|
| Status |
Public on Aug 01, 2008 |
| Title |
fib_ZT22 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Hypothalamus from 4 bezafibrate-treated mice at ZT22
|
| Organism |
Mus musculus |
| Characteristics |
Strain; ICR, Gender; Male, Age; 17 wks, Tissue; Hypothalamus, The time of sacrifice; ZT22.
These mice were fed diet including 0.5% bezafibrate between 11 and 12 wks age.
Equivalent amount of total RNA from hypothalamus of 4 mice were mixed equally and used for microarray.
|
| Treatment protocol |
Mice of 8wks age were fed with a normal diet (MF, Oriental Yeast, Tokyo, Japan) for two weeks, after which their feed was supplemented with 0.5% bezafibrate (Sigma Chemical Co., St. Louis, MO, USA) for two weeks. After that, the mice were returned to their normal diet for five weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The square area containing the hypothalamus was dissected from the brain immediately after decapitation at ZT22 and stored in RNAlater stabilization reagent for two hours. Total RNA was isolated following Qiagen's RNA isolation protocol (RNeasy Mini kit; Qiagen P/N 74104, Hilden, Germany). Contaminating DNA was removed using an RNase-free DNase set (Qiagen P/N 79254) during the process of RNA purification. The quality of the purified RNA applicable for microarray analysis was assessed by Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis – Protocol. These protocols are available for download at http://www.chem.agilent.com/scripts/generic.asp?lpage=11617&indcol=N&prodcol=Y.
The microarrays used were Agilent’s Whole Mouse Genome Oligo Microarrays (P/N G4122F). Probe sequence information is publicly available at http://www.chem.agilent.com/cag/bsp/bsp_register.asp.
Labeled cRNAs were generated from 400 ng of total RNA using Agilent’s Low RNA Input Linear Amplification Kit (P/N 5188-5339).
|
| |
|
| Channel 2 |
| Source name |
Hypothalamus from 4 control mice at ZT22
|
| Organism |
Mus musculus |
| Characteristics |
Strain; ICR, Gender; Male, Age; 17 wks, Tissue; Hypothalamus, The time of sacrifice; ZT22.
Equivalent amount of total RNA from hypothalamus of 4 mice were mixed equally and used for microarray.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The square area containing the hypothalamus was dissected from the brain immediately after decapitation at ZT22 and stored in RNAlater stabilization reagent for two hours. Total RNA was isolated following Qiagen's RNA isolation protocol (RNeasy Mini kit; Qiagen P/N 74104, Hilden, Germany). Contaminating DNA was removed using an RNase-free DNase set (Qiagen P/N 79254) during the process of RNA purification. The quality of the purified RNA applicable for microarray analysis was assessed by Agilent 2100 Bioanalyzer using an RNA 6000 Nano Labchip kit (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Sample labeling, array processing and scanning, and data extraction were performed as described in One-Color Microarray-Based Gene Expression Analysis â?? Protocol. These protocols are available for download at http://www.chem.agilent.com/scripts/generic.asp?lpage=11617&indcol=N&prodcol=Y.
The microarrays used were Agilentâ??s Whole Mouse Genome Oligo Microarrays (P/N G4122F). Probe sequence information is publicly available at http://www.chem.agilent.com/cag/bsp/bsp_register.asp.
Labeled cRNAs were generated from 400 ng of total RNA using Agilentâ??s Low RNA Input Linear Amplification Kit (P/N 5188-5339).
|
| |
|
| |
| Hybridization protocol |
Hybridizations were performed using GE Hybridization Kit (P/N 5188-5242) and GE Wash Buffer 1 and 2 (P/N 5188-5325, -5326) as following Agilent's protocol.
|
| Scan protocol |
Microarrays were scanned using Agilent’s DNA Microarray Scanner BA (P/N G2565BA) and data extracted using Agilent's Feature Extraction software, version 9.5 (P/N G2567AA).
|
| Description |
Four bezafibrate-treated mice at time ZT22 are divided by the control sample for all present spots.
|
| Data processing |
Data were processed using Agilent’s GeneSpring® GX software, version 7.3 (P/N G1745). Data were transformed by setting all measurements less than 0.01. Data points that did not have detectable signal and those that represent microarray controls were labeled as Absent, those representing either non-uniform or saturated features were labeled as Marginal, and all remaining data points were labeled as Present. All data points were 50 percentile scaled using the 50 percentile of signal intensity value that cut off 10 for data points labeled as Present. Then the data from each "spot ID" was subdivided by that of control sample.
|
| |
|
| Submission date |
Feb 05, 2008 |
| Last update date |
Jun 23, 2008 |
| Contact name |
Tomoko Kawai |
| E-mail(s) |
kawaito@basic.med.tokushima-u.ac.jp
|
| Phone |
81 88 633 7784
|
| Organization name |
The University of Tokushima Graduate School
|
| Department |
Institute of Health Biosciences
|
| Street address |
3-18-15 Kuramoto-cho
|
| City |
Tokushima |
| ZIP/Postal code |
770-8503 |
| Country |
Japan |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE10417 |
The effect of PPAR-alpha agonist on the gene expression in mice hypothalamus. |
|
