title: 387S4-2 j2

status: Public on Sep 25 2009

type: genomic

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67305.gif
Individual: 387
Disease State: Duodenal Ulcer
Replicate: 4

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1960, 35080; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 80038; Parameter Laser Power = 3.44; Parameter Scan Time = 08:38:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.55; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 80467; Parameter Laser Power = 3.70; Parameter Scan Time = 08:38:26; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.55; Performer: Nina,,Salama

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: genomic DNA

organism:
Helicobacter pylori 26695
Helicobacter pylori J99

source_name: 0.25 ng 26695/J99 genomic DNA mix

label_protocol: not provided

extract_protocol: not provided

tag: 0.25 ng 26695/J99 genomic DNA mix

organism: Helicobacter pylori

source_name: 500 ng 387S4-2 j2, Disease State: Duodenal Ulcer


title: 510S4-4 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67313.gif
Individual: 510
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2410, 35530; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 80068; Parameter Laser Power = 3.44; Parameter Scan Time = 09:08:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 80497; Parameter Laser Power = 3.73; Parameter Scan Time = 09:08:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Nina,,Salama

source_name: 500 ng 510S4-4 j2, Disease State: Gastric Cancer


title: 535S4-1 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67308.gif
Individual: 535
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2190, 35710; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 79973; Parameter Laser Power = 3.53; Parameter Scan Time = 09:14:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.35; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 80402; Parameter Laser Power = 3.74; Parameter Scan Time = 09:14:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.35; Performer: Nina,,Salama

source_name: 500 ng 535S4-1 j1, Disease State: Gastric Cancer


title: 535S4-1 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67309.gif
Individual: 535
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2330, 35520; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 80047; Parameter Laser Power = 3.44; Parameter Scan Time = 08:47:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.64; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 80475; Parameter Laser Power = 3.71; Parameter Scan Time = 08:47:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.64; Performer: Nina,,Salama

source_name: 500 ng 535S4-1 j2, Disease State: Gastric Cancer


title: 386S3-6 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67320.gif
Individual: 386
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2430, 35630; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 80012; Parameter Laser Power = 3.55; Parameter Scan Time = 09:54:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.77; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 710; Parameter Scan Power = 100; Parameter Laser on time = 80441; Parameter Laser Power = 3.77; Parameter Scan Time = 09:54:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.77; Performer: Nina,,Salama

source_name: 500 ng 386S3-6 j1, Disease State: Non-atrophic Gastritis


title: 110S3-3 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67314.gif
Individual: 110
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1960, 8880; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 80002; Parameter Laser Power = 3.54; Parameter Scan Time = 09:44:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 710; Parameter Scan Power = 100; Parameter Laser on time = 80431; Parameter Laser Power = 3.76; Parameter Scan Time = 09:44:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.62; Performer: Nina,,Salama

source_name: 500 ng 110S3-3 j1, Disease State: Non-atrophic Gastritis


title: 387S3-1 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67322.gif
Individual: 387
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2260, 9040; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 640; Parameter Laser on time = 80022; Parameter Laser Power = 3.55; Parameter Scan Time = 10:04:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.90; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 80451; Parameter Laser Power = 3.77; Parameter Scan Time = 10:04:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.90; Performer: Nina,,Salama

source_name: 500 ng 387S3-1 j1, Disease State: Duodenal Ulcer


title: 510S4-4 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67312.gif
Individual: 510
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2050, 35160; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 79993; Parameter Laser Power = 3.54; Parameter Scan Time = 09:35:14; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.53; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 80422; Parameter Laser Power = 3.74; Parameter Scan Time = 09:35:14; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.53; Performer: Nina,,Salama

source_name: 500 ng 510S4-4 j1, Disease State: Gastric Cancer


title: 320S4-1 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67310.gif
Individual: 320
Disease State: Non-atrophic Gastritis
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2040, 9120; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 79986; Parameter Laser Power = 3.54; Parameter Scan Time = 09:28:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 80415; Parameter Laser Power = 3.74; Parameter Scan Time = 09:28:30; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.50; Performer: Nina,,Salama

source_name: 500 ng 320S4-1 j1, Disease State: Non-atrophic Gastritis


title: 370S3-5 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67307.gif
Individual: 370
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2330, 9130; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 80057; Parameter Laser Power = 3.44; Parameter Scan Time = 08:57:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.77; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 610; Parameter Scan Power = 100; Parameter Laser on time = 80485; Parameter Laser Power = 3.73; Parameter Scan Time = 08:57:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.77; Performer: Nina,,Salama

source_name: 500 ng 370S3-5 j2, Disease State: Non-atrophic Gastritis


title: 103S3-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61520.gif
Individual: 103
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 680, 8560; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 64321; Parameter Laser Power = 3.48; Parameter Scan Time = 15:45:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.01; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 660; Parameter Scan Power = 100; Parameter Laser on time = 64202; Parameter Laser Power = 3.79; Parameter Scan Time = 15:45:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.01; Performer: Nina,,Salama

source_name: 500 ng 103S3-1-1, Disease State: Non-atrophic Gastritis


title: 370S3-5 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67306.gif
Individual: 370
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2400, 9700; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 620; Parameter Laser on time = 79980; Parameter Laser Power = 3.53; Parameter Scan Time = 09:22:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.47; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 710; Parameter Scan Power = 100; Parameter Laser on time = 80408; Parameter Laser Power = 3.74; Parameter Scan Time = 09:22:16; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.47; Performer: Nina,,Salama

source_name: 500 ng 370S3-5 j1, Disease State: Non-atrophic Gastritis


title: 386S3-6 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67321.gif
Individual: 386
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2130, 35430; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 80088; Parameter Laser Power = 3.44; Parameter Scan Time = 09:29:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.16; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 80517; Parameter Laser Power = 3.73; Parameter Scan Time = 09:29:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.16; Performer: Nina,,Salama

source_name: 500 ng 386S3-6 j2, Disease State: Non-atrophic Gastritis


title: 110S3-3 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67315.gif
Individual: 110
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2640, 9930; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 80081; Parameter Laser Power = 3.44; Parameter Scan Time = 09:21:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.07; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 80510; Parameter Laser Power = 3.73; Parameter Scan Time = 09:21:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.07; Performer: Nina,,Salama

source_name: 500 ng 110S3-3 j2, Disease State: Non-atrophic Gastritis


title: 174S4-3 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67319.gif
Individual: 174
Disease State: Duodenal Ulcer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2050, 9160; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 80086; Parameter Laser Power = 3.44; Parameter Scan Time = 09:26:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.13; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 80515; Parameter Laser Power = 3.73; Parameter Scan Time = 09:26:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.13; Performer: Nina,,Salama

source_name: 500 ng 174S4-3 j2, Disease State: Duodenal Ulcer


title: 357S3-1 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67303.gif
Individual: 357
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2240, 8560; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 80031; Parameter Laser Power = 3.44; Parameter Scan Time = 08:31:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 80460; Parameter Laser Power = 3.69; Parameter Scan Time = 08:31:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Nina,,Salama

source_name: 500 ng 357S3-1 j2, Disease State: Non-atrophic Gastritis


title: 320S4-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61525.gif
Individual: 320
Disease State: Non-atrophic Gastritis
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 8880; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 64475; Parameter Laser Power = 3.65; Parameter Scan Time = 11:33:27; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.94; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 64449; Parameter Laser Power = 3.74; Parameter Scan Time = 11:33:27; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.94; Performer: Nina,,Salama

source_name: 0.25 ng 26695/J99 genomic DNA mix

source_name: 500 ng 320S4-1-1, Disease State: Non-atrophic Gastritis


title: 387S3-1 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67323.gif
Individual: 387
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2250, 9600; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 80101; Parameter Laser Power = 3.44; Parameter Scan Time = 09:42:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.32; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 590; Parameter Scan Power = 100; Parameter Laser on time = 80530; Parameter Laser Power = 3.74; Parameter Scan Time = 09:42:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.32; Performer: Nina,,Salama

source_name: 500 ng 387S3-1 j2, Disease State: Duodenal Ulcer


title: 174S4-3 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67318.gif
Individual: 174
Disease State: Duodenal Ulcer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2510, 8880; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 80009; Parameter Laser Power = 3.55; Parameter Scan Time = 09:51:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.71; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 80437; Parameter Laser Power = 3.76; Parameter Scan Time = 09:51:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.71; Performer: Nina,,Salama

source_name: 500 ng 174S4-3 j1, Disease State: Duodenal Ulcer


title: 372S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61498.gif
Individual: 372
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 8360; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 63460; Parameter Laser Power = 3.40; Parameter Scan Time = 11:16:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.42; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 63170; Parameter Laser Power = 3.71; Parameter Scan Time = 11:16:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.42; Performer: Nina,,Salama

source_name: 500 ng 372S3-2-1, Disease State: Duodenal Ulcer


title: 443S6-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61507.gif
Individual: 443
Disease State: Gastric Cancer
Replicate: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1490, 35250; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 63771; Parameter Laser Power = 3.46; Parameter Scan Time = 10:04:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.81; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 730; Parameter Scan Power = 100; Parameter Laser on time = 63508; Parameter Laser Power = 3.67; Parameter Scan Time = 10:04:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.81; Performer: Nina,,Salama

source_name: 500 ng 443S6-1-1, Disease State: Gastric Cancer


title: 103S4-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61494.gif
Individual: 103
Disease State: Non-atrophic Gastritis
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 640, 8120; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 65609; Parameter Laser Power = 3.49; Parameter Scan Time = 12:32:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.34; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 65830; Parameter Laser Power = 3.77; Parameter Scan Time = 12:32:39; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.34; Performer: Nina,,Salama

source_name: 500 ng 103S4-1-1, Disease State: Non-atrophic Gastritis


title: 535S4-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61509.gif
Individual: 535
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1010, 8550; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 63971; Parameter Laser Power = 3.49; Parameter Scan Time = 13:43:42; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.46; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 63820; Parameter Laser Power = 3.76; Parameter Scan Time = 13:43:42; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.46; Performer: Nina,,Salama

source_name: 500 ng 535S4-1-1, Disease State: Gastric Cancer


title: 204S4-3-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61515.gif
Individual: 204
Disease State: Duodenal Ulcer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 440, 6720; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 64282; Parameter Laser Power = 3.48; Parameter Scan Time = 15:02:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 64163; Parameter Laser Power = 3.79; Parameter Scan Time = 15:02:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Nina,,Salama

source_name: 500 ng 204S4-3-1, Disease State: Duodenal Ulcer


title: 320S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61510.gif
Individual: 320
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 930, 35130; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 63976; Parameter Laser Power = 3.49; Parameter Scan Time = 13:47:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.49; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 750; Parameter Scan Power = 100; Parameter Laser on time = 63825; Parameter Laser Power = 3.76; Parameter Scan Time = 13:47:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.49; Performer: Nina,,Salama

source_name: 500 ng 320S3-2-1, Disease State: Non-atrophic Gastritis


title: 401S4-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61506.gif
Individual: 401
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 8510; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 63768; Parameter Laser Power = 3.61; Parameter Scan Time = 10:01:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.72; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 63504; Parameter Laser Power = 3.68; Parameter Scan Time = 10:01:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.72; Performer: Nina,,Salama

source_name: 500 ng 401S4-1-1, Disease State: Gastric Cancer


title: 357S3-1 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67302.gif
Individual: 357
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 8730; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 670; Parameter Laser on time = 79952; Parameter Laser Power = 3.52; Parameter Scan Time = 08:53:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 690; Parameter Scan Power = 100; Parameter Laser on time = 80381; Parameter Laser Power = 3.72; Parameter Scan Time = 08:53:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Nina,,Salama

source_name: 500 ng 357S3-1 j1, Disease State: Non-atrophic Gastritis


title: 387S4-2 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67304.gif
Individual: 387
Disease State: Duodenal Ulcer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2190, 35230; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 79965; Parameter Laser Power = 3.53; Parameter Scan Time = 09:07:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.29; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 80394; Parameter Laser Power = 3.72; Parameter Scan Time = 09:07:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.29; Performer: Nina,,Salama

source_name: 500 ng 387S4-2 j1, Disease State: Duodenal Ulcer


title: 320S4-1 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67311.gif
Individual: 320
Disease State: Non-atrophic Gastritis
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2180, 9250; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 80062; Parameter Laser Power = 3.44; Parameter Scan Time = 09:03:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 540; Parameter Scan Power = 100; Parameter Laser on time = 80491; Parameter Laser Power = 3.73; Parameter Scan Time = 09:03:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.86; Performer: Nina,,Salama

source_name: 500 ng 320S4-1 j2, Disease State: Non-atrophic Gastritis


title: 372S3-3 j1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67316.gif
Individual: 372
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2050, 35160; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 79998; Parameter Laser Power = 3.54; Parameter Scan Time = 09:39:47; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 80426; Parameter Laser Power = 3.75; Parameter Scan Time = 09:39:47; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.59; Performer: Nina,,Salama

source_name: 500 ng 372S3-3 j1, Disease State: Duodenal Ulcer


title: 456S6-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61519.gif
Individual: 456
Disease State: Gastric Cancer
Replicate: 6

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 0, 33900; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 64314; Parameter Laser Power = 3.49; Parameter Scan Time = 15:39:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 64196; Parameter Laser Power = 3.80; Parameter Scan Time = 15:39:38; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Nina,,Salama

source_name: 500 ng 456S6-2-1, Disease State: Gastric Cancer


title: 379S4-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61496.gif
Individual: 379
Disease State: Duodenal Ulcer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 600, 8240; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 65555; Parameter Laser Power = 3.49; Parameter Scan Time = 11:37:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.16; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 65776; Parameter Laser Power = 3.74; Parameter Scan Time = 11:37:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.16; Performer: Nina,,Salama

source_name: 500 ng 379S4-2-1, Disease State: Duodenal Ulcer


title: 372S3-3 j2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67317.gif
Individual: 372
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2040, 36020; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 570; Parameter Laser on time = 80073; Parameter Laser Power = 3.44; Parameter Scan Time = 09:13:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.01; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-24; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 80502; Parameter Laser Power = 3.74; Parameter Scan Time = 09:13:37; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.01; Performer: Nina,,Salama

source_name: 0.25 ng 26695/J99 genomic DNA mix

source_name: 500 ng 372S3-3 j2, Disease State: Duodenal Ulcer


title: 110S3-3-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61495.gif
Individual: 110
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 710, 34700; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 490; Parameter Laser on time = 65616; Parameter Laser Power = 3.49; Parameter Scan Time = 12:39:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.37; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 65837; Parameter Laser Power = 3.77; Parameter Scan Time = 12:39:35; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.37; Performer: Nina,,Salama

source_name: 500 ng 110S3-3-1, Disease State: Non-atrophic Gastritis


title: 204S4-6-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61522.gif
Individual: 204
Disease State: Duodenal Ulcer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 280, 7200; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 64331; Parameter Laser Power = 3.48; Parameter Scan Time = 15:54:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 64212; Parameter Laser Power = 3.80; Parameter Scan Time = 15:54:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Nina,,Salama

source_name: 500 ng 204S4-6-1, Disease State: Duodenal Ulcer


title: 370S3-5-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61511.gif
Individual: 370
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1010, 34970; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 63981; Parameter Laser Power = 3.49; Parameter Scan Time = 13:53:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 63830; Parameter Laser Power = 3.76; Parameter Scan Time = 13:53:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.52; Performer: Nina,,Salama

source_name: 500 ng 370S3-5-1, Disease State: Non-atrophic Gastritis


title: 284S4-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61491.gif
Individual: 284
Disease State: Non-atrophic Gastritis
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 390, 35170; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 450; Parameter Laser on time = 65151; Parameter Laser Power = 3.38; Parameter Scan Time = 11:30:49; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.58; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 640; Parameter Scan Power = 100; Parameter Laser on time = 65291; Parameter Laser Power = 3.71; Parameter Scan Time = 11:30:49; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.58; Performer: Nina,,Salama

source_name: 500 ng 284S4-1-1, Disease State: Non-atrophic Gastritis


title: 261S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61513.gif
Individual: 261
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 860, 35130; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 63989; Parameter Laser Power = 3.49; Parameter Scan Time = 14:01:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.58; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 63838; Parameter Laser Power = 3.77; Parameter Scan Time = 14:01:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.58; Performer: Nina,,Salama

source_name: 500 ng 261S3-2-1, Disease State: Duodenal Ulcer


title: 510S4-3-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61502.gif
Individual: 510
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 8640; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 63596; Parameter Laser Power = 3.43; Parameter Scan Time = 10:53:49; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.39; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 63311; Parameter Laser Power = 3.70; Parameter Scan Time = 10:53:49; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.39; Performer: Nina,,Salama

source_name: 500 ng 510S4-3-1, Disease State: Gastric Cancer


title: 188S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61504.gif
Individual: 188
Disease State: Gastric Cancer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 8040; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 63760; Parameter Laser Power = 3.63; Parameter Scan Time = 09:54:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.63; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 63497; Parameter Laser Power = 3.66; Parameter Scan Time = 09:54:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.63; Performer: Nina,,Salama

source_name: 500 ng 188S3-2-1, Disease State: Gastric Cancer


title: 206S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61524.gif
Individual: 206
Disease State: Gastric Cancer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1280, 8680; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 650; Parameter Laser on time = 64465; Parameter Laser Power = 3.44; Parameter Scan Time = 11:23:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.91; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 530; Parameter Scan Power = 100; Parameter Laser on time = 64439; Parameter Laser Power = 3.73; Parameter Scan Time = 11:23:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.91; Performer: Nina,,Salama

source_name: 500 ng 206S3-2-1, Disease State: Gastric Cancer


title: 174S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61512.gif
Individual: 174
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 940, 8540; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 63987; Parameter Laser Power = 3.49; Parameter Scan Time = 13:58:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.58; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 720; Parameter Scan Power = 100; Parameter Laser on time = 63836; Parameter Laser Power = 3.77; Parameter Scan Time = 13:58:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.58; Performer: Nina,,Salama

source_name: 500 ng 174S3-2-1, Disease State: Duodenal Ulcer


title: 331S3-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61521.gif
Individual: 331
Disease State: Gastric Cancer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 680, 34280; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 64324; Parameter Laser Power = 3.48; Parameter Scan Time = 15:48:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.01; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 660; Parameter Scan Power = 100; Parameter Laser on time = 64206; Parameter Laser Power = 3.80; Parameter Scan Time = 15:48:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.01; Performer: Nina,,Salama

source_name: 500 ng 331S3-1-1, Disease State: Gastric Cancer


title: 386S4-3-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61493.gif
Individual: 386
Disease State: Non-atrophic Gastritis
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 630, 34150; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 65548; Parameter Laser Power = 3.50; Parameter Scan Time = 11:31:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.13; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 65769; Parameter Laser Power = 3.74; Parameter Scan Time = 11:31:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.13; Performer: Nina,,Salama

source_name: 500 ng 386S4-3-1, Disease State: Non-atrophic Gastritis


title: 510S3-4-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61501.gif
Individual: 510
Disease State: Gastric Cancer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 34910; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 63589; Parameter Laser Power = 3.49; Parameter Scan Time = 10:51:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.33; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 63304; Parameter Laser Power = 3.70; Parameter Scan Time = 10:51:10; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.33; Performer: Nina,,Salama

source_name: 500 ng 510S3-4-1, Disease State: Gastric Cancer


title: 362S3-6-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61490.gif
Individual: 362
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 80, 7640; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 65142; Parameter Laser Power = 3.57; Parameter Scan Time = 11:22:02; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.39; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 65282; Parameter Laser Power = 3.70; Parameter Scan Time = 11:22:02; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.39; Performer: Nina,,Salama

source_name: 500 ng 362S3-6-1, Disease State: Duodenal Ulcer


title: Murine model of gastrointestinal stromal tumors harboring a germline Kit K641E oncogenic mutant_Biological replica 3_2

type: RNA

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: Sample were hybridized to MEEBO arrays containing 38784 mouse 70mer oligonucleotide probes (Stanford Functional Genomics Facility, California, USA).

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of mouse cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and expression levels were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing:
A non-linear Lowess (locally weighted scatter plot) normalization method applied to each individual block (print-tip option) was carried out.
VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2

molecule: total RNA

organism: Mus musculus

source_name: Antrum  harboring a germline Kit K641E oncogenic mutant

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30min in 50% DMSO at room temperature in a dark environment.

growth_protocol: No growth

extract_protocol: Antrum total RNA was extracted using the Mirvana kit (Ambion, Texas, USA)

treatment_protocol: Animals were housed in a temperature (21±1°C) and humidity (55±10%)-controlled room with a 12 h light: 12 h dark cycle. Food and water were available ad libitum. Animal procedures were conducted in accordance with the guidelines of the European Communities Directive 86/609/EEC regulating animal research and were approved by the Local Ethical Committee of the Faculty of medicine, Université Libre de Bruxelles, Brussels, Belgium.

tag: A mouse model of gastrointestinal stromal tumor (GIST) has been developed by a knock-in gene targeting strategy, which introduced a Kit gene K641E mutation, originally identified in sporadic human GISTs and in the germ line of familial GIST syndrome patients. All Kit K641E homozygotes die by age 3 weeks due to gastrointestinal obstruction by hyperplastic interstitial cells of Cajal or GISTs. Total RNA was extracted from antral tissue of three independent Kit K641E:Neo homozygote littermates at P14 stage. Biological replica 3, technical replica 2 (dye-swap)

source_name: Antrum Kit wt/wt

treatment_protocol: Animals were maintained and experiments performed as described above.

tag: Reference RNA  was extracted from the antrum of a Kit wt/wt of the same littermate P14 as the knock-in GIST Kit K641E mice.


title: colorectal cancer DNA hypermethylome: TSA vs mock in SW480

status: Public on Sep 23 2009

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

institute: Ghent University

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in SW480

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufacturer's protocol (G4140-90050)

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays. with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor

organism: Homo sapiens

source_name: Mock treated SW480 cells

label_protocol: Agilent low RNA input linear amplification kit

growth_protocol: McCoy's 5A medium with 10% BCS and 1x P/S

extract_protocol: TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment

treatment_protocol: 1x PBS for 96 hours

tag: SW480 human colorectal cancer cell line

source_name: TSA treated SW480 cells

treatment_protocol: 300 nanomolar TSA for 18 hours

tag: SW480 human colorectal cancer cell line treated with TSA


title: colorectal cancer DNA hypermethylome: DAC vs mock in SW480

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in SW480

source_name: 5-AZA treated SW480 cells

treatment_protocol: 5 micromolar 5-AZA for 96 hours

tag: SW480 human colorectal cancer cell line treated with 5-AZA


title: Murine model of gastrointestinal stromal tumors harboring a germline Kit K641E oncogenic mutant_Biological replica 3_1

tag: A mouse model of gastrointestinal stromal tumor (GIST) has been developed by a knock-in gene targeting strategy, which introduced a Kit gene K641E mutation, originally identified in sporadic human GISTs and in the germ line of familial GIST syndrome patients. All Kit K641E homozygotes die by age 3 weeks due to gastrointestinal obstruction by hyperplastic interstitial cells of Cajal or GISTs. Total RNA was extracted from antral tissue of three independent Kit K641E:Neo homozygote littermates at P14 stage. Biological replica 3, technical replica 1 (dye-swap)


title: Murine model of gastrointestinal stromal tumors harboring a germline Kit K641E oncogenic mutant_Biological replica 2_2

tag: A mouse model of gastrointestinal stromal tumor (GIST) has been developed by a knock-in gene targeting strategy, which introduced a Kit gene K641E mutation, originally identified in sporadic human GISTs and in the germ line of familial GIST syndrome patients. All Kit K641E homozygotes die by age 3 weeks due to gastrointestinal obstruction by hyperplastic interstitial cells of Cajal or GISTs. Total RNA was extracted from antral tissue of three independent Kit K641E:Neo homozygote littermates at P14 stage. Biological replica 2, technical replica 2 (dye-swap)


title: 386S3-6-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61497.gif
Individual: 386
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 450, 34900; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 450; Parameter Laser on time = 65562; Parameter Laser Power = 3.49; Parameter Scan Time = 11:45:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.16; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 65783; Parameter Laser Power = 3.75; Parameter Scan Time = 11:45:21; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.16; Performer: Nina,,Salama

source_name: 0.25 ng 26695/J99 genomic DNA mix

source_name: 500 ng 386S3-6-1, Disease State: Non-atrophic Gastritis


title: 357S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61526.gif
Individual: 357
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 160, 34140; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-11; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 64478; Parameter Laser Power = 3.63; Parameter Scan Time = 11:36:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.97; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-11; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 64452; Parameter Laser Power = 3.74; Parameter Scan Time = 11:36:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.97; Performer: Nina,,Salama

source_name: 500 ng 357S3-2-1, Disease State: Non-atrophic Gastritis


title: 345S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61517.gif
Individual: 345
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 600, 8120; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 64301; Parameter Laser Power = 3.49; Parameter Scan Time = 15:23:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 64182; Parameter Laser Power = 3.79; Parameter Scan Time = 15:23:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Nina,,Salama

source_name: 500 ng 345S3-2-1, Disease State: Non-atrophic Gastritis


title: 377S4-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61505.gif
Individual: 377
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 35490; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 63763; Parameter Laser Power = 3.46; Parameter Scan Time = 09:58:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.66; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 63500; Parameter Laser Power = 3.67; Parameter Scan Time = 09:58:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.66; Performer: Nina,,Salama

source_name: 500 ng 377S4-2-1, Disease State: Gastric Cancer


title: 357S3-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61514.gif
Individual: 357
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 600, 34320; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 64120; Parameter Laser Power = 3.61; Parameter Scan Time = 11:37:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.73; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 610; Parameter Scan Power = 100; Parameter Laser on time = 64001; Parameter Laser Power = 3.71; Parameter Scan Time = 11:37:07; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.73; Performer: Nina,,Salama

source_name: 500 ng 357S3-1-1, Disease State: Non-atrophic Gastritis