|
| Status |
Public on Feb 19, 2014 |
| Title |
miR-126-/-_S1 |
| Sample type |
RNA |
| |
|
| Source name |
miR-126-/-_wire-injured carotid artery_target
|
| Organism |
Mus musculus |
| Characteristics |
gender: female
age: 6 weeks
genotype/variation: miR-126-/-/ApoE-/-
tissue: carotid artery
|
| Treatment protocol |
Wire-induced carotid injury was performed in miR-126+/+ApoE-/- (control group) and miR-126-/-ApoE-/- (target group) mice on western-type diet. RNA was isolated after 14 days following vascular injury (n=4 each group) and hybridized to the Agilent mouse microarrays.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy micro Kit (QIAGEN) following the manufacturer's instruction. The protocol includes tissue lysis, hemogenization, and an on-column DNase digestion. RNA was quantified using a NanoDrop spectrophotometer and quality was measured with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
100 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into labeled cRNA by in-vitro transcription (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies) incorporating Cyanine-3-CTP.
|
| |
|
| Hybridization protocol |
Following cRNA clean-up and quantification, 825 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Each single cRNA sample was hybridized at 65°C for 17 hrs on separate SurePrint G3 Mouse GE Microarrays (8x60K format). The microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).
|
| Scan protocol |
Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 028005_D_F_20101029.xml.
|
| Description |
RS-188_05
Genomewide expression profile of miR-126-/-/ApoE-/- mouse 14 days after vascular injury - mouse carotid artery
The mouse strain in this experiment have a mixed genetic background.
|
| Data processing |
The software tools Feature Extraction 10.7.3.1, GeneSpring GX 11.5 and Spotfire Decision Site 9.1.2 were used for quality control, statistical data analysis, Gene ontology annotation and visualization. Quantile normalization was applied to the data set. After normalization, data is returned as log2 transformed values and filtered based on flags.
|
| |
|
| Submission date |
Dec 08, 2011 |
| Last update date |
Feb 19, 2014 |
| Contact name |
Andreas Schober |
| E-mail(s) |
aschober@med.lmu.de
|
| Organization name |
Ludwig-Maximilians-University
|
| Department |
Institute for Cardiovascular Prevention
|
| Street address |
Pettenkoferstr. 9
|
| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
80336 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE34262 |
Genomewide expression profile of wire-injured carotid arteries harvested from either miR-126+/+/ApoE-/- or miR-126-/-/ApoE-/- mice during neointima development |
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