Comment[ArrayExpressAccession]	E-GEOD-44092
MAGE-TAB Version	1.1		
Public Release Date	2013-02-14
Investigation Title	Bisulfite-Seq profiling of undifferentiated ESCs, and in vitro derived primordial germ cells (iPGCs)		
Comment[Submitted Name]	Bisulfite-Seq profiling of undifferentiated ESCs, and in vitro derived primordial germ cells (iPGCs)
Experiment Description	We report that in vitro derived PGCs undergo genome-wide DNA demethylation and that this demethylation does not require Tet1/Tet2 Examination of methylation in ESCs, iPGCs, and Tet2-/- iPGCs depleted of Tet1 by shRNA lentiviruses		
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	Vincent	Vincent	Clark
Person First Name	John	John	Amander
Person Mid Initials		J	T
Person Email	jvincent@ucla.edu		
Person Affiliation	UCLA		
Person Address	MCDB, UCLA, 621 Charles E Young Dr. S, Los Angeles, USA		
Person Roles	submitter		
Protocol Name	P-GSE44092-2	P-GSE44092-1	P-GSE44092-3
Protocol Description	Genomic DNA was isolated via Zymo gDNA Mini Prep columns and subjected to sonication. Briefly, sonicated DNA was end repaired with T4/Klenow DNA polymerases and T4 polynucleotide kinase, adenylated, and ligated to pre-methylated single end Illumina Adapters with T4 DNA ligase. Following purification and size selection (150-300bp), samples were bisulfite converted with CpG Genome Kit (Millipore). Libraries were then subjected to one round of PCR amplification (15 cycles)	ESCs were cultured under standard conditions in LIF on feeders. iPGCs were generated via ESC differentiation for 6 days following selection of SSEA1+/cKitbright cells by FACS. Indicated viruses were transduced into ESCs prior to embryoid body differentiation.	BS-seq reads were aligned to the mm9 genome assembly using BS Seeker, allowing up to 10 mismatches. Alignments with three consecutive methylated non-CG sites are removed. If multiple alignments mapped to the same location only one is kept. Genome_build: mm9 Supplementary_files_format_and_content: Processed data (CGmap) is in text format. column 1=chromosome id (see mouse_mm9_chr_name_id.txt); column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.
Protocol Type	nucleic acid library construction protocol	grow	feature_extraction
Experimental Factor Name	LENTIVIRUS	CELL TYPE	GENOTYPE
Experimental Factor Type	lentivirus	cell type	genotype
Comment[SecondaryAccession]	GSE44092		
Comment[GEOReleaseDate]	2013-02-14		
Comment[ArrayExpressSubmissionDate]	2013-02-05		
Comment[GEOLastUpdateDate]	2013-03-08		
Comment[AEExperimentType]	methylation profiling by high throughput sequencing		
Comment[AdditionalFile:Data1]	GSE44092_mouse_mm9_chr_name_id.txt		
Comment[SecondaryAccession]	SRP018523		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR688514-SRR688535		
SDRF File	E-GEOD-44092.sdrf.txt