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Status |
Public on Dec 10, 2014 |
Title |
Dahl Salt Resistant rats (Dahl R) 2 |
Sample type |
RNA |
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Source name |
Dahl R Rat fed with Low-salt (0.3%) diet
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Organism |
Rattus norvegicus |
Characteristics |
strain: Dahl Salt Resistant rats (Dahl R) tissue: Kidney gender: Male age: 53 days
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Treatment protocol |
After weaning all rats were fed with Low-salt (0.3%) diet (Harlan Teklad diet TD 7034; Harlan–Sprague-Dawley).
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Growth protocol |
All rats born on the same day were selected and weaned at 30 days of age.
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Extracted molecule |
total RNA |
Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
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Label |
Cy3
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Label protocol |
Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, for each sample 1 μg of total RNA were linearly amplified and labeled with Cy3-dCTP. Labelled cRNAs purified with Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol cy3/μg cRNA) were measured in a NanoDrop® ND-1000 spectrophotometer.
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Hybridization protocol |
A total of 1μg of labeled cRNA was prepared for fragmentation adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, heated at 60 °C for 30 min, and finally diluted by addition with 55μl 2×GE Hybridization buffer. A volume of 100μl of hybridization solution was then dispensed in the gasket slide and assembled to the custom Rat Long Non-coding RNA Array microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven.
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Scan protocol |
The hybridized arrays were washed, fixed and scanned using the Agilent DNA microarray scanner (part number G2505B) following Agilent Technologies’ guidelines.
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Description |
mRNA and LncRNA expression
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Data processing |
Raw data .txt files were extracted using Agilent Feature Extraction Software (version 10.5.1.1) and imported into the Agilent GeneSpring GX software (version11.0) for further analysis. The 9 microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (Quantile normalization). Differentially expressed lncRNAs and genes with statistically significance were identified through Volcano Plot filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.0). GO analysis and Pathway analysis was performed in the standard enrichment computation method.
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Submission date |
Jul 07, 2014 |
Last update date |
Dec 10, 2014 |
Contact name |
Bina Joe |
E-mail(s) |
bina.joe@utoledo.edu
|
Phone |
419-383-4415
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Organization name |
University of Toledo, College of Medicine and Life Sciences
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Department |
Department of Physiology and Pharmacology
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Lab |
Center for Hypertension and Personalized Medicine
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Street address |
Block Health Science Bldg, 3000 Arlington Ave
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City |
Toledo |
State/province |
Ohio |
ZIP/Postal code |
43614 |
Country |
USA |
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Platform ID |
GPL15690 |
Series (1) |
GSE59165 |
Genome-wide identification of rat long non-coding RNAs (microarray) |
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