Comment[ArrayExpressAccession]	E-GEOD-41753
MAGE-TAB Version	1.1				
Public Release Date	2013-06-04
Investigation Title	Single-base resolution DNA methylomes of soybean recombinant inbred lines reveals heritability patterns of natural methylation variants				
Comment[Submitted Name]	Single-base resolution DNA methylomes of soybean recombinant inbred lines reveals heritability patterns of natural methylation variants
Experiment Description	The epigenomics approaches presented here provide the first comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations paving the way for understanding how methylation variants contribute to phenotypic variation. MethylC-Seq and RNA-Seq data collected from Glycine max leaves of two parental lines of a RIL population and two individual RILs. Additionally gDNA-Seq was performed on the two parental lines [SRA060034].				
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	Ecker	Schmitz	Ecker		
Person First Name	Joseph	Robert	Joseph		
Person Mid Initials	R	J	R		
Person Email	ecker@salk.edu				
Person Affiliation	Salk-Institute				
Person Phone	8584534100				
Person Address	PBIO, Salk-Institute, 10010 North Torrey Pines Road, La Jolla, CA, USA				
Person Roles	submitter				
Protocol Name	P-GSE41753-5	P-GSE41753-3	P-GSE41753-2	P-GSE41753-4	P-GSE41753-1
Protocol Description	Data were mapped to the Glycine max 1.0 reference genome MethylC-Seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013). RNA-Seq RPKM data were generated using Bowtie version 0.12.7 and Tophat version 1.3.3 (flags = -g 1, –F 0). Gene expression values were calculated using Cufflinks version 1.1.0 (flags = -F 0, -b, -N) Genome_build: Gm1.0	Data were mapped to the Glycine max 1.0 reference genome MethylC-Seq analysis were performed as described in Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-36 (2008), PMID: 18423832. RNA-Seq RPKM data were generated using Bowtie version 0.12.7 and Tophat version 1.3.3 (flags = -g 1, –F 0). Gene expression values were calculated using Cufflinks version 1.1.0 (flags = -F 0, -b, -N). Genome_build: Gm1.0 Supplementary_files_format_and_content: mc*.txt file represents MethylC-Seq data. Supplementary_files_format_and_content: RPKM file represents RNA-Seq data.	Genomic DNA (gDNA) was purified from 0.5 g of leaves by using DNeasy Plant MiniKit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. MethylC-Seq libraries were constructed according to Schmitz, R.J. et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369-73 (2011).	Total RNA was purified from 0.5 g of leaves by using Trizol Reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions, and subsequently purified using chloroform extraction. RNA-Seq libraries were constructed using the Illumina TruSeq Kit v2 (Illumina, San Diego, CA) according to the manufacturer’s guidelines.	Seeds were surface sterilized [30% bleach, rinsed several times with sterile, double-distillated H2O (ddiH2O)], planted in soil-less medium (SogeMix “SM-2”-general purpose growing medium), and germinated in growth chambers (190 mmol PAR m-2s-1, 230C, 60% R.H., and 16 h photoperiod)
Protocol Type	normalization data transformation protocol	normalization data transformation protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	GENOTYPE	ECOTYPE			
Experimental Factor Type	genotype	ecotype			
Comment[SecondaryAccession]	GSE41753				
Comment[GEOReleaseDate]	2013-06-04				
Comment[ArrayExpressSubmissionDate]	2012-10-22				
Comment[GEOLastUpdateDate]	2013-06-04				
Comment[AEExperimentType]	methylation profiling by high throughput sequencing				
Comment[AEExperimentType]	RNA-seq of coding RNA				
Comment[AdditionalFile:Data1]	GSE41753_README.txt				
Comment[AdditionalFile:Data2]	GSE41753_RPKM_soybean.txt				
Comment[AdditionalFile:Data3]	GSE41753_processedfiles_column_header_descriptions.txt				
Comment[SecondaryAccession]	SRP016593				
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR605670-SRR605694,SRR847605-SRR847686				
SDRF File	E-GEOD-41753.sdrf.txt