Search results for the GEO ID: GSE34599  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM851708 | GPL570 |
|
patient 7G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: stable disease SD
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851708
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851708/suppl/GSM851708_2147_4559_25260_7.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851709 | GPL570 |
|
patient 8G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: complete response CR
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851709
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851709/suppl/GSM851709_2147_4559_25261_8.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851710 | GPL570 |
|
patient 9G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: complete response CR
genotype: Braf-WT Nras-mutant
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851710
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851710/suppl/GSM851710_2147_4559_25262_9.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851711 | GPL570 |
|
patient 13G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: non-evaluable n.e.
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851711
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851711/suppl/GSM851711_2147_4559_25263_13.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851712 | GPL570 |
|
patient 15G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: non-evaluable n.e.
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851712
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851712/suppl/GSM851712_2147_4559_25265_15.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851713 | GPL570 |
|
patient 16G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: complete response CR
genotype: Braf-mutant Nras-WT
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851713
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851713/suppl/GSM851713_2147_4559_25266_16.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851714 | GPL570 |
|
patient 18G-A
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: progressive disease PD
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851714
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851714/suppl/GSM851714_2147_4559_25268_18.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851715 | GPL570 |
|
patient 18G-B
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: progressive disease PD
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851715
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851715/suppl/GSM851715_2147_4559_25269_18B_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851716 | GPL570 |
|
patient 19G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: progressive disease PD
genotype: Braf-mutant Nras-WT
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851716
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851716/suppl/GSM851716_2147_4559_25270_19.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851717 | GPL570 |
|
patient 20G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: complete response CR
genotype: Braf-mutant Nras-WT
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851717
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851717/suppl/GSM851717_2147_4559_25271_20.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851718 | GPL570 |
|
patient 21G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: non-evaluable n.e.
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851718
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851718/suppl/GSM851718_2147_4559_25272_21.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851719 | GPL570 |
|
patient 22G-A
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: non-evaluable n.e.
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851719
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851719/suppl/GSM851719_2147_4559_25273_22A_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851720 | GPL570 |
|
patient 22G-B
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: non-evaluable n.e.
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851720
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851720/suppl/GSM851720_2147_4559_25274_22B_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851721 | GPL570 |
|
patient 23G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: non-evaluable n.e.
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851721
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851721/suppl/GSM851721_2147_4559_25275_23.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851722 | GPL570 |
|
patient 24G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: complete response CR
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851722
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851722/suppl/GSM851722_2147_4559_25276_24.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851723 | GPL570 |
|
patient 25G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: progressive disease PD
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851723
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851723/suppl/GSM851723_2147_4559_25277_25.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851724 | GPL570 |
|
patient 26G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: partial response PR
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851724
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851724/suppl/GSM851724_2147_4559_25278_26.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851725 | GPL570 |
|
patient 27G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb perfusion w/ melphalan
response: complete response CR
genotype: Braf-WT Nras-mutant
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851725
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851725/suppl/GSM851725_2147_4559_25279_27.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851726 | GPL570 |
|
patient 28G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: progressive disease PD
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851726
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851726/suppl/GSM851726_2147_4559_25280_28.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851727 | GPL570 |
|
patient 29G
|
melanoma
|
disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: complete response CR
tissue: melanoma biopsy
|
|
| Sample_geo_accession | GSM851727
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851727/suppl/GSM851727_2147_4559_25281_29.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
| | |
|
GSM851728 | GPL570 |
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patient 30G
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melanoma
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disease state: in-transit melanoma
treatment: isolated limb infusion w/ melphalan
response: stable disease SD
tissue: melanoma biopsy
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| Sample_geo_accession | GSM851728
| | Sample_status | Public on Dec 22 2011
| | Sample_submission_date | Dec 21 2011
| | Sample_last_update_date | Dec 22 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | 4mm punch biopsies were obtained prior to isolated-limb-infusion or isolated limb perfusion with melphalan following a protocol approved by the Duke University institutional review board. Biopsies were snap frozen and stored at -130.
| | Sample_growth_protocol_ch1 | N/A
| | 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 total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA
| | Sample_hyb_protocol | labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip 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 were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair using the Affymetrix GeneChip Operating System (GCOS). A present/absent call (based on a statistical p-value) is included.
| | 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/GSM851nnn/GSM851728/suppl/GSM851728_2147_4559_25282_30.0_HG-U133+Plus+2.CEL.gz
| | Sample_series_id | GSE34599
| | Sample_data_row_count | 54675
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