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Series GSE4776 Query DataSets for GSE4776
Status Public on Jun 06, 2006
Title Thrivikraman-5P50MH058922-050002
Organism Rattus norvegicus
Experiment type Expression profiling by array
Summary It is suggested that the stress induced activation of the HPA axis and associated increases in plasma ACTH and glucocorticoids (corticosterone, B in the rat) are contributing factors in the development of many psychopathologies. However, the circadian fluctuation of the HPA axis activity (characterized by a zenith in the plasma ACTH and B, before the beginning of the active awake state and the nadir during the inactive sleeping period) occurs throughout the life and is important for normal physiological and behavioral functioning. A blunting or enhancement of this rhythm through changes in the trough or in the peak is a characteristic feature of many pathological states. At the CNS level, the circadian fluctuation of the HPA axis activity is associated with changes in the expression profile of structural, functional, and immediate early genes. However, little is known about the specific role of B in the modulation of the circadian pattern of gene regulation in the CNS.
Thus, during the circadian cycle B is a major factor, which could influence the expression profile of a large family of genes. Accordingly, the microarray technology, because of its characteristic feature that facilitates the identification of the expression profiles of a wide range of genes simultaneously, is an ideal technique. Because the B status of animals can be easily manipulated by adrenalectomy (ADX) surgery with or without B replacement, this model will be used in these studies. Thus, the proposed studies are intended to characterize, by the use of the microarray technique, the effects of the B milieu on diurnal gene expression profiles in selected rat brain regions strongly influenced by: a.) B status: amygdala, hippocampus, hypothalamus, and septum; and b.) Circadian Activity: dorsal raphe, frontal Cortex and locus coeruleus.
The gradient of the B response during the circadian cycle implies that at the beginning of the sleep cycle MR are predominantly occupied while at the end of the sleep cycle, both MR and GR are occupied. Thus, we propose that differing ratios of activation of these nuclear receptors could differentially modulate gene expression and impart temporal characteristics in the expression profile of a large family of genes. Furthermore, we propose that these effects may be region specific, reflecting regional differences in GR and MR distribution, B uptake, and neural activity. B may exert these circadian effects on regional gene expression profiles either directly or indirectly via interneurons. However, little is known about the circadian effect of B on gene expression profiles in different brain regions. Such knowledge is important to identify the specific role of B in circadian differences in CNS function and, potentially, the development of psychopathologies.
After arrival at the facility the rats (male Long Evans) will be maintained on 12:12 h LD cycle ('lights-on" at 0700 h) with food and water ad libitum. One week after, they will undergo bilateral ADX under survival anesthetics (day-0). The study will include three groups (n=10); (a) ADX: rats with no adrenals, (b) pADX: ADX rats with subcutaneous 40 percent B pellet (fused cholesterol and B), and (c) SHAM: rats undergoing flank incisions without the removal of the adrenals. After surgery, rats will be housed individually. The ADX rats will receive 0.5 percent saline in addition to regular tap water. On post-surgical day-7, 15 rats (five/group) will be sacrificed by decapitation 2h after 'lights-on", and the remaining 15, 2h after "lights-off". The brains will be removed immediately, frozen on dry ice, and stored at -80 C. The trunk blood will be collected with EDTA and plasma frozen for ACTH and B RIA. The brains from rats with confirmed ADX will be used for free hand dissection of brain regions: frontal cortex, septum, hypothalamus, amygdala, hippocampus, dorsal raphe, and locus coeruleus. Tissue will be stored at -80 C. Total RNA will be extracted from individual brain regions using Qiagen RNeasy Lipid Tissue kit. Initial evaluation of quality and quantity of the RNA will be done by the absorbance method. Frozen samples containing 0.5 ul total RNA or higher will be sent to the NINDS-NIMH Microarray Consortium in dry ice for evaluation of the integrity of 28S and 18S RNA on an Agilent Bioanalyzer. If the integrity of RNA is not good, the experiment will be repeated and new RNA samples will be provided. Replicates of each brain region with 28S/18S ratio of 1.7 and higher will be selected for assay using Affymetrix Rat U34A array. The RNA samples from one region from all the brains will be processed together. A total of 84 chips may be utilized in these studies, however the final number will depend upon integrity of the total RNA.
Keywords: other
 
 
Contributor(s) Thrivikraman KV
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date May 04, 2006
Last update date Jul 31, 2017
Contact name Winnie Liang
Organization name Translational Genomics
Street address 445 N. Fifth Street
City Phoenix
State/province AZ
ZIP/Postal code 85012
Country USA
 
Platforms (1)
GPL1355 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array
Samples (82)
GSM107895 brain, frontal cortex: LabeledExtract2
GSM107896 brain, frontal cortex: LabeledExtract3
GSM107897 brain, frontal cortex: pADX AM FC_e1_le1
Relations
BioProject PRJNA95547

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE4776_RAW.tar 193.9 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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