Search results for the GEO ID: GSE13276 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM335185 | GPL96 |
|
Core sample 1
|
Human glioblastoma tumor mass
|
Tumor mass samples were retrieved from patients operated for supratentorial GBM with "en bloc" total removal technique. All specimens were collected and submitted to the study under institutional review board-approved protocols. Classification and grading of the tumors were performed according to the criteria of the World Health Organization (WHO). All tumors included in this protocol were classified as WHO grade IV.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335185
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335185/suppl/GSM335185.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335185/suppl/GSM335185.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335186 | GPL96 |
|
Core sample 2
|
Human glioblastoma tumor mass
|
Tumor mass samples were retrieved from patients operated for supratentorial GBM with "en bloc" total removal technique. All specimens were collected and submitted to the study under institutional review board-approved protocols. Classification and grading of the tumors were performed according to the criteria of the World Health Organization (WHO). All tumors included in this protocol were classified as WHO grade IV.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335186
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335186/suppl/GSM335186.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335186/suppl/GSM335186.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335187 | GPL96 |
|
Core sample 3
|
Human glioblastoma tumor mass
|
Tumor mass samples were retrieved from patients operated for supratentorial GBM with "en bloc" total removal technique. All specimens were collected and submitted to the study under institutional review board-approved protocols. Classification and grading of the tumors were performed according to the criteria of the World Health Organization (WHO). All tumors included in this protocol were classified as WHO grade IV.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335187
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335187/suppl/GSM335187.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335187/suppl/GSM335187.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335188 | GPL96 |
|
Core sample 4
|
Human glioblastoma tumor mass
|
Tumor mass samples were retrieved from patients operated for supratentorial GBM with "en bloc" total removal technique. All specimens were collected and submitted to the study under institutional review board-approved protocols. Classification and grading of the tumors were performed according to the criteria of the World Health Organization (WHO). All tumors included in this protocol were classified as WHO grade IV.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335188
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335188/suppl/GSM335188.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335188/suppl/GSM335188.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335189 | GPL96 |
|
Core sample 5
|
Human glioblastoma tumor mass
|
Tumor mass samples were retrieved from patients operated for supratentorial GBM with "en bloc" total removal technique. All specimens were collected and submitted to the study under institutional review board-approved protocols. Classification and grading of the tumors were performed according to the criteria of the World Health Organization (WHO). All tumors included in this protocol were classified as WHO grade IV.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335189
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335189/suppl/GSM335189.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335189/suppl/GSM335189.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335190 | GPL96 |
|
GBM surrounding tissue 1
|
GBM surrounding tissue
|
GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335190
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor surrounding tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335190/suppl/GSM335190.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335190/suppl/GSM335190.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335191 | GPL96 |
|
GBM surrounding tissue 2
|
GBM surrounding tissue
|
GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335191
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor surrounding tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335191/suppl/GSM335191.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335191/suppl/GSM335191.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335192 | GPL96 |
|
GBM surrounding tissue 3
|
GBM surrounding tissue
|
GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335192
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor surrounding tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335192/suppl/GSM335192.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335192/suppl/GSM335192.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335193 | GPL96 |
|
GBM surrounding tissue 3R
|
GBM surrounding tissue
|
GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border. This is a biological replicate of GBM surrounding tissue 3, harvested independently.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335193
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor surrounding tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335193/suppl/GSM335193.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335193/suppl/GSM335193.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335194 | GPL96 |
|
GBM surrounding tissue 4
|
GBM surrounding tissue
|
GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335194
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor surrounding tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335194/suppl/GSM335194.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335194/suppl/GSM335194.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335195 | GPL96 |
|
GBM surrounding tissue 4R
|
GBM surrounding tissue
|
GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border. This sample is a biological replicate of GBM surrounding tissue sample 4, harvested independently.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335195
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor surrounding tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335195/suppl/GSM335195.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335195/suppl/GSM335195.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335196 | GPL96 |
|
GBM surrounding tissue 5
|
GBM surrounding tissue
|
GBM surrounding tissue was retrieved from not infiltrated white matter sited at 2cm from the macroscopic tumor border.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335196
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen tumor surrounding tissue. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335196/suppl/GSM335196.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335196/suppl/GSM335196.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335197 | GPL96 |
|
White matter control 1
|
human white matter
|
White matter control biopsies were retrieved from patients operated on for deep intracerebral cavernomas.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335197
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen biopsies. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335197/suppl/GSM335197.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335197/suppl/GSM335197.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335198 | GPL96 |
|
White matter control 2
|
human white matter
|
White matter control biopsies were retrieved from patients operated on for deep intracerebral cavernomas.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335198
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen biopsies. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335198/suppl/GSM335198.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335198/suppl/GSM335198.CHP.gz
| Sample_series_id | GSE13276
| Sample_data_row_count | 22283
| |
|
GSM335199 | GPL96 |
|
White matter control 3
|
human white matter
|
White matter control biopsies were retrieved from patients operated on for deep intracerebral cavernomas.
|
Glioblastoma is a highly locally invasive tumor. Key genetic mutations defining GBM are well-characterized, while poor informations are available about the surrounding tumor tissue, that represents the site of tumor recurrence in 90% of the cases. Knowledges of the molecular mechanisms that encode this invasive phenotype may help to develop new therapeutic options.
|
Sample_geo_accession | GSM335199
| Sample_status | Public on Jun 15 2009
| Sample_submission_date | Oct 20 2008
| Sample_last_update_date | Apr 08 2009
| 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 extracted from frozen biopsies. Samples were homogenized in 1ml guanidine isothiocyanate solution. RNA was extracted by standard phenol/chloroform extraction method, followed by isopropanol precipitation. Finally, RNA was purified onto columns (Qiagen) with an additional DNase digestion step.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| Sample_label_protocol_ch1 |
| Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human U133A array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| Sample_scan_protocol | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to GeneSpring software for normalization, statistical analysis and functional categorization.
| Sample_platform_id | GPL96
| Sample_contact_name | Nathalie,,Saulnier
| Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| Sample_contact_phone | +39 0630154915
| Sample_contact_fax | +39 0630154813
| Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| Sample_contact_address | Largo Francesco Vito,1
| Sample_contact_city | Roma
| Sample_contact_zip/postal_code | 00168
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335199/suppl/GSM335199.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM335nnn/GSM335199/suppl/GSM335199.CHP.gz
| Sample_series_id | GSE13276
| 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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