|
| Status |
Public on Jun 01, 2009 |
| Title |
Peripheral blood cells in patients with Systemic Lupus Erythematosus (SLE)-9 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Peripheral blood cells from SLE patient 9
|
| Organism |
Homo sapiens |
| Characteristics |
Gender : female, Age : 32, Disease : Systemic Lupus Erythematosus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA). Total RNA was extracted using PAXGene Blood RNA kit with the optimal on-column DNase digestion according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3.
|
| |
|
| Channel 2 |
| Source name |
Peripheral blood cells from 12 healthy women
|
| Organism |
Homo sapiens |
| Characteristics |
Healthy women without any identified diseases.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA). Total RNA was extracted using PAXGene Blood RNA kit with the optimal on-column DNase digestion according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy5.
|
| |
|
| |
| Hybridization protocol |
The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16 hours at 42℃. Slides were washed in 2xSSC+0.1% SDS, 2xSSC, 1xSSC and 0.1xSSC before air pressure drying and scanning.
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Lite (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).
|
| Description |
Genes expressed in peripheral blood cells from patients with SLE.
|
| Data processing |
The median background intensities were subtracted from median intensities of Channel 1 (Cy3) or Channel 2 (Cy5). Log2 ratios of Cy3 to Cy5 were calculated. The VALUE shown were log2 Cy3/Cy5 ratios of all spots on the DNA microarray which were normalized by the method of global ratio median normalization.
|
| |
|
| Submission date |
Aug 07, 2008 |
| Last update date |
Jun 01, 2009 |
| Contact name |
Norihiro Nishimoto |
| E-mail(s) |
norichan@wakayama-med.ac.jp
|
| Phone |
+81-72-646-8039
|
| Fax |
+81-72-646-8140
|
| Organization name |
Wakayama Medical University
|
| Lab |
Laboratory of Immune Regulation
|
| Street address |
7-7-20, Saito-Asagi
|
| City |
Ibaraki |
| State/province |
Osaka |
| ZIP/Postal code |
567-0085 |
| Country |
Japan |
| |
|
| Platform ID |
GPL1291 |
| Series (1) |
| GSE12374 |
Interactions of cytokines in peripheral blood cells from Systemic Lupus Erythematosus |
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