E-GEOD-2162 - Transcription profiling of mouse liver from adrenalectomized (ADX) and sham-operated mice to identofy circadian expressed genes regulated by endogenous glucocorticoids

Status
Submitted on 15 January 2005, released on 12 June 2008, last updated on 27 March 2012
Organism
Mus musculus
Samples (4)
Array (1)
Protocols (2)
Description
Genome-wide expression analysis of two circadian oscillatory mechanisms in the mouse liver; To identify the genes of which the circadian expression is regulated by endogenous glucocorticoids, we performed DNA microarray analysis using hepatic RNA from adrenalectomized (ADX) and sham-operated mice. Mice were housed in a 12:12 h light-dark cycle (LD12:12; lights on at zeitgeber time (ZT) 0) for at least two weeks before the day of the experiment. Liver samples were dissected, quickly frozen, and stored in liquid nitrogen. Total RNA was purified from pools of 3 animal tissues collected at each time-point using ISOGEN (Nippon Gene Co., Ltd., Japan). Hybridization to Affymetrix GeneChip (MG-U74Av2) arrays proceeded as described (Oishi K et al., J Biol Chem, 278, 41519-41527, 2003). The average difference (AD) value for each gene was provided by GeneChip software. To identify putative glucocorticoid-regulated circadian genes, we compared AD values between two time points (ZT2 and ZT14) in sham operated and in ADX mice. We applied three criteria to the selection of putative glucocorticoid-regulated circadian genes: (i) the AD value is marked as “present” by the GeneChip software in at least one of two time points, (ii) the AD value exhibits a 2-fold or greater change in sham-operated mice and (iii) the fold change is below 2-fold in ADX mice. We identified 169 genes that fluctuated between day and night in the livers of sham-operated mice. Among these, 100 lost circadian rhythmicity in ADX mice. On the other hand, the circadian expression of clock or clock-related genes such as mPer2 and DBP remained almost totally intact in the liver of ADX mice. The present study showed that the circadian expression of one type of liver genes in the mouse is governed by core components of the circadian clock such as CLOCK and BMAL1, and the other depends on endogenous glucocorticoids.
Experiment types
transcription profiling by array, growth condition, time series
Contact
Citation
Genome-wide expression analysis reveals 100 adrenal gland-dependent circadian genes in the mouse liver. Katsutaka Oishi, Noriko Amagai, Hidenori Shirai, Koji Kadota, Naoki Ohkura, Norio Ishida. DNA Res 12(3):191-202 (2005)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-2162.idf.txt
Sample and data relationshipE-GEOD-2162.sdrf.txt
Raw data (1)E-GEOD-2162.raw.1.zip
Processed data (1)E-GEOD-2162.processed.1.zip
Array designA-AFFY-6.adf.txt
R ExpressionSetE-GEOD-2162.eSet.r
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