Search results for the GEO ID: GSE26526  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM652229 | GPL570 |
|
CLL_del11q rep1_case22
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: UT
net insr expression by facs: 7.61%
delta ctm insr-gapd: 7.3
zap70%+ mean: 13
mutated]: UM
FISH (>25% of nuclei): 11q,trisomy 12, 13q
FISH-all: 11q,trisomy 12, 13q
snp 6.0 total subchromosomal and chromosomal lesions: 3
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652229
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652229/suppl/GSM652229.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652230 | GPL570 |
|
CLL_del11q rep2_case24
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: UT
net insr expression by facs: 6.01%
delta ctm insr-gapd: 6.6
zap70%+ mean: 22
mutated]: UM
FISH (>25% of nuclei): 6q, 11q,
FISH-all: 6q, 11q,
snp 6.0 total subchromosomal and chromosomal lesions: 20
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652230
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652230/suppl/GSM652230.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652231 | GPL570 |
|
CLL_del11q rep3_case32
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flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: T
net insr expression by facs: 7.31%
delta ctm insr-gapd: 9.4
zap70%+ mean: 87
mutated]: UM
FISH (>25% of nuclei): 11q, trisomy 12
FISH-all: 11q, trisomy 12
snp 6.0 total subchromosomal and chromosomal lesions: 2
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652231
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652231/suppl/GSM652231.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652232 | GPL570 |
|
CLL_del11q rep4_case52
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: UT
net insr expression by facs: 3.30%
delta ctm insr-gapd: 9.3
zap70%+ mean: 32
mutated]: UM
FISH (>25% of nuclei): 6q, 11q
FISH-all: 6q, 11q
snp 6.0 total subchromosomal and chromosomal lesions: 6
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652232
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652232/suppl/GSM652232.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652233 | GPL570 |
|
CLL_del11q rep5_case81
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: UT
net insr expression by facs: 24.55%
delta ctm insr-gapd: 5.6
zap70%+ mean: 1
mutated]: UM
FISH (>25% of nuclei): 11q, 13q
FISH-all: 11q, 13q
snp 6.0 total subchromosomal and chromosomal lesions: 3
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652233
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652233/suppl/GSM652233.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652234 | GPL570 |
|
CLL_del11q rep6_case101
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: UT
net insr expression by facs: 40.27%
delta ctm insr-gapd: 5.2
zap70%+ mean: 59
mutated]: UM
FISH (>25% of nuclei): 11q
FISH-all: 11q
snp 6.0 total subchromosomal and chromosomal lesions: 1
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652234
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652234/suppl/GSM652234.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652235 | GPL570 |
|
CLL_del11q rep7_case103
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: UT
net insr expression by facs: 28.59%
delta ctm insr-gapd: 6.1
zap70%+ mean: 63
mutated]: UM
FISH (>25% of nuclei): 13q, 11q
FISH-all: 13q, 11q
snp 6.0 total subchromosomal and chromosomal lesions: 2
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652235
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652235/suppl/GSM652235.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652236 | GPL570 |
|
CLL_del11q rep8_case155
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: UT
net insr expression by facs: 5.10%
delta ctm insr-gapd: absent
zap70%+ mean: 49
mutated]: UM
FISH (>25% of nuclei): 11q
FISH-all: 11q
snp 6.0 total subchromosomal and chromosomal lesions: 2
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652236
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652236/suppl/GSM652236.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652237 | GPL570 |
|
CLL_del11q rep9_case171
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: T
net insr expression by facs: 37.17%
delta ctm insr-gapd: 4.5
zap70%+ mean: 30
mutated]: UM
FISH (>25% of nuclei): 11q, 13q
FISH-all: 11q, 13q
snp 6.0 total subchromosomal and chromosomal lesions: 2
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652237
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652237/suppl/GSM652237.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652238 | GPL570 |
|
CLL_del11q rep10_case173
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; del11q present.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: del11q present
treated]: T
net insr expression by facs: 2.61%
delta ctm insr-gapd: 13.4
zap70%+ mean: 7
mutated]: M
FISH (>25% of nuclei): 11q, 13q
FISH-all: 11q, 13q
snp 6.0 total subchromosomal and chromosomal lesions: 2
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652238
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652238/suppl/GSM652238.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652239 | GPL570 |
|
CLL_non-del11q_rep1_case17
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: T
net insr expression by facs: 4.32%
delta ctm insr-gapd: absent
zap70%+ mean: 76
mutated]: UM
FISH (>25% of nuclei): normal
FISH-all: normal
snp 6.0 total subchromosomal and chromosomal lesions: 0
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652239
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652239/suppl/GSM652239.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652240 | GPL570 |
|
CLL_non-del11q_rep2_case19
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: T
net insr expression by facs: 4.36%
delta ctm insr-gapd: 13.3
zap70%+ mean: 88
mutated]: UM
FISH (>25% of nuclei): normal
FISH-all: normal
snp 6.0 total subchromosomal and chromosomal lesions: 0
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652240
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652240/suppl/GSM652240.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652241 | GPL570 |
|
CLL_non-del11q_rep3_case27
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: UT
net insr expression by facs: 1.70%
delta ctm insr-gapd: absent
zap70%+ mean: 89
mutated]: M
FISH (>25% of nuclei): normal
FISH-all: normal
snp 6.0 total subchromosomal and chromosomal lesions: 0
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652241
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652241/suppl/GSM652241.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652242 | GPL570 |
|
CLL_non-del11q_rep4_case55
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: UT
net insr expression by facs: 4.17%
delta ctm insr-gapd: absent
zap70%+ mean: 91
mutated]: UM
FISH (>25% of nuclei): normal
FISH-all: 13q
snp 6.0 total subchromosomal and chromosomal lesions: 0
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652242
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652242/suppl/GSM652242.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652243 | GPL570 |
|
CLL_non-del11q_rep5_case57
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: UT
net insr expression by facs: 5.44%
delta ctm insr-gapd: 12.1
zap70%+ mean: 56
mutated]: UM
FISH (>25% of nuclei): trisomy 12
FISH-all: trisomy 12
snp 6.0 total subchromosomal and chromosomal lesions: 1
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652243
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652243/suppl/GSM652243.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652244 | GPL570 |
|
CLL_non-del11q_rep6_case59
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: UT
net insr expression by facs: 3.30%
delta ctm insr-gapd: absent
zap70%+ mean: 16
mutated]: M
FISH (>25% of nuclei): normal
FISH-all: normal
snp 6.0 total subchromosomal and chromosomal lesions: 0
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652244
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652244/suppl/GSM652244.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652245 | GPL570 |
|
CLL_non-del11q_rep7_case66
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: UT
net insr expression by facs: 2.64%
delta ctm insr-gapd: absent
zap70%+ mean: 73
mutated]: M
FISH (>25% of nuclei): normal
FISH-all: normal
snp 6.0 total subchromosomal and chromosomal lesions: 0
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652245
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652245/suppl/GSM652245.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652246 | GPL570 |
|
CLL_non-del11q_rep8_case77
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: T
net insr expression by facs: 1.41%
delta ctm insr-gapd: absent
zap70%+ mean: 39
mutated]: UM
FISH (>25% of nuclei): 13q
FISH-all: 13q
snp 6.0 total subchromosomal and chromosomal lesions: 0
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652246
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652246/suppl/GSM652246.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
|
GSM652247 | GPL570 |
|
CLL_non-del11q_rep9_case132
|
flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient; non-del11q.
|
cell type: flow-sorted CD19+ cells from peripheral blood of chronic lymphocytic leukemia patient
del11q status: non-del11q
treated]: UT
net insr expression by facs: 3.31%
delta ctm insr-gapd: 11.9
zap70%+ mean: 5
mutated]: UM
FISH (>25% of nuclei): normal
FISH-all: normal
snp 6.0 total subchromosomal and chromosomal lesions: 0
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM652247
| | Sample_status | Public on May 06 2011
| | Sample_submission_date | Jan 10 2011
| | Sample_last_update_date | May 06 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Material used was cryopreserved primary human peripheral blood cells, prepared as below.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | 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).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 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.
| | Sample_hyb_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.
| | Sample_scan_protocol | Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.
| | Sample_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.
| | Sample_data_processing | 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.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sami,N,Malek
| | Sample_contact_email | smalek@med.umich.edu, pouillet@med.umich.edu
| | Sample_contact_phone | 734-763-1222
| | Sample_contact_department | Internal Medicine, Hematology-Oncology
| | Sample_contact_institute | University of Michigan
| | Sample_contact_address | 4410 Cancer Center; 1500 E Medical Center Dr
| | Sample_contact_city | Ann Arbor
| | Sample_contact_state | MI
| | Sample_contact_zip/postal_code | 48109
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM652nnn/GSM652247/suppl/GSM652247.CEL.gz
| | Sample_series_id | GSE26526
| | Sample_data_row_count | 54675
| | |
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