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E-GEOD-59460 - 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

Status
Released on 6 January 2015, last updated on 22 June 2015
Organism
Mus musculus
Samples (10)
Array (1)
Protocols (7)
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).
Experiment type
transcription profiling by array 
Contacts
Logan J Everett <loganje@mail.med.upenn.edu>, Ankur Roy, Bin Fang, Dan Feng, Erika Briggs, Jennifer Jager, Mitchell A Lazar, Sean M Armour, Zachary Gerhart-Hines, Zheng Sun
Citation
Circadian enhancers coordinate multiple phases of rhythmic gene transcription in vivo. Fang B, Everett LJ, Jager J, Briggs E, Armour SM, Feng D, Roy A, Gerhart-Hines Z, Sun Z, Lazar MA.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-59460.idf.txt
Sample and data relationshipE-GEOD-59460.sdrf.txt
Raw data (1)E-GEOD-59460.raw.1.zip
Processed data (1)E-GEOD-59460.processed.1.zip
Array designA-AFFY-130.adf.txt
Links