Comment[ArrayExpressAccession]	E-GEOD-59460										
MAGE-TAB Version	1.1										
Public Release Date	2015-01-06										
Investigation Title	Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo										
Comment[Submitted Name]	Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo										
Comment[AEExperimentDisplayName]	Transcription profiling by array of liver tissues from wild type and Rev-erb{alpha} knockout (Nr1d1-/-) mice to study direct targets of Nr1d1 in rhythmic (circadian) transcription										
Experiment Description	Mammalian transcriptomes display complex circadian rhythms with multiple phases of gene expression that cannot be accounted for by current models of the molecular clock.  We have determined the underlying mechanisms by measuring nascent RNA transcription around the clock in mouse liver.  Unbiased examination of eRNAs that cluster in specific circadian phases identified functional enhancers driven by distinct transcription factors (TFs).  We further identify on a global scale the components of the TF cistromes that function to orchestrate circadian gene expression.  Integrated genomic analyses also revealed novel mechanisms by which a single circadian factor controls opposing transcriptional phases.  These findings shed new light on the diversity and specificity of TF function in the generation of multiple phases of circadian gene transcription in a mammalian organ. The goal of this experiment was to determine direct targets of Rev-erb{alpha} in mouse liver. All samples were collected at ZT10, when Rev-erb{alpha} protein levels and genomic binding are maximal. All mice were housed and harvested together (n=5 per genotype). All mice were male, 10-12 week old on C57Bl/6 background. RNA was extracted, processed, and hybridized from each mouse liver individually (each sample represents a single mouse).										
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	Everett	Fang	Everett	Jager	Briggs	Armour	Feng	Roy	Gerhart-Hines	Sun	Lazar
Person First Name	Logan	Bin	Logan	Jennifer	Erika	Sean	Dan	Ankur	Zachary	Zheng	Mitchell
Person Mid Initials	J		J			M					A
Person Email	loganje@mail.med.upenn.edu										
Person Affiliation	University of Pennsylvania										
Person Address	Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, USA										
Person Roles	submitter										
Protocol Name	P-GSE59460-1	P-GSE59460-5	P-GSE59460-6	P-GSE59460-2	P-GSE59460-3	P-GSE59460-4	P-GSE59460-7				
Protocol Description	Raw images were analyzed using Partek Genomics Suite to extract individual probe intensities. Subsequent data analysis was performed using BioConductor. Raw probe signal values were background and quantile normalized and summarized by probe sets using the RMA algorithm. Final differential expression calls were determined using the SAM algorithm with 10% false-discovery rate and an absolute fold-change threshold of 1.3. ID_REF =  VALUE = RMA signal (NOT log2)	RNA from each liver was individually processed with the Ambion WT expression kit and GeneChIP WT terminal labeling and control kit (Affymetrix) and hybridized to the Mouse Gene 1.0 ST arrays (Affymetrix)	About 2ug cDNA was hybridized at 45�C for 16h to the Mouse Gene 1.0ST array. Arrays were washed and stained using the GeneChIP Hybridization, Wash and Stain Kit (Affymetrix).	Mice were euthanized at 5pm (ZT10).	Wild-type (WT) C57Bl/6 mice were purchased from the Jackson Laboratories. The Rev-erb{alpha} -/- mice were obtained from B. Vennström, and backcrossed at least 7 generations with C57Bl/6 mice. 10-12 weeks old WT and mutant male mice were fed normal chow and housed under standard 12h-light/12h-dark cycles, with lights on (ZT0) at 7AM and lights off (ZT12) at 7PM. All animal care and procedures followed the guidelines of the Institutional Animal Care and Use Committee of the University of Pennsylvania.	Total RNA was extracted from each mouse liver sample using Trizol extraction followed by QIAGEN Rneasy Kit according to the manufacture's instructions.	Array images were captured on a GCS3000 laser scanner (Affymetrix)				
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol				
Experimental Factor Name	genotype										
Experimental Factor Type	genotype										
Publication Title	Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo.										
Publication Author List	Fang B, Everett LJ, Jager J, Briggs E, Armour SM, Feng D, Roy A, Gerhart-Hines Z, Sun Z, Lazar MA										
PubMed ID	25416951										
Publication DOI	10.1016/j.cell.2014.10.022										
Comment[SecondaryAccession]	GSE59460										
Comment[GEOReleaseDate]	2015-01-06										
Comment[ArrayExpressSubmissionDate]	2014-07-16										
Comment[GEOLastUpdateDate]	2015-01-07										
Comment[AEExperimentType]	transcription profiling by array										
SDRF File	E-GEOD-59460.sdrf.txt