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| Status |
Public on Aug 03, 2013 |
| Title |
BM_High density culture_15Days_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
endothelial progenitor cells (EPCs)
|
| Organism |
Rattus norvegicus |
| Characteristics |
background strain: Wistar
tissue type: bone marrow
age: 6 weeks
|
| Treatment protocol |
After 15 days of culture at regular or high density, total RNA was extracted from the cells with Trizol (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction 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 and array hybridization were 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. 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 the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.
|
| |
|
| Hybridization protocol |
100 μl 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 G2505B).
|
| Description |
Gene expression after 15days high density culture of rat bone marrow cells
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After Quantile normalization of the raw data, genes that at least 2 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.0).
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| |
|
| Submission date |
Aug 02, 2013 |
| Last update date |
Aug 03, 2013 |
| Contact name |
Yang Lu |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
639 Zhi Zao Ju Road
|
| City |
Shanghai |
| ZIP/Postal code |
200011 |
| Country |
China |
| |
|
| Platform ID |
GPL14746 |
| Series (1) |
| GSE49510 |
Global gene expression pattern difference between the high density and the regular density cultured rat bone marrow cells |
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