title: PT265_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48742.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 11:07:49; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147883; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 11:07:49; Parameter PMT Volts = 660; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512786; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT265_1 DNA

tag: Prostate genomic DNA; PT265_1 DNA


title: PT187_3  DNA

status: Public on Oct 03 2007

type: genomic

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

country: USA

institute: Stanford University

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52830.gif

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.69; Parameter Scan Time = 10:07:25; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167374; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.69; Parameter Scan Time = 10:07:25; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532278; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.95; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

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: Homo sapiens

source_name: Normal male genomic DNA

label_protocol: not provided

extract_protocol: not provided

tag: Normal male genomic DNA

tag: LabeledExtract

source_name: PT187_3  DNA

tag: Prostate genomic DNA; PT187_3  DNA

tag: Prostate genomic DNA; LabeledExtract


title: PT103_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52828.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 09:41:17; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 167349; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 09:41:17; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 532252; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT103_1 DNA

tag: Prostate genomic DNA; PT103_1 DNA


title: PT83_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48743.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.96; Parameter Scan Time = 11:27:10; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147902; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.96; Parameter Scan Time = 11:27:10; Parameter PMT Volts = 670; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512805; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.06; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT83_2 DNA

tag: Prostate genomic DNA; PT83_2 DNA


title: PT315_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48740.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.34; Parameter Scan Time = 10:24:13; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147839; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.34; Parameter Scan Time = 10:24:13; Parameter PMT Volts = 660; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512743; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.05; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT315_2 DNA

tag: Prostate genomic DNA; PT315_2 DNA


title: PT148_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47183.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 4760; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.11; Parameter Scan Time = 09:53:31; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136798; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.11; Parameter Scan Time = 09:53:31; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501863; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT148_1 DNA

tag: Prostate genomic DNA; PT148_1 DNA


title: PT07_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52826.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.85; Parameter Scan Time = 10:33:32; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 166598; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.85; Parameter Scan Time = 10:33:32; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 531502; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.05; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT07_2 DNA

tag: Prostate genomic DNA; PT07_2 DNA


title: PT229_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49681.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.69; Parameter Scan Time = 09:58:08; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149989; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.69; Parameter Scan Time = 09:58:08; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514892; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT229_1 DNA

tag: Prostate genomic DNA; PT229_1 DNA


title: PT177_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47167.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5530; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 11:28:02; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135327; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 11:28:02; Parameter PMT Volts = 680; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500392; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PL177_2 DNA

tag: Prostate genomic DNA; PL177_2 DNA


title: PT87_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48744.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.05; Parameter Scan Time = 11:39:58; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147914; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.05; Parameter Scan Time = 11:39:58; Parameter PMT Volts = 670; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512818; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.07; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT87_1 DNA

tag: Prostate genomic DNA; PT87_1 DNA


title: PT37_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47186.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.98; Parameter Scan Time = 09:40:18; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136784; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.98; Parameter Scan Time = 09:40:18; Parameter PMT Volts = 670; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501850; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT37_1 DNA

tag: Prostate genomic DNA; PT37_1 DNA


title: PT14_3 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52827.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.91; Parameter Scan Time = 10:45:59; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 166611; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.91; Parameter Scan Time = 10:45:59; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 531514; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT14_3 DNA

tag: Prostate genomic DNA; PT14_3 DNA


title: PT19_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52822.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.06; Parameter Scan Time = 11:01:54; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 166624; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.06; Parameter Scan Time = 11:01:54; Parameter PMT Volts = 730; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 531527; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT19_2 DNA

tag: Prostate genomic DNA; PT19_2 DNA


title: PT41_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53659.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.86; Parameter Scan Time = 09:51:35; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-10; Parameter Pixel Size = 10; Parameter Laser on time = 174158; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.86; Parameter Scan Time = 09:51:35; Parameter PMT Volts = 730; Parameter Scan Date = 2004-07-10; Parameter Pixel Size = 10; Parameter Laser on time = 538962; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT41_2 DNA

tag: Prostate genomic DNA; PT41_2 DNA


title: PT310_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47181.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 4760; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.16; Parameter Scan Time = 08:34:45; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136720; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.16; Parameter Scan Time = 08:34:45; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501785; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT310_2 DNA

tag: Prostate genomic DNA; PT310_2 DNA


title: PT05_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52825.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.72; Parameter Scan Time = 10:19:39; Parameter PMT Volts = 650; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 166585; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.72; Parameter Scan Time = 10:19:39; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-25; Parameter Pixel Size = 10; Parameter Laser on time = 531488; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: Normal male genomic DNA

source_name: PT05_1 DNA

tag: Prostate genomic DNA; PT05_1 DNA


title: PT233_4 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49682.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.83; Parameter Scan Time = 10:10:52; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 150002; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.83; Parameter Scan Time = 10:10:52; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514906; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.27; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: LabeledExtract

source_name: PT233_4 DNA

tag: Prostate genomic DNA; PT233_4 DNA


title: PT313_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47177.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.85; Parameter Scan Time = 10:59:33; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136066; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.85; Parameter Scan Time = 10:59:33; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501132; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.23; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: Normal male genomic DNA

source_name: PT313_2 DNA

tag: Prostate genomic DNA; PT313_2 DNA

tag: Prostate genomic DNA; LabeledExtract


title: PT309_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47175.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.55; Parameter Scan Time = 10:31:01; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136037; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.55; Parameter Scan Time = 10:31:01; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501103; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.15; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT309_2 DNA

tag: Prostate genomic DNA; PT309_2 DNA


title: PT250_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48741.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 10:54:36; Parameter PMT Volts = 650; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 147870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 10:54:36; Parameter PMT Volts = 670; Parameter Scan Date = 2004-01-27; Parameter Pixel Size = 10; Parameter Laser on time = 512773; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.11; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT250_1 DNA

tag: Prostate genomic DNA; PT250_1 DNA


title: PT311_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47174.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.42; Parameter Scan Time = 10:17:01; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136023; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.42; Parameter Scan Time = 10:17:01; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501088; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.16; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT311_2 DNA

tag: Prostate genomic DNA; PT311_2 DNA


title: PT100_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47182.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 4720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.44; Parameter Scan Time = 08:47:38; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136732; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.44; Parameter Scan Time = 08:47:38; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501797; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.06; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT100_1 DNA

tag: Prostate genomic DNA; PT100_1 DNA


title: Former Smoker, Sample 84

status: Public on Oct 02 2007

type: RNA

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

description: RNA isolated from Bronchial Epithelial cells obtained from the large airway during time of bronchosocpy

hyb_protocol: Affymetrix Suggest Protocol

scan_protocol: Affymetrix Suggest Protocol

data_processing: GCRMA generated expression value

label: Biotin

molecule: total RNA

source_name: Bronchial Epithelium

label_protocol: Affymetrix Suggest Protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Former Smoker

tag: Age:45 Packyears:2 Time Since Quit Smoking (months):14


title: PT312_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47176.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.76; Parameter Scan Time = 10:46:42; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136054; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.76; Parameter Scan Time = 10:46:42; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501119; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.19; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT312_2 DNA

tag: Prostate genomic DNA; PT312_2 DNA


title: Former Smoker, Sample 77

tag: Age:43 Packyears:10 Time Since Quit Smoking (months):4


title: PT112_5 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49679.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.38; Parameter Scan Time = 09:31:06; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149962; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.38; Parameter Scan Time = 09:31:06; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.19; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT112_5 DNA

tag: Prostate genomic DNA; PT112_5 DNA


title: Former Smoker, Sample 87

tag: Age:40 Packyears:30 Time Since Quit Smoking (months):14


title: Former Smoker, Sample 95

tag: Age:50 Packyears:8.25 Time Since Quit Smoking (months):252


title: PT92_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49675.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.86; Parameter Scan Time = 09:55:24; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 148647; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.86; Parameter Scan Time = 09:55:24; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 513550; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.18; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: Normal male genomic DNA

source_name: PT92_1 DNA

tag: Prostate genomic DNA; PT92_1 DNA


title: PT308_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47173.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.27; Parameter Scan Time = 10:01:59; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 136010; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.27; Parameter Scan Time = 10:01:59; Parameter PMT Volts = 640; Parameter Scan Date = 2003-11-12; Parameter Pixel Size = 10; Parameter Laser on time = 501075; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.15; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: LabeledExtract

source_name: PT308_2 DNA

tag: Prostate genomic DNA; PT308_2 DNA


title: Former Smoker, Sample 72

tag: Age:38 Packyears:21.75 Time Since Quit Smoking (months):14


title: Former Smoker, Sample 69

tag: Age:62 Packyears:47.5 Time Since Quit Smoking (months):8


title: Former Smoker, Sample 326

tag: Age:80 Packyears:65 Time Since Quit Smoking (months):120


title: PT224_3 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49680.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.51; Parameter Scan Time = 09:45:26; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149977; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.51; Parameter Scan Time = 09:45:26; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514880; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.20; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT224_3 DNA

tag: Prostate genomic DNA; PT224_3 DNA

tag: Prostate genomic DNA; LabeledExtract


title: Former Smoker, Sample 61

tag: Age:71 Packyears:56 Time Since Quit Smoking (months):3


title: PL116_4 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49671.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.87; Parameter Scan Time = 11:07:03; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 148359; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.87; Parameter Scan Time = 11:07:03; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-03; Parameter Pixel Size = 10; Parameter Laser on time = 513262; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PL116_4 DNA

tag: Prostate genomic DNA; PL116_4 DNA


title: Former Smoker, Sample 63

tag: Former Smoker

tag: Age:27 Packyears:0.5 Time Since Quit Smoking (months):6


title: PT168_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49676.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.96; Parameter Scan Time = 09:02:28; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149933; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.96; Parameter Scan Time = 09:02:28; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514836; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.19; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT168_2 DNA

tag: Prostate genomic DNA; PT168_2 DNA


title: PT316_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48003.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 490, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 12:05:15; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 142669; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.74; Parameter Scan Time = 12:05:15; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 507734; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.23; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT316_2 DNA

tag: Prostate genomic DNA; PT316_2 DNA


title: PT335_6 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49674.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.71; Parameter Scan Time = 09:42:28; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 148633; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.71; Parameter Scan Time = 09:42:28; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 513537; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.20; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT335_6 DNA

tag: Prostate genomic DNA; PT335_6 DNA


title: Former Smoker, Sample 317

tag: Age:71 Packyears:67 Time Since Quit Smoking (months):66


title: PT181_4 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47169.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5530; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.28; Parameter Scan Time = 12:04:14; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 135363; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.28; Parameter Scan Time = 12:04:14; Parameter PMT Volts = 690; Parameter Scan Date = 2003-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 500428; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: Normal male genomic DNA

source_name: PT181_4 DNA

tag: Prostate genomic DNA; PT181_4 DNA


title: PT314_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48000.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 4960; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.45; Parameter Scan Time = 11:24:37; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 142628; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.45; Parameter Scan Time = 11:24:37; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 507693; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.15; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: Normal male genomic DNA

tag: LabeledExtract

source_name: PT314_2 DNA

tag: Prostate genomic DNA; PT314_2 DNA


title: PT317_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48002.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 4960; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.66; Parameter Scan Time = 11:52:27; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 142656; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.66; Parameter Scan Time = 11:52:27; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 507721; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.22; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT317_2 DNA

tag: Prostate genomic DNA; PT317_2 DNA


title: PT205_3 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49673.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.61; Parameter Scan Time = 09:26:53; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 148618; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.61; Parameter Scan Time = 09:26:53; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 513521; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.15; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT205_3 DNA

tag: Prostate genomic DNA; PT205_3 DNA


title: Former Smoker, Sample 296

tag: Age:71 Packyears:45 Time Since Quit Smoking (months):6


title: Former Smoker, Sample 262

tag: Age:59 Packyears:5.5 Time Since Quit Smoking (months):468


title: Former Smoker, Sample 301

tag: Age:53 Packyears:70 Time Since Quit Smoking (months):36


title: Former Smoker, Sample 316

tag: Age:65 Packyears:99 Time Since Quit Smoking (months):1


title: PT32_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47185.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 09:28:20; Parameter PMT Volts = 650; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 136773; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 09:28:20; Parameter PMT Volts = 660; Parameter Scan Date = 2003-11-14; Parameter Pixel Size = 10; Parameter Laser on time = 501838; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT32_1 DNA

tag: Prostate genomic DNA; PT32_1 DNA

tag: Prostate genomic DNA; LabeledExtract


title: Former Smoker, Sample 250

tag: Former Smoker

tag: Age:46 Packyears:24 Time Since Quit Smoking (months):24


title: PT111_1 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49678.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.21; Parameter Scan Time = 09:18:41; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 149950; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.21; Parameter Scan Time = 09:18:41; Parameter PMT Volts = 660; Parameter Scan Date = 2004-02-11; Parameter Pixel Size = 10; Parameter Laser on time = 514853; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.19; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT111_1 DNA

tag: Prostate genomic DNA; PT111_1 DNA


title: Former Smoker, Sample 304

source_name: Bronchial Epithelium

tag: Age:63 Packyears:84 Time Since Quit Smoking (months):24


title: Former Smoker, Sample 173

tag: Age:63 Packyears:0.5 Time Since Quit Smoking (months):504


title: Former Smoker, Sample 140

tag: Age:76 Packyears:35 Time Since Quit Smoking (months):300


title: Former Smoker, Sample 247

tag: Age:74 Packyears:100 Time Since Quit Smoking (months):156


title: Former Smoker, Sample 263

tag: Age:64 Packyears:24.25 Time Since Quit Smoking (months):108


title: Former Smoker, Sample 162

tag: Age:40 Packyears:21 Time Since Quit Smoking (months):60


title: Former Smoker, Sample 119

tag: Age:48 Packyears:64 Time Since Quit Smoking (months):12


title: Former Smoker, Sample 240

tag: Age:76 Packyears:31 Time Since Quit Smoking (months):372


title: Former Smoker, Sample 172

tag: Age:59 Packyears:5 Time Since Quit Smoking (months):468


title: Former Smoker, Sample 246

tag: Age:74 Packyears:60 Time Since Quit Smoking (months):336


title: Former Smoker, Sample 196

tag: Age:53 Packyears:40 Time Since Quit Smoking (months):96


title: Former Smoker, Sample 125

tag: Age:26 Packyears:1.1 Time Since Quit Smoking (months):9


title: PT319_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48001.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 4960; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.56; Parameter Scan Time = 11:38:04; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 142641; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.56; Parameter Scan Time = 11:38:04; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-19; Parameter Pixel Size = 10; Parameter Laser on time = 507707; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.17; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

tag: Normal male genomic DNA

tag: LabeledExtract

source_name: PT319_2 DNA

tag: Prostate genomic DNA; PT319_2 DNA


title: Former Smoker, Sample 147

description: RNA isolated from Bronchial Epithelial cells obtained from the large airway during time of bronchosocpy

scan_protocol: Affymetrix Suggest Protocol

tag: Former Smoker

tag: Age:59 Packyears:13 Time Since Quit Smoking (months):360


title: Former Smoker, Sample 104

tag: Age:40 Packyears:5 Time Since Quit Smoking (months):252


title: Current Smoker, Sample 98

tag: Current Smoker

tag: Age:42 Packyears:1


title: Former Smoker, Sample 141

tag: Age:55 Packyears:10 Time Since Quit Smoking (months):252


title: Current Smoker, Sample 97

tag: Age:54 Packyears:20.5


title: PT215_2 DNA

description:
Simple annotation: Prostate, aCGH tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49672.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jacques,,Lapointe Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.33; Parameter Scan Time = 09:12:41; Parameter PMT Volts = 650; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 148604; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.33; Parameter Scan Time = 09:12:41; Parameter PMT Volts = 670; Parameter Scan Date = 2004-02-06; Parameter Pixel Size = 10; Parameter Laser on time = 513508; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.13; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jacques,,Lapointe

source_name: PT215_2 DNA

tag: Prostate genomic DNA; PT215_2 DNA

tag: Prostate genomic DNA; LabeledExtract


title: Current Smoker, Sample 92

tag: Age:33 Packyears:3.5


title: Current Smoker, Sample 91

tag: Age:32 Packyears:8


title: Current Smoker, Sample 88

tag: Age:39 Packyears:20


title: Current Smoker, Sample 82

tag: Age:26 Packyears:22.5


title: Current Smoker, Sample 83

tag: Age:41 Packyears:28.25


title: Current Smoker, Sample 71

tag: Age:23 Packyears:7


title: Current Smoker, Sample 81

tag: Age:54 Packyears:9.75


title: Current Smoker, Sample 85

tag: Age:39 Packyears:25


title: Current Smoker, Sample 56

tag: Age:73 Packyears:51


title: Current Smoker, Sample 79

tag: Age:39 Packyears:23


title: Current Smoker, Sample 300

tag: Age:66 Packyears:4


title: Current Smoker, Sample 58

tag: Current Smoker

tag: Age:32 Packyears:2


title: Current Smoker, Sample 73

tag: Age:42 Packyears:28


title: Current Smoker, Sample 336

tag: Age:50 Packyears:57


title: Current Smoker, Sample 309

tag: Age:68 Packyears:53


title: Current Smoker, Sample 67

tag: Age:48 Packyears:21


title: Current Smoker, Sample 307

tag: Age:47 Packyears:39.5


title: Current Smoker, Sample 283

tag: Age:34 Packyears:17


title: Current Smoker, Sample 286

tag: Age:45 Packyears:14


title: Current Smoker, Sample 330

tag: Age:44 Packyears:45


title: Current Smoker, Sample 333

tag: Age:40 Packyears:27.5


title: Current Smoker, Sample 86

tag: Age:30 Packyears:4


title: Current Smoker, Sample 75

tag: Age:37 Packyears:19


title: Current Smoker, Sample 241

tag: Age:51 Packyears:45


title: Current Smoker, Sample 292

tag: Age:45 Packyears:16


title: Current Smoker, Sample 282

tag: Age:66 Packyears:85


title: Former Smoker, Sample 89

tag: Former Smoker

tag: Age:43 Packyears:7 Time Since Quit Smoking (months):156


title: Current Smoker, Sample 225

tag: Current Smoker

tag: Age:71 Packyears:80


title: Current Smoker, Sample 68

tag: Age:38 Packyears:28


title: Current Smoker, Sample 226

tag: Age:69 Packyears:25


title: Current Smoker, Sample 265

tag: Age:79 Packyears:180


title: Current Smoker, Sample 223

tag: Age:69 Packyears:114


title: Current Smoker, Sample 244

tag: Age:68 Packyears:105


title: Current Smoker, Sample 195

tag: Age:50 Packyears:5


title: Current Smoker, Sample 161

tag: Age:59 Packyears:70.5


title: Current Smoker, Sample 220

tag: Age:58 Packyears:22


title: Current Smoker, Sample 116

tag: Age:38 Packyears:25


title: Current Smoker, Sample 151

tag: Age:49 Packyears:34


title: Current Smoker, Sample 113

tag: Age:36 Packyears:10.5


title: Current Smoker, Sample 106

tag: Age:37 Packyears:13


title: Current Smoker, Sample 143

tag: Age:56 Packyears:42


title: Current Smoker, Sample 102

tag: Age:27 Packyears:8.13


title: Current Smoker, Sample 176

tag: Age:65 Packyears:50


title: Never Smoker, Sample 96

tag: Never Smoker


title: Never Smoker, Sample 94


title: Never Smoker, Sample 78


title: Current Smoker, Sample 124

tag: Current Smoker

tag: Age:54 Packyears:90


title: Current Smoker, Sample 134

tag: Age:23 Packyears:7


title: Current Smoker, Sample 109

tag: Age:49 Packyears:0.5


title: Current Smoker, Sample 207

tag: Age:71 Packyears:61


title: Current Smoker, Sample 112

tag: Age:69 Packyears:30


title: Current Smoker, Sample 120

tag: Age:35 Packyears:25


title: Never Smoker, Sample 70


title: Never Smoker, Sample 59


title: Never Smoker, Sample 334


title: Never Smoker, Sample 332


title: Never Smoker, Sample 60


title: Never Smoker, Sample 259


title: Never Smoker, Sample 254


title: Never Smoker, Sample 293


title: Never Smoker, Sample 105


title: Never Smoker, Sample 311


title: Never Smoker, Sample 118


title: Never Smoker, Sample 132


title: Never Smoker, Sample 194


title: Current Smoker, Sample 238

tag: Age:79 Packyears:64


title: Never Smoker, Sample 108


title: Never Smoker, Sample 127


title: Immature_ear_H99vsF1_fwd_rep2

status: Public on Oct 01 2007

city: Milan

first: Giorgio

last: Pea

address: via Celoria 26

department: Department of Biomolecular Sciences and Biotechnology

country: Italy

institute: University of Milan

description:
Slide number 606.01.04.024.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)

hyb_protocol: After adding 12 ug of Polydeoxyadenylic Acid (Amersham Bioscience, Little Chalfont, UK) the probe was lyophilized in SpeedVac SVC-100 H (Savant Instruments/E-C Apparatus, Holbrook, NY) and then resuspended in 29 uL Array Hyb Low Temp Hybridization Buffer (Sigma-Aldrich, St. Louis, MO) and 2 uL salmon sperm DNA (20 ug/uL). Slides were re-hydrated 7 min in water-saturated atmosphere and briefly dried on heating plate (3-4 sec); spotted cDNA were cross-linked to the silane-glass support applying twice 65 mJ/cm2 UV light (254 nm; Stratalinker 2400 UV cross-linker, Stratagene, La Jolla, CA). After rinsing 2 min in SDS at R.T., spotted cDNA were denatured by immersion of slides in mQ water for 2 min at 95 C. Unspecific binding sites were blocked for 40 min at 65 C in 1% BSA, 3.5X SSC, 0.2% SDS. Slides were rinsed at R.T. in mQ water 50 times in each of four trays, then in iso-propanol (10 immersions), and finally air-dried and stored in a clean box until hybridization. After denaturation (2 min, 98 C in mQ water) probe was hybridized on microarray slides o. n. at 50 C in a dark hybridization chamber (CMT-Hybridization Chamber, Corning Inc., Corning, NY). Slides were then washed in SDS 1% solutions at increasing stringency (SSC concentration 2X, 1X, 0.1X; 10 min each, 65 C), then in SSC 0.1X (5 min, 65 C, twice), air-dried and stored in the dark at room temperature until image acquisition.

scan_protocol: Microarray images for Cy3 and Cy5 channels were acquired using ScanArray software on SA4000 Scanner (v3.1, Packard BioScience, Wellesley, MA), setting laser power to 90% and auto-adjusting photo-multiplicator gain to the maximum sub-saturating value for each channel. Signal and background intensities and spot parameters were quantified by QuantArray (v3.0, Packard BioScience, Wellesley, MA).

data_processing: Records corresponding to single bad-quality spots were manually removed. Intensity data were imported into GeneSpring (Agilent Technologies, Palo Alto, CA), where local background subtraction as well as per-chip LOWESS and 50th percentile within-array normalization functions were performed on log-two transformed data. Base two logarithms of hybrid/inbred expression ratios for each EST, calculated from the average over three replicate spots within the slide, were exported from GeneSpring to perform all subsequent analyses.

molecule: polyA RNA

organism: Zea mays

source_name: F1 immature ear

label_protocol: 1 ug of purified poly(A+) RNA was independently retrotranscribed using 400 U of SuperScript II RNase H- Reverse Transcriptase (Invitrogen, Carlsbad, CA) and 2 ug Oligo(dT)23 Anchored (Sigma-Aldrich, St. Louis, MO) as primer, in 30 uL final volume (2 hours, 42 C). cDNA probes were labeled by direct incorporation of Cy3/Cy5 modified dCTP 0.3 mM (Amersham Bioscience, Little Chalfont, UK); dATP, dGTP and dTTP 0.5 mM each, dCTP 0.2 mM. Reaction was stopped adding 1.5 uL EDTA (0.5 M – pH 8.0) and 3.75 uL NaOH (1 M) (10 min, 65 C) and then neutralized with 0.75 uL HCl (5 M) and 9 uL Tris HCl (1 M – pH 6.9). Probe was purified with Nucleo Spin Extract kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany), protocol #4.2 with double wash in NT3 buffer.

growth_protocol: Immature ears were harvested from plants cultivated in open field (2003), at 12 p.m. along 3 different days

extract_protocol: After harvesting, plant material was immediately frozen after removing silks and ear apexes and stored at - 80 C. Tissues were ground in liquid nitrogen using mortars and pestles. Total RNA was isolated using the TRizol protocol (Invitrogen, Carlsbad, CA), as indicated by the manufacturer (except for 5 min extra time centrifugation in TRizol reagent), including a second step in chloroform for lowering protein contamination. Poly(A+) RNA was purified from 1 mg of total RNA derived from a minimum of three independent extractions using mRNA Purification Kit (Amersham Bioscience, Little Chalfont, UK). Both total and poly(A+) RNA were tested for quality by electrophoresis on 1.5% agarose gel and quantified by absorbance at 260 nm.

tag: Genotype

value: B73xH99 F1 hybrid

tag: Tissue

value: Immature ear

tag: Stage

tag: Origin

value: bulk of 10 individuals

source_name: H99 immature ear

growth_protocol: Immature ears were harvested from 10 individuals cultivated in open field (2003), at 12 p.m. along 3 different days


title: Immature_ear_H99vsF1_fwd_rep1

description:
Slide number 606.01.04.022.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)


title: Immature_ear_H99vsF1_rev_rep5

description:
Slide number 606.01.04.036.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)


title: Never Smoker, Sample 100


title: Never Smoker, Sample 149


title: Immature_ear_B73vsF1_rev_rep5

description:
Slide number 606.01.04.034.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)

source_name: B73 immature ear


title: Immature_ear_B73vsF1_rev_rep4

description:
Slide number 606.01.04.033.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)


title: Immature_ear_B73vsF1_fwd_rep2

description:
Slide number 606.01.04.028.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)


title: Immature_ear_B73vsF1_fwd_rep3

description:
Slide number 606.01.04.029.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)


title: Immature_ear_B73vsF1_fwd_rep1

description:
Slide number 606.01.04.026.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)

value: B73xH99 F1 hybrid.

value: Immature ear.

value: bulk of 10 individuals.


title: Immature_ear_H99vsF1_rev_rep4

description:
Slide number 606.01.04.035.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)


title: Immature_ear_H99vsF1_fwd_rep3

description:
Slide number 606.01.04.025.
For a detailed description of the experiment see:
Pea G, Ferron S, Gianfranceschi L, Krajewski P, Pe' ME (2007) Gene expression non-additivity in immature ears of a heterotic F1 maize hybrid. Plant Science (DOI:10.1016/j.plantsci.2007.09.005)


title: HCT116 6.7uM/48h

city: Oslo

first: Nur

last: Duale

address: Lovisenbergg. 8, P.O.Box 4404 Nydalen,

department: Division of Climate and Environment Health

country: Norway

institute: Norwegian Institute of Public Health

description: Cell culture and treatment: The human colon cancer derived cell line, HCT116 from (ATCC-CCL-247, Manassas, VA). The HCT116 cells were grown in cell culture flasks (Corning Inc., USA) in McCoy’s 5A medium with L-glutamine supplemented with 10% fetal calf serum and 1% penicillin-streptomycin mixture (Cambrex, Belgium). The cell line was grown at 37oC in a humidified atmosphere of 5% of CO2 in air. Cells were seeded in 100 mm cell culture dishes (Corning Inc, USA) and allowed to attach 24 h prior to cisplatin (Cis-Diamminedichloroplatinum(II) or CDDP, Sigma) treatment. Cells in exponential growth phase were exposed to cisplatin and the cells were harvested after 48 h of exposure and prepared for further analysis. RNA preparation: Total RNA was isolated from cisplatin treated and control cell lines by GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Microarrays: 21K human oligonucleotide microarrays were printed at the Norwegian Microarray Consortium using OPERON hum oligo v2.0. The microarrays consist of 70 mer, oligos representing 21,329 genes from UniGene Database. cDNA synthesis and labeling:Labeled cDNAs were synthesized according to the manufacturer's protocol, FairPlay cDNA labeling kit (Stratagene, La Jolla, CA). Briefly, 20 μg of total RNA (from cisplatin treated and control cell lines) in 13 μl of nuclease-free water was combined with 1 μl of 500 ng/μl oligo-d(T)12–18. The mixture was incubated at 70°C for 10 min and cooled on ice. For each reaction, 2 μl of 10X StrataScript reaction buffer, 1 μl of unlabeled 20X dNTP mix containing amino-allyl dUTP, 1.5 μl of 0.1 M dithiothreitol and 0.5 μl of RNase Block (40 U/μl) were prepared and mixed with the RNA sample and 1 μl of 50 U/μl StrataScript RT. After incubation at 48°C for 30 min an additional 1 μl of StrataScript RT was added and incubation was continued for 30 additional minutes. RNA was degraded by adding 10 μl of 1 M NaOH, followed by a 10-min incubation at 70°C and the mixture neutralized with 10 μl of 1 M HCl. Unincorporated nucleotides were removed by precipitation of the cDNA with 4 μl of 3 M sodium acetate, 1 μl of 20 mg/ml glycogen and 100 μl of 95% ethanol at -20°C for 1 h. After centrifugation and washing the pellet with 70% ethanol, it was resuspended in 5 μl of 2x coupling buffer provided in the kit. Cy3 or Cy5 dye (Amersham), resuspended in 45 ul of DMSO, was added and the reaction incubated for 2 h at room temperature in the dark. Dye-coupled cDNA was purified with a DNA-binding spin cup, combined and concentrated by vacuum drier.

hyb_protocol: Microarray slides were prehybridized in buffer containing 5X SSC, 1% Bovine Serum Albumin and 0.1% SDS at 42°C for 1 h to block nonspecific binding and washed by dipping several times in double distilled water. The slides were then dipped in isopropanol and centrifuged to dry in 50 ml un-capped centrifuge tubes at 480 x g for 5 min. Labeled cDNAs were added to hybridization buffer (50% formamide, 5x SSC, 0.1% SDS, 4 µg/µl yeast tRNA, and 0.6 µg/µl human Cot-1 DNA), denatured for 5 min at 95°C, and applied to the arrays using a cover slip (LifterSlip, Erie Scientific). Arrays were placed in a hybridization chamber and the hybridization chamber was incubated overnight at 42°C water bath. After hybridization, washing was performed as follows: 5 min washing with  2×SSC, 0.1% SDS at 42°C, 10 min washing with  0.1x SSC, 0.1% SDS and 4x1 min washing with  0.1×SSC at room temperature. The slide was dried by centrifuging at 480x g for 5 min and scanned with an Agilent microarray laser Scanner (Agilent, Palo Alto, CA).

scan_protocol: According to the manufacturer's protocol, Agilent microarray laser Scanner (Agilent, Palo Alto, CA)

data_processing: Quality control of the scanned images (tiff-files) and conversion to numerical values were performed using the GenePix Pro 4.1 (Axon Instruments). The gpr-files obtained were further analyzed using J-Express Pro2.7 (http://www.molmine.com). Mean FG intensities were used as input values. Controls as well as flagged or empty spots were filtered away before Global Lowess Normalization. Further quality control was performed using the various Plot and Spot Image View options in J-Express. The relevant data were transferred to Excel. The average ratios, as well as average red and green intensities were calculated.

source_name: HCT116 treated with 6.7uM cisplatin

extract_protocol: Total RNA was isolated from cisplatin treated and control cell lines by GenElute kit (Sigma). RNA isolated from three individual treatments was mixed. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer. RNA integrity was determined by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). RNA from at least three independent experiments was pooled together before labeling and hybridization to reduce possible bias for single treatment.

treatment_protocol: Treatment of cell cultures: HCT116 cell line in exponential growth phase was exposed to 6.7uM (2.0ug/ml) cisplatin 48h after plating. Cells were harvested after 24h of exposure and prepared for further analysis.

tag: Human colon cancer derived cell line, HCT116 (ATCC-CCL-247, Manassas, VA)

source_name: HCT116 CTL


title: Ap 48 hr YE vs 48 hr YES Slide 10B

city: Mississippi State

first: Jeff

last: Wilkinson

state: MS

department: Biochemistry and Molecular Biology

institute: Mississippi State University

description: The independent TIFF images from each channel were analyzed using TIGR Spotfinder software program.  After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values.

hyb_protocol: Pre-hybridization was performed according to TIGR’s protocols and washed according to post-hybridization instructions for the 3DNA Array 900MPXTM Kit (Genisphere Inc., Hatfield, PA). Hybridizations were performed using the 3DNA Array 900MPXTM Kit (Genisphere Inc.), according to the manufacturer’s protocol.  Each experiment consisted of one 48 hour YE sample coupled to either a 3, 6, 12, 24, or 48 hour sample from the YE to YES shift.  The 48 hour YE to 3, 6, 12 and 24 hour YES comparisons were repeated with duplicate biological replicates and with duplicate dye-flip; the 0 hour to 48 hour comparisons were done in triplicate each with a dye-flip.  Briefly, 3 µg of total RNA was used to generate cDNA using Genisphere’s random and MPX dT primers with Supercript II, dithiotreitol and 5X SuperScript II First Strand Buffer (Invitrogen Corp., Carlsbad, CA) as per Genisphere’s instructions.  The generated cDNA’s were purified using Qiagen MiniElute PCR Purification Kit (Qiagen Inc., Valencia, CA) as well as after terminal deoxynucleotidyl transferase tailing reaction and ligation to 3DNA capture sequence reactions. cDNA hybridizations were performed using the 2X Formamide-Based Hybridization Buffer overnight at 49oC in Hybridization Cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA), unbound cDNA was removed by washing as per Genisphere’s instructions.  Hybridization of the 3DNA Capture reagent containing the fluorescent dyes were performed using the 2X Formamide-Based Hybridization Buffer at 49oC for 4 hours in Hybridization Cassette and washed as per Genisphere’s instructions to remove non-specific background.

scan_protocol: Hybridized slides were scanned using either a ScanArray5000XL (GSI Lumonics, Packard Biochip, Packard BioScience Company, Billerica, MA) or a GenePix 4000B (Axon Instruments, Molecular Devices, Sunnyvale, CA).

data_processing: To remove the non-specific background signals, the raw data was normalized using a local regression technique, LOWESS (LOcally WEighted Scatterplot Smoothing), using the MIDAS software tool.  The LOWESS normalized dye-flips were then combined to minimize any artifacts introduced by the Cy3 or Cy5 dyes.  The resulting data were averaged over duplicate gene features on each array for each replicate experiment.  Some genes are represented by two separate non-overlapping fragments, therefore since a gene may be detected by each fragment they are defined as features so that gene count will not be over reported.  All calculated gene expression ratios were log2-transformed when imported into TIGR MeV software [31].  Only genes that gave detectable signals in all replicate experiments were used for further analysis.

organism: Aspergillus parasiticus

source_name: Aspergillus parasiticus SU-1 48 hr YE

growth_protocol:
A. parasiticus SRRC 143 ATCC 56775 (or SU-1), a wild type strain previously used for biochemical and genetic studies of both B group (B1 and B2) and G group (G1 and G2) aflatoxins, was selected for this study.  Fresh conidia were generated by plating 50 µl of 108 spore per ml onto Difco Potato-Dextrose Agar (PDA) (American Scientific Products, Charlotte, N.C.) and incubated at 30oC for 5 days.  The conidia were collected from 5-day cultures with sterile aqueous 0.05% Triton X-100.
A. parasiticus spores were inoculated to a final concentration of 105 spores/ml in 200 ml yeast extract (YE) liquid medium consisting of 25 g/L of yeast extract (DIFCO) and incubated for 48 hours at 30oC with constant shaking at 150 rpm.  The fungal mycelia were harvested by filtration in vacuo.  The harvested mycelia were divided into 1 gram aliquots.  Each aliquot was used to inoculate 100 ml of YES medium (60 g/L of sucrose and 25 g/L of yeast extract) for harvesting at different time points.  The cultures shifted from YE to YES were grown at 30oC with 150 rpm shaking until harvested at 3, 6, 12, 24, and 48 hours post-inoculation.  The harvested fungal mycelial samples were fresh frozen in liquid nitrogen and stored at -80oC for RNA preparation and aflatoxin extraction.

extract_protocol: The frozen fungal mycelia were ground to a fine powder in liquid nitrogen using mortar and pestle.  Total RNA was extracted from approximately 100 mg of ground mycelium in 1 ml of TRIZOL® (Molecular Research Center, Inc., Cincinnati, OH) according to manufacturer's instructions.  Total RNA was quantified using a ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and visualized by agarose gel electrophoresis to ensure quality.

tag: Aspergillus parasiticus SU-1 RNA collected from 48 hr YE cultures

source_name: Aspergillus parasiticus SU-1 48 hr YES

tag: Aspergillus parasiticus SU-1 RNA collected 48 hr post shift from 48 hr YE to YES