Comment[ArrayExpressAccession]	E-GEOD-39777
MAGE-TAB Version	1.1					
Public Release Date	2013-03-28
Investigation Title	Comparison of DNA methylation in human tissues					
Comment[Submitted Name]	Comparison of DNA methylation in human tissues
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series					
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	Schroeder					
Person First Name	Diane					
Person Mid Initials	Irene					
Person Email	dischroed@ucdavis.edu					
Person Affiliation	UC Davis					
Person Address	UC Davis, 1 Shields Ave, Davis, CA, USA					
Person Roles	submitter					
Protocol Name	P-GSE39777-5	P-GSE39777-1	P-GSE39777-4	P-GSE39777-3	P-GSE39777-6	P-GSE39777-2
Protocol Description	RNA was extracted using the NuGEN Ovation RNA-Seq System. Indexed adapters were added using the NuGEN Encore NGS Library System I.	Tissue DNA was purified using Qiagen's Puregene kit. The genomic DNA was sonicated to ~300 bp and methylated Illumina adapters were ligated to the ends. 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurboCx Hotstart DNA Polymerase (Stratagene) for 14 cycles using Illumina's standard amplification protocol.	Reads were aligned to the genome using BS Seeker. 76 bp reads were processed with BS Seeker parameters -e 75 -m 2. Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0% Genome_build: hg18 Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site	Reads were aligned to the genome using BS Seeker. 100 bp reads were trimmed at the 3' end to 75 bp for BS Seeker alignment. BS Seeker parameters: -e 75 -m 2. Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0% Genome_build: hg18 Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site	Sequencing index was in first 4 bases of sequencing read. For raw fastq files, first four bases were removed and separate fastq files were made for each indexed replicate. Reads were mapped to the hg18 version of the genome using TopHat (version 1). Parameters: --library-type fr-unstranded –GTF –butterfly-search –no-novel-juncs --prefilter-multihits Cufflinks was used to assemble the mapped reads into transcripts, omitting reads that did not align to known transcripts. Parameters: --library-type fr-unstranded – GTF –frag-bias-correct –multi-read-correct –frag-len-mean 390 –compatible-hits-norm Genome_build: hg18 Supplementary_files_format_and_content: fpkm_tracking file from Cufflinks	Reads were aligned to the genome using BS Seeker. 100 bp reads were trimmed at the 3' end to 85 bp for BS Seeker alignment. BS Seeker parameters: -e 85 -m 3 -a adapter2. Custom Perl scripts were used to calculate percent methylation for each genomic CpG site with read coverage. Methylation data for both DNA strands were combined. Only one read starting at a given genomic coordinate was kept to eliminate clonal replicates. Red=80-100% methylation, green=60-80%, blue=1-60%, black=0% Genome_build: hg18 Supplementary_files_format_and_content: BED file with the name field giving the % methylation at that CpG site
Protocol Type	nucleic acid library construction protocol	nucleic acid library construction protocol	feature_extraction	feature_extraction	feature_extraction	feature_extraction
Experimental Factor Name	ORGANISM PART					
Experimental Factor Type	organism part					
Publication Title	The human placenta methylome.					
Publication Author List	Schroeder DI, Blair JD, Lott P, Yu HO, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, Lasalle JM					
PubMed ID	23530188					
Publication DOI	10.1073/pnas.1215145110					
Comment[SecondaryAccession]	GSE39777					
Comment[GEOReleaseDate]	2013-03-28					
Comment[ArrayExpressSubmissionDate]	2012-07-31					
Comment[GEOLastUpdateDate]	2013-04-04					
Comment[AEExperimentType]	methylation profiling by high throughput sequencing					
Comment[AEExperimentType]	RNA-seq of coding RNA					
SDRF File	E-GEOD-39777.sdrf.txt