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Search results for the GEO ID: GSE7127
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GSM162902
GPL570
Melanoma cell line HT144 Melanoma cell line HT144 Melanoma cell line HT144 established from a metastatic melanoma. For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162904
GPL570
Melanoma cell line MM127 Melanoma cell line MM127 Melanoma cell line established from a metastatic melanoma. For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162905
GPL570
Melanoma cell line MM170 Melanoma cell line MM170 Melanoma cell line MM170 established from a metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162906
GPL570
Melanoma cell line A2058 Melanoma cell line A2058 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162928
GPL570
Melanoma cell line A11 Melanoma cell line A11 Melanoma cell line established from a metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162929
GPL570
Melanoma cell line MM370 Melanoma cell line MM370 Melanoma cell line MM370 established from a metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162930
GPL570
Melanoma cell line AF6 Melanoma cell line AF6 Melanoma cell line For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162931
GPL570
Melanoma cell line C-32 Melanoma cell line C-32 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162932
GPL570
melanoma cell line MM386 Melanoma cell line MM386 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162933
GPL570
Melanoma cell line MM415 Melanoma cell line MM415 Melanoma cell line MM415 established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162934
GPL570
Melanoma cell line COLOF Melanoma cell line COLOF Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162935
GPL570
Melanoma cell line MM200 Melanoma cell line MM200 Melanoma cell line established from primary nodular melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162936
GPL570
Melanoma cell line MM466 Melanoma cell line MM466 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162937
GPL570
Melanoma cell line MM537 Melanoma cell line MM537 Melanoma cell line MM537 established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162938
GPL570
Melanoma cell line D04 Melanoma cell line D04 Melanoma cell line D04 established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162939
GPL570
Melanoma cell line D05 Melanoma cell line D05 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162940
GPL570
Melanoma cell line MM253 Melanoma cell line MM253 Melanoma cell line MM253 established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162941
GPL570
Melanoma cell line MM455 Melanoma cell line MM455 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162942
GPL570
Melanoma cell line MM648 Melanoma cell line MM648 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM162943
GPL570
Melanoma cell line MM649 Melanoma cell line MM649 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM169524
GPL570
Melanoma cell line D24 Melanoma cell line D24 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM169525
GPL570
Melanoma cell line D25 Melanoma cell line D25 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM169526
GPL570
Melanoma cell line D22 Melanoma cell line D22 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM169527
GPL570
melanoma cell line D20 Melanoma cell line D20 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM169528
GPL570
melanoma cell line D17 Melanoma cell line D17 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM169529
GPL570
melanoma cell line D14 melanoma cell line D14 melanoma cell line D14 established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM169530
GPL570
melanoma cell line D11 melanoma cell line D11 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM169531
GPL570
Melanoma cell line D10 Melanoma cell line D10 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170588
GPL570
Melanoma cell line D28 Melanoma cell line D28 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170589
GPL570
Melanoma cell line D29 Melanoma cell line D29 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170590
GPL570
Melanoma cell line D35 Melanoma cell line D35 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170591
GPL570
Melanoma cell line D36 Melanoma cell line D36 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170592
GPL570
Melanoma cell line D38 Melanoma cell line D38 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170593
GPL570
Melanoma cell line D40 Melanoma cell line D40 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170594
GPL570
Melanoma cell line D41 Melanoma cell line D41 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170595
GPL570
Melanoma cell line A02 Melanoma cell line A02 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170596
GPL570
Melanoma cell line MM595 Melanoma cell line MM595 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170597
GPL570
Melanoma cell line MM603 Melanoma cell line MM603 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170823
GPL570
Melanoma cell line BL Melanoma cell line BL Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170833
GPL570
Melanoma cell line A13 Melanoma cell line A13 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170835
GPL570
Melanoma cell line MM473 Melanoma cell line MM473 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170841
GPL570
Melanoma cell line MM329 Melanoma cell line MM329 Melanoma cell line established from primary melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170843
GPL570
Melanoma cell line MM383 Melanoma cell line MM383 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170844
GPL570
Melanoma cell line A06 Melanoma cell line A06 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170848
GPL570
Melanoma cell line MM426 Melanoma cell line MM426 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170849
GPL570
Melanoma cell line MM485 Melanoma cell line MM485 Melanoma cell line established in metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170850
GPL570
Melanoma cell line MM576 Melanoma cell line MM576 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170853
GPL570
Melanoma cell line D01 Melanoma cell line D01 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170855
GPL570
Melanoma cell line D08 Melanoma cell line D08 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170857
GPL570
Melanoma cell line MM608 Melanoma cell line MM608 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170858
GPL570
Melanoma cell line MM622 Melanoma cell line MM622 Melanoma cell line established from primary melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170862
GPL570
Melanoma cell line A15 Melanoma cell line A15 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170865
GPL570
Melanoma cell line CJM Melanoma cell line CJM Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170866
GPL570
Melanoma cell line MM229 Melanoma cell line MM229 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170867
GPL570
Melanoma cell line MM540 Melanoma cell line MM540 Melanoma cell line established from primary melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170978
GPL570
Melanoma cell line MM548 Melanoma cell line MM548 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170979
GPL570
Melanoma cell line MM96L Melanoma cell line MM96L Melanoma cell line established from primary melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170980
GPL570
Melanoma cell line SKMEL13 Melanoma cell line SKMEL13 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170983
GPL570
Melanoma cell line WSB Melanoma cell line WSB Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM170992
GPL570
Melanoma cell line A04 Melanoma cell line A04 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM171011
GPL570
Melanoma cell line SKMEL5 Melanoma cell line SKMEL5 Melanoma cell line established from metastatic melanoma For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM171012
GPL570
Melanoma cell line SKMEL28 Melanoma cell line SKMEL28 Melanoma cell line For each sample, 5 μg of total RNA were used for target preparation using Eukaryotic One-cycle Target Labelling and Control Reagents kits according to the manufacturer’s instructions (Affymetrix). First-strand complementary DNA (cDNA) was synthesized using a T7-Oligo(dT) primer followed by second-strand cDNA synthesis from these samples using T4 polymerase. An in-vitro transcription reaction was then performed to produce biotin-labelled complementary RNA (cRNA). This cRNA was fragmented and 15 μg were hybridized to an Affymetrix Human Genome U133 Plus 2.0 Array in an Affymetrix Hybridization Oven 640 for 16 h at 45oC. Chips were then washed and post-stained with streptavidin phycoerythrin and normal goat IgG solutions on an Affymetrix Fluidics Station 450. Chips were scanned on an Affymetrix GeneChip Scanner 3000, and raw image data files obtained using Affymetrix GeneChip Operating Software (GCOS Version 1.2). Relative expression values were generated for each probe set using the Affymetrix PLIER algorithm in ArrayAssist® Version 4.20 (Stratagene) and further log transformed to base 2. The resulting data were imported into GeneSpring GX v7.3 (Agilent Technologies). Data values less than 0.1 were set to 0.1 and the logarithm of data values were used as expression values. The expression values were normalized in two steps. First, values were centralized sample by sample, such that the median expression value was zero for each sample. Second, expression values were centralized gene by gene such that the median expression value was zero for each probe set.
GSM171597
GPL570
Melanoma cell line D32 Melanoma cell line D32 Melanoma cell line established from metastatic melanoma No other data to add
 
 
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