title: Wt5FGF-replicate

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50554.gif

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6280; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.99; Parameter Scan Time = 12:17:05; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 79340; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.07; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.99; Parameter Scan Time = 12:17:05; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 79340; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.07; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

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)

source_name: universal

label_protocol: not provided

extract_protocol: not provided

tag: universal


title: MMJ192-NIH

status: Public on Nov 10 2006

type: RNA

city: Stanford

state: CA

country: USA

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41183.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 860, 7650; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 31.58; Parameter Scan Time = 10:29:44; Parameter PMT Volts = 610; Parameter Scan Date = 2003-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 33915; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 31.58; Parameter Scan Time = 10:29:44; Parameter PMT Volts = 810; Parameter Scan Date = 2003-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 103682; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

molecule: total RNA

organism: Mus musculus

source_name: amp univ

tag: amp univ

source_name: NIH Alone

tag: NIH Alone


title: MMJ194-NIH Pooled

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41185.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 860, 7510; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 31.73; Parameter Scan Time = 10:41:32; Parameter PMT Volts = 610; Parameter Scan Date = 2003-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 33927; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 31.73; Parameter Scan Time = 10:41:32; Parameter PMT Volts = 810; Parameter Scan Date = 2003-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 103694; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

source_name: NIH Pooled

tag: NIH Pooled


title: Squamous cell carcinoma 76981_B

city: st louis

first: Yan

last: Lu

state: MO

address: 660 s. euclid ave

institute: washington univ.

description: Squamous cell carcinoma

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Robust Multichip Average

label: biotin

organism: Homo sapiens

source_name: Squamous cell carcinoma

label_protocol: Approximately 1 to 5 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: standard Affymetrix procedures

tag: Gender

value: M; age:76; stage:T2N0


title: Wt4FGF-replicate

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50553.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 7080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.96; Parameter Scan Time = 12:03:07; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 79328; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.96; Parameter Scan Time = 12:03:07; Parameter PMT Volts = 780; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 148829; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: Squamous cell carcinoma 48556_B

description: Squamous cell carcinoma

value: M; age:78; stage:T2N0


title: MMJ196-NIH Clone 1

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41186.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 860, 7510; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 31.88; Parameter Scan Time = 10:59:09; Parameter PMT Volts = 560; Parameter Scan Date = 2003-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 33945; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.02; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 31.88; Parameter Scan Time = 10:59:09; Parameter PMT Volts = 780; Parameter Scan Date = 2003-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 103712; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

source_name: NIH Clone 1

tag: NIH Clone 1


title: HMW1-replicate

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50550.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5640; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.84; Parameter Scan Time = 11:10:11; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 79274; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.07; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.84; Parameter Scan Time = 11:10:11; Parameter PMT Volts = 700; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 148775; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: MMJ193-NIH Vector

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41184.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 860, 7650; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 31.64; Parameter Scan Time = 10:35:34; Parameter PMT Volts = 610; Parameter Scan Date = 2003-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 33922; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 31.64; Parameter Scan Time = 10:35:34; Parameter PMT Volts = 810; Parameter Scan Date = 2003-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 103689; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.50; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

source_name: NIH Vector

tag: NIH Vector


title: Squamous cell carcinoma 57774_B

description: Squamous cell carcinoma

value: M; age:76; stage:T1N0


title: RGWCAF10

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62149.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1800, 6880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.59; Parameter Scan Time = 09:35:43; Parameter PMT Volts = 600; Parameter Scan Date = 2005-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 218706; 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: Hongjuan,,Zhao 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 = 38.59; Parameter Scan Time = 09:35:43; Parameter PMT Volts = 620; Parameter Scan Date = 2005-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 583510; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.88; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: Universal human reference RNA

tag: Universal human reference RNA

source_name: RGWCAF10 total RNA

tag: RGWCAF10 total RNA


title: KGBPHF8

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62146.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.64; Parameter Scan Time = 12:57:09; Parameter PMT Volts = 570; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 220045; 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: Hongjuan,,Zhao 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 = 38.64; Parameter Scan Time = 12:57:09; Parameter PMT Volts = 620; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 584849; 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: Hongjuan,,Zhao

source_name: KGBPHF8 total RNA

tag: KGBPHF8 total RNA


title: WIBCAF14

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62156.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 6800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.99; Parameter Scan Time = 13:22:06; Parameter PMT Volts = 560; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 220070; 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: Hongjuan,,Zhao 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 = 38.99; Parameter Scan Time = 13:22:06; Parameter PMT Volts = 630; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 584874; 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: Hongjuan,,Zhao

source_name: WIBCAF14 total RNA

tag: WIBCAF14 total RNA


title: Wt6FGF-replicate

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50555.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6360; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.99; Parameter Scan Time = 12:29:48; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 79353; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.99; Parameter Scan Time = 12:29:48; Parameter PMT Volts = 780; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 148855; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.60; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: LMW3-replicate

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50552.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.90; Parameter Scan Time = 12:43:39; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 79368; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.90; Parameter Scan Time = 12:43:39; Parameter PMT Volts = 780; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 148869; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.60; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: RAFPZ(L)F17

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62148.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1800, 7160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 09:29:15; Parameter PMT Volts = 610; Parameter Scan Date = 2005-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 218700; 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: Hongjuan,,Zhao 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 = 09:29:15; Parameter PMT Volts = 620; Parameter Scan Date = 2005-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 583504; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.88; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: RAFPZ(L)F17 total RNA

tag: RAFPZ(L)F17 total RNA


title: DAHPZF16

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62137.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 37.87; Parameter Scan Time = 10:36:18; Parameter PMT Volts = 580; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 219781; 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: Hongjuan,,Zhao 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 = 37.87; Parameter Scan Time = 10:36:18; Parameter PMT Volts = 600; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 584585; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: DAHPZF16 total RNA

tag: DAHPZF16 total RNA


title: WJCTZF14

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62159.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 6760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 13:03:18; Parameter PMT Volts = 570; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 220051; 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: Hongjuan,,Zhao 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 = 13:03:18; Parameter PMT Volts = 620; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 584855; 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: Hongjuan,,Zhao

source_name: WJCTZF14 total RNA

tag: WJCTZF14 total RNA


title: HMW2-replicate

description:
Simple annotation: gene overexpression, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50551.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.96; Parameter Scan Time = 11:30:27; Parameter PMT Volts = 560; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 79294; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.10; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.96; Parameter Scan Time = 11:30:27; Parameter PMT Volts = 700; Parameter Scan Date = 2004-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 148795; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: DCMCA(PZ)F11-du

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62161.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.35; Parameter Scan Time = 12:37:36; Parameter PMT Volts = 560; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 220026; 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: Hongjuan,,Zhao 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 = 38.35; Parameter Scan Time = 12:37:36; Parameter PMT Volts = 630; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 584830; 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: Hongjuan,,Zhao


title: DCMCA(PZ)F11

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62138.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1800, 6640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 09:42:19; Parameter PMT Volts = 610; Parameter Scan Date = 2005-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 218713; 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: Hongjuan,,Zhao 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 = 09:42:19; Parameter PMT Volts = 620; Parameter Scan Date = 2005-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 583517; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.90; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: DCMCA(PZ)F11 total RNA

tag: DCMCA(PZ)F11 total RNA


title: GOPZ(L)F

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62139.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.02; Parameter Scan Time = 10:45:03; Parameter PMT Volts = 580; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 219790; 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: Hongjuan,,Zhao 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 = 38.02; Parameter Scan Time = 10:45:03; Parameter PMT Volts = 630; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 584593; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.92; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: GOPZ(L)F total RNA

tag: GOPZ(L)F total RNA


title: ALTBPHF10

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62135.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 37.68; Parameter Scan Time = 10:21:35; Parameter PMT Volts = 550; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 219766; 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: Hongjuan,,Zhao 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 = 37.68; Parameter Scan Time = 10:21:35; Parameter PMT Volts = 600; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 584570; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.91; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: ALTBPHF10 total RNA

tag: ALTBPHF10 total RNA


title: MASCAF10

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62147.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 12:50:55; Parameter PMT Volts = 560; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 220039; 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: Hongjuan,,Zhao 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 = 12:50:55; Parameter PMT Volts = 620; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 584843; 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: Hongjuan,,Zhao

source_name: MASCAF10 total RNA

tag: MASCAF10 total RNA


title: JENAPZF19

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62143.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 13:16:15; Parameter PMT Volts = 580; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 220064; 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: Hongjuan,,Zhao 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 = 13:16:15; Parameter PMT Volts = 630; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 584868; 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: Hongjuan,,Zhao

source_name: JENAPZF19 total RNA

tag: JENAPZF19 total RNA


title: Squamous cell carcinoma 48536_B

description: Squamous cell carcinoma

scan_protocol: standard Affymetrix procedures

value: M; age:80; stage:T2N0


title: JMSPZF15

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62145.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 6880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 09:48:37; Parameter PMT Volts = 590; Parameter Scan Date = 2005-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 218719; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao 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 = 09:48:37; Parameter PMT Volts = 620; Parameter Scan Date = 2005-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 583523; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.91; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: JMSPZF15 total RNA

tag: JMSPZF15 total RNA


title: Squamous cell carcinoma 48549_B

description: Squamous cell carcinoma

value: F; age:62; stage:T1N0


title: WERCAF8

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62153.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 6920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.17; Parameter Scan Time = 12:28:06; Parameter PMT Volts = 570; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 220016; 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: Hongjuan,,Zhao 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 = 38.17; Parameter Scan Time = 12:28:06; Parameter PMT Volts = 630; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 584820; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.08; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: WERCAF8 total RNA

tag: WERCAF8 total RNA


title: Squamous cell carcinoma 48521_B

description: Squamous cell carcinoma

source_name: Squamous cell carcinoma

tag: Gender

value: M; age:70; stage:T2N0


title: Squamous cell carcinoma 44661_B

description: Squamous cell carcinoma

value: M; age:64; stage:T2N0


title: APABPHF11

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62136.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 6840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 37.76; Parameter Scan Time = 10:28:48; Parameter PMT Volts = 580; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 219773; 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: Hongjuan,,Zhao 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 = 37.76; Parameter Scan Time = 10:28:48; Parameter PMT Volts = 610; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 584577; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.90; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: APABPHF11 total RNA

tag: APABPHF11 total RNA


title: AKPZF15

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62134.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 37.47; Parameter Scan Time = 10:10:25; Parameter PMT Volts = 550; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 219755; 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: Hongjuan,,Zhao 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 = 37.47; Parameter Scan Time = 10:10:25; Parameter PMT Volts = 590; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 584559; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.91; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: AKPZF15 total RNA

tag: AKPZF15 total RNA


title: Squamous cell carcinoma 42613_B

description: Squamous cell carcinoma

value: M; age:73; stage:T2N0


title: Squamous cell carcinoma 44693_B

description: Squamous cell carcinoma

value: F; age:66; stage:T2N0


title: Squamous cell carcinoma 44656_B

description: Squamous cell carcinoma

value: F; age:76; stage:T2N0


title: Squamous cell carcinoma 42616_B

description: Squamous cell carcinoma

value: M; age:63; stage:T1N0


title: SKTZF16

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62150.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.43; Parameter Scan Time = 12:44:11; Parameter PMT Volts = 560; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 220032; 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: Hongjuan,,Zhao 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 = 38.43; Parameter Scan Time = 12:44:11; Parameter PMT Volts = 630; Parameter Scan Date = 2005-06-06; Parameter Pixel Size = 10; Parameter Laser on time = 584836; 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: Hongjuan,,Zhao

source_name: Universal human reference RNA

tag: Universal human reference RNA

source_name: SKTZF16 total RNA

tag: SKTZF16 total RNA


title: Squamous cell carcinoma 44680_B

description: Squamous cell carcinoma

value: F; age:70; stage:T1N0


title: Squamous cell carcinoma 41932_B

description: Squamous cell carcinoma

value: F; age:62; stage:T2N0


title: GSLPZF11

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62140.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 5840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.32; Parameter Scan Time = 11:17:11; Parameter PMT Volts = 560; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 219822; 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: Hongjuan,,Zhao 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 = 38.32; Parameter Scan Time = 11:17:11; Parameter PMT Volts = 630; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 584626; 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: Hongjuan,,Zhao

source_name: GSLPZF11 total RNA

tag: GSLPZF11 total RNA


title: WT237

description:
Simple annotation: Cell-line, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46442.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 8040; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.48; Parameter Scan Time = 11:09:05; Parameter PMT Volts = 520; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 60427; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.86; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.48; Parameter Scan Time = 11:09:05; Parameter PMT Volts = 620; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 129988; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

source_name: Amplified Universal

tag: Amplified Universal

source_name: Wt FGF

tag: Wt FGF


title: LMW185

description:
Simple annotation: gene overexpression, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46865.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 8000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 30.32; Parameter Scan Time = 11:19:13; Parameter PMT Volts = 530; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 60570; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.89; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 30.32; Parameter Scan Time = 11:19:13; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 130131; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

source_name: universal

tag: universal


title: Squamous cell carcinoma 42081_B

description: Squamous cell carcinoma

value: F; age:73; stage:T2N0


title: LMW184

description:
Simple annotation: gene overexpression, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46864.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 8000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 30.23; Parameter Scan Time = 11:09:39; Parameter PMT Volts = 530; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 60560; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.89; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 30.23; Parameter Scan Time = 11:09:39; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 130121; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: LMW239

description:
Simple annotation: Cell-line, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46444.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1290, 7950; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.48; Parameter Scan Time = 11:33:46; Parameter PMT Volts = 520; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 60451; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.48; Parameter Scan Time = 11:33:46; Parameter PMT Volts = 620; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 130013; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.60; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: Squamous cell carcinoma 41923_B

description: Squamous cell carcinoma

value: M; age:65; stage:T1N0


title: GVNBPHF14

description:
Simple annotation: Prostate, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62141.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 7000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao 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 = 38.07; Parameter Scan Time = 10:51:08; Parameter PMT Volts = 580; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 219796; 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: Hongjuan,,Zhao 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 = 38.07; Parameter Scan Time = 10:51:08; Parameter PMT Volts = 630; Parameter Scan Date = 2005-06-04; Parameter Pixel Size = 10; Parameter Laser on time = 584600; 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: Hongjuan,,Zhao

source_name: GVNBPHF14 total RNA

tag: GVNBPHF14 total RNA


title: Squamous cell carcinoma 40430_B

description: Squamous cell carcinoma

value: M; age:75; stage:T2N0


title: HMW182

description:
Simple annotation: gene overexpression, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46862.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 7760; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 30.08; Parameter Scan Time = 10:46:49; Parameter PMT Volts = 530; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 60535; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.89; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 30.08; Parameter Scan Time = 10:46:49; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 130097; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

source_name: Universal Mouse

tag: Universal Mouse


title: rat gastrocnemius muscle chip9

city: Stockholm

first: Mikael

last: Altun

address: Retzius väg 8

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: experiment was dye swapt. values were inverted before processed.

hyb_protocol: 8. Neutralize by addition of 7,5μl of 1.0M Tris-HCl (pH 7,5). At this time, start the prehybridisation of the array. Refer to protocol below. 9. Mix the two probes into a centrion-30 tube and add 400μl of filtered TE (Wash 1). Spin 9 min (or more if needed) at 13 kRPM. 10. Remove flow-through. Wash 2: Add 450μl TE and spin 9 min at 13 kRPM. 11. Wash 3: Add 450μl TE, 20μg of Cot1 DNA, 2μl of 10μg/μl polyA RNA and 2μl of 10μg/μl tRNA. Spin 7 min at 13kRPM (may need longer time). Try to concentrate to a volume less than 10μl. 12. Invert the centricon into a clean tube and spin briefly at 4 kRPM to recover the probe 13. Adjust vol. to 12μl with TE for 22x22mm array (to 20μl if using 22x40mm array). 14. For final probe preparation add 2.55μl 20xSSC and 0.45μl 10%SDS. (for 20x40mm array add: 4.25μl 20xSSC & 0.75μl 10%SDS) 15. Denature probe by heating for 2 min. at 100°C, and incubate at RT for 15-20 min. At this incubation time, wash the prehybridized array and spin dry it at 670 RPM for 3 min. 16. Place the probe (25μl) on the array under a cover slip. Remember to humidify the incubation chamber with one drop of 3xSSC on both ends of the slide. Incubate at 65°C for 14 to 18 hr.

scan_protocol: Genepix 4200A laser scanner (Axon Instruments, Union City, CA). For each array, the photomultiplier tubes (PMT) and power of the laser were adjusted so that the overall count ratio of Cy5 to Cy3 signal was approximately 1. Image analysis was performed using the GenePix 6.0 software (Axon Instruments). Automatic flagging was used to localize absent or very weak spots, which were excluded from further analysis.

data_processing: Expression ratios calculated as Cy5/Cy3 signals was normalized using the “LOWESS” method in the SMA (Statistical Analysis of Macroarrays) package. The significance of the expression ratios of the aged animals in the different stage groups was estimated using the SAM software

organism: Rattus norvegicus

source_name: rat gastrocnemuis muscle adults 4 months

label_protocol:
1. To anneal primer, mix 20-30μg of totalRNA with 2,5μg of anchored oligo-dT primer in a total vol. of 15μl (use DEPC-H2O):
2. Heat to 70°C for 10 min and quickly cool on ice.
3. Add 9,6μl of reaction mixture to each Cy3 reactions:
4. Add 3μl Cy3 (1mM) to each reaction. Keep everything in the dark from this step.
5. Incubate at 42°C for 2 minutes, add 2μl Superscript II enzyme. Incubate for 1 hour, then add another 1μl to the reaction and continue incubation for another 30-60 min.
6. Add 4μl of 500mM EDTA to stop reaction.
1. To anneal primer, mix 20-30μg of totalRNA with 2,5μg of anchored oligo-dT primer in a total vol. of 15μl (use DEPC-H2O):
2. Heat to 70°C for 10 min and quickly cool on ice.
3. Add 9,6μl of reaction mixture to each Cy3 reactions:
4. Add 3μl Cy3 (1mM) to each reaction. Keep everything in the dark from this step.
5. Incubate at 42°C for 2 minutes, add 2μl Superscript II enzyme. Incubate for 1 hour, then add another 1μl to the reaction and continue incubation for another 30-60 min.
6. Add 4μl of 500mM EDTA to stop reaction.
7. Degrade RNA by addition 7,5μl of 1.0M NaOH, and incubation at 65°C for 20min

extract_protocol: Total RNA was isolated from tissues according to Trizol protocol (GibcoBRL, Life Technologies, Täby, Sweden). RNA amount and purity was measured in a spectophotometer (Pharmacia Ultrospec-Plus, Uppsala, Sweden) and by running a denaturing agarose gel. RNA used in real-time PCR experiments were DNAse treated (DNA-free, Ambion Inc., TX) according to the manufacturer’s protocol, resulting in OD 260/280 values above 1.9.

treatment_protocol: adult animals

tag: Strain

value: Sprauge-Dawley

value: Male

source_name: rat gastrocnemuis muscle aged 30 months stage III

label_protocol:
1. To anneal primer, mix 20-30μg of totalRNA with 2,5μg of anchored oligo-dT primer in a total vol. of 15μl (use DEPC-H2O):
2. Heat to 70°C for 10 min and quickly cool on ice.
3. Add 9,6μl of reaction mixture to each Cy5 reactions:
4. Add 3μl Cy5 (1mM) to each reaction. Keep everything in the dark from this step.
5. Incubate at 42°C for 2 minutes, add 2μl Superscript II enzyme. Incubate for 1 hour, then add another 1μl to the reaction and continue incubation for another 30-60 min.
6. Add 4μl of 500mM EDTA to stop reaction.
1. To anneal primer, mix 20-30μg of totalRNA with 2,5μg of anchored oligo-dT primer in a total vol. of 15μl (use DEPC-H2O):
2. Heat to 70°C for 10 min and quickly cool on ice.
3. Add 9,6μl of reaction mixture to each Cy5 reactions:
4. Add 3μl Cy3 (1mM) to each reaction. Keep everything in the dark from this step.
5. Incubate at 42°C for 2 minutes, add 2μl Superscript II enzyme. Incubate for 1 hour, then add another 1μl to the reaction and continue incubation for another 30-60 min.
6. Add 4μl of 500mM EDTA to stop reaction.
7. Degrade RNA by addition 7,5μl of 1.0M NaOH, and incubation at 65°C for 20min

extract_protocol: Total RNA was isolated from tissues according to Trizol protocol (GibcoBRL, Life Technologies, Täby, Sweden). RNA amount and purity was measured in a spectophotometer (Pharmacia Ultrospec-Plus, Uppsala, Sweden) and by running a denaturing agarose gel. RNA used in real-time PCR experiments were DNAse treated (DNA-free, Ambion Inc., TX) according to the manufacturer’s protocol, resulting in OD 260/280 values above 1.9.


title: V240

description:
Simple annotation: gene overexpression, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46866.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 6000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 29.99; Parameter Scan Time = 10:35:31; Parameter PMT Volts = 530; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 60519; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.89; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 29.99; Parameter Scan Time = 10:35:31; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 130081; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: V236

description:
Simple annotation: Cell-line, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46441.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 8080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.51; Parameter Scan Time = 10:57:49; Parameter PMT Volts = 520; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 60415; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.51; Parameter Scan Time = 10:57:49; Parameter PMT Volts = 620; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 129976; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: rat gastrocnemius muscle chip6

source_name: rat gastrocnemius muscle adults 4 months

source_name: rat gastrocnemius muscle aged 30 months stage II


title: rat gastrocnemius muscle chip8

source_name: rat gatrocnemius muscle adults 4 months

source_name: rat gatrocnemius muscle aged 30 months Stage III


title: rat gastrocnemius muscle chip4

source_name: rat gatrocnemius muscle aged 30 months Stage II


title: HMW183

description:
Simple annotation: gene overexpression, Signal transduction
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46863.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 8000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 30.11; Parameter Scan Time = 10:59:15; Parameter PMT Volts = 530; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 60550; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.89; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 30.11; Parameter Scan Time = 10:59:15; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 130111; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong

source_name: Mouse Universal

tag: Mouse Universal


title: HMW238

description:
Simple annotation: Cell-line, FGF pathway
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46443.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 8080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Kenton,,Fong 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 = 34.48; Parameter Scan Time = 11:20:51; Parameter PMT Volts = 520; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 60438; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong 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 = 34.48; Parameter Scan Time = 11:20:51; Parameter PMT Volts = 620; Parameter Scan Date = 2003-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 130000; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Kenton,,Fong


title: rat gastrocnemius muscle chip5

description: dye swapt experiment. values were inverted before further processed


title: rat gastrocnemius muscle chip3

description: Dye swapt run. Values were inverted before further processing.

source_name: rat gastrocnemius of adults 4 months

source_name: rat gastrocnemius muscle aged 30 month stage I

tag: Under these conditions the median survival time is 30 months (plus/minus 2 months across cohorts), and based on this the 30-month-old rats are defined as aged. All aged rats used in this study showed signs of behavioral sensorimotor disturbances, defined by using two parameters as a guide to select a stage, namely

value: (a) is a limb weight bearing? (b) does a limb show a complete gait cycle coordinated with the other limb(s)? The animals were ranked in stage 0-III:Stage 0 animals show no signs of insufficiency concerning these two variables; Stage I animals show some signs, including a lowering of the trunk towards the supportive surface and minor signs of gait cycle aberrations; Stage II animals show clear gait cycle aberrations, often involving a poorer coordination between limbs. Body weight bearing is often clearly incapacitated in at least one limb; Stage III animals show severe gait cycle aberrations, often involving a poorer coordination between limbs. Only minor efforts to initiate a gait cycle may.


title: rat gastrocnemius muscle chip7

tag: Geder

source_name: rat gastrocnemius muscle aged 30 months Stage III


title: rat gastrocnemius muscle chip2

source_name: gatrocnemius muscle adults 4 months

source_name: gastrocnemius muscle aged 30 month stage I


title: rat gastrocnemius muscle chip1

source_name: Rat gatrocnemius muscle adults 4 month

value: SD

tag: Gender Male

source_name: Rat gatrocnemius muscle aged 30 month stage I


title: Retransformed ME-B-T/t cells: breast cancer cell line

city: Berlin

first: Andreas

last: Klein

address: Charitéplatz 1

department: Institute of Biochemistry

country: Germany

institute: Charité (CCO)

description: see: Klein A, Guhl E, Zollinger R, Tzeng YJ, Wessel R, Hummel M, Graessmann M, Graessmann A. Gene expression profiling: cell cycle deregulation and aneuploidy do not cause breast cancer formation in WAP-SVT/t transgenic animals. J Mol Med. 2005 May;83(5):362-76.

hyb_protocol: The Affymetrix GeneChip was hybridized with the biotin-labelled cRNA fragments for 16 hr at 45°C. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.

scan_protocol: Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.

data_processing: The raw experimental microarray data were normalized with the Affymetrix Microarray Suite (MAS 5.0) based on the housekeeping gene method. Further analyses were performed with the software CorrXpression.

source_name: breast cancer cell line

label_protocol: The dsDNA was in vitro transcribed into biotinylated cRNA by RNA Transcript labeling Kit (Enzo Life Sciences, Inc).

extract_protocol: RNA was isolated from mammary gland tissue segments stored in liquid nitrogen. The frozen tissue segments were ground to a fine powder using a liquid nitrogen chilled mortar and pestle. Total RNA was extracted with RNAzol reagent in accordance with the manufacturer’s protocol (PeQLab, Biotechnology), and the isolated RNA was treated with RNasefree DNase (DNA-free Ambion, Austin, Tex., USA). The integrity of RNA was verified with the Agilent Bioanalyzer (Agilent Technologies) by the presence of prominent 28S and 18S bands on agarose gels and an A260/280 ratio in the range of 1.9–2.1.

tag: The revertant-ME-B cells were again reconverted into tumor cells by SV40 T/t. The pSVT/t DNA construct was transfected into revertant-ME-B cells and SV40 T/t-antigen positive cell clones were G418 selected. These clones were collected and designated as retransformed ME-B-T/t cells. The ME-B-T/t cells regained the morphology and growth characteristic of breast cancer cells.


title: Revertant ME-B cells: breast cancer cell line

tag: Small tissue segments from the 583 tumor 1 were isolated and used to establish the revertant ME-B cells. These cells show (in contrast to the ME-A cells) a downregulation of the WAP-SVT/t gene expression. These cells, that were formerly of tumor origin regain the morphology and growth characteristic of non-tumor cells. This transition occurs mostly within the first days after plating under standard tissue culture conditions (DME-medium, 10% FCS).


title: EPO  donor 1

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53412.gif
Compound Based Treatment: 1

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:53:19; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-27; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:53:19; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-27; Performer: Einar Andreas,,Sivertsen

source_name: Amplified Universal Human Reference RNA (Stratagene)

source_name: Amplified RNA from early erythroid progenitors stimulated with EPO


title: Medium donor 2

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53455.gif
Compound Based Treatment: 0

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:31:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-30; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:31:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-30; Performer: Einar Andreas,,Sivertsen

tag: Amplified Universal Human Reference RNA (Stratagene)

source_name: Amplified RNA from early erythroid progenitors cultured in medium


title: LY  donor 1

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53392.gif
Compound Based Treatment: 0

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:47:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:47:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; Performer: Einar Andreas,,Sivertsen

source_name: Amplified RNA from early erythroid progenitors stimulated with LY


title: Medium donor 3

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53457.gif
Compound Based Treatment: 0

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:20:40; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:20:40; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen

tag: Amplified RNA from early erythroid progenitors cultured in medium


title: ME-A cells: breast cancer cell line

tag: Small tissue segments from the 583 tumor 1 were isolated and used to establish the ME-A cells. These cells show continuous T/t-antigen synthesis and are permanently T/t-antigen positive. They exhibit the morphology and growth characteristics of tumor cells.


title: Case_8_2004090139

status: Public on Nov 08 2006

type: genomic

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Comparison between individual with Gastrointestinal stromal tumor (GIST) vs normal individual

hyb_protocol: Probe preparation and preblocking of the slide were performed as described by Fiegler et al. (2003). Equal amounts (200 pmol) of Cy5- and Cy3-labeled probe were combined with 100 ug Cot-1 DNA followed by an ethanol precipitation. Resuspension of the pellet was done in hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween 20, 2 x SSC, and 10 mM Tris HCl, pH 7.5) containing 400 ug yeast tRNA to hybridize a spotting area of 24 x 60 mm.  The slide was blocked with 50 ug Cot-1 DNA and 300 ug salmon sperm DNA dissolved in 60 ul hybridization buffer. Blocking solution and probe mixture were denaturated for 10 min in a water bath at 75C. Blocking solution was then placed on the slide covered with a coverslip (24 x 60 mm) and placed in a humid chamber. Meanwhile, the probe was placed at 37C for preannealing. After 1 hr of blocking, the coverslip was removed and probe was placed on the slide. After placing a coverslip (24 x 60 mm), the slide was placed in a humid chamber saturated with 20% formamide and 2 x SSC. Hybridization was allowed to take place for two nights at 37C. Posthybridization washes were performed as described by Fiegler et al. (2003). The coverslip was removed by placing the slide in PBS with 0.05% Tween 20, followed by a 10- min wash in a fresh solution of PBS/Tween 20 at room temperature, 30 min in 50% formamide/2 x SSC at 42C, and 10 min in PBS/0.05% Tween 20 at room temperature. Slides were spin dried at 1000 rpm for 5 min. See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

scan_protocol: Array slides were scanned with a GenePix 4000B scanner and hybridization signals were evaluated using GenePixPro 3.0 image analysis software.

data_processing: All data analysis was performed with Excel. Spot intensities were corrected for local background, and only spots with signal intensities at least two fold above background signal intensities were included in the final analysis. For each clone, a ratio of Cy5 to Cy3 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of the autosomes followed by the 2D normalization. Normalized ratios of the duplicates were averaged and a log2 value was calculated. Precise localizations of clones spotted on the array were obtained from the Ensemble database (www.ensembl.org/Homo_sapiens). The Normalized ratio is not included  in the submitted raw data.

molecule: genomic DNA

source_name: 48/F Stomach

label_protocol: The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy5-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

extract_protocol: Genomic DNA was extracted from a frozen fragment of the tumor, using a microdissection technique to reduce contamination with non-neoplastic tissue. DNA was extracted using a standard proteinase K digestion followed by phenol/chloroform extraction and ethanol precipitation.

tag: Age

value: 48, Gender:female, tissue :stomach

source_name: control DNA

label_protocol: The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy3-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

extract_protocol: Genomic DNA was isolated from lymphocytes of normal individuals.

tag: normal individual, Tissue

value: lymphocyte


title: LY donor 3

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53415.gif
Compound Based Treatment: 0

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:29:49; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:29:49; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen

tag: Amplified RNA from early erythroid progenitors stimulated with LY


title: Case_66_2004121327

source_name: 72/F Duodenum

value: 72, Gender:female, tissue :Duodenum


title: EPO+LY donor 1

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53454.gif
Compound Based Treatment: 1

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:44:31; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-27; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:44:31; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-27; Performer: Einar Andreas,,Sivertsen

source_name: Amplified RNA from early erythroid progenitors stimulated with EPO and LY


title: EPO donor 3

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53416.gif
Compound Based Treatment: 1

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:38:51; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:38:51; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen

tag: Amplified RNA from early erythroid progenitors stimulated with EPO


title: LY donor 2

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53456.gif
Compound Based Treatment: 0

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:22:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-30; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:22:24; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-04-30; Performer: Einar Andreas,,Sivertsen


title: Case_9_2004121332

source_name: 64/M Stomach

value: 64, Gender:male, tissue :stomach


title: Case_6_2004070116

scan_protocol: Array slides were scanned with an Agilent G2565 scanner and hybridisation signals were evaluated using Array Vision V7 image analysis software.

source_name: 51/M Stomach

value: 51, Gender:male, tissue :stomach


title: Case_63_2004070151

source_name: 74/M Stomach

value: 74, Gender:male, tissue :stomach


title: Case_63_2004070150


title: Case_6_2004070117


title: EPO+LY donor 2

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53453.gif
Compound Based Treatment: 1

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:37:48; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:37:48; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; Performer: Einar Andreas,,Sivertsen

tag: Amplified RNA from early erythroid progenitors stimulated with EPO and LY


title: Case_62_2004090155

source_name: 47/F Duodenum

value: 47, Gender:female, tissue :duodenum


title: Case_7_2004090138

source_name: 67/F Omentum

value: 67, Gender:female, tissue :omentum


title: EPO donor 2

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53452.gif
Compound Based Treatment: 1

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:28:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:28:03; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-12; Performer: Einar Andreas,,Sivertsen


title: Case_55_2005061522

source_name: 59/M Small intestin

value: 59, Gender:male, tissue :small intestin


title: Case_56_2004121311

source_name: 53/F Stomach

value: 53, Gender:female, tissue :stomach


title: Case_60_2004121339

source_name: 61/F Stomach

value: 61, Gender:female, tissue :Stomach


title: Case_57_2004121349

source_name: 75/M Stomach

value: 75, Gender:male, tissue :stomach


title: Case_55_2005061521


title: Case_53_2004121325

source_name: 65/F Stomach

value: 65, Gender:female, tissue:Stomach


title: Case_55_2004121321


title: Case_54_2004121331

source_name: 69/F Stomach

value: 69, Gender:female, tissue :Stomach


title: Case_45_2005061515

source_name: 46/F small intestin

value: 46, Gender:female, tissue :small intestin


title: Case_5_2004070112

source_name: 62/M Stomach

value: 62, Gender:male, tissue :stomach


title: Case_5_2004070111


title: Case_51_2004121350


title: Case_43_2005090104

source_name: 49/F Mesent.

value: 49, Gender:female, tissue :Mesent.


title: Case_43_2005090105

source_name: control DNA


title: Case_48_2004070166

source_name: 68/F duodenum

value: 68, Gender:female, tissue :duodenum


title: Case_48_2004070165

value: lymphocyte


title: Case_50_2004121319

source_name: 66/F Stomach

value: 66, Gender:female, tissue :stomach


title: Case_33_2005090106

source_name: 82/F Stomach

value: 82, Gender:female, tissue :stomach


title: Case_35_2005061512

source_name: 44/F Stomach

value: 44, Gender:female, tissue :stomach


title: Case_45_2004062310


title: Case_45_2004062311


title: Case_33_2005061519