|
| Status |
Public on Jun 01, 2008 |
| Title |
Bcell-lowBMD-5 |
| Sample type |
RNA |
| |
|
| Source name |
B cells in blood
|
| Organism |
Homo sapiens |
| Characteristics |
postmenopause, age=58,Spine Z-score=-0.7,Hip Z-score=-0.47
|
| Treatment protocol |
B cells isolated from 70mL of whole blood using a B cells positive method Dynabeads CD19 (Pan B)Kit (Invitrogen Life Technologies Dynal Biotech Inc.,CA) following manufacturer's instructions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from B cells was extracted using Qiagen Rneasy Mini Kit (Qiagen Inc.,CA)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from low BMD postmenopausal females
|
| Data processing |
The probe level data generated by Microarray Suite 5.0 (MAS 5.0, Affymetrix) CEL files were converted into expression measures and normalized by Robust Multiarray Algorithm using the Affy package from Bioconductor in R environment.Transformed data were analyzed by Bioconductor's Multtest package to identify differentially expressed genes between the high and the low BMD subgroups using t-statistics. Benjamini and Hochberg (BH) stepwise procedure was used for multiple-testing adjustment and FDR (false discovery rate)<0.05 was used as the significant criterion.
|
| |
|
| Submission date |
Apr 02, 2007 |
| Last update date |
Jan 02, 2009 |
| Contact name |
Peng Xiao |
| E-mail(s) |
[email protected]
|
| Phone |
402-280-4283
|
| Fax |
402-280-4284
|
| Organization name |
Creighton University Medical Center
|
| Department |
Biomedical Sciences & Osteoporosis Research Center
|
| Lab |
Genetic Lab
|
| Street address |
601 N 30th ST Suite 6730
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68131 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE7429 |
Gene Expression of Circulating B Lymphocytes for Osteoporosis |
| GSE13850 |
Gene Expression of Circulating B Lymphocytes for Smoking-related Osteoporosis in Postmenopausal Females |
|
