Comment[ArrayExpressAccession]	E-GEOD-41472
MAGE-TAB Version	1.1			
Public Release Date	2014-02-11
Investigation Title	Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression			
Comment[Submitted Name]	Epigenetic regulation of gene expression is instructed by promoter sequence and refined by developmental progression
Experiment Description	A large body of literature suggests that local features of chromatin are crucial in determining functional properties of underlying DNA.  The extent to which DNA sequence plays an active role in the establishment and maintenance of patterns of histone and DNA modification at promoters in cells and tissues in an adult animal remains poorly understood.  Likewise, whether passage through development is required for refinement of transcriptional states and chromatin marks characteristic of fully differentiated adult cells remains unclear.  Here we undertook analysis of gene expression along with the genomic distribution of DNA methylation and a set of histone marks in primary tissues derived from different primordial germ layers in adult mice.  We find that promoter CpG content correlated strongly with specific repressive mechanisms.  Likewise, RNA polymerase II occupancy and active histone marks were omnipresent on CpG rich promoters regardless of transcriptional output and of cell type.  However, these same chromatin features cleanly demarcate transcriptional activity on promoters with low CpG content.  While these observations imply an instructive role for DNA sequence in establishment and maintenance of epigenetic states, experimental evidence presented here also suggests an additional role for development in refining these features at individual promoters. Examination of H3K36me3, S5ph pol2, and S2ph pol2 in liver using ChIP-seq.			
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	Du	Li	Wade	Grimm
Person First Name	Ying	Ruifang	Paul	Sara
Person Mid Initials			A	
Person Email	ying.du@nih.gov			
Person Affiliation	NIEHS			
Person Address	NIEHS, 111 Alexander Avenue , Durham, NC, USA			
Person Roles	submitter			
Protocol Name	P-GSE41472-3	P-GSE41472-1	P-GSE41472-2	
Protocol Description	Basecalls performed using CASAVA version 1.8 ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with parameters -m 1 -v 2 Only reads that were mapped to an unambiguous ‘best’ genomic location with no more than 2 mismatches were accepted Duplicate reads were removed to limit PCR amplification bias, and all alignments were extended at the 3’ end to a length of 150 bases Genome_build: mm9 Supplementary_files_format_and_content: BedGraph files were generated from these mapped, non-duplicate, extended reads for visualization of aggregate genomic coverage.	Liver was dissected and washed in PBS then was snap frozen on dry ice.	30 mg of liver tissue was pulverized then incubated in 1% formaldehyde in PBS for 15 min at room temperature. Cross-linking was terminated by addition of glycine. The cells were spun down and rinsed in ice-cold PBS two times. The cell lysates were sonicated using a Bioruptor (Diagenode) to generate 150–350 bp fragments for immunoprecipitation. The following antibodies were used for ChIP: H3K36me3 (Abcam), S5ph pol2 (Abcam), S2ph pol2 (Abcam). libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kits v1 following the manufacturer’s instructions.	
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	
Experimental Factor Name	CHIP ANTIBODY			
Experimental Factor Type	chip antibody			
Comment[SecondaryAccession]	GSE41472			
Comment[GEOReleaseDate]	2014-02-11			
Comment[ArrayExpressSubmissionDate]	2012-10-10			
Comment[GEOLastUpdateDate]	2014-02-11			
Comment[AEExperimentType]	ChIP-seq			
Comment[AdditionalFile:Data1]	GSE41472_H3K36me3.bedGraph			
Comment[AdditionalFile:Data2]	GSE41472_S2phPol2.bedGraph			
Comment[AdditionalFile:Data3]	GSE41472_S5phPol2.bedGraph			
Comment[AdditionalFile:Data4]	GSE41472_input.bedGraph			
Comment[SecondaryAccession]	SRP016061			
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR585641-SRR585647			
SDRF File	E-GEOD-41472.sdrf.txt