Comment[ArrayExpressAccession]	E-MTAB-2037
MAGE-TAB Version	1.1																										
Investigation Title	Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.																										
Comment[Submitted Name]	Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.
Experiment Description	Expression in seven tissues from Oryza sativa L. ssp japonica Nipponbare was profiled using RNA-sequencing: callus, leaf, root, seed, shoot, panicle before flowering, and panicle after flowering. The original experiment examined gene expression in the seven tissues, and utilized the data both to compare gene expression patterns between retrogenes and their parents and to compare patterns of expression divergence between RNA-based duplicates and DNA-based duplicates Note: All samples in SRA were assigned the same sample accession (DRS000668). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.																										
Experimental Design	organism part comparison design																										
Experimental Design Term Source REF	EFO																										
Experimental Design Term Accession Number																											
Experimental Factor Name	organism part																										
Experimental Factor Type	organism part																										
Experimental Factor Term Source REF	EFO																										
Experimental Factor Term Accession Number																											
Person Last Name	National Institute of Agrobiological Sciences	Gaut	Keays																								
Person First Name		Brandon	Maria																								
Person Mid Initials		S	C																								
Person Email		bgaut@uci.edu 	mkeays@ebi.ac.uk																								
Person Phone																											
Person Fax																											
Person Address	Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan																										
Person Affiliation	National Institute of Agrobiological Sciences	University of California, Irvine	EMBL-EBI																								
Person Roles	investigator	investigator	submitter																								
Person Roles Term Source REF																											
Person Roles Term Accession Number																											
Quality Control Type																											
Quality Control Term Source REF																											
Quality Control Term Accession Number																											
Replicate Type																											
Replicate Term Source REF																											
Replicate Term Accession Number																											
Normalization Type																											
Normalization Term Source REF																											
Normalization Term Accession Number																											
Date of Experiment																											
Public Release Date	2011-12-21																										
PubMed ID	22042334																										
Publication DOI	10.1093/gbe/evr111																										
Publication Author List	Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS.																										
Publication Title	Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.																										
Publication Status	published																										
Publication Status Term Source REF	EFO																										
Publication Status Term Accession Number																											
Protocol Name	P-MTAB-35714	P-MTAB-35715	P-MTAB-35716	P-MTAB-35717
Protocol Type	growth protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol																							
Protocol Term Source REF	EFO	EFO	EFO	EFO																							
Protocol Term Accession Number	EFO_0003789		EFO_0004184	EFO_0004170																							
Protocol Description	We obtained seeds (accession number ‘‘JP229579’’) from the GENE bank in the National Institute of Agrobiological Sciences, Japan (http://www.gene.affrc.go.jp/about_en.php). The seeds were germinated in a growth chamber at 28degreesC under a 16-h light/8-h dark regime. Seven days after germination, shoots and roots were collected. In the meantime, plants were grown in paddy fields, where leaves (7 days before heading to 7 days after flowering) and panicles (7 days before and 0–7 days after heading to flowering) were collected. Callus was induced on N6D medium according to a previous protocol (Ozawa 2009).	For RNA extraction from each plant tissue, at least 10 plants were collected, immediately frozen in liquid nitrogen, and mixed, to minimize the effect of transcriptome unevenness among plants. Total RNA was extracted from each tissue with the RNeasy Plantmini kit (Qiagen).	cDNA was synthesized with mRNAseq 8-sample prep kit (Illumina) (Mizuno et al. 2010). We constructed cDNA libraries for the seven tissues individually.	Illumina Genome Analyzer IIx. We sequenced single ends of each library on the Illumina GAIIx platform for four separate runs (three at 36 cycles and one at 76 cycles).																							
Protocol Parameters																											
Protocol Hardware				Illumina Genome Analyzer IIx																							
Protocol Software																											
Protocol Contact																											
Term Source Name	NCBI Taxonomy	EFO
Term Source File	http://www.ncbi.nlm.nih.gov/Taxonomy/	http://www.ebi.ac.uk/efo																									
Term Source Version		2.34																									
Comment[SecondaryAccession]	DRP000391																										
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/DRR001024-DRR001051																										
Comment[AEExperimentType]	RNA-seq of coding RNA																										
Comment[SRASubmissionDate]	2011-12-21																										
Comment[AEExperimentDisplayName]	Transcription profiling by RNA-seq of seven tissues from Oryza sativa japonica Nipponbare																										
SDRF File	E-MTAB-2037.sdrf.txt