Search results for the GEO ID: GSE12090  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM305099 | GPL570 |
|
Oncocytoma: 0B03-123_U133
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305099
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305099/suppl/GSM305099.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305100 | GPL570 |
|
Oncocytoma: 0B04-340_U133
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305100
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305100/suppl/GSM305100.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305101 | GPL570 |
|
Chromophobe: 0B05-268_U133
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305101
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305101/suppl/GSM305101.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305102 | GPL570 |
|
Oncocytoma: 0B05-305_U133
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305102
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305102/suppl/GSM305102.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305103 | GPL570 |
|
Chromophobe: 0B05-335_U133
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305103
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305103/suppl/GSM305103.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305104 | GPL570 |
|
Chromophobe: OB05-178_U133
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305104
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305104/suppl/GSM305104.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305105 | GPL570 |
|
Chromophobe: OB03-110A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305105
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305105/suppl/GSM305105.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305106 | GPL570 |
|
Chromophobe: OB03-1A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305106
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305106/suppl/GSM305106.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305107 | GPL570 |
|
Oncocytoma: OB03-44A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305107
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305107/suppl/GSM305107.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305108 | GPL570 |
|
Chromophobe: OB03-59A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305108
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305108/suppl/GSM305108.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305109 | GPL570 |
|
Oncocytoma: OB03-78A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305109
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305109/suppl/GSM305109.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305110 | GPL570 |
|
Oncocytoma: OB03-97A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305110
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305110/suppl/GSM305110.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305111 | GPL570 |
|
Oncocytoma: OB04-123A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305111
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305111/suppl/GSM305111.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305112 | GPL570 |
|
Oncocytoma: OB04-133A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305112
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305112/suppl/GSM305112.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305113 | GPL570 |
|
Chromophobe: OB04-20A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305113
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305113/suppl/GSM305113.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305114 | GPL570 |
|
Chromophobe: OB04-210A4
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305114
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305114/suppl/GSM305114.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305115 | GPL570 |
|
Oncocytoma: OB04-22A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305115
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305115/suppl/GSM305115.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
GSM305116 | GPL570 |
|
Chromophobe: OB04-65A1
|
renal cell carcinoma tissue obtained surgically
|
renal cell carcinoma
|
none
|
| Sample_geo_accession | GSM305116
| | Sample_status | Public on Jul 12 2008
| | Sample_submission_date | Jul 11 2008
| | Sample_last_update_date | Jul 11 2008
| | 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 fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the Total RNA was extracted from fresh tissues using RNeasy mini kit (Qiagen) following the manufacturer’s protocol using rotor-stator homogenization. Approximately 30 mg of fresh tissues was used for each sample. For extraction of RNA from paraffin-embedded tissue, the Optimum FFPE RNA isolation kit (Ambion) was used, using materials derived from four 8m sections. The non-tumor areas on the slides were manually removed with surgical blades, and the remaining tissue on the slide was scraped into an Eppendorf tube for RNA extraction.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA was reverse-transcribed and in vitro transcribed and biotin-labeled using Affymetrix one-cycle cDNA synthesis and IVT labeling kits (Affymetrix)
| | Sample_hyb_protocol | Following biotinylation and fragmentation, hybridization was performed against the Affymetrix Human HG-U133 plus 2.0 GeneChips according to the manufacturers directions.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | Raw data probeset intensity data was extracted from the CEL files using the RMA algorithm in GeneSpring 7.2 and the data was then median normalized per chip.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Piali,,Mukherjee
| | Sample_contact_email | pim2001@med.cornell.edu
| | Sample_contact_department | Physiology and Biophysics
| | Sample_contact_institute | Weill Medical Cornell
| | Sample_contact_address | 1305 York Avenue
| | Sample_contact_city | New York
| | Sample_contact_state | NY
| | Sample_contact_zip/postal_code | 10021
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM305nnn/GSM305116/suppl/GSM305116.CEL.gz
| | Sample_series_id | GSE12090
| | Sample_data_row_count | 54675
| | |
|
| |
| |
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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