|
| Status |
Public on May 20, 2010 |
| Title |
C590 |
| Sample type |
RNA |
| |
|
| Source name |
sorted CML CD34+CD38- cells treated with IM
|
| Organism |
Homo sapiens |
| Characteristics |
subjectid: 5269
imatinib: IM
lbh589: NoLBH
|
| Treatment protocol |
CML CD34+CD38- cells were selected using flow cytometry sorting and treated with IM, LBH and the combination of IM and LBH or cultured without exposure to drugs (controls) for 24 hours (n=3 each).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 5000 cells was extracted using the RNeasy kit (Qiagen), amplified and labeled using GeneChip Two-Cycle Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol (15 µg cRNA from each sample was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays)
|
| Scan protocol |
Standard Affymetrix protocol
|
| Description |
n/a
|
| Data processing |
Microarray data analyses were performed using R (version 2.9) with genomic analysis packages from Bioconductor (version 2.4).
Expression data were normalized using the robust multiarray average (RMA) algorithm, with background adjustment, quantile normalization and median polish summarization.
Differentially expressed genes were identified by calculating empirical Bayes moderated t-statistic, and p-values were adjusted by FDR using the “LIMMA” package.
Gene Set Enrichment Analyses (GSEA) was performed using GSEA software version 2.04 [http://www.broadinstitute.org/gsea/] to detect enrichment of predetermined gene sets using t-scores and gene sets in C2 (curated gene sets) category from the Molecular Signature Database (MsigDB).
|
| |
|
| Submission date |
Mar 15, 2010 |
| Last update date |
Apr 21, 2010 |
| Contact name |
Ravi Bhatia |
| E-mail(s) |
rbhatia@coh.org
|
| Phone |
6263598111
|
| Fax |
6263018973
|
| Organization name |
City of Hope Beckman Research Institute
|
| Department |
Hematopoietic Stem Cell and Leukemia Research
|
| Street address |
1500 E Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE20876 |
Effective Targeting of Quiescent Chronic Myelogenous Leukemia Stem Cells by Histone Deacetylase Inhibitors in Combination with Imatinib Mesylate |
|
