|
| Status |
Public on Jun 29, 2013 |
| Title |
Artery_uninjured_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
CommonCarotidArtery, uninjured, replicate1
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: wistar rat
tissue: whole artery
gender: male
treatment: uninjured
|
| Treatment protocol |
Harvested arteries were flushed rapidly with ice-cold phosphate buffer saline (PBS). These specimens were frozen in a -86°C freezer (Thermo Scientific Forma ULT; USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the frozen common carotid artery of each animal using TRIzol® reagent (Invitrogen) according to the manufacturer's instructions.Total RNA from each sample was quantified using the NanoDrop ND-1000 Spectrophotometer and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
One microgram of RNA was amplified and transcribed into fluorescent cRNA using the One-Color Quick Amp Labeling protocol (version 5.7, Agilent Technologies), followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65ug of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was incubated at 60°C for exactly 30 minutes to fragment RNA in a reaction volume of 55ul containing 25x Agilent Fragmentation Buffer and 10x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x GExHybridization Buffer was added to the fragmentation mixture and hybridized onto the Whole Rat Genome Oligo Microarray (4x44K, Agilent Technologies) for 17 hours at 65°C in an Agilent hybridization oven rotator. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then slowly remove the slide rack minimizing droplets on the slides.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in uninjured wistar rat common carotid artery
|
| Data processing |
Quantile normalization and subsequent data processing was performed using Agilent Feature Extraction software (version 10.7.3.1) and the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, then genes that at least 5 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
Please note: Two raw data files, Sample 1 and Sample 3, contain raw data hybridized to the Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Probe Name version) array. The raw data file of Sample 2 is from a later batch and contains raw data from the Agilent-028282 Whole Rat Genome Microarray 4x44K v3 (Probe Name version). The ProbeNames in the Sample data table are from a median merger of each probe in both arrays according to the GenBank Accession numbers. Then the arrays are quantile standardized. So the ProbeNames in the matrix are the names that were merged for the same GenBank Accession corresponding to the later edition of the Agilent microarray probes names.
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| |
|
| Submission date |
Jun 25, 2013 |
| Last update date |
Jun 29, 2013 |
| Contact name |
Dong ye Li |
| E-mail(s) |
[email protected]
|
| Phone |
0086-516-85582763
|
| Organization name |
Xuzhou Medical College
|
| Department |
Institute of Cardiovascular Disease Research
|
| Lab |
Institute of Cardiovascular Disease Research
|
| Street address |
No. 84 West Huaihai Road
|
| City |
Xuzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
221002 |
| Country |
China |
| |
|
| Platform ID |
GPL14746 |
| Series (1) |
| GSE48279 |
Balloon injury-induced gene expression in common carotid arteries of wistar rat |
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