.

Transcriptomes measurements
Total RNA was extracted using TRIzol® reagents, following manufacturer's instructions (Invitrogen, Carlsbad, California). Quality and purity of RNA were determined by 1% of agarose gels and nano-drop (IMPLEN, California, USA), respectively. RNA integrity was evaluated via Agilent Bioanalyzer 2100 system (Agilent Technologies, California, USA). The total amount of RNA per sample was normalized to 1.5 mg, which was used as an input for RNA sequencing. Sequencing libraries were generated using NEB-Next® UltraTMRNA Library Prep Kit for Illumina® (NEB, USA). Sequencing libraries was featured by Illumina Hiseq 4000 platform with 150bp pair-read was generated [7]. The original read was aligned with B73 reference genome (RefGen_v3), using TopHat2.0.8 and STAR, with a minimum inner length set to 20bp. The gene and heterogeneous are quantified using the GTF annotation file generated by PacBio sequencing. To reduce transcription noise, gene is included only if FPKM value is < 0.01. The value is selected based on the genetic coverage saturation analysis as reported previously [8].