Comment[ArrayExpressAccession]	E-GEOD-48040
MAGE-TAB Version	1.1			
Public Release Date	2013-07-15
Investigation Title	A global profiling of  gene expression under cold stress in Brachypodium			
Comment[Submitted Name]	A global profiling of  gene expression under cold stress in Brachypodium
Experiment Description	RNA-Seq was performed to study the change of gene expression before and after cold treatment  in Brachypodium. Different change patterns were identified. We have provided a complete view of  transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 12-day-old Brachypodium seedlings with and without cold treatment  (4 M-BM-0C for 24 h)  were generated by deep sequencing using  Illumina HiSeqM-bM-^DM-" 2000.			
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl		
Person Last Name	jingyu	Zhang		
Person First Name	zhang	Jingyu		
Person Email	jingyu_zhang@hotmail.com			
Person Affiliation	Institute od botany			
Person Address	Institute od botany, Nanxincun #20, Beijing, China			
Person Roles	submitter			
Protocol Name	P-GSE48040-4	P-GSE48040-1	P-GSE48040-3	P-GSE48040-2
Protocol Description	Illumina GA Pipeline v1.3 used for basecalling. After low quality reads being removed, the remaining Illumina sequencing reads were mapped to the Brachypodium genome (v1.2 ,http://www.brachypodium.org) using SOAP. The gene expression level is calculated by using RPKM (Reads Per kb per Million reads) method (Mortazavi et al, 2008, Nature Methods. 5: 621-8.) Genome_build: Brachypodium distachyon Supplementary_files_format_and_content: text file showing RPKM value for all the samples	The aerial part of seedlings treated or untreated with cold stress (4 M-0C for 24 h) were pooled and used for library construction	Total RNA was extracted from 12-day-old ABR5 seedlings using the mirVana miRNA Isolation Kit (Ambion, Austin, USA) following the manufacturer's protocol. The mRNAs were enriched by using oligo(dT) magnetic beads and broken into short fragments (about 200 bp). The first strand cDNA was synthesized using random hexamer primer with mRNA fragments as templates. DNA polymerase I (EpicentreM-. Biotechnologies, Madison, USA) was used to synthesize the second strand. The double-strand cDNA was purified with the QiaQuick PCR extraction kit (Qiagen). Then, sequencing adaptors were added and the obtained fragments were purified using agarose gels and enriched by PCR amplification. The resultant products were used for sequencing analysis via Illumina HiSeqM-bM-^DM-" 2000.	Seeds of the Brachypodium distachyon (L.) Beauv. diploid line ABR5 were placed in petri dishes containing two layers of damp sterile filter paper. The seeds were first stratified at 4 M-0C for one week to promote synchronous germination, then grown in a growth chamber at 24 M-0C under a 16 hour/8 hour (light/dark) photoperiod with light intensity of approximately 5,000 lux.
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	TREATMENT			
Experimental Factor Type	treatment			
Comment[SecondaryAccession]	GSE48040			
Comment[GEOReleaseDate]	2013-07-15			
Comment[ArrayExpressSubmissionDate]	2013-06-17			
Comment[GEOLastUpdateDate]	2013-07-18			
Comment[AEExperimentType]	RNA-seq of coding RNA			
Comment[SecondaryAccession]	SRP026261			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR921317-SRR921318			
SDRF File	E-GEOD-48040.sdrf.txt