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Sample GSM652242 Query DataSets for GSM652242
Status Public on May 06, 2011
Title CLL_non-del11q_rep4_case55
Sample type RNA
 
Source name flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
Organism Homo sapiens
Characteristics cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treatment status prior to enrollment [ut = untreated; t = treated]: UT
net insr expression by facs: 4.17%
delta ctm insr-gapd: absent
zap70%+ mean: 91
igvh (98%) [um = unmutated; m = mutated]: UM
FISH (>25% of nuclei): normal
FISH-all: 13q
snp 6.0 total subchromosomal and chromosomal lesions: 0
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.
 
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.
 
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.

Data table header descriptions
ID_REF
VALUE log2 RMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 9.673894341
1053_at 7.551364514
117_at 8.389402627
121_at 6.225368127
1255_g_at 2.394211488
1294_at 9.456358512
1316_at 6.594029663
1320_at 4.482153891
1405_i_at 6.011024982
1431_at 6.282632213
1438_at 4.088694802
1487_at 8.015392532
1494_f_at 4.363860664
1552256_a_at 4.686997907
1552257_a_at 8.236152723
1552258_at 3.727652036
1552261_at 4.008922262
1552263_at 5.920239743
1552264_a_at 7.285815076
1552266_at 3.695100139

Total number of rows: 54675

Table truncated, full table size 1211 Kbytes.




Supplementary file Size Download File type/resource
GSM652242.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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