|
| Status |
Public on Apr 04, 2016 |
| Title |
Dahl-S_colon_tumor-induced_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Dahl salt-senstive rat, colon tissue, Azoxymethane-induced colon tumors
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: S
treatment: Azoxymethane
tissue: colon
gender: male
age: 30 weeks
|
| Treatment protocol |
Dahl salt-sensitive rats (SS/Jr) were from our colony and will be referred to S. The congenic rat strain we used in this study is the S.LEW(10)x12x2x3x5 (S.LEW) congenic strain and will be referred to S.LEW congenic rat [Hypertension. 2007 Nov;50(5):891-8]. All the experimental rats were weaned at 28-30 d of age and fed with a low salt (0.3% NaCl) Harlan Teklad diet after weaning. At six weeks of age, both S and S.LEW congenic rats received intraperitoneal (IP) injection of AOM in sterial saline at a dose of 15mg/kg body weight once a week for two consecutive weeks. Then two animals per plastic cage, one S rat and one congenic rat, were housed in barrier-sustained animal room with a 12-h light/dark cycle. At 30 weeks of age, all the rats were euthanized through carbon dioxide inhalation. The colon tissue was harvested, dissected longitudinally, and washed with saline.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from colons of 3 S and 3 S.LEW congenic rats were prepared for microarray study using TRIzol Reagent (Life Technologies) following the manufacturer's protocol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
Array hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Description |
S3
Gene expression in colon of 30-week-old Dahl salt-sensitive rat receiving Azoxymethane to induce colon tumors at 6 weeks of age
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (All Targets Value) were chosen for further data analysis.
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| |
|
| Submission date |
Nov 21, 2015 |
| Last update date |
Apr 04, 2016 |
| Contact name |
Bina Joe |
| E-mail(s) |
[email protected]
|
| Phone |
419-383-4415
|
| Organization name |
University of Toledo, College of Medicine and Life Sciences
|
| Department |
Department of Physiology and Pharmacology
|
| Lab |
Center for Hypertension and Personalized Medicine
|
| Street address |
Block Health Science Bldg, 3000 Arlington Ave
|
| City |
Toledo |
| State/province |
Ohio |
| ZIP/Postal code |
43614 |
| Country |
USA |
| |
|
| Platform ID |
GPL14746 |
| Series (1) |
| GSE75280 |
Azoxymethane-induced colorectal tumorigenesis in hypertensive rat models |
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