|
| Status |
Public on Jul 01, 2014 |
| Title |
BM01 |
| Sample type |
RNA |
| |
|
| Source name |
Cultured bone marrow mesenchymal stem cells (Millipore)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: bone marrow mesenchymal stem cells
|
| Treatment protocol |
No specific treatment.
|
| Growth protocol |
Cell culturing methods.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted when the culture was near confluent. About 2-3 x 10^6 cells from each sample were lysed and total RNA was isolated using the RNeasy kit (Qiagen Hamburg GmbH, Hamburg, Germany) according to the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Prior to Cy3 labeling, 2uL of Agilent One-Colour Spike Mix dilution was added to 100ng of total RNA for each sample. The total RNA was converted to cDNA and then to Cy3-labeled cRNA by using the Agilent One-Colour RNA Spike-In Kit as per the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
The labeled cRNA was purified and quantitated before subjected to hybridization in a hybridization oven at 65 °C for 17 hr.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Dye channel is set to Green and Green PMT).
|
| Description |
US83503546_252800412748_S01_GE1_107_Sep09_1_1
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal. Data analysis was done by using GeneSpring 11.5 (Agilent Technologies, Santa Clara, CA). The threshold was set to intensity value of 1.0. Log base 2 transformation was carried out for threshold data. Normalization was done by 75th percentile shift. Baseline transformation was based on the median of samples. The data were futher filtered by probeset on flags and expression less than 20. Unpaired Student’s T test was used for statistical analysis. Genes up- or down-regulated by two-fold change were selected for further analysis.
|
| |
|
| Submission date |
Jun 26, 2012 |
| Last update date |
Jul 01, 2014 |
| Contact name |
Moon Nian Lim |
| E-mail(s) |
limmn@imr.gov.my
|
| Phone |
603-26162714
|
| Organization name |
Institute for Medical Research
|
| Department |
Haematology Unit
|
| Lab |
Stem Cell Laboratory
|
| Street address |
Jalan Pahang
|
| City |
Kuala Lumpur |
| ZIP/Postal code |
50588 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL14550 |
| Series (1) |
| GSE38947 |
Comparative gene expression profile of human limbal stromal cells, bone marrow mesenchymal cells, adipose cells and foreskin fibroblasts |
|
