|
| Status |
Public on Nov 30, 2012 |
| Title |
Contol4 ZP35 mRNA |
| Sample type |
RNA |
| |
|
| Source name |
Contol4 ZP35
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: dermal mesenchymal stem cell
age: 36 years
gender: male
pasi: ——
|
| Growth protocol |
The dermises were separated from the epidermis by dispase and monoplast suspension was obtained by pipetting. The MSCs were cultured by adherent assay. Cells of 3rd passage were enrolled in the microarry.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
|
| Label |
Cy3
|
| Label protocol |
1 μg of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The Labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA
|
| |
|
| Hybridization protocol |
100μl 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. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).
|
| Scan protocol |
scanned with using the Agilent DNA Microarray Scanner (part number G2505B).
|
| Data processing |
Agilent Feature Extraction software (version 10.7.3.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 12 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through volcano plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method
|
| |
|
| Submission date |
Nov 29, 2012 |
| Last update date |
Nov 30, 2012 |
| Contact name |
Ruixia Hou |
| E-mail(s) |
hrx0205@163.com
|
| Organization name |
Taiyuan City Central Hospital
|
| Department |
Dermatology
|
| Street address |
1,Dong San Dao Xiang, Jiefang Road
|
| City |
Taiyuan |
| State/province |
Shanxi |
| ZIP/Postal code |
030009 |
| Country |
China |
| |
|
| Platform ID |
GPL13497 |
| Series (1) |
| GSE42632 |
mRNA expression profile of dermal MSCs derived from psoriasis patients and normal control |
|
