|
| Status |
Public on Jun 01, 2006 |
| Title |
U133Plus-P002 (TT2 pre-treatment) |
| Sample type |
RNA |
| |
|
| Source name |
pre-treatment bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
[SURIND=0 (Indicator of disease-related death; integer, 0=alive or death by other cause, 1=disease related death, na=death cause undetermined)]
[SURTIM=69.24 (Follow-up time in months from Pre-Treatment baseline; integer)]
[PCTCELLS=0%/1%/5%/91%/3% (Percentage of cells with 0 copy/1 copy/2 copies/3 copies/4+ copies; percentage)]
[AMPIND=3 copies (Indicator of FISH 1q21 Amplification; string, na=not available)]
[Subgrp7=CD1]
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
As recommended by manufacturer
|
| |
|
| Hybridization protocol |
As recommended by manufacturer
|
| Scan protocol |
As recommended by manufacturer
|
| Description |
Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA)
More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining
The clinic survival follow-up is through November 5, 2004
Disease-related survival: Deaths were coded as disease-related according to a physician chart review. Three deaths had not been coded as of the time of the analysis and these corresponding to the three missing status indicators in the data set. Non-disease related deaths are competing risks, so distribution estimates should use cumulative incidence of disease-related death as the outcome, rather than survival
Censored data analysis: Analyses using the status indicator as a grouping variable directly are not recommended. Tests for censored data can be applied, gene-by-gene, as in the published analysis, or disease-related deaths can be matched to a random sample of longer survivors
Keywords = CKS1B in Multiple Myeloma
|
| Data processing |
All data used in these analyses were derived with the Affymetrix Microarray Suite GCOS1.1 software.
CEL files are available upon request via a Materials Transfer Agreement. Please contact Dr. John Shaughnessy for details.
|
| |
|
| Submission date |
May 13, 2005 |
| Last update date |
Apr 01, 2010 |
| Contact name |
Shaughnessy Jr. John |
| E-mail(s) |
shaughnessyjohn@uams.edu
|
| Phone |
(501)296-1503 1410
|
| Organization name |
Myeloma Institute for Research and Therapy
|
| Department |
|
| Lab |
Donna D. and Donald M. Lambert Laboratory of Myeloma Genetics
|
| Street address |
4301 West Markham St., Slot 776
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72205 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (3) |
| GSE2658 |
Gene Expression Profiles of Multiple Myeloma |
| GSE4204 |
Gene Expression Profiles of Multiple Myeloma Before Treatment |
| GSE4581 |
Gene Expression Profiles of Multiple Myeloma (N=414) Before Treatment |
|
