title: N4_b: uninfected+IFNg 4h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67656.gif
Infection: None
Measurement: time(absolute) 4 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1800, 7160; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 38.25; Parameter Scan Time = 11:37:56; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 49657; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 38.25; Parameter Scan Time = 11:37:56; Parameter PMT Volts = 770; Parameter Scan Date = 2006-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 122792; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: 250 ng universal reference cDNA

tag: 250 ng universal reference cDNA

source_name: N4_b: uninfected+IFNg 4h

tag: 300 ng sample cDNA


title: Basal epidermal cells (+/+) -UVB (3) vs. Reference

status: Public on Jul 19 2007

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50216.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 8160; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.70; Parameter Scan Time = 13:11:19; Parameter PMT Volts = 570; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 171501; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.34; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.70; Parameter Scan Time = 13:11:19; Parameter PMT Volts = 710; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 170498; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.24; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

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

molecule: total RNA

organism: Mus musculus

source_name: Reference (brain, liver, neonate, whole dorsal skin) (20ug)

label_protocol: not provided

extract_protocol: not provided

source_name: Basal epidermal cells (+/+) -UVB (3) (20ug)


title: Basal epidermal cells (KitW-v/KitW-v) +UVB (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50232.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 8000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 40.99; Parameter Scan Time = 14:54:47; Parameter PMT Volts = 600; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171850; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.36; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 40.99; Parameter Scan Time = 14:54:47; Parameter PMT Volts = 760; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170847; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.27; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

tag: Reference (brain, liver, neonate, whole dorsal skin) (20ug)

source_name: Basal epidermal cells (KitW-v/KitW-v) +UVB (1) (20ug)


title: Basal epidermal cells (+/+) -UVB (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50214.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 8520; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.42; Parameter Scan Time = 12:50:56; Parameter PMT Volts = 570; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 171480; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.28; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.42; Parameter Scan Time = 12:50:56; Parameter PMT Volts = 720; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 170478; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.23; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (+/+) -UVB (2) (20ug)


title: Basal epidermal cells (+/+) +UVB (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50223.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 7920; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.89; Parameter Scan Time = 12:05:14; Parameter PMT Volts = 590; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171680; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.35; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.89; Parameter Scan Time = 12:05:14; Parameter PMT Volts = 710; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170678; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.24; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (+/+) +UVB (1) (20ug)


title: N0_a: uninfected+IFNg 0h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67608.gif
Infection: None
Measurement: time(absolute) 0 h
Measurement: concentration(absolute) IFNg, 0 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 6680; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.26; Parameter Scan Time = 10:31:56; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-15; Parameter Pixel Size = 10; Parameter Laser on time = 49459; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.26; Parameter Scan Time = 10:31:56; Parameter PMT Volts = 760; Parameter Scan Date = 2006-03-15; Parameter Pixel Size = 10; Parameter Laser on time = 122594; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

organism: Homo sapiens

source_name: 250 ng reference cDNA

tag: 250 ng reference cDNA

source_name: N0_a: uninfected+IFNg 0h


title: P2_b: infected+IFNg 2h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67650.gif
Infection: Toxoplasma
Measurement: time(absolute) 2 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 6520; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.36; Parameter Scan Time = 11:08:52; Parameter PMT Volts = 650; Parameter Scan Date = 2006-03-13; Parameter Pixel Size = 10; Parameter Laser on time = 49375; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.36; Parameter Scan Time = 11:08:52; Parameter PMT Volts = 800; Parameter Scan Date = 2006-03-13; Parameter Pixel Size = 10; Parameter Laser on time = 122510; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.27; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: universal reference cDNA 250 ng

tag: universal reference cDNA 250 ng

source_name: P2_b: infected+IFNg 2h

tag: sample cDNA 300 ng


title: N2_b: uninfected+IFNg 2h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67654.gif
Infection: None
Measurement: time(absolute) 2 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1840, 7040; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.75; Parameter Scan Time = 10:52:16; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 49610; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.75; Parameter Scan Time = 10:52:16; Parameter PMT Volts = 710; Parameter Scan Date = 2006-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 122745; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: N2_b: uninfected+IFNg 2h


title: N4_a: uninfected+IFNg 4h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68112.gif
Infection: None
Measurement: time(absolute) 4 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1640, 5800; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.92; Parameter Scan Time = 11:15:10; Parameter PMT Volts = 690; Parameter Scan Date = 2006-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 50318; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.92; Parameter Scan Time = 11:15:10; Parameter PMT Volts = 770; Parameter Scan Date = 2006-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 123453; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: N4_a: uninfected+IFNg 4h


title: N8_b: uninfected+IFNg 8h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67609.gif
Infection: None
Measurement: time(absolute) 8 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 7080; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.48; Parameter Scan Time = 10:55:03; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-15; Parameter Pixel Size = 10; Parameter Laser on time = 49481; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.20; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.48; Parameter Scan Time = 10:55:03; Parameter PMT Volts = 760; Parameter Scan Date = 2006-03-15; Parameter Pixel Size = 10; Parameter Laser on time = 122616; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.07; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: N8_b: uninfected+IFNg 8h


title: P0_b: infected+IFNg 0h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67649.gif
Infection: Toxoplasma
Measurement: time(absolute) 0 h
Measurement: concentration(absolute) IFNg, 0 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 7520; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.54; Parameter Scan Time = 11:21:35; Parameter PMT Volts = 650; Parameter Scan Date = 2006-03-13; Parameter Pixel Size = 10; Parameter Laser on time = 49387; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.54; Parameter Scan Time = 11:21:35; Parameter PMT Volts = 800; Parameter Scan Date = 2006-03-13; Parameter Pixel Size = 10; Parameter Laser on time = 122522; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.26; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: P0_b: infected+IFNg 0h


title: Basal epidermal cells (Mc1re/Mc1re) +UVB (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50228.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 8120; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 40.48; Parameter Scan Time = 13:32:18; Parameter PMT Volts = 590; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171766; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 40.48; Parameter Scan Time = 13:32:18; Parameter PMT Volts = 690; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170764; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.25; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (Mc1re/Mc1re) +UVB (3) (20ug)


title: N2 (red, channel 2) vs. lin-14 (n179ts) (green, channel 1)-repeat #2

description:
Simple annotation: Development, lin-14
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2033.gif

scan_protocol: not provided

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

organism: Caenorhabditis elegans

source_name: lin-14 (n179ts) (green)

tag: lin-14 (n179ts) (green)

source_name: N2 (red)

tag: N2 (red)


title: Basal epidermal cells (KitW-v/KitW-v) -UVB (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51888.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 7800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Craig,,April Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.64; Parameter Scan Time = 11:29:11; Parameter PMT Volts = 590; Parameter Scan Date = 2004-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 179269; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.08; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Craig,,April Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.64; Parameter Scan Time = 11:29:11; Parameter PMT Volts = 710; Parameter Scan Date = 2004-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 178495; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.20; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (KitW-v/KitW-v) -UVB (2) (20ug)


title: P4_a: infected+IFNg 4h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/68113.gif
Infection: Toxoplasma
Measurement: time(absolute) 4 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1640, 6600; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.15; Parameter Scan Time = 11:31:28; Parameter PMT Volts = 690; Parameter Scan Date = 2006-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 50334; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.29; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.15; Parameter Scan Time = 11:31:28; Parameter PMT Volts = 760; Parameter Scan Date = 2006-04-19; Parameter Pixel Size = 10; Parameter Laser on time = 123469; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: P4_a: infected+IFNg 4h


title: Basal epidermal cells (Mc1re/Mc1re) -UVB (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50219.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 7840; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 40.26; Parameter Scan Time = 13:55:23; Parameter PMT Volts = 570; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 171544; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 40.26; Parameter Scan Time = 13:55:23; Parameter PMT Volts = 700; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 170541; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.25; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Reference (brain, liver, neonate, whole dorsal skin) (20ug)

source_name: Basal epidermal cells (Mc1re/Mc1re) -UVB (3) (20ug)


title: Basal epidermal cells (KitW-v/KitW-v) -UVB (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51889.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 7720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Craig,,April Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.86; Parameter Scan Time = 11:42:26; Parameter PMT Volts = 590; Parameter Scan Date = 2004-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 179281; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Craig,,April Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.86; Parameter Scan Time = 11:42:26; Parameter PMT Volts = 710; Parameter Scan Date = 2004-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 178508; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.21; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (KitW-v/KitW-v) -UVB (3) (20ug)


title: N8_a: uninfected+IFNg 8h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67668.gif
Infection: None
Measurement: time(absolute) 8 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 6840; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.97; Parameter Scan Time = 11:10:52; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 49629; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.97; Parameter Scan Time = 11:10:52; Parameter PMT Volts = 710; Parameter Scan Date = 2006-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 122764; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.26; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: 250 ng universal reference cDNA

source_name: N8_a: uninfected+IFNg 8h


title: P8_a: infected+IFNg 8h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67652.gif
Infection: Toxoplasma
Measurement: time(absolute) 8 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 6680; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.08; Parameter Scan Time = 10:44:27; Parameter PMT Volts = 680; Parameter Scan Date = 2006-03-13; Parameter Pixel Size = 10; Parameter Laser on time = 49347; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.08; Parameter Scan Time = 10:44:27; Parameter PMT Volts = 780; Parameter Scan Date = 2006-03-13; Parameter Pixel Size = 10; Parameter Laser on time = 122482; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: P8_a: infected+IFNg 8h


title: Basal epidermal cells (KitW-v/KitW-v) -UVB (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/51886.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 7920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Craig,,April Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.31; Parameter Scan Time = 11:09:20; Parameter PMT Volts = 590; Parameter Scan Date = 2004-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 179246; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.95; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Craig,,April Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.31; Parameter Scan Time = 11:09:20; Parameter PMT Volts = 740; Parameter Scan Date = 2004-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 178472; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.20; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (KitW-v/KitW-v) -UVB (1) (20ug)


title: P2_a: infected+IFNg 2hr

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67607.gif
Infection: Toxoplasma
Measurement: time(absolute) 2 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 5920; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.72; Parameter Scan Time = 10:39:50; Parameter PMT Volts = 610; Parameter Scan Date = 2006-03-09; Parameter Pixel Size = 10; Parameter Laser on time = 49279; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.73; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.72; Parameter Scan Time = 10:39:50; Parameter PMT Volts = 720; Parameter Scan Date = 2006-03-09; Parameter Pixel Size = 10; Parameter Laser on time = 122414; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.80; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: P2_a: infected+IFNg 2hr


title: Basal epidermal cells (+/+) -UVB (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50213.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 8120; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.22; Parameter Scan Time = 12:35:35; Parameter PMT Volts = 530; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 171465; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.22; Parameter Scan Time = 12:35:35; Parameter PMT Volts = 750; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 170462; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.23; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (+/+) -UVB (1) (20ug)


title: Basal epidermal cells (Mc1re/Mc1re) +UVB (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50227.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 7720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 40.44; Parameter Scan Time = 13:20:09; Parameter PMT Volts = 590; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171754; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 40.44; Parameter Scan Time = 13:20:09; Parameter PMT Volts = 690; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170751; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.25; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (Mc1re/Mc1re) +UVB (2) (20ug)


title: N0_b: uninfected+IFNg 0h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67669.gif
Infection: None
Measurement: time(absolute) 0 h
Measurement: concentration(absolute) IFNg, 0 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 7160; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.60; Parameter Scan Time = 10:39:18; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 49597; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.60; Parameter Scan Time = 10:39:18; Parameter PMT Volts = 710; Parameter Scan Date = 2006-03-16; Parameter Pixel Size = 10; Parameter Laser on time = 122732; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: 250 ng reference cDNA

source_name: N0_b: uninfected+IFNg 0h


title: N2 (red, channel 2) vs. lin-14 (n179ts) (green, channel 1)- repeat #1

description:
Simple annotation: Development, lin-14
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2125.gif


title: N2_a: uninfected+IFNg 2h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67605.gif
Infection: None
Measurement: time(absolute) 2 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 6200; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 11:08:03; Parameter PMT Volts = 610; Parameter Scan Date = 2006-03-09; Parameter Pixel Size = 10; Parameter Laser on time = 49307; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.82; Parameter Scan Time = 11:08:03; Parameter PMT Volts = 720; Parameter Scan Date = 2006-03-09; Parameter Pixel Size = 10; Parameter Laser on time = 122442; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.84; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: N2_a: uninfected+IFNg 2h


title: Basal epidermal cells (Mc1re/Mc1re) -UVB (2) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50218.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 8360; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 40.09; Parameter Scan Time = 13:38:37; Parameter PMT Volts = 570; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 171527; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 40.09; Parameter Scan Time = 13:38:37; Parameter PMT Volts = 740; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 170525; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.24; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (Mc1re/Mc1re) -UVB (2) (20ug)


title: N2 (red, channel 2) vs. lin-14 (n179ts) (green, channel 1)

description:
Simple annotation: Development, lin-14
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2124.gif

source_name: lin-14 (n179ts) (green)

source_name: N2 (red)


title: Group 4 PEITC + NMBA treated, pool # EP 18 vs. reference pool

status: Public on Jul 18 2007

city: Columbus

first: Gary

middle: D

last: Stoner

state: OH

address: 2001 Polaris Pkwy

department: The Ohio State University

institute: Department of Internal Medicine

description: Barcode: 251316210195

hyb_protocol: Agilent 60-mer Oligo Microarray Processing Protocol Version 4.1 using the Agilent In situ Hybridization Kit. In the hybridization reaction 0.75 ug of Cyanine 3 labeled cRNA and 0.75 ug of Cyanine 5 labeled cRNA were mixed together and allowed to co-hybridize on an Agilent Rat Whole Genome Oligo Microarray (44K) for 17 hours at 60°C. Slide was washed and dried according to Agilent's 60-mer Oligo microarray processing protocol for SSC wash.

scan_protocol: Slides were scanned with an Agilent dual laser scanner. PMT settings were set at 100% for both channels.

data_processing: Tiff images were analyzed using Agilent’s feature extraction software (version 7.5) to obtain fluorescent intensities for each spot on the array. Local background subtraction was performed. Linear&LOWESS normalization was performed on the intensity values.

label: Cyanine 3

organism: Rattus norvegicus

source_name: Stratagene Rat reference RNA

label_protocol: Agilent Low Input Fluorescent Linear Amplification Kit, Protocol Version 2.0.

treatment_protocol: Untreated reference pool.

tag: Commercial reference RNA standard, Stratagene.

label: Cyanine 5

source_name: Rat Esophagus, Group 4 PEITC + NMBA  treated, pool # EP 18

extract_protocol: RNA extraction. Total cellular RNA was isolated from frozen tissue using TRIzol reagent (Life Technologies, Gaithersburg, MD), according to the manufacture’s instructions, and cleaned using RNeasy Mini kit (Qiagen, Valencia, CA). The integrity of the RNA samples was checked by resolving the total RNA on an agarose gel and visualizing the 18S and 28S ribosomal bands after staining the gel with ethidium bromide. Samples were aliquoted and frozen at -80C. Further quality control check of total RNA from each biological sample was made using an Agilent 2100 Bioanalyzer and the 6000 Nano Assay kit (Agilent Technologies, Palo Alto, CA), and analyzed for purity using a spectrophotometer; a 260/280 ratio in the range of 1.9-2.2 was considered acceptable. Samples having apparent degradation were excluded from the study.

treatment_protocol: Rats were randomized into four experimental groups of nine animals each. Rats in Groups 1 and 3 were placed on control AIN-76A diet and those in Groups 2 and 4 were given AIN-76A diet plus 5µmole PEITC. During the third week of dietary treatment, Group 1 (Vehicle-control) and Group 2 (PEITC-control) rats each received 3 s.c. injections of 20% DMSO in water (the vehicle for NMBA). During the same week, Group 3 (NMBA-control) and Group 4 (PEITC+NMBA) rats were given 3 s.c. injections of NMBA (0.5 mg/kg b.w.). All rats were sacrificed 24h after the last NMBA treatment, and their esophagi excised, opened longitudinally, and sectioned into two parts. One part was stripped of the submucosal and muscularis layers, added to 1 ml of TRIzol solution, quick frozen in liquid nitrogen, and stored at minus 80C until extraction of RNA.

tag: 4-5 week old male Fischer-344 rats (F344)


title: P8_b: infected+IFNg 8h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67611.gif
Infection: Toxoplasma
Measurement: time(absolute) 8 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 7160; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.70; Parameter Scan Time = 11:18:41; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-15; Parameter Pixel Size = 10; Parameter Laser on time = 49506; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.70; Parameter Scan Time = 11:18:41; Parameter PMT Volts = 760; Parameter Scan Date = 2006-03-15; Parameter Pixel Size = 10; Parameter Laser on time = 122641; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: P8_b: infected+IFNg 8h


title: Group 2 PEITC treated, EP#15 vs. reference pool

description: Barcode: 251316210185

source_name: Rat Esophagus, Group 2 PEITC treated pool # EP15


title: Group 1 Control Untreated pool # EP3 vs. reference pool

description: Barcode: 251316210241

source_name: Rat Esophagus, Group 1 Control  pool # EP3


title: Basal epidermal cells (Mc1re/Mc1re) +UVB (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50226.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 8560; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 40.39; Parameter Scan Time = 13:05:13; Parameter PMT Volts = 590; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171739; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 40.39; Parameter Scan Time = 13:05:13; Parameter PMT Volts = 690; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170737; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.25; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Reference (brain, liver, neonate, whole dorsal skin) (20ug)

source_name: Basal epidermal cells (Mc1re/Mc1re) +UVB (1) (20ug)


title: Group 2 PEITC treated, pool #EP13 vs. reference pool

description: Barcode: 251316210183

source_name: Rat Esophagus, Group 2 PEITC treated, pool #EP13


title: Basal epidermal cells (Mc1re/Mc1re) -UVB (1) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50217.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 8400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.90; Parameter Scan Time = 13:24:31; Parameter PMT Volts = 570; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 171514; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.90; Parameter Scan Time = 13:24:31; Parameter PMT Volts = 720; Parameter Scan Date = 2004-01-17; Parameter Pixel Size = 10; Parameter Laser on time = 170511; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.24; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Basal epidermal cells (Mc1re/Mc1re) -UVB (1) (20ug)


title: P0_a: Infected+IFNg 0h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67606.gif
Infection: Toxoplasma
Measurement: time(absolute) 0 h
Measurement: concentration(absolute) IFNg, 0 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1840, 6000; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.87; Parameter Scan Time = 11:19:38; Parameter PMT Volts = 610; Parameter Scan Date = 2006-03-09; Parameter Pixel Size = 10; Parameter Laser on time = 49319; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.87; Parameter Scan Time = 11:19:38; Parameter PMT Volts = 720; Parameter Scan Date = 2006-03-09; Parameter Pixel Size = 10; Parameter Laser on time = 122454; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.97; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: 250 ng universal reference cDNA

source_name: P0_a: Infected+IFNg 0h


title: Group 4 PEITC + NMBA  treated, pool # EP 16 vs. reference pool

description: Barcode: 251316210193

source_name: Rat Esophagus, Group 4 PEITC + NMBA  treated, pool # EP 16


title: Group 3 NMBA treated, pool #EP4 vs. reference pool

description: Barcode: 251316210242

source_name: Rat Esophagus, Group 3 NMBA treated, pool #EP4


title: Group 1 Control Untreated, pool #EP1 vs. reference pool

description: Barcode: 251316210236

source_name: Rat Esophagus, Group 1 CONTROL treated, pool #EP1


title: 9a5ccy5 x Fb7cy3-Replica 1

type: genomic

city: Santo André

first: Luiz

middle: R.

last: Nunes

state: SP

address: Rua Santa Adélia 166

department: Centro de Ciências Naturais e Humanas

country: Brazil

institute: UFABC - Universidade Federal do ABC

description: This hybridization is part of an experiment aimed at performing comparative genomic analyses among different isolates of Xylella fastidiosa

hyb_protocol: Labelled DNAs were mixed, dried in a Savant speed vacuum and resuspended in 100 ul of 1X Hybridization buffer, containing 6X SSC, 5X Denhardts solution, 0,25 mg/ml salmon sperm DNA, 0,01% SDS´and 50% formamide. Arrays were hybridized overnight (42oC) in a Gene-Tac Hybridization Station (Genomic Solutions, Inc., Ann Arbor, MI) and washed twice (42oC) in 0.5 X SSC, 0.01 % SDS, followed by two washes in 0.06 X SSC, 0.01 % SDS and two final washes in 0.06 X SSC. All washing steps consisted of 1 min of flow, followed by 5 min of incubation. Slides were then dried and subjected to fluorescent detection

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

data_processing: Hybridized arrays were scanned in an Affymetrix 418 Array Scanner and images were analyzed with Affymetrix Jaguar v 2.0. Quality control of the hybridized spots was automatically performed by the software, based on spot morphology and local signal-to-background ratio, using the Easy Threshold and Variable Circle Size Algorithms. In all experiments, reliable hybridization signals could be obtained for more than 90% of the arrayed probes. Normalization between the intensities in the two channels was achieved with the Jaguar Control Spots option, using a list of 30 control ORFs that shared sequence identity in the genomes of strains 9a5c and Temecula-1.

molecule: genomic DNA

organism: Xylella fastidiosa

source_name: Xylella fastidiosa Fb7 cells grown in PW medium

label_protocol: DNA labelling was performed as described by: Behr, M.A., Wilson, M.A., Gill, W.P., Salamon, H., Schoolnik, G.K., Rane, S. and Small, P.M. (1999) Comparative genomics of BCG vaccines by whole-genome DNA Microarray. Science 284, 1520-1523.

growth_protocol: Bacteria have been recovered from -70oC glycerol stocks and inoculated onto PW agar plates. Plates were maintained for 10 days at 28oC. The colonies were transferred once to new plates containing the same medium, grown for 20 days and harvested for DNA extraction

extract_protocol: Total genomic DNA was extracted according to : Dungan, D. (1989) in: Current Protocols in Molecular Biology (Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. and Struhl, K., Eds.), pp. 241-242. John Wiley and Sons, New York.

tag: Total DNA from Xylella fastidiosa (isolate Fb7), grown on solid PW medium

source_name: Xylella fastidiosa 9a5c cells grown in PW medium

tag: Total DNA from Xylella fastidiosa (isolate 9a5c), grown on solid PW medium


title: 9a5ccy5 x Fb7cy3-Replica 2

treatment_protocol: Bacteria have been recovered from -70oC glycerol stocks and inoculated onto PW agar plates. Plates were maintained for 10 days at 28oC. The colonies were transferred once to new plates containing the same medium, grown for 20 days and harvested for DNA extraction


title: Group 3 NMBA treated, pool # EP6 vs. reference pool

description: Barcode: 251316210198

source_name: Rat Esophagus, Group 3 NMBA treated, pool # EP6


title: Group 4 PEITC + NMBA  treated, pool # EP 17 vs. reference pool

source_name: Stratagene Rat reference RNA

source_name: Rat Esophagus, Group 4 PEITC + NMBA  treated, pool # EP 17


title: Group 3 NMBA treated, pool #EP5 vs. reference pool

source_name: Rat Esophagus, Group 3 NMBA treated, pool #EP5


title: Group 1 Control Untreated, pool #EP2 vs. reference pool

description: Barcode: 251316210240

tag: Commercial reference RNA standard, Stratagene

source_name: Rat Esophagus, Group 1 CONTROL treated, pool #EP2


title: 9a5ccy3 x Cv21cy5-Replica 2

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 80% PMT gain

source_name: Xylella fastidiosa Cv21 cells grown in PW medium

tag: Total DNA from Xylella fastidiosa (isolate Cv21), grown on solid PW medium


title: 9a5ccy5 x CV21cy3-Replica 2

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 70% PMT gain Cy5 channel was scanned at 100% laser power and 70% PMT gain


title: 9a5ccy5 x Cv21cy3-Replica 1


title: 9a5ccy3 x Fb7cy5-Replica 1


title: 9a5ccy3 x Cv21cy5-Replica 1


title: 9a5ccy5 x 9.12ccy3-Replica 2

source_name: Xylella fastidiosa 9.12c cells grown in PW medium

tag: Total DNA from Xylella fastidiosa (isolate 9.12c), grown on solid PW medium


title: Group 2 PEITC treated, pool #EP 14 vs. reference pool

description: Barcode: 251316210184

source_name: Rat Esophagus, Group 2  PEITC treated, pool #EP 14


title: 9a5ccy5 x 9.12ccy3-Replica 1


title: Basal epidermal cells (KitW-v/KitW-v) +UVB (3) vs. Reference

description:
Simple annotation: Pigmentation, Skin
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50234.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 8080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Craig,,April 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 = 41.11; Parameter Scan Time = 15:30:54; Parameter PMT Volts = 560; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 171886; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.36; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Craig,,April 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 = 41.11; Parameter Scan Time = 15:30:54; Parameter PMT Volts = 780; Parameter Scan Date = 2004-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 170883; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.28; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Craig,,April

source_name: Reference (brain, liver, neonate, whole dorsal skin) (20ug)

source_name: Basal epidermal cells (KitW-v/KitW-v) +UVB (3) (20ug)


title: HeLa transfected with miR181a duplex versus control transfected HeLa, 12 hours

city: Seattle

first: Lee

last: Lim

state: WA

institute: Rosetta Inpharmatics

description: Transfection of miRNA duplexes into cell lines as described in Grimson et al., Molecular Cell, 2007

hyb_protocol: Hybridization to Agilent microarrays as described in Hughes et al, Nature Biotechnology (2001), 19(4):342-7.

scan_protocol: Agilent LP2 laser scanner

data_processing: Error model as described in Hughes et al and in US patent #6,351,712

source_name: Mock transfected HeLa, 24 hours

label_protocol: Customized Ambion MessageAmp II

extract_protocol: Qiagen RNAeasy

tag: Mock transfected HeLa, 24 hours

source_name: HeLa transfected with miR181a duplex, 24 hours


title: HeLa transfected with miR181a duplex versus control transfected HeLa, 24 hours

tag: HeLa transfected with miR181a duplex, 24 hours


title: Restore-Cy5 vs WT-Cy3-2

city: Buffalo

first: Wansheng

last: Li

state: NY

address: 3435 main st.

department: Oral Biology

institute: University at Buffalo

description: Candida albicans restoration strain by restoring one copy of TRK1 gene of the mutant strain compared to wild-type strain

hyb_protocol: The appropriate Cy3-cDNA and Cy5-cDNA samples were then mixed and heated for 2 min at 100°C before application to the microarray slide. Samples were hybridized for 20 h at 42°C, and the slides washed, dried, and scanned.

scan_protocol: As described in the the manufacturer's instructions of GenePix 4000A scanner (Axon Instruments).

data_processing: Slides have been scanned by Axon scanner 4000A and image analysis analyzed by GenePix Version 3.0. Post analysis was performed using TIGR microarray software suite(http://www.tm4.org). ExprConverter v1.7 to transform GPR format to Mev file, Midias 2.19 to normalize the data, and Mev4.0 to do statistical analysis. The VALUE column is the log2 based expression level after background correction, total intensity normaliztion,Lowess normalization. if VALUE=null, then this spot was bad.

organism: Candida albicans

source_name: Candida albicans wild-type strain

label_protocol: The dried cDNA was coupled with fluorescent dyes Cy3 dye (GE Healthcare) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a SpeedVac. The labeled cDNA samples were resuspended in a solution containing 50 % formamide, 10x SSC, and 0.2% SDS.

growth_protocol: Cells were grown overnight in 10 ml of YNB medium, 2% glucose with the addition of uridine when required.

extract_protocol: cDNA was synthesized from total RNA samples using Superscript II RT (Invitrogen) in reaction mixtures containing 0.5 mM deoxynucleoside triphosphates (aminoallyl-dUTP and deoxynucleoside triphosphates). After cDNA synthesis, RNA was hydrolyzed with 1 M NaOH and 0.5 M EDTA, followed by neutralization with 1 M HCl. The cDNA was purified using the Qiagen QIAquick PCR purification kit and dried by SpeedVac.

tag: Candida albicans wild-type strain

label_protocol: The dried cDNA was coupled with fluorescent dyes Cy5 dye (GE Healthcare) for 1 h at room temperature in the dark. Unincorporated dye was removed using a Qiagen QIAquick PCR purification kit, and the samples were dried in a SpeedVac. The labeled cDNA samples were resuspended in a solution containing 50 % formamide, 10x SSC, and 0.2% SDS.

tag: a restoration strain (trk1/TRK1/rp10::TRK1) in which we restored the second copy of TRK1 using the mutant strain (trk1/TRK1 ) as parent.


title: 9a5ccy3 x 9.12ccy5-Replica 2


title: 9a5ccy3 x 9.12ccy5-Replica 1


title: 9a5ccy5 x 56acy3-Replica 2

source_name: Xylella fastidiosa 56a cells grown in PW medium

tag: Total DNA from Xylella fastidiosa (isolate 56a), grown on solid PW medium


title: HeLa transfected with miR148b duplex versus control transfected HeLa, 24 hours

source_name: HeLa transfected with miR148b duplex, 24 hours


title: HeLa transfected with miR142 duplex versus control transfected HeLa, 12 hours

source_name: HeLa transfected with miR142 duplex, 24 hours


title: Restore-Cy5 vs WT-Cy3-1

source_name: restoration strain by restoring one copy of TRK1 gene of the mutant strain


title: 9a5ccy3 x 56acy5-Replica 1

scan_protocol: Slides were subjected to fluorescent detection with a GMS (Affymetrix) 418 Array Scanner (Affymetrix Inc., Santa Clara, CA) Cy3 channel was scanned at 100% laser power and 80% PMT gain Cy5 channel was scanned at 100% laser power and 70% PMT gain

source_name: Xylella fastidiosa 9a5c cells grown in PW medium


title: OverExp-Cy5 vs WT-Cy3-2

description: Candida albicans mutant strain overexpressing TRK1 gene compared to wild-type strain

scan_protocol: As described in the the manufacturer's instructions of GenePix 4000B scanner (Axon Instruments).

data_processing: Slides have been scanned by Axon scanner 4000B and image analysis analyzed by GenePix Version 4.0. Post analysis was performed using TIGR microarray software suite(http://www.tm4.org). ExprConverter v1.7 to transform GPR format to Mev file, Midias 2.19 to normalize the data, and Mev4.0 to do statistical analysis. The VALUE column is the log2 based expression level after background correction, total intensity normaliztion,Lowess normalization. if VALUE=null, then this spot was bad.

source_name: mutant strain overexpressing TRK1 gene

tag: mutant strain overexpressing TRK1 gene.


title: 9a5ccy3 x 56acy5-Replica 2


title: HeLa transfected with miR133a duplex versus control transfected HeLa, 12 hours

source_name: HeLa transfected with miR133a duplex, 24 hours


title: HeLa transfected with miR148b duplex versus control transfected HeLa, 12 hours

tag: HeLa transfected with miR148b duplex, 24 hours


title: Restore-Cy3 vs WT-Cy5-2


title: HeLa transfected with miR133a duplex versus control transfected HeLa, 24 hours

tag: HeLa transfected with miR133a duplex, 24 hours


title: HeLa transfected with miR142 duplex versus control transfected HeLa, 24 hours

tag: HeLa transfected with miR142 duplex, 24 hours


title: OverExp-Cy5 vs WT-Cy3-1


title: OverExp-Cy3 vs WT-Cy5-2.


title: 9a5ccy5 x 56acy3-Replica 1


title: HeLa transfected with miR132 duplex versus control transfected HeLa, 12 hours

source_name: HeLa transfected with miR132 duplex, 24 hours


title: 9a5ccy5 x 36fcy3-Replica 1

source_name: Xylella fastidiosa 36f cells grown in PW medium

tag: Total DNA from Xylella fastidiosa (isolate 36f), grown on solid PW medium


title: 9a5ccy5 x 36fcy3-Replica 2


title: Mutant-Cy3 vs WT-Cy5-2

description: Candida albicans TRK1 mutant strain compared to wild-type strain

source_name: TRK1 mutant strain

tag: Candida albicans wild type strain was mutated by deleting one of TRK1 genes.


title: Mutant-Cy3 vs WT-Cy5-1


title: HeLa transfected with miR132 duplex versus control transfected HeLa, 24 hours

tag: HeLa transfected with miR132 duplex, 24 hours


title: OverExp-Cy3 vs WT-Cy5-1


title: Restore-Cy3 vs WT-Cy5-1


title: HeLa transfected with miR128a duplex versus control transfected HeLa, 24 hours

source_name: HeLa transfected with miR128a duplex, 24 hours


title: 9a5ccy3 x 36fcy5-Replica 2


title: 9a5ccy3 x 36fcy5-Replica 1


title: Mutant-Cy5 vs WT-Cy3-2


title: 9a5ccy5 x 187bcy3-Replica 2

source_name: Xylella fastidiosa 187b cells grown in PW medium

tag: Total DNA from Xylella fastidiosa (isolate 187b), grown on solid PW medium


title: 9a5ccy5 x 187bcy3-Replica 1

tag: Total DNA from Xylella fastidiosa (isolate 9a5c), grown on solid PW medium


title: P4_b: infected+IFNg 4h

description:
Simple annotation: Toxoplasma, interferon
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67610.gif
Infection: Toxoplasma
Measurement: time(absolute) 4 h
Measurement: concentration(absolute) IFNg, 30 pM

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 7160; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Seon,,Kim 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 = 37.60; Parameter Scan Time = 11:06:04; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-15; Parameter Pixel Size = 10; Parameter Laser on time = 49492; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim 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 = 37.60; Parameter Scan Time = 11:06:04; Parameter PMT Volts = 760; Parameter Scan Date = 2006-03-15; Parameter Pixel Size = 10; Parameter Laser on time = 122627; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Seon,,Kim

source_name: 250 ng universal reference cDNA

tag: 250 ng universal reference cDNA

source_name: P4_b: infected+IFNg 4h

tag: 300 ng sample cDNA


title: 9a5ccy3 x 187bcy5-Replica 2


title: Mutant-Cy5 vs WT-Cy3-1

description: Candida albicans TRK1 mutant strain compared to wild-type strain CAI4

tag: Candida albicans wild-type strain CAI4


title: 9a5ccy3 x 187bcy5-Replica 1


title: Hst5-Cy3 vs CAI4-Cy5

description: Candida albicans Hst5 treated wild-type strain compared to wild-type strain CAI4

scan_protocol: As described in the the manufacturer's instructions of GenePix 4200A scanner (Axon Instruments).

data_processing: Slides have been scanned by Axon scanner 4200A and image analysis analyzed by GenePix Version 6.0. Post analysis was performed using TIGR microarray software suite(http://www.tm4.org). ExprConverter v1.7 to transform GPR format to Mev file, Midias 2.19 to normalize the data, and Mev4.0 to do statistical analysis. The VALUE column is the log2 based expression level after background correction, total intensity normaliztion,Lowess normalization. if VALUE=null, then this spot was bad.

source_name: wild-type strain CAI4

source_name: Hst5 treated wild-type strain

growth_protocol: Cells were grown overnight in 10 ml of YNB medium, 2% glucose with the addition of uridine when required. AFTER this, the cells were treated using Hst5.

treatment_protocol: wild-type CAI4 cells were harvested, washed twice with 10 mM NaPB, pH 7.4 and reconstituted in the same buffer. About 3x10^8 cells were incubated with 500uM Hst 5 (an LD40 dose) for 60 min.

tag: wild-type strain CAI4 treated 60min. with Hst5.


title: HeLa transfected with miR122a duplex versus control transfected HeLa, 12 hours

source_name: Mock transfected HeLa, 24 hours

tag: Mock transfected HeLa, 24 hours

source_name: HeLa transfected with miR122a duplex, 24 hours


title: HeLa transfected with miR122a duplex versus control transfected HeLa, 24 hours

tag: HeLa transfected with miR122a duplex, 24 hours


title: HeLa transfected with miR7 duplex versus control transfected HeLa, 24 hours

source_name: HeLa transfected with miR7 duplex, 24 hours


title: HeLa transfected with miR7 duplex versus control transfected HeLa, 12 hours

tag: HeLa transfected with miR7 duplex, 24 hours


title: HeLa transfected with miR9 duplex versus control transfected HeLa, 12 hours

source_name: HeLa transfected with miR9 duplex, 24 hours


title: HeLa transfected with miR128a duplex versus control transfected HeLa, 12 hours

tag: HeLa transfected with miR128a duplex, 24 hours


title: HeLa transfected with miR9 duplex versus control transfected HeLa, 24 hours

tag: HeLa transfected with miR9 duplex, 24 hours


title: Expt192 W5-82

status: Public on Jul 17 2007

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66219.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 480, 27870; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 40.25; Parameter Scan Time = 12:44:00; Parameter PMT Volts = 520; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 58326; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 40.25; Parameter Scan Time = 12:44:00; Parameter PMT Volts = 640; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 204251; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.37; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller

organism: Vibrio cholerae


title: Expt192 N16961

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66211.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 27470; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 40.66; Parameter Scan Time = 14:38:34; Parameter PMT Volts = 510; Parameter Scan Date = 2005-12-21; Parameter Pixel Size = 10; Parameter Laser on time = 59852; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 40.66; Parameter Scan Time = 14:38:34; Parameter PMT Volts = 610; Parameter Scan Date = 2005-12-21; Parameter Pixel Size = 10; Parameter Laser on time = 205777; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.33; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt192 W5-22

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66214.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 480, 27560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.89; Parameter Scan Time = 12:09:14; Parameter PMT Volts = 530; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 58291; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.89; Parameter Scan Time = 12:09:14; Parameter PMT Volts = 640; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 204216; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.36; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt192 W5-62

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66216.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 480, 27870; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 40.09; Parameter Scan Time = 12:26:09; Parameter PMT Volts = 540; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 58307; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.58; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 40.09; Parameter Scan Time = 12:26:09; Parameter PMT Volts = 640; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 204232; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.35; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt168 W5 - 22A amp

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62298.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 430, 27770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 38.65; Parameter Scan Time = 10:26:51; Parameter PMT Volts = 560; Parameter Scan Date = 2005-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 224257; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 38.65; Parameter Scan Time = 10:26:51; Parameter PMT Volts = 600; Parameter Scan Date = 2005-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 589061; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.86; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt129 SP6G 2 amp

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57250.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 27200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.79; Parameter Scan Time = 08:34:56; Parameter PMT Volts = 590; Parameter Scan Date = 2004-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 190029; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.24; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.79; Parameter Scan Time = 08:34:56; Parameter PMT Volts = 690; Parameter Scan Date = 2004-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 189409; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.21; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt168 PS5 - 34A amp

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62297.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 27760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 38.67; Parameter Scan Time = 10:32:47; Parameter PMT Volts = 550; Parameter Scan Date = 2005-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 224264; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 38.67; Parameter Scan Time = 10:32:47; Parameter PMT Volts = 600; Parameter Scan Date = 2005-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 589068; 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: Michael,,Miller


title: Expt192 W5-61

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66215.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 480, 27560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 40.02; Parameter Scan Time = 12:16:45; Parameter PMT Volts = 520; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 58298; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 40.02; Parameter Scan Time = 12:16:45; Parameter PMT Volts = 640; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 204223; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.35; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt192 PS5-32

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66213.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 480, 27560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.72; Parameter Scan Time = 11:46:29; Parameter PMT Volts = 510; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 58268; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.72; Parameter Scan Time = 11:46:29; Parameter PMT Volts = 630; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 204193; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.36; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt129 W6G  2 amp

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57252.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1390, 26900; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 40.05; Parameter Scan Time = 08:53:57; Parameter PMT Volts = 590; Parameter Scan Date = 2004-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 190049; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 40.05; Parameter Scan Time = 08:53:57; Parameter PMT Volts = 690; Parameter Scan Date = 2004-11-09; Parameter Pixel Size = 10; Parameter Laser on time = 189429; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.21; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt168 W5 - 61A amp

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62299.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 28120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 38.50; Parameter Scan Time = 10:21:32; Parameter PMT Volts = 560; Parameter Scan Date = 2005-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 224253; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 38.50; Parameter Scan Time = 10:21:32; Parameter PMT Volts = 610; Parameter Scan Date = 2005-06-30; Parameter Pixel Size = 10; Parameter Laser on time = 589057; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.86; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt192 W5-81

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66218.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 480, 27870; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller 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 = 40.26; Parameter Scan Time = 12:38:09; Parameter PMT Volts = 510; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 58320; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller 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 = 40.26; Parameter Scan Time = 12:38:09; Parameter PMT Volts = 640; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 204245; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.36; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller


title: Expt192 E5-64

description:
Simple annotation: Genome comparison, Profiling
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66212.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 27240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Michael,,Miller Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.63; Parameter Scan Time = 11:37:36; Parameter PMT Volts = 510; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 58259; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.63; Parameter Scan Time = 11:37:36; Parameter PMT Volts = 670; Parameter Scan Date = 2005-11-17; Parameter Pixel Size = 10; Parameter Laser on time = 204184; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.36; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Michael,,Miller