|
| Status |
Public on Dec 31, 2011 |
| Title |
Butyrate-DMH-Notumor_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Normal colonic mucosa,Butyrate group without tumors,replicate 3
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR
tissue: normal colonic mucosa
tumor status: with tumors
agent: Butyrate-DMH
|
| Treatment protocol |
The mice of DMH group were received normal drink water normal diet and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks,the mice of Butyrate group were received drink water with 1.5% Butyrate and subcutaneous injection of 1,2-Dimethylhydrazine at a dose of 20 mg/kg once weekly for 20 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs of the normal colonic mucosa are harvested using TRIzol(Invitrogen) and the Rneasy kit(Qiagen) according to manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55μl of 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).
|
| Description |
Gene expression in mice of Butyrate group without tumors
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The 9 microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization). The positive effect of this median normalization is illustrated in Box-plot, and genes marked present in all samples were chosen for data analysis. Differentially expressed genes were identified through Fold-change and T-test p-value screening.
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| |
|
| Submission date |
Dec 06, 2010 |
| Last update date |
Dec 31, 2011 |
| Contact name |
Jing-Yuan Fang |
| E-mail(s) |
jingyuanfang2007@126.com
|
| Organization name |
Shanghai Jiao-Tong University School of Medicine Ren-Ji Hospital
|
| Department |
Division of Gastroenterology
|
| Lab |
Shanghai Institute of Digestive Disease
|
| Street address |
145 Middle Shandong Rd
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200001 |
| Country |
China |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE25858 |
Gene expression profile of butyrate mediated prevention of coloractal cancer in a mouse model |
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