Comment[GEAAccession]	E-GEAD-428
MAGE-TAB Version	1.1
Investigation Title	DNA microarray analysis of gene expression of etiolated maize seedlings grown under microgravity conditions in space
Experiment Description	This data introduces the use of microarray data technology with the Agilent Maize Oligo Microarray (Design ID 016047) to characterize global changes in the transcript abundance of etiolated Zea mays (cv. Golden Cross Bantam) seedlings grown under microgravity (micro-g) conditions on the International Space Station (ISS) compared with those grown under 1 g conditions on Earth. Gene array data were analyzed according to stringent criteria that restricted the scored genes for specific hybridization values at least two fold. Of the 32152 - 32616 transcripts detected, 1030 and 590 transcripts were significantly different in the coleoptiles and in the mesocotyls. Of the transcripts detected, 877 and 428 transcripts were found to increase under micro-g conditions in the coleoptiles and the mesocotyls, respectively. Venn diagram analysis showed that 154 transcripts commonly increased and 10 decreased under micro-g conditions irrespective of the organ difference. Of these, phytohormone-related genes were focused, indicating that some of them were responsive to gravity. These results support the commonly accepted idea that phytohormone-related genes play a significant role in regulating plant growth and development under different gravity conditions.
Experimental Design	stimulus or stress design
Experimental Factor Name	gravity] Factor Value[tissue
Experimental Factor Type	gravity] Factor Value[tissue
Person Last Name	Kamada
Person First Name	Motoshi
Person Affiliation	Future Development Division, Advanced Engineering Service Corporation
Person Roles	submitter
Public Release Date	2021-05-14
Protocol Name	P-GEAD-814	P-GEAD-815	P-GEAD-816	P-GEAD-817	P-GEAD-818	P-GEAD-819
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol
Protocol Description	Maize (Zea mays L. cv. Golden Cross Bantam) was used in the ISS space experiment. As the seed bed, dry rockwool block (the thickness: 32 mm; Culture Mat; Nippon Rockwool, Tokyo, Japan) was fitted in an acrylic resin maize box (W 62 mm ???????? D 100 mm ???????? H 150 mm), which had six holes (1 cm in diameter) and covered with the hydrophobic fluoropore membrane, MilliSeal (Merck Millipore, Tokyo, Japan) for ventilation was used. Twenty dry maize seeds were inserted beneath the block surface with the seed axis longitudinal to the maize box. After an astronaut supplied 120 mL of water (Milli-Q water, autoclaved) to each maize box, the boxes were kept in the Measurement Experiment Unit, and then placed in the micro-g compartment in an incubator, the Cell Biology Experiment Facility (CBEF). The maize seeds were allowed to germinate and grow at 25 degree_C in the dark for four days (96 h 27 m) under micro-g conditions in space. The maize seedlings were frozen at -95 degree_C in the Minus Eighty-Degree Celsius Laboratory Freezer for ISS (MELFI) for later analysis of gene expression. These samples were returned to Earth by the Cargo Dragon capsule and sent to our laboratory; their storage temperature maintained with dry ice. The frozen seedlings were then stored at -80 degree_C until RNA extraction.	Micro Smash, TRI reagent	Cy3	The degrees of hybridization signal, or intensity of the fluorescence, on the microarray slides were calculated using Feature Extraction Software (Agilent Technologies).	The microarray slides were washed and scanned using the SureScan Microarray Scanner System (Model; G4900DA, Agilent Technologies).	Microarray analysis was conducted on three independent RNA samples obtained from etiolated maize seedlings grown in three independent maize boxes. Microarray data were analyzed using Gene Spring GX ver. 14.9.1 software (Tomy Digital Biology, Tokyo, Japan) and the maize microarray annotation database. Data were produced by normalizing to 75 percentile shift protocol and the baseline-to-median control sample protocol. Arrays were filtered on expression 20-100th percentile in the raw data. The P value was corrected by the False Discovery Rate (FDR) method. Data were produced by normalizing to 75 percentile shift protocol and the baseline-to-median 1g sample protocol
SDRF File	E-GEAD-428.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEOD-5440
Comment[AEExperimentType]	transcription profiling by array
Comment[BioProject]	PRJDB11348
Comment[Last Update Date]	2021-05-14