Search results for the GEO ID: GSE9250  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM234840 | GPL570 |
|
CLL_del13q_rep1
|
chronic lymphocytic leukemia (CLL) with del13q
|
female
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234840
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234840/suppl/GSM234840.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234841 | GPL570 |
|
CLL_del13q_rep2
|
chronic lymphocytic leukemia (CLL) with del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234841
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234841/suppl/GSM234841.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234842 | GPL570 |
|
CLL_FISHnormal_rep1
|
chronic lymphocytic leukemia (CLL) with no del13q
|
female
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234842
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234842/suppl/GSM234842.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234843 | GPL570 |
|
CLL_FISHnormal_rep2
|
chronic lymphocytic leukemia (CLL) with no del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234843
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234843/suppl/GSM234843.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234844 | GPL570 |
|
CLL_del13q_rep3
|
chronic lymphocytic leukemia (CLL) with del13q
|
female
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234844
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234844/suppl/GSM234844.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234845 | GPL570 |
|
CLL_del13q_rep4
|
chronic lymphocytic leukemia (CLL) with del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234845
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234845/suppl/GSM234845.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234846 | GPL570 |
|
CLL_FISHnormal_rep3
|
chronic lymphocytic leukemia (CLL) with no del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234846
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234846/suppl/GSM234846.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234847 | GPL570 |
|
CLL_del13q_rep5
|
chronic lymphocytic leukemia (CLL) with del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234847
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234847/suppl/GSM234847.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234848 | GPL570 |
|
CLL_del13q_rep6
|
chronic lymphocytic leukemia (CLL) with del13q
|
female
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234848
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234848/suppl/GSM234848.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234849 | GPL570 |
|
CLL_FISHnormal_rep4
|
chronic lymphocytic leukemia (CLL) with no del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234849
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234849/suppl/GSM234849.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234850 | GPL570 |
|
CLL_FISHnormal_rep5
|
chronic lymphocytic leukemia (CLL) with no del13q
|
female
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234850
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234850/suppl/GSM234850.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234851 | GPL570 |
|
CLL_FISHnormal_rep6
|
chronic lymphocytic leukemia (CLL) with no del13q
|
female
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234851
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234851/suppl/GSM234851.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234852 | GPL570 |
|
CLL_del13q_rep7
|
chronic lymphocytic leukemia (CLL) with del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234852
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234852/suppl/GSM234852.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234853 | GPL570 |
|
CLL_FISHnormal_rep7
|
chronic lymphocytic leukemia (CLL) with no del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234853
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234853/suppl/GSM234853.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234854 | GPL570 |
|
CLL_FISHnormal_rep8
|
chronic lymphocytic leukemia (CLL) with no del13q
|
female
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234854
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234854/suppl/GSM234854.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234855 | GPL570 |
|
CLL_FISHnormal_rep9
|
chronic lymphocytic leukemia (CLL) with no del13q
|
female
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234855
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234855/suppl/GSM234855.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234856 | GPL570 |
|
CLL_del13q_rep8
|
chronic lymphocytic leukemia (CLL) with del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234856
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234856/suppl/GSM234856.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234857 | GPL570 |
|
CLL_del13q_rep9
|
chronic lymphocytic leukemia (CLL) with del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234857
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234857/suppl/GSM234857.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234858 | GPL570 |
|
CLL_FISHnormal_rep10
|
chronic lymphocytic leukemia (CLL) with no del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234858
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234858/suppl/GSM234858.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
GSM234859 | GPL570 |
|
CLL_del13q_rep10
|
chronic lymphocytic leukemia (CLL) with del13q
|
male
|
50 ng total RNA amplified with Ovation RNA Amplification system (NuGen, Inc.)
|
| Sample_geo_accession | GSM234859
| | Sample_status | Public on Oct 06 2007
| | Sample_submission_date | Oct 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Not applicable.
| | Sample_growth_protocol_ch1 | Not applicable. 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). 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_label_ch1 | FL-Ovation cDNA Biotin module (NuGen, Inc.)
| | Sample_label_protocol_ch1 | See extract protocol.
| | Sample_hyb_protocol | Affymetrix Hybridization Oven 640 for 16 hrs at 480C 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 follows. 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. Briefly, the raw perfect match (PM) probes were quartile normalized to remove any non biological variability (due to differential binding, chip effects, etc). The normalized probe data were then converted to an expression measure for each gene on each chip using a robust modeling strategy. For differential expression analysis relating to 13q14 deletion status, we first removed the bottom 25% of probe sets in terms of overall variability. After this filtering step, 41007 probe sets remained. Two-way analysis of variance (ANOVA) was then used to identify differentially expressed genes while accounting for the two-batch design of the study. Main effects for the presence of 13q14 deletion and for batch were included in the model. Standardized ANOVA coefficient estimates for the 13q14 deletion factor were then analyzed using false discovery rates (FDR).
| | 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/GSM234nnn/GSM234859/suppl/GSM234859.CEL.gz
| | Sample_series_id | GSE9250
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
