characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-11-21T17:03:39Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-05-16T18:32:12Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104041779
characteristics.characteristic: External Id
characteristics.text: unspecified
characteristics.characteristic: INSDC center name
characteristics.text: 2017-11-21T17:03:39Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-05-16T18:32:12Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1705672
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5709:BR4_normoxia_28h
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: soybean
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCIT_C72010
characteristics.characteristic: common name
characteristics.text: BR4
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001236
characteristics.characteristic: cultivar
characteristics.text: Protocols: Soybean seeds from cultivar BR 4 were germinated on moist filter paper and maintained in a growth chamber at 25 ± 1ºC and approximately 90% relative humidity. The experiment was carried out in a greenhouse using a hydroponic system. Plantlets were transferred to polystyrene supports, which were placed on blue plastic boxes (59 cm × 38 cm × 16 cm) containing 36 L of Hoagland solution (Hoagland and Arnon, 1950). Plantlets were grown under natural daylight at 27 ± 3ºC (day) and 24 ± 2ºC (night), with humidity at 64 ± 9 (day) to 71 ± 5% (night) until the V1 stage (Fehr et al., 1971). The nutrient solution was kept at pH 6.6 and constantly aerated with atmospheric air. Plantlets were placed in a randomized block design comprising two oxygen conditions and three treatment sampling times, each with three biological replicates (four plantlets per replicate). At the V1 stage, the plantlets were randomly divided into two groups: plants under normoxia (the control condition with plantlets under constant atmospheric aeration) and plantlets under hypoxia (the nutrient solution was constantly bubbled with nitrogen gas). The oxygen concentration was determined before the start of the experiment. The boxes were sealed to avoid the reoxygenation of the nutrient solutions. The oxygen dissolved in the nutrient solution was measured using a portable oxymeter (HI 9146, Hanna). Normoxic conditions contained oxygen concentrations between 7.1 mg/L and 7.8 mg/L, whereas for the hypoxic group, the oxygen concentration was between 0.1 mg/L and 0.3 mg/L (Figure S1). Plantlets were maintained under normoxic (control plants) or hypoxic conditions for 0.5 h, 4 h, and 28 h. At each time point, root tissues were collected and immediately frozen in liquid nitrogen before being stored at −80ºC. Fehr WR, Caviness CE, Burmood DT, Pernnigton JS (1971) Stage of development description for soybeans [Glycine max (L.) Merrill]. Crop Sci. 11: 929-931. Hoagland DR, Arnon DI (1950) The water-culture method for growing for plants without soil. AES Circ. 347: 1-32. Total RNA was extracted from root tissues using Trizol reagent (Invitrogen) according to manufacturer instructions. RNA concentration and purity were measured using a spectrophotometer (NanoDrop, ND-1000), and the integrity of the molecules was analyzed on 1% agarose gels stained with ethidium bromide. For each of twelve treatments {two cultivars (Embrapa 45 and BR 4), two oxygen conditions [fully aerobic state (normoxy) and hypoxic], and three treatment sampling times (0.5h, 4h, and 28h), each with three biological replicates (four plantlets per replicate)}, equimolar quantities of purified total RNA from roots of twelve plants were pooled to result one library. The twelve libraries were sent to Fasteris SA (Plan-les-Ouates, Switzerland) for processing and sequencing. Libraries were prepared according to standard Illumina protocols and deep sequenced on the Illumina HiSeq 2000 platform. After processing the twelve libraries (poly-A purification, fractionation, cDNA synthesis using random primers, and ligation to bar-coded adapters), fragments of 150-250 pb were isolated and multiplexed, resulting one sequencing library (a pooled of equimolar quantities from twelve initial libraries; each library with a specific barcode for further bioinformatic discrimination). Then, sequencing library was used to produce clusters for a 1 x 100 bp single end-sequencing run into one lane on a flow cell for sequencing in a Hi-Seq 2000 (Illumina). The raw data was uploaded to the GeneSifter database (Geospiza, Seattle, WA) for alignment with the soybean reference genome (assembly Glyma 1.1) (Schmutz et al., 2010). The mapping of reads and transcripts analysis was done as described previously (Rodrigues et al., 2015). Rodrigues, F. A., Fuganti-Pagliarini, R., Marcolino-Gomes, J., Nakayama, T. J., Molinari, H. B. C., Lobo, F. P., et al. (2015). Daytime soybean transcriptome fluctuations during water deficit stress. BMC Genomics 16, 505. doi:10.1186/s12864-015-1731-x. Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183. doi:10.1038/nature08670.
characteristics.characteristic: description
characteristics.text: normoxia
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0001461
characteristics.characteristic: growth condition
characteristics.text: Glycine max
characteristics.characteristic: organism
characteristics.text: Glycine max
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_3847
characteristics.characteristic: organism
characteristics.text: root
characteristics.characteristic: organism part
characteristics.text: Glycine max
characteristics.characteristic: scientific_name
characteristics.text: BR4_normoxia_28h
characteristics.characteristic: title