Comment[ArrayExpressAccession]	E-GEOD-56463
MAGE-TAB Version	1.1					
Public Release Date	2015-11-25
Investigation Title	Transcriptome profiling of various organs at different developmental stages in rice (single-end)					
Comment[Submitted Name]	Transcriptome profiling of various organs at different developmental stages in rice (single-end)
Experiment Description	To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using stranded single-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.					
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	Wang	Wang	Wu	Ye	Liu	Chua
Person First Name	Huan	Huan	Hui-Wen	Jian	Jun	Nam-Hai
Person Email	hwang01@rockefeller.edu					
Person Affiliation	The Rockefeller University					
Person Address	The Rockefeller University, 1230 York Avenue, New York, New York, USA					
Person Roles	submitter					
Protocol Name	P-GSE56463-2	P-GSE56463-1				
Protocol Description	RNA was extracted using the Qiagen RNeasy Plant Mini kit. Total RNA was treated with Turbo DNase I (Life Technologies AM2238) according to product specification. DNase I treated RNA was then applied again to an RNeasy spin column with 0.5 volumes of ethanol, washed and eluted according to the manufacturer’s instructions. Sequencing libraries were prepared using the Illumina Stranded mRNA sample Prep kit, set A (RS-122-2101, Illumina Inc.) according to the manufacturer's instructions. The quality and size of cDNA libraries for sequencing were checked using the Agilent 2200 TapeStation system (Agilent Inc.). The libraries were sequenced for 100 cycles on HiseqTM 2500 (Illumina Inc.)	Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica were grown in a greenhouse in Singapore . Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at the before- and after-flowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected.				
Protocol Type	nucleic acid library construction protocol	growth protocol				
Experimental Factor Name	organism part					
Experimental Factor Type	organism part					
Publication Title	Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits.					
Publication Author List	Wang H, Niu QW, Wu HW, Liu J, Ye J, Yu N, Chua NH					
PubMed ID	26387578					
Publication DOI	10.1111/tpj.13018					
Comment[SecondaryAccession]	GSE56463					
Comment[GEOReleaseDate]	2015-11-25					
Comment[ArrayExpressSubmissionDate]	2014-04-02					
Comment[GEOLastUpdateDate]	2015-11-25					
Comment[AEExperimentType]	RNA-seq of coding RNA					
Comment[AdditionalFile:Data1]	GSE56463_ssRNA-seq_fpkm.txt					
Comment[SecondaryAccession]	SRP040813					
SDRF File	E-GEOD-56463.sdrf.txt