Search results for the GEO ID: GSE9662  |
(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 |
GSM243724 | GPL96 |
|
pool 1a
|
breast cancer patients without relapse
|
Sample name: pool 1 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243724
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243724/suppl/GSM243724.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243725 | GPL96 |
|
pool 1b
|
breast cancer patients without relapse
|
Sample name: pool 1 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243725
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243725/suppl/GSM243725.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243726 | GPL96 |
|
pool 3a
|
breast cancer patients without relapse
|
Sample name: pool 3 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243726
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243726/suppl/GSM243726.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243729 | GPL96 |
|
pool 3b
|
breast cancer patients without relapse
|
Sample name: pool 3 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243729
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243729/suppl/GSM243729.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243760 | GPL96 |
|
pool 5a
|
breast cancer patients without relapse
|
Sample name: pool 5 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243760
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243760/suppl/GSM243760.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243761 | GPL96 |
|
pool 5b
|
breast cancer patients without relapse
|
Sample name: pool 5 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243761
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243761/suppl/GSM243761.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243762 | GPL96 |
|
pool 7a
|
breast cancer patients without relapse
|
Sample name: pool 7 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243762
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243762/suppl/GSM243762.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243763 | GPL96 |
|
pool 7b
|
breast cancer patients without relapse
|
Sample name: pool 7 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243763
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243763/suppl/GSM243763.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243764 | GPL96 |
|
pool 9a
|
breast cancer patients without relapse
|
Sample name: pool 9 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243764
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243764/suppl/GSM243764.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243765 | GPL96 |
|
pool 9b
|
breast cancer patients without relapse
|
Sample name: pool 9 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243765
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243765/suppl/GSM243765.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243766 | GPL96 |
|
pool 11a
|
breast cancer patients without relapse
|
Sample name: pool 11 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243766
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243766/suppl/GSM243766.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243767 | GPL96 |
|
pool 11b
|
breast cancer patients without relapse
|
Sample name: pool 11 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients without relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243767
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243767/suppl/GSM243767.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243768 | GPL96 |
|
pool 2a
|
breast cancer patients with relapse
|
Sample name: pool 2 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243768
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243768/suppl/GSM243768.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243769 | GPL96 |
|
pool 2b
|
breast cancer patients with relapse
|
Sample name: pool 2 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243769
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243769/suppl/GSM243769.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243770 | GPL96 |
|
pool 4a
|
breast cancer patients with relapse
|
Sample name: pool 4 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243770
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243770/suppl/GSM243770.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243771 | GPL96 |
|
pool 4b
|
breast cancer patients with relapse
|
Sample name: pool 4 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243771
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243771/suppl/GSM243771.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243772 | GPL96 |
|
pool 6a
|
breast cancer patients with relapse
|
Sample name: pool 6 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243772
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243772/suppl/GSM243772.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243773 | GPL96 |
|
pool 6b
|
breast cancer patients with relapse
|
Sample name: pool 6 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243773
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243773/suppl/GSM243773.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243774 | GPL96 |
|
pool 8a
|
breast cancer patients with relapse
|
Sample name: pool 8 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243774
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243774/suppl/GSM243774.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243775 | GPL96 |
|
pool 8b
|
breast cancer patients with relapse
|
Sample name: pool 8 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243775
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243775/suppl/GSM243775.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243776 | GPL96 |
|
pool 10a
|
breast cancer patients with relapse
|
Sample name: pool 10 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243776
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243776/suppl/GSM243776.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243777 | GPL96 |
|
pool 10b
|
breast cancer patients with relapse
|
Sample name: pool 10 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243777
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243777/suppl/GSM243777.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243778 | GPL96 |
|
pool 12a
|
breast cancer patients with relapse
|
Sample name: pool 12 replicate a
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243778
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243778/suppl/GSM243778.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
| | |
|
GSM243779 | GPL96 |
|
pool 12b
|
breast cancer patients with relapse
|
Sample name: pool 12 replicate b
|
Tumor samples of ductal invasive breast carcinoma from patients with relapse within 72 months from surgery
|
| Sample_geo_accession | GSM243779
| | Sample_status | Public on Nov 19 2008
| | Sample_submission_date | Nov 20 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_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was isolated with Concert Cytoplasmic RNA Reagent (Invitrogen Corporation) from 20 to 50 mg tumor tissues, according to the manufacturer's guidelines. Frozen tumors were placed in this reagent and homogenized using a ball mill (MM200, Retsch, Düsseldorf, Germany). 10 µg aliquots of total RNA was treated with DNase I, using a commercially available kit (DNA free, Ambion, Inc., Austin, TX) to eliminate genomic DNA contamination. The quantity and quality of the RNA samples were determined using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Approximately 2 microgram of total RNA was processed to produce biotinylated cRNA targets.
| | Sample_hyb_protocol | standard Affymetrix procedures
| | Sample_scan_protocol | standard Affymetrix procedures
| | Sample_data_processing | GCRMA Bioconductor
| | Sample_platform_id | GPL96
| | Sample_contact_name | Daniela,,Cimino
| | Sample_contact_email | daniela.cimino@unito.it
| | Sample_contact_phone | 00390116706448
| | Sample_contact_department | Oncological Science
| | Sample_contact_institute | Molecular Biotechnology Center
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | Torino
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM243nnn/GSM243779/suppl/GSM243779.CEL.gz
| | Sample_series_id | GSE9662
| | Sample_data_row_count | 22283
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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