Search results for the GEO ID: GSE10282 |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM259617 | GPL570 |
|
patient_1_a
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IV
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259617
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259617/suppl/GSM259617.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259618 | GPL570 |
|
patient_1_b
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IV
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259618
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259618/suppl/GSM259618.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259619 | GPL570 |
|
patient_1_c
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IV
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259619
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259619/suppl/GSM259619.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259620 | GPL570 |
|
patient_2_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259620
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259620/suppl/GSM259620.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259621 | GPL570 |
|
patient_2_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259621
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259621/suppl/GSM259621.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259622 | GPL570 |
|
patient_3_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259622
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259622/suppl/GSM259622.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259623 | GPL570 |
|
patient_3_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259623
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259623/suppl/GSM259623.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259624 | GPL570 |
|
patient_3_c
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259624
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259624/suppl/GSM259624.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259625 | GPL570 |
|
patient_4_a
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIB
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259625
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259625/suppl/GSM259625.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259626 | GPL570 |
|
patient_4_b
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIB
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259626
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259626/suppl/GSM259626.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259627 | GPL570 |
|
patient_4_c
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIB
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259627
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259627/suppl/GSM259627.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259628 | GPL570 |
|
patient_4_d
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIB
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259628
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259628/suppl/GSM259628.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259629 | GPL570 |
|
patient_5_a
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-WT_Nras-mutant
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259629
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259629/suppl/GSM259629.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259630 | GPL570 |
|
patient_5_b
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-WT_Nras-mutant
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259630
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259630/suppl/GSM259630.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259631 | GPL570 |
|
patient_5_c
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-WT_Nras-mutant
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259631
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259631/suppl/GSM259631.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259632 | GPL570 |
|
patient_6_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259632
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259632/suppl/GSM259632.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259633 | GPL570 |
|
patient_6_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259633
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259633/suppl/GSM259633.CEL.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259634 | GPL570 |
|
patient_10_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-WT_Nras-mutant
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259634
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259634/suppl/GSM259634.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259634/suppl/GSM259634.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259635 | GPL570 |
|
patient_10_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-WT_Nras-mutant
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259635
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259635/suppl/GSM259635.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259635/suppl/GSM259635.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259636 | GPL570 |
|
patient_11_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-WT_Nras-mutant
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259636
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259636/suppl/GSM259636.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259636/suppl/GSM259636.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259637 | GPL570 |
|
patient_11_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-WT_Nras-mutant
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259637
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259637/suppl/GSM259637.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259637/suppl/GSM259637.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259638 | GPL570 |
|
patient_11_c
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-WT_Nras-mutant
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259638
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259638/suppl/GSM259638.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259638/suppl/GSM259638.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259639 | GPL570 |
|
patient_12_a
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259639
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259639/suppl/GSM259639.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259639/suppl/GSM259639.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259640 | GPL570 |
|
patient_12_c
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259640
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259640/suppl/GSM259640.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259640/suppl/GSM259640.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259641 | GPL570 |
|
patient_13_a
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259641
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259641/suppl/GSM259641.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259641/suppl/GSM259641.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259642 | GPL570 |
|
patient_13_b
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259642
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259642/suppl/GSM259642.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259642/suppl/GSM259642.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259643 | GPL570 |
|
patient_13_c
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259643
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259643/suppl/GSM259643.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259643/suppl/GSM259643.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259644 | GPL570 |
|
patient_14_a
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259644
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259644/suppl/GSM259644.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259644/suppl/GSM259644.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259645 | GPL570 |
|
patient_14_b
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259645
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259645/suppl/GSM259645.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259645/suppl/GSM259645.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259646 | GPL570 |
|
patient_15_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259646
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259646/suppl/GSM259646.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259646/suppl/GSM259646.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259647 | GPL570 |
|
patient_15_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259647
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259647/suppl/GSM259647.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259647/suppl/GSM259647.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259648 | GPL570 |
|
patient_15_c
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259648
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259648/suppl/GSM259648.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259648/suppl/GSM259648.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259649 | GPL570 |
|
patient_16_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259649
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259649/suppl/GSM259649.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259649/suppl/GSM259649.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259650 | GPL570 |
|
patient_16_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259650
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259650/suppl/GSM259650.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259650/suppl/GSM259650.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259651 | GPL570 |
|
patient_16_c
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIB
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259651
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259651/suppl/GSM259651.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259651/suppl/GSM259651.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259652 | GPL570 |
|
patient_17_a
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IV
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259652
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259652/suppl/GSM259652.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259652/suppl/GSM259652.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259653 | GPL570 |
|
patient_17_b
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IV
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259653
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259653/suppl/GSM259653.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259653/suppl/GSM259653.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259654 | GPL570 |
|
patient_18_a
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259654
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259654/suppl/GSM259654.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259654/suppl/GSM259654.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259655 | GPL570 |
|
patient_18_b
|
melanoma
|
punch biopsy
in-transit disease
M_stage_IIIC
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259655
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259655/suppl/GSM259655.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259655/suppl/GSM259655.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259656 | GPL570 |
|
patient_19_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259656
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259656/suppl/GSM259656.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259656/suppl/GSM259656.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259657 | GPL570 |
|
patient_19_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IIIC
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259657
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259657/suppl/GSM259657.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259657/suppl/GSM259657.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259658 | GPL570 |
|
patient_20_a
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IV
Braf-mutant_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259658
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259658/suppl/GSM259658.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259658/suppl/GSM259658.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
GSM259659 | GPL570 |
|
patient_20_b
|
melanoma
|
punch biopsy
in-transit disease
F_stage_IV
Braf-WT_Nras-WT
|
In the Sample title, number refers to patient, letter refers to the lesion. For example, samples 1a, 1b and 1c are all from patient #1. For patient #1, we had 3 lesions from the extremity region harboring the melanoma disease.
|
Sample_geo_accession | GSM259659
| Sample_status | Public on Oct 30 2008
| Sample_submission_date | Jan 25 2008
| Sample_last_update_date | Jan 25 2008
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Melanoma biopsies were obtained before initiation of isolated-limb-infusion (ILI) with melphalan from 17 patients after general anesthesia was administered using a 4-mm punch. The samples were snap frozen and stored at -133°C until ready for further analysis. All patients were enrolled after obtaining written informed consent and tissue samples collected according to a protocol approved by Duke University Medical Center Institutional Review Board.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Tissue was homogenized and RNA isolated using Qiagen Rneasy kit. A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue. Each RNA isolation included treatment with Dnase to minimize genomic DNA.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | one-cycle cDNA synthesis of 1ug total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols
| Sample_scan_protocol | Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000
| Sample_data_processing | Expression values across 54675 probe sets or genes were calculated using the Robust Multichip Average (RMA) method. RMA estimates are based upon a robust average of background corrected perfect match (PM) probe intensities. Normalization was done using quantile normalization. Expression values were then transformed by taking Logarithm base 2
| Sample_platform_id | GPL570
| Sample_contact_name | Christina,,Augustine
| Sample_contact_email | christi.augustine@duke.edu
| Sample_contact_department | Surgery
| Sample_contact_institute | Duke University Medical Center
| Sample_contact_address | VAMC RmE4001 508 Fulton St.
| Sample_contact_city | Durham
| Sample_contact_state | NC
| Sample_contact_zip/postal_code | 27705
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259659/suppl/GSM259659.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259659/suppl/GSM259659.EXP.gz
| Sample_series_id | GSE10282
| Sample_data_row_count | 54613
| |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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Select GSMs and click on "Add groups" |
Enter the group name here: |
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