|
| Status |
Public on May 06, 2011 |
| Title |
CLL_del11q rep9_case171 |
| Sample type |
RNA |
| |
|
| Source name |
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treatment status prior to enrollment [ut = untreated; t = treated]: T
net insr expression by facs: 37.17%
delta ctm insr-gapd: 4.5
zap70%+ mean: 30
igvh (98%) [um = unmutated; m = mutated]: UM
FISH (>25% of nuclei): 11q, 13q
FISH-all: 11q, 13q
snp 6.0 total subchromosomal and chromosomal lesions: 2
|
| Growth protocol |
Material used was cryopreserved primary human peripheral blood cells, prepared as below.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CLL peripheral blood mononuclear cells were stained with propidium iodide and CD19*PE, then sorted using a high-speed FACS Aria (Becton Dickinson) sorter to purity. RNA was extracted using the Trizol reagent. RNA was further purified using the RNAeasy kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
50ng total RNA was amplified using the Ovation RNA Amplification system (NuGen, Inc.), labeled with the FL-Ovation cDNA Biotin module (NuGen, Inc.) and hybridized to the Human 133 2.0 plus GeneChip (Affymetrix) following the manufacturer's recommended protocols.
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| |
|
| Hybridization protocol |
Affymetrix Hybridization Oven 640 for 16 hrs at 48 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.
|
| Scan protocol |
Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
|
| Description |
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Data processing |
Affymetrix GeneChip data were analyzed as described (Ouillette et al., Cancer Res. 2008;68:1012-21). Raw probe-level data were converted to expression measures using the Robust Multi-array Average (RMA) method, which is implemented in the Affymetrix package of Bioconductor (Izarry et al., Biostatistics. 2003;4:249-64; R version 2.7.0, Bioconductor Affymetrix package version 1.17.5). Briefly, the raw perfect match (PM) probes are first quartile normalized to reduce array-to-array variation. The normalized probe data are then converted to an expression measure (log scale) for each gene on each chip. For differential expression analysis relating to 11q deletion status, we used two-sample Z-tests to compare the mean log-scale expression level between del11q and non-del11q samples. Genes with a False Discovery Rate (33) below 0.1 were selected, then fold-changes, FDR values, and Z-scores were used to identify genes having a strong association with 11q deletion status.
Robust multi-array average (RMA)-computed expression values (Izarry et al., Biostatistics, 4:249-64, 2003). Note that the expression values are log2-transformed data.
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| |
|
| Submission date |
Jan 10, 2011 |
| Last update date |
May 06, 2011 |
| Contact name |
Sami N Malek |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
734-763-1222
|
| Organization name |
University of Michigan
|
| Department |
Internal Medicine, Hematology-Oncology
|
| Street address |
4410 Cancer Center; 1500 E Medical Center Dr
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE26526 |
A Pathobiological Role of the Insulin Receptor in CLL. |
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