Search results for the GEO ID: GSE12345  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM309986 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; ctrl 14
|
pleural tissue
|
Pleural tissue was obtained from patients undergoing resection for lung cancer at an area distant from the tumour site.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM309986
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309986/suppl/GSM309986.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM309987 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; ctrl 8
|
pleural tissue
|
Pleural tissue was obtained from patients undergoing resection for lung cancer at an area distant from the tumour site.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM309987
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309987/suppl/GSM309987.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM309988 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; ctrl 48
|
pleural tissue
|
Pleural tissue was obtained from patients undergoing resection for lung cancer at an area distant from the tumour site.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM309988
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309988/suppl/GSM309988.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM309989 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; ctrl 47
|
pleural tissue
|
Pleural tissue was obtained from patients undergoing resection for lung cancer at an area distant from the tumour site.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM309989
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309989/suppl/GSM309989.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM309990 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; meso 21
|
mesothelioma tissue
|
Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM309990
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309990/suppl/GSM309990.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM309991 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; meso 23
|
mesothelioma tissue
|
Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM309991
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM309nnn/GSM309991/suppl/GSM309991.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM310012 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; meso 35
|
mesothelioma tissue
|
Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM310012
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310012/suppl/GSM310012.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM310013 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; meso 36
|
mesothelioma tissue
|
Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM310013
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310013/suppl/GSM310013.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM310014 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; meso 4
|
mesothelioma tissue
|
Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM310014
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310014/suppl/GSM310014.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM310015 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; meso 7
|
mesothelioma tissue
|
Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM310015
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310015/suppl/GSM310015.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM310068 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; meso 38
|
mesothelioma tissue
|
Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction. mm
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM310068
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310068/suppl/GSM310068.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
|
GSM310070 | GPL570 |
|
Global gene expression profiling of human pleural mesotheliomas; meso 10
|
mesothelioma tissue
|
Mesothelioma tissue was obtained from those patients with a confirmed pathological diagnosis and who had not received prior therapy. Intraoperative malignant mesothelial samples and nodules were dissected from associated fat and connective tissue, but no microdissection was performed. H&E staining was performed to verify the presence of neoplastic cells and to determine the histological subtype. Samples were stored in RNAlater (Ambion) following the manufacturer’s protocol until RNA extraction.
|
9 mesothelioma mixed type tumors were compared to the normal pleura of 4 donors.
|
| Sample_geo_accession | GSM310070
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Aug 05 2008
| | Sample_last_update_date | Jul 30 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 | Total RNA was extracted from each of the tumor and control samples using the RNeasy Mini kit (Qiagen, Valencia, CA).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA target was produced starting from 3 µg of total RNA in according to Affymetrix (Santa Clara, CA) instructions and for each sample 15 µg were fragmented to a length of 20-200 bp
| | Sample_hyb_protocol | All the hybridization, washing, staining procedures were done using a Genechip Affymetrix station (Fluidics station 450), GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_scan_protocol | Scanning was done using a Genechip Affymetrix station (GeneChip Scanner 3000) as raccomended by manufacturer.
| | Sample_data_processing | Microarray quality control and statistical validation were performed using Bioconductor The presence of hybridization/construction artifacts was evaluated with the fitPLM function. The probe (PM) intensity distribution was evaluated using hist function (Bioconductor package affy). Probe set intensities were obtained by means of GCRMA and normalization was done according to quantiles method.Bioconductor OneChannelGUI, a graphical interface to Bioconductor packages, was used to run any of the described analyses.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Raffaele,A,Calogero
| | Sample_contact_email | raffaele.calogero@unito.it
| | Sample_contact_phone | ++39 0116706457
| | Sample_contact_laboratory | Bioinformatics and Genomics Unit
| | Sample_contact_department | Molecular Biotechnology Center
| | Sample_contact_institute | University of Torino
| | Sample_contact_address | Via Nizza 52
| | Sample_contact_city | Torino
| | Sample_contact_state | To
| | Sample_contact_zip/postal_code | 10126
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM310nnn/GSM310070/suppl/GSM310070.CEL.gz
| | Sample_series_id | GSE12345
| | Sample_data_row_count | 54675
| | |
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