Comment[ArrayExpressAccession]	E-MEXP-3718
Investigation Title	Global expression profiling of low temperature induced genes in chilling tolerant japonica rice
Comment[Submitted Name]	Global expression profiling of low temperature induced genes in chilling tolerant japonica rice
Comment[AEExperimentDisplayName]	Transcriptional profiling by array of chilling-tolerant japonica rice to study low temperature induced genes
Comment[MIAMExpressLogin]	fxrider
Comment[MIAMExpressSubmissionID]	8401
Experiment Description	Three week old seedlings of rice cultivar Jumli Marshi (spp. Japonica) was exposed to cold (+4C) temperatures for varying time periods. Tissue samples were collected in replicates. Microarray data analysis was then performed on the extracted totalRNA from the samples.
Experimental Design	physiological_process_design	co-expression_design	time_series_design	replicate_design
Comment[AEExperimentType]	transcription profiling by array
Experimental Factor Name	Time
Experimental Factor Type	time
Person Last Name	Chawade
Person First Name	Aakash
Person Email	aakash.chawade@croptailor.com
Person Phone	4646227469
Person Affiliation	CropTailor AB
Person Address	R&D, Applied Biochemistry, Lund University, Box 124, Lund, Lund, 22100, Sweden
Person Roles	submitter
Person Roles Term Source REF	MGED Ontology
Quality Control Type	biological_replicate
Public Release Date	2013-05-01
Comment[ArrayExpressSubmissionDate]	2012-08-21 14:03
Publication Status	not yet submitted
Protocol Name	P-MTAB-28073	P-MTAB-28074	P-MTAB-28075	P-MTAB-28076
Protocol Description	At mid-day, three week old plants were transferred to growth chambers (Percival) in the same photoperiod, but with an air temperature of 4 degrees C and a light intensity of 100 umol m2 s-1. Pooled leaf tissue from five individual Jumli Marshi plants was harvested at 0, 0.5, 2, 4, 8, and 24 hours, frozen in liquid nitrogen and stored at -80 degrees C until further analysis. 	Total RNA was extracted from JM leaf tissue with TRIZOL reagents (Invitrogen) according to the manufacturerM-^Rs protocol and purified by RNeasy MinElute Cleanup Kit (Qiagen). (Parameters: Extracted product = total_RNA, Amplification = none)	Biotinylated target cRNA was prepared from 4 M-5g of total RNA following the manufacturerM-^Rs specifications (Affymetrix). The samples were then hybridized to Affymetrix GeneChip(r) Rice Genome Arrays, which contain probes to query ~51K transcripts representing both the Japonica and Indica cultivars. The chips were thereafter washed and stained in a GeneChip(r) Fluidics Station 450. Scanning was carried out with GeneChip(r) Scanner 3000 and image analysis was performed using GeneChip(r) Operating Software. (Parameters: Scanning hardware = GeneChip Scanner 3000 [Affymetrix], Scanning software = Scanning software)	Seeds of two rice cultivars, Oryza sativa, ssp. Japonica, cv. Jumli Marshi (JM) and ssp. Indica, cv. IR64 (IR64), were first soaked in water for 16 hours at room temperature and thereafter grown on standard soil in 14 hours photoperiod, with a day/night air temperature of 25 degrees C/20 degrees C and 250 M-5mol m2 s-1 light. (Parameters: time unit = seconds, temperature unit = C)
Protocol Type	specified_biomaterial_action	nucleic_acid_extraction	image_acquisition	grow
Protocol Term Source REF	MGED Ontology	MGED Ontology	MGED Ontology	MGED Ontology
Term Source Name	MGED Ontology	ArrayExpress
Term Source File	http://mged.sourceforge.net/ontologies/MGEDontology.php	http://www.ebi.ac.uk/arrayexpress
SDRF File	E-MEXP-3718.sdrf.txt
PubMed ID	24349120
Publication Author List	Chawade A, LindlM-CM-6f A, Olsson B, Olsson O.
Publication Title	Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice jumli marshi.
Publication DOI	10.1371/journal.pone.0081729