Comment[ArrayExpressAccession]	E-GEOD-43763
MAGE-TAB Version	1.1					
Public Release Date	2013-03-18
Investigation Title	EBF2 determines and maintains brown adipocyte identity					
Comment[Submitted Name]	EBF2 determines and maintains brown adipocyte identity
Experiment Description	We compared PPARg binding sites in BAT and eWAT to identify regulatory elements that contribute to BAT identity and to find an important factor that bind those elements. To this end, we performed PPARg ChIP-seq in both tissues and called each tissue-spsecific binding sites. PPARg ChIP-seq in BAT and eWAT of mice					
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	Lim	Rajakumari	Ishibashi	Lim	Won	Seale
Person First Name	Hee-Woong	Sona	Jeff	Hee-Woong	Kyoung-Jae	Parick
Person Email	geo@ncbi.nlm.nih.gov					
Person Affiliation	University of Pennsylvania					
Person Address	Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, 3400 Civic Center Boulevard, Phildelphia, USA					
Person Roles	submitter					
Protocol Name	P-GSE43763-1	P-GSE43763-3	P-GSE43763-2	P-GSE43763-4		
Protocol Description	Mice were euthanized and BAT/eWAT were removed at ZT10, 5pm. BAT and eWAT samples were cross-linked with 1% formaldehyde, and used for ChIP with PPARg antibody.	Nuclei were lysed and sonicated. Protein-DNA complexes were isolated from lysates using antibodies, and DNA were extracted. For each condition, ChIP was performed on lysates from 4 different mice, and ChIPed DNA or input DNA samples were pooled for sequencing. ChIPed DNA or input DNA samples were pooled for sequencing.	8-10 week old male Sv129 mice has been housed in regular 12h light/12h dark cycles on normal chow diet.	Sequencing: High throughput sequencing was done by the Functional Genomics Core of the Penn Diabetes Research Center using the Illumina Genome Analyzer IIx or HiSeq 2000, and the reads were aligned to the mm8 genome assembly genome using Bowtie. In each ChIP-seq sample, all the duplicate reads were removed except for one before downstream analysis. Peak Calling: To identify depot-specific Pparg peaks, we performed peak calling for one depot sample as foreground and the other sample as background, and vice versa. All the peak calling were performed using Homer with options, peak size 200bp and minimum distance 200bp (-size 200 -minDist 200), then 1 rpm cutoff was applied. Common Pparg peaks were defined as follows. First, Pparg peaks were called for each depot using a matching input sample, then all the peaks were pooled and overlapping peaks were merged. Among these peaks, any peak that overlaps with the depot-specific Pparg peaks were eliminated, and the remaining peaks were defined as common Pparg peaks. It should be noted that our definition of common peak here is naïve in the sense that some peaks might show different peak height between different depots. However, this should not be a problem in this work because our primary target is to identify depot-specific (especially BAT-specific) Pparg binding sites. Genome_build: mm9 Supplementary_files_format_and_content: Peak calling results for each tissue-specific PPARg binding sites in bed format		
Protocol Type	specified_biomaterial_action	nucleic acid library construction protocol	grow	feature_extraction		
Experimental Factor Name	ORGANISM PART					
Experimental Factor Type	organism part					
Comment[SecondaryAccession]	GSE43763					
Comment[GEOReleaseDate]	2013-03-18					
Comment[ArrayExpressSubmissionDate]	2013-01-25					
Comment[GEOLastUpdateDate]	2013-03-18					
Comment[AEExperimentType]	ChIP-seq					
Comment[SecondaryAccession]	SRP018214					
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR653007-SRR653008					
SDRF File	E-GEOD-43763.sdrf.txt