title: NSH57 8-1 1mo: S, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52252.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 9120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:44:53; Parameter PMT Volts = 400; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45667; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:44:53; Parameter PMT Volts = 450; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45675; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.78; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 8-1 1mo; S, 2C

tag: output mouse NSH57 8-1 1mo; S, 2C


title: NSH57 18-3 1mo: N3, 2C

status: Public on Dec 15 2006

type: genomic

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59512.gif

hyb_protocol: pubmed ID 17101654

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1270, 34400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.58; Parameter Scan Time = 11:16:37; Parameter PMT Volts = 410; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 58199; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.63; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.58; Parameter Scan Time = 11:16:37; Parameter PMT Volts = 520; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 57947; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.77; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

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

molecule: genomic DNA

organism: Helicobacter pylori

source_name: input mouse NSH57 18.2i; N3, 2C

label_protocol: pubmed ID 17101654

extract_protocol: pubmed ID 17101654

tag: input mouse NSH57 18.2i; N3, 2C

source_name: output mouse NSH57 18-3 1mo; N3, 2C

tag: output mouse NSH57 18-3 1mo; N3, 2C


title: NSH57 18-2 1wk: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59511.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1110, 7890; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 11:12:26; Parameter PMT Volts = 410; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 58195; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 11:12:26; Parameter PMT Volts = 500; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 57942; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.76; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 18.1i; N3, 2C

tag: input mouse NSH57 18.1i; N3, 2C

source_name: output mouse NSH57 18-2 1wk; N3, 2C

tag: output mouse NSH57 18-2 1wk; N3, 2C


title: NSH57 17-1 1mo: S, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59515.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 8370; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.85; Parameter Scan Time = 13:54:30; Parameter PMT Volts = 400; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 58515; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.85; Parameter Scan Time = 13:54:30; Parameter PMT Volts = 570; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 58263; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.76; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 17.1i; S, 2C

tag: input mouse NSH57 17.1i; S, 2C

source_name: output mouse NSH57 17-1 1mo; S, 2C

tag: output mouse NSH57 17-1 1mo; S, 2C


title: NSH57 18-1 1wk: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59510.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1340, 34550; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.51; Parameter Scan Time = 11:09:06; Parameter PMT Volts = 440; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 58191; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.63; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.51; Parameter Scan Time = 11:09:06; Parameter PMT Volts = 410; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 57939; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.76; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 18-1 1wk; N3, 2C

tag: output mouse NSH57 18-1 1wk; N3, 2C


title: NSH57 17-4 1mo: S, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59517.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1210, 8450; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.85; Parameter Scan Time = 14:00:44; Parameter PMT Volts = 420; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 58522; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.85; Parameter Scan Time = 14:00:44; Parameter PMT Volts = 510; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 58269; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.77; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 17.2i; S, 2C

tag: input mouse NSH57 17.2i; S, 2C

source_name: output mouse NSH57 17-4 1mo; S, 2C

tag: output mouse NSH57 17-4 1mo; S, 2C


title: NSH57 5-4 1wk: S, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54715.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 34730; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin 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 = 32.03; Parameter Scan Time = 13:01:28; Parameter PMT Volts = 520; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49533; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin 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 = 32.03; Parameter Scan Time = 13:01:28; Parameter PMT Volts = 600; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49459; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.79; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 5.2i; S, 2C

tag: input mouse NSH57 5.2i; S, 2C

source_name: output mouse NSH57 5-4 1wk; S, 2C

tag: output mouse NSH57 5-4 1wk; S, 2C


title: NSH57 5-3 1wk: S, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54714.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1130, 8930; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin 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 = 32.00; Parameter Scan Time = 12:59:12; Parameter PMT Volts = 520; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49530; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin 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 = 32.00; Parameter Scan Time = 12:59:12; Parameter PMT Volts = 600; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49457; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.79; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 5-3 1wk; S, 2C

tag: output mouse NSH57 5-3 1wk; S, 2C


title: NSH57 11-4 1wk: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54717.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 34830; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 11:00:47; Parameter PMT Volts = 600; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 49687; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 11:00:47; Parameter PMT Volts = 550; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 49613; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.78; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 11.2i; N3, 2C

tag: input mouse NSH57 11.2i; N3, 2C

source_name: output mouse NSH57 11-4 1wk; N3, 2C

tag: output mouse NSH57 11-4 1wk; N3, 2C


title: NSH57 8-2 1mo: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52250.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1920, 35790; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:42:02; Parameter PMT Volts = 380; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45664; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:42:02; Parameter PMT Volts = 480; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45672; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.78; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: NSH57 8 input 1 N3, 2C

tag: NSH57 8 input 1 N3, 2C

source_name: output mouse NSH57 8-2 1mo; N3, 2C

tag: output mouse NSH57 8-2 1mo; N3, 2C


title: NSH57 11-3 1wk: S, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54719.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 34830; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin 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 = 32.03; Parameter Scan Time = 11:06:16; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 49692; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin 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 = 32.03; Parameter Scan Time = 11:06:16; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 49619; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.79; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 11.2i; S, 2C

tag: input mouse NSH57 11.2i; S, 2C

source_name: output mouse NSH57 11-3 1wk; S, 2C

tag: output mouse NSH57 11-3 1wk; S, 2C


title: NSH57 11-4 1mo: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54718.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 8480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin 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 = 32.00; Parameter Scan Time = 11:03:59; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 49690; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin 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 = 32.00; Parameter Scan Time = 11:03:59; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 49616; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.78; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 11-4 1mo; N3, 2C

tag: output mouse NSH57 11-4 1mo; N3, 2C


title: NSH57 5-1 1wk: S, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54712.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 8700; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.91; Parameter Scan Time = 12:53:31; Parameter PMT Volts = 520; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49525; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.91; Parameter Scan Time = 12:53:31; Parameter PMT Volts = 560; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49451; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.79; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 5.1i; S, 2C

tag: input mouse NSH57 5.1i; S, 2C

source_name: output mouse NSH57 5-1 1wk; S, 2C

tag: output mouse NSH57 5-1 1wk; S, 2C


title: NSH57 8-3 1wk: S, 2C PCRtest

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52101.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1530, 9190; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.27; Parameter Scan Time = 10:02:40; Parameter PMT Volts = 390; Parameter Scan Date = 2004-05-14; Parameter Pixel Size = 10; Parameter Laser on time = 46053; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.27; Parameter Scan Time = 10:02:40; Parameter PMT Volts = 540; Parameter Scan Date = 2004-05-14; Parameter Pixel Size = 10; Parameter Laser on time = 45996; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.78; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: NSH57 8 input 2 S, 2C

tag: NSH57 8 input 2 S, 2C

source_name: output mouse NSH57 8-3 1wk; S, 2C

tag: output mouse NSH57 8-3 1wk; S, 2C


title: NSH57 17-4 1mo: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59509.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1110, 7890; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 10:59:51; Parameter PMT Volts = 400; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 58182; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 10:59:51; Parameter PMT Volts = 520; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 57930; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.75; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 17.2i; N3, 2C

tag: input mouse NSH57 17.2i; N3, 2C

source_name: output mouse NSH57 17-4 1mo; N3, 2C

tag: output mouse NSH57 17-4 1mo; N3, 2C


title: NSH57 5-1 1mo: S, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54713.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 35050; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 12:56:11; Parameter PMT Volts = 520; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49527; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 12:56:11; Parameter PMT Volts = 560; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49453; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.79; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 5-1 1mo; S, 2C

tag: output mouse NSH57 5-1 1mo; S, 2C


title: NSH57 17-3 1mo: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59508.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1270, 34630; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 10:56:26; Parameter PMT Volts = 410; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 58180; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.55; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 10:56:26; Parameter PMT Volts = 500; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 57928; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.73; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 17-3 1mo; N3, 2C

tag: output mouse NSH57 17-3 1mo; N3, 2C


title: NSH57 5-3 1wk: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54710.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1270, 8390; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 12:42:07; Parameter PMT Volts = 510; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49514; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 12:42:07; Parameter PMT Volts = 580; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49440; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.77; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 5.2i; N3, 2C

tag: input mouse NSH57 5.2i; N3, 2C

source_name: output mouse NSH57 5-3 1wk; N3, 2C

tag: output mouse NSH57 5-3 1wk; N3, 2C


title: NSH57 17-1 1mo: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59507.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 8280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 10:52:28; Parameter PMT Volts = 420; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 58176; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 10:52:28; Parameter PMT Volts = 480; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 57923; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.74; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 17.1i; N3, 2C

tag: input mouse NSH57 17.1i; N3, 2C

source_name: output mouse NSH57 17-1 1mo; N3, 2C

tag: output mouse NSH57 17-1 1mo; N3, 2C


title: NSH57 5-4 1wk: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54711.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1350, 35130; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.79; Parameter Scan Time = 12:45:16; Parameter PMT Volts = 500; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49517; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.79; Parameter Scan Time = 12:45:16; Parameter PMT Volts = 610; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 49443; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.78; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 5-4 1wk; N3, 2C

tag: output mouse NSH57 5-4 1wk; N3, 2C


title: 10700_array 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5365.gif

scan_protocol: pubmed ID 17101654

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)

source_name: 0.7 ug 26695 genomic DNA + 0.7 ug J99 genomic DNA

source_name: 2 ug 10700(ss1 premouse) genomic DNA

tag: 2 ug 10700(ss1 premouse) genomic DNA


title: NSH57 11-3 1wk: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54716.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 8400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.88; Parameter Scan Time = 10:57:55; Parameter PMT Volts = 520; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 49684; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.88; Parameter Scan Time = 10:57:55; Parameter PMT Volts = 680; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 49611; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.77; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: input mouse NSH57 11.2i; N3, 2C

tag: input mouse NSH57 11.2i; N3, 2C

source_name: output mouse NSH57 11-3 1wk; N3, 2C

tag: output mouse NSH57 11-3 1wk; N3, 2C


title: NSH57 6-6 1mo: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52244.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2140, 35550; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:36:44; Parameter PMT Volts = 360; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45659; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:36:44; Parameter PMT Volts = 500; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45667; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.78; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: NSH57 6 input 3 N3, 2C

tag: NSH57 6 input 3 N3, 2C

source_name: output mouse NSH57 6-6 1mo; N3, 2C

tag: output mouse NSH57 6-6 1mo; N3, 2C


title: NSH57 8-1 1mo: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52246.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1830, 8490; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:39:22; Parameter PMT Volts = 360; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45661; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.34; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.39; Parameter Scan Time = 10:39:22; Parameter PMT Volts = 500; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45669; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.77; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: NSH57 8 input 1 N3, 2C

tag: NSH57 8 input 1 N3, 2C

source_name: output mouse NSH57 8-1 1mo; N3, 2C

tag: output mouse NSH57 8-1 1mo; N3, 2C


title: 10700_array 1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5364.gif

tag: 0.7 ug 26695 genomic DNA + 0.7 ug J99 genomic DNA


title: NSH57 6-5 1mo: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2004-05/52242.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 9120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 10:33:19; Parameter PMT Volts = 390; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45656; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 10:33:19; Parameter PMT Volts = 450; Parameter Scan Date = 2004-05-11; Parameter Pixel Size = 10; Parameter Laser on time = 45663; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.78; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 6-5 1mo; N3, 2C

tag: output mouse NSH57 6-5 1mo; N3, 2C


title: NSH57 17-2 1wk: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59506.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 34750; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 10:47:09; Parameter PMT Volts = 400; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 58169; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.63; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 10:47:09; Parameter PMT Volts = 500; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 57917; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.73; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 17-2 1wk; N3, 2C

tag: output mouse NSH57 17-2 1wk; N3, 2C


title: G27 O.25 ug 2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23696.gif

source_name: 0.25 ug 26695/J99 Reference

tag: 0.25 ug 26695/J99 Reference

source_name: G27 genomic DNA O.25 ug

tag: G27 genomic DNA O.25 ug


title: NSH57 17-1 1wk: N3, 2C

description:
Simple annotation: Method testing, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59505.gif

scan_protocol: pubmed ID 17101654 Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 8240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: David,,Baldwin Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 10:43:35; Parameter PMT Volts = 400; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 58168; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 10:43:35; Parameter PMT Volts = 500; Parameter Scan Date = 2005-02-09; Parameter Pixel Size = 10; Parameter Laser on time = 57915; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.72; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: David,,Baldwin

source_name: output mouse NSH57 17-1 1wk; N3, 2C

tag: output mouse NSH57 17-1 1wk; N3, 2C


title: G27 0.25 ug

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/23695.gif


title: SS1 (A.L.)  2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5683.gif

source_name: 0.7 ug 26695 genomic DNA + 0.7 ug 26695 genomic DNA

source_name: 2 ug SS1 (AL) genomic DNA

tag: 2 ug SS1 (AL) genomic DNA


title: Histone H3 IP during expontential growth culture #14

status: Public on Nov 30 2006

city: Chapel Hill

first: Jason

middle: D.

last: Lieb

state: NC

department: Biology

institute: Univeristy of North Carolina at Chapel Hill

description: Histone H3 ChIP-chip using H3-AB (Lab generated) on BY4741 culture # 14 during expontential growth OD 0.8384. Strain - BY4741

hyb_protocol: Direct hybridization 4X SSC, 0.2% SDS

scan_protocol: Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)

data_processing: The normalized median log2 ratios (ch2/ch1) were download from UNC microarray database, dye swapped experiments were inverted

organism: Saccharomyces cerevisiae

source_name: Ref BY4741 log #14

label_protocol: samples and references were amplified using a random primed PCR-based method (see Bohlander et al., 1992)

growth_protocol: Expontential Growth (OD 0.6-1.0)

extract_protocol: Input genomic DNA, 1/20 of WCE for IP used as input.  Reversed and crosslinked, purified, and amplified using Rnd A/B/C.

treatment_protocol: Rich Media (YPD 2% Glucose)

tag: Ref BY4741 log #14

source_name: H3 IP from Log #14

extract_protocol: IP DNA isoloated from 1mg protein from WCE by IP with AB towards Histone H3.

tag: H3 IP from Log #14


title: NSH79

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5682.gif

source_name: 0.7 ug 26695 genomic DNA + 0.7 ug J99 genomic DNA


title: Histone H3 IP during expontential growth culture #12

description: Histone H3 ChIP-chip using H3-AB (Lab generated) on BY4741 culture # 12 during expontential growth OD 0.7388. Strain - BY4741

source_name: Ref BY4741 expontential growth #12

tag: Ref BY4741 expontential growth #12

source_name: H3 IP from expontential growth #12

tag: H3 IP from expontential growth #12


title: Histone H3 IP during post-diuaxic shift (72hrs) culture #13

description: Histone H3 ChIP-chip using H3-AB (Lab generated) on BY4741 culture # 13 during post-diuaxic shift (72hrs) OD 5.958. Strain - BY4741

source_name: Ref BY4741 post-diuaxic shift (72hrs) #13

growth_protocol: Post-Diuaxic Shift (72 hrs)

source_name: H3 IP from post-diuaxic shift (72hrs) #13


title: Histone H3 IP during post-diuaxic shift (72hrs) culture #12

description:
Histone H3 ChIP-chip using H3-AB (Lab generated) on BY4741 culture # 12 during post-diuaxic shift(72hrs) OD 5.098.
Strain - BY4741

source_name: Ref BY4741 during post-diuaxic shift (72hrs) culture #12

growth_protocol: Post-diuaxic shift (72 hrs)


title: Histone H3 IP during expontential growth culture #13

description: Histone H3 ChIP-chip using H3-AB (Lab generated) on BY4741 culture # 13 during expontential growth OD 0.8114. Strain - BY4741

source_name: Ref BY4741 expontential growth #13

tag: Ref BY4741 expontential growth #13

source_name: H3 IP from expontential growth #13

tag: H3 IP fromexpontential growth #13


title: Rap1 IP with AB on BY4741 during expontential growth in Etoh #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on BY4741 culture # 3 during expontential growth in Ethanol OD 0.5453. Strain - BY4741

source_name: Ref BY4741 #3 + EtOH

treatment_protocol: Ethanol Media (YP EtOH)

tag: Ref BY4741 #3 + EtOH

source_name: Rap1 IP BY4741 #3 + EtOH

extract_protocol: IP DNA isoloated from 1mg protein from WCE by IP with AB Y-300.

tag: Rap1 IP BY4741 #3 + EtOH


title: Rap1 IP with AB on BY4741 during expontential growth in Etoh #4

description: Rap1 ChIP-chip using RAP1-AB (y-300) on BY4741 culture # 4 during expontential growth in Ethanol OD 0.5691. Strain - BY4741

source_name: Ref BY4741 #4 + EtOH

tag: Ref BY4741 #4 + EtOH

source_name: Rap1 IP BY4741 #4 + EtOH

tag: Rap1 IP BY4741 #4 + EtOH


title: Sut1-Tap IP during expontential growth culture #2

description: Sut1-Tap ChIP-chip using Tap affinity tag on culture # 2 during expontential growth OD 0.7972. Strain - Sut1-Tap, BY4741

source_name: Ref Sut1-tap #2

tag: Ref Sut1-tap #2

source_name: Sut1-Tap IP expontential growth #2

extract_protocol: IP DNA isoloated from 1mg protein from WCE by affinity purification of the Tap-tagged protein.

tag: Sut1-Tap IP expontential growth #2


title: Sut1-Tap IP during expontential growth culture #1

description: Sut1-Tap ChIP-chip using Tap affinity tag on culture # 1 during expontential growth OD 0.7140. Strain - Sut1-Tap, BY4741

source_name: Ref Sut1-tap #1

tag: Ref Sut1-tap #1

source_name: Sut1-Tap IP expontential growth phase #1


title: Histone H3 IP during post-diuaxic shift (72hrs) culture #14

description: Histone H3 ChIP-chip using H3-AB (Lab generated) on BY4741 culture # 14 during post-diuaxic shift (72hrs) OD .Strain - BY4741

source_name: Ref BY4741 post-diuaxic shift (72hrs) #14

source_name: H3 IP from post-diuaxic shift (72hrs) #14


title: Sut1-Tap IP during post-diauxic shift (72 hrs) culture #3

description: Sut1-Tap ChIP-chip using Tap affinity tag on culture # 3 during post-diauxic shift (72 hrs) OD 6.025. Strain - Sut1-Tap, BY4741

source_name: Ref Sut1-Tap post-diauxic shift (72 hrs) #3

growth_protocol: Post-Diauxic Shift (72 hrs)

source_name: Sut1-Tap IP post-diauxic shift (72 hrs) # 3


title: Rap1 IP with AB on BY4741 during expontential growth in Etoh #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on BY4741 culture # 2 during expontential growth in Ethanol OD 0.6079. Strain - BY4741

source_name: Ref BY4741 #2 + EtOH

tag: Ref BY4741 #2 + EtOH

source_name: Rap1 IP BY4741 #2 + EtOH

tag: Rap1 IP BY4741 #2 + EtOH


title: Sut1-Tap IP during expontential growth culture #4

description: Sut1-Tap ChIP-chip using Tap affinity tag on culture # 4 during expontential growth OD 0.7817. Strain - Sut1-Tap, BY4741

source_name: Ref Sut1-tap #4

tag: Ref Sut1-tap #4

source_name: Sut1-Tap IP expontential growth #4

tag: Sut1-Tap IP expontential growth #4


title: Tup1-Tap IP during expontential growth culture #1 Rep

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 1 during expontential growth OD 0.680. Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Log phase # 1

tag: Ref Tup1-tap Log phase # 1

source_name: Tup1-tap IP Log phase # 1

tag: Tup1-tap IP Log phase # 1


title: Tup1-Tap IP during post-diauxic shift (72 hrs) #2 Redo

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 2 during post-diuxic shift OD 6.088. Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Day 3 #2

growth_protocol: Post-Diauxic shift (72 hrs)

tag: Ref Tup1-tap Day 3 #2

source_name: Tup1-tap IP #2 Day 3

tag: Tup1-tap IP #2 Day 3


title: Rap1 IP with AB on BY4741 during expontential growth in Etoh #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on BY4741 culture # 1 during expontential growth in Ethanol OD 0.6584. Strain - BY4741

source_name: Ref BY4741 #1 + EtOH

tag: Ref BY4741 #1 + EtOH

source_name: Rap1 IP BY4741 #1 + EtOH

tag: Rap1 IP BY4741 #1 + EtOH


title: Sut1-Tap IP during expontential growth culture #3

description: Sut1-Tap ChIP-chip using Tap affinity tag on culture # 3 during expontential growth OD 0.6906. Strain - Sut1-Tap, BY4741

source_name: Ref Sut1-tap #3

tag: Ref Sut1-tap #3

source_name: Sut1-Tap IP expontential growth #3

tag: Sut1-Tap IP expontential growth #3


title: Tup1-Tap IP during expontential growth culture #6

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 6 during expontential growth OD 0.6256. DYE-SWAPStrain - Tup1-Tap, BY4741

source_name: Tup1-tap Log phase # 6

tag: Tup1-tap Log phase # 6

source_name: Ref Tup1-tap Log phase # 6

tag: Ref Tup1-tap Log phase # 6


title: Tup1-Tap IP during expontential growth culture #5

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 5 during expontential growth OD 0.6433. Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Log phase # 5

tag: Ref Tup1-tap Log phase # 5

source_name: Tup1-tap IP Log phase # 5

tag: Tup1-tap IP Log phase # 5


title: Tup1-Tap IP during expontential growth culture #7

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 7 during expontential growth OD 0.5756. Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Log phase # 7

tag: Ref Tup1-tap Log phase # 7

source_name: Tup1-tap IP Log phase # 7

tag: Tup1-tap IP Log phase # 7


title: Tup1-Tap IP during post-diauxic shift (72 hrs) #6

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 6 during post-diuxic shift OD 16.30. DYE-SWAPStrain - Tup1-Tap, BY4741

source_name: Tup1-tap IP #6 Day 3

tag: Tup1-tap IP #6 Day 3

source_name: Ref Tup1-tap Day 3 #6

tag: Ref Tup1-tap Day 3 #6


title: Tup1-Tap IP during post-diauxic shift (72 hrs) #7

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 7 during post-diuxic shift OD 15.70. Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Day 3 #7

tag: Ref Tup1-tap Day 3 #7

source_name: Tup1-tap IP #7 Day 3

tag: Tup1-tap IP #7 Day 3


title: Tup1-Tap IP during expontential growth culture #4

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 4 during expontential growth OD 0.5245. Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Log phase # 4

tag: Ref Tup1-tap Log phase # 4

source_name: Tup1-tap IP Log phase # 4

tag: Tup1-tap IP Log phase # 4


title: Tup1-Tap IP during expontential growth culture #1

source_name: Ref Tup1-tap Log phase # 1

tag: Ref Tup1-tap Log phase # 1

source_name: Tup1-tap IP Log phase # 1

tag: Tup1-tap IP Log phase # 1


title: Tup1-Tap IP during post-diauxic shift (72 hrs) #3

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 3 during post-diuxic shift OD 7.164. Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Day 3 #3

tag: Ref Tup1-tap Day 3 #3

source_name: Tup1-tap IP #3 Day 3

tag: Tup1-tap IP #3 Day 3


title: Rap1 IP with AB on isw2del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on isw2del culture # 1 during expontential growth OD 0.6505. Strain - isw2del, BY4741

source_name: Ref Isw2del log phase #1

tag: Ref Isw2del log phase #1

source_name: Rap1 IP with AB on Isw2del log #1

tag: Rap1-IP on Isw2del #1


title: Rap1 IP with AB on tup1del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on tup1del culture # 1 during expontential growth OD 1.003.Strain - tup1del, BY4741

source_name: Ref Tup1del #1

tag: Ref Tup1del #1

source_name: Rap1 IP with AB in Tup1del Log #1

tag: Rap1 IP with AB in Tup1del Log #1


title: Rap1 IP with AB on hda1del during expontential growth culture #4

description: Rap1 ChIP-chip using RAP1-AB (y-300) on hda1del culture # 4 during expontential growth OD 0.8218. DYE-SWAP Strain - hda1del, BY4741

source_name: Rap1 IP with AB in Hda1del #4

tag: Rap1 IP with AB in Hda1del #4

source_name: Ref Hda1del #4

tag: Ref Hda1del #4


title: Tup1-Tap IP during post-diauxic shift (72 hrs) #2

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 2 during post-diuxic shift OD 6.088.Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Day 3 #2

tag: Ref Tup1-tap Day 3 #2

source_name: Tup1-tap IP #2 Day 3

tag: Tup1-tap IP #2 Day 3


title: Rap1 IP with AB on hda1del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on hda1del culture # 1 during expontential growth OD 0.6622.Strain - hda1del, BY4741

source_name: Ref Hda1del #1

tag: Ref Hda1del #1

source_name: Rap1-IP on Hda1del #1

tag: Rap1-IP on Hda1del #1


title: Rap1 IP with AB on hda1del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on hda1del culture # 2 during expontential growth OD 0.7067.Strain - hda1del, BY4741

source_name: Ref Hda1del #2

tag: Ref Hda1del #2

source_name: Rap1-IP on Hda1del #2

tag: Rap1-IP on Hda1del #2


title: Rap1 IP with AB on tup1del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on tup1del culture # 2 during expontential growth OD 0.6600.Strain - tup1del, BY4741

source_name: Ref Tup1del #2

tag: Ref Tup1del #2

source_name: Rap1 IP with AB in Tup1del Log #2

tag: Rap1 IP with AB in Tup1del Log #2


title: Rap1 IP with AB on gat1del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on gat1del culture # 2 during expontential growth OD 0.6619. Strain - gat1del, BY4741

source_name: Ref for Gat1del # 2

tag: Ref for Gat1del # 2

source_name: Rap1 IP with AB Gat1del Log # 2

tag: Rap1 IP with AB Gat1del Log # 2


title: Rap1 IP with AB on isw2del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on isw2del culture # 2 during expontential growth OD 0.7052. Strain - isw2del, BY4741

source_name: Ref Isw2del log phase #2

tag: Ref Isw2del log phase #2

source_name: Rap1-IP on Isw2del #2

tag: Rap1-IP on Isw2del #2


title: Rap1 IP with AB on tup1del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on tup1del culture # 3 during expontential growth OD 0.8063. Strain - tup1del, BY4741

source_name: Ref Tup1del #3

tag: Ref Tup1del #3

source_name: Rap1 IP with AB in Tup1del Log #3

tag: Rap1 IP with AB in Tup1del Log #3


title: Tup1-Tap IP during expontential growth culture #2

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 2 during expontential growth OD 0.7118.Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Log phase # 2

tag: Ref Tup1-tap Log phase # 2

source_name: Tup1-tap IP Log phase # 2

tag: Tup1-tap IP Log phase # 2


title: Rap1 IP with AB on gat1del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on gat1del culture # 1 during expontential growth OD 0.8160. Strain - gat1del, BY4741

source_name: Ref for Gat1del # 1

tag: Ref for Gat1del # 1

source_name: Rap1 IP with AB Gat1del Log # 1

tag: Rap1 IP with AB Gat1del Log # 1


title: Rap1 IP with AB on isw2del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on isw2del culture # 3 during expontential growth OD 0.5953. Strain - isw2del, BY4741

source_name: Rap1 ip in Isw2del

tag: Rap1 ip in Isw2del

source_name: Ref Isw2del

tag: Ref Isw2del


title: Rap1 IP with AB on gat1del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on gat1del culture # 3 during expontential growth OD 0.8160. DYE-SWAP Strain - gat1del, BY4741

source_name: Rap1 ip in GAT1del

tag: Rap1 ip in GAT1del

source_name: Ref GAT1del

tag: Ref GAT1del


title: Tup1-Tap IP during expontential growth culture #3

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 3 during expontential growth OD 0.7498. Strain - Tup1-Tap, BY4741

source_name: Ref Tup1-tap Log phase # 3

tag: Ref Tup1-tap Log phase # 3

source_name: Tup1-tap IP Log phase # 3

tag: Tup1-tap IP Log phase # 3


title: Rap1 IP with AB on hda1del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on hda1del culture # 3 during expontential growth OD 0.6846. DYE-swap Strain - hda1del, BY4741

source_name: Rap1 IP with AB in Hda1del #3

tag: Rap1 IP with AB in Hda1del #3

source_name: Ref Hda1del #3

tag: Ref Hda1del #3


title: Rap1 IP with AB on mig1del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on mig1del culture # 2 during expontential growth OD 0.6456.Strain - mig1del, BY4741

source_name: Ref Rap1 IP on Mig1del culture # 2

tag: Ref Rap1 IP on Mig1del culture # 2

source_name: Rap1 IP on Mig1del #2

tag: Rap1 IP on Mig1del #2


title: Rap1 IP with AB on mig1del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on mig1del culture # 3 during expontential growth OD 0.6644. Strain - mig1del, BY4741

source_name: Ref Rap1 IP on Mig1del culture # 3

tag: Ref Rap1 IP on Mig1del culture # 3

source_name: Rap1 IP on Mig1del #3

tag: Rap1 IP on Mig1del #3


title: Rap1 IP with AB on tup1del during expontential growth culture #3 -DS

description: Rap1 ChIP-chip using RAP1-AB (y-300) on dot6del culture # 3 during expontential growth OD 0.8063. DYE-SWAP Strain - tup1del, BY4741

source_name: Rap1-IP Tup1del #3

tag: Rap1-IP Tup1del #3

source_name: Ref Tup1del #3

tag: Ref Tup1del #3


title: Tup1-Tap IP during post-diauxic shift (72 hrs) #5

description: Tup1-Tap ChIP-chip using Tap affinity tag on culture # 5 during post-diuxic shift OD 15.72. Strain - Tup1-Tap, BY4741

source_name: Tup1-tap IP #5 Day 3

tag: Tup1-tap IP #5 Day 3

source_name: Ref Tup1-tap Day 3 #5

tag: Ref Tup1-tap Day 3 #5


title: Rap1 IP with AB on sko1del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sko1del culture # 3 during expontential growth OD 0.8221. Strain - sko1del, BY4741

source_name: Ref Sko1del #3

tag: Ref Sko1del #3

source_name: Rap1 IP with AB in Sko1del #3 log phase

tag: Rap1 IP with AB in Sko1del #3 log phase


title: Rap1 IP with AB on mig1del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on mig1del culture # 1 during expontential growth OD 0.6877. Strain - mig1del, BY4741

source_name: Ref Rap1 IP on Mig1del culture # 1

tag: Ref Rap1 IP on Mig1del culture # 1

source_name: Rap1 IP on Mig1del #1

tag: Rap1 IP on Mig1del #1


title: Rap1 IP with AB on sko1del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sko1del culture # 2 during expontential growth OD 0.8582. Strain - sko1del, BY4741

source_name: Ref Sko1del #2

tag: Ref Sko1del #2

source_name: Rap1 IP with AB in Sko1del #2 log phase

tag: Rap1 IP with AB in Sko1del #2 log phase


title: Rap1 IP with AB on tup1del during expontential growth culture #2 Redo

description: Rap1 ChIP-chip using RAP1-AB (y-300) on tup1del culture # 2 during expontential growth OD 0.6600. Redo Strain - tup1del, BY4741

source_name: Ref Tup1del #2

tag: Ref Tup1del #2

source_name: Rap1 IP with AB in Tup1del Log #2

tag: Rap1 IP with AB in Tup1del Log #2


title: Rap1 IP with AB on nrg1del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on nrg1del culture # 1 during expontential growth OD 0.7596.Strain - nrg1del, BY4741

source_name: Ref for Nrg1del #1

tag: Ref for Nrg1del #1

source_name: Rap1 IP on Nrg1del #1 during log phase

tag: Rap1 IP on Nrg1del #1 during log phase


title: Rap1 IP with AB on dot6del during expontential growth culture #4

description: Rap1 ChIP-chip using RAP1-AB (y-300) on dot6del culture # 4 during expontential growth OD 0.7905. DYE-SWAP Strain - dot6del, BY4741

source_name: Rap1 IP with AB in Dot6del #4

tag: Rap1 IP with AB in Dot6del #4

source_name: Ref Dot6del #4

tag: Ref Dot6del #4


title: Rap1 IP with AB on dot6del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on dot6del culture # 1 during expontential growth OD 0.7815.Strain - dot6del, BY4741

source_name: Ref for Dot6del # 1

tag: Ref for Dot6del # 1

source_name: Rap1 IP with AB Dot6del Log # 1

tag: Rap1 IP with AB Dot6del Log # 1


title: Rap1 IP with AB on sko1del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sko1del culture # 1 during expontential growth OD 0.8221.Strain - sko1del, BY4741

source_name: Ref Sko1del #1

tag: Ref Sko1del #1

source_name: Rap1 IP with AB in Sko1del #1 log phase

tag: Rap1 IP with AB in Sko1del #1 log phase


title: Rap1 IP with AB on sut1del during diauxic shift (24 hrs) culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sut1del culture # 1 during diauxic shift (24 hrs)OD 6.808. Strain - sut1del, BY4741

source_name: Ref Sut1del

growth_protocol: Diauxic Shift 24 hrs

tag: Ref Sut1del

source_name: Rap1 IP with AB in sut1del culture # 1

tag: Rap1 IP with AB in sut1del culture # 1


title: Rap1 IP with AB on sut1del during diauxic shift (24 hrs) culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sut1del culture # 2 during diauxic shift (24 hrs)OD 6.332.Strain - sut1del, BY4741

source_name: Rap1 IP with AB in sut1del culture # 2

tag: Rap1 IP with AB in sut1del culture # 2


title: Rap1 IP with AB on sut1del during diauxic shift (72 hrs) culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sut1del culture # 1 during post-diauxic shift (72 hrs)OD 7.269. Strain - sut1del, BY4741

growth_protocol: Post-Diauxic Shift 72 hrs


title: Rap1 IP with AB on sut1del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sut1del culture # 2 during expontential growth OD 0.6633. Strain - sut1del, BY4741


title: Rap1 IP with AB on nrg1del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on nrg1del culture # 2 during expontential growth OD 0.8993.Strain - nrg1del, BY4741

source_name: Ref for Nrg1del #2

tag: Ref for Nrg1del #2

source_name: Rap1 IP on Nrg1del #2 during log phase

tag: Rap1 IP on Nrg1del #2 during log phase


title: Rap1 IP with AB on BY4741 during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on BY4741 culture # 1 during expontential growth OD 0.7388. Strain - BY4741

source_name: Ref for BY4741

tag: Ref for BY4741

source_name: Rap1 IP with AB in BY4741


title: Rap1 IP with AB on nrg1del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on nrg1del culture # 3 during expontential growth OD 0.6073. DYE-SWAP Strain - nrg1del, BY4741

source_name: Rap1 IP with AB in nrg1del

tag: Rap1 IP with AB in nrg1del

source_name: Ref nrg1del

tag: Ref nrg1del


title: Rap1 IP with AB on BY4741 during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on BY4741 culture # 3 during expontential growth OD 0.8384. Strain - BY4741


title: Rap1 IP with AB on BY4741 during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on BY4741 culture # 2 during expontential growth OD 0.8114. Strain - BY4741


title: Rap1 IP with AB on sut1del during expontential growth culture #1

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sut1del culture # 1 during expontential growth OD 0.7365. Strain - sut1del, BY4741


title: Rap1 IP with AB on dot6del during expontential growth culture #2

description: Rap1 ChIP-chip using RAP1-AB (y-300) on dot6del culture # 2 during expontential growth OD 0.6112.Strain - dot6del, BY4741

source_name: Ref for Dot6del # 2

tag: Ref for Dot6del # 2

source_name: Rap1 IP with AB Dot6del Log # 2

tag: Rap1 IP with AB Dot6del Log # 2


title: Mock-Tap IP post-diauxic shift (72 hrs) #1

description: Mock ChIP-chip using Tap affinity tag on untagged strain (BY4741) during post-diauxic-shift OD 6.034 #1.Strain - BY4741

source_name: Mock Reference DNA

tag: Mock Reference DNA

extract_protocol: IP DNA isoloated from 1mg protein from WCE by affinity purification of Rap1-Tap.  Using Tap-Tag TEV cleavage protocol.


title: Rap1 IP with AB on dot6del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on dot6del culture # 3 during expontential growth OD 0.9003. DYE-SWAP. Strain - dot6del, BY4741

source_name: Rap1 IP with AB in Dot6del #3

tag: Rap1 IP with AB in Dot6del #3

source_name: Ref Dot6del #3

tag: Ref Dot6del #3


title: Mock-Tap IP diauxic shift (24 hrs) #2

description: Mock ChIP-chip using Tap affinity tag on untagged strain (BY4741) during diauxic-shift OD 5.964 #2. Dye-swap Strain - BY4741

source_name: Mock-Tap IP

tag: Mock-Tap IP diauxic shift (24 hrs) #2


title: Rap1 IP with AB on sut1del during expontential growth culture #3

description: Rap1 ChIP-chip using RAP1-AB (y-300) on sut1del culture # 3 during expontential growth OD 0.6675. Strain - sut1del, BY4741

source_name: Rap1 IP with AB in sut1del culture # 3

tag: Rap1 IP with AB in sut1del culture # 3


title: Mock-Tap IP post-diauxic shift (168 hrs) #1

description: Mock ChIP-chip using Tap affinity tag on untagged strain (BY4741) during post- diauxic-shift (168 hrs) OD 6.00 #1.Strain -BY4741

growth_protocol: Post-Diauxic Shift 168 hrs


title: Mock-Tap IP diauxic shift (24 hrs) #1

description: Mock ChIP-chip using Tap affinity tag on untagged strain (BY4741) during diauxic-shift OD 6.320 #1.Strain - BY4741

source_name: Mock-Tap IP diauxic shift (24 hrs) #1

tag: Mock-Tap IP diauxic shift (24 hrs) #1


title: Mock-Tap IP during expontential growth #1

description: Mock ChIP-chip using Tap affinity tag on untagged strain (S288C) during expontential growth OD 0.7750 #1.Strain - S288C


title: Mock-Tap IP post-diauxic shift (168 hrs) #2

description: Mock ChIP-chip using Tap affinity tag on untagged strain (BY4741) during post- diauxic-shift (168 hrs) OD 5.50 #2. Dye-swap.Strain - BY4741


title: Mock-Tap IP during expontential growth #2

description: Mock ChIP-chip using Tap affinity tag on untagged strain (S288C) during expontential growth OD 0.7267 #2.Strain - S288C


title: Mock-Tap IP post-diauxic shift (72 hrs) #2

description: Mock ChIP-chip using Tap affinity tag on untagged strain (BY4741) during post- diauxic-shift (72 hrs) OD 5.880 #2. Dye-swapStrain - BY4741


title: Rap1-Tap IP during post-diauxic shift (168 hrs) culture #10

description: Rap1 ChIP-chip using Tap affinity tag on culture # 10 during post-diuaxic shift (168 hrs) OD 3.735 in the absence of glucose. Dye-swap.Strain - Rap1-Tap, BY4741

source_name: Rap1-Tap IP

source_name: Rap1-Tap Ref

tag: Rap1-Tap Input Reference


title: Rap1-Tap IP during post-diauxic shift (72 hrs) culture #10

description: Rap1 ChIP-chip using Tap affinity tag on culture # 10 during post-diuaxic shift (72 hrs) OD 4.136 in the absence of glucose. Strain - Rap1-Tap, BY4741

source_name: Rap1-Tap Reference DNA

tag: Rap1-Tap Reference DNA


title: Rap1-Tap IP during diauxic shift (24 hrs) culture #11

description: Rap1 ChIP-chip using Tap affinity tag on culture # 11 during diuaxic shift (24 hrs) OD 2.661 in the absence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during stationary phase (504 hrs) culture #5

description: Rap1 ChIP-chip using Tap affinity tag on culture # 5 during stationary phase (504 hrs) OD 3.790 in the absence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741

growth_protocol: Stationary Phase 504 hrs


title: Rap1-Tap IP during diauxic shift (24 hrs) culture #10

description: Rap1 ChIP-chip using Tap affinity tag on culture # 10 during diuaxic shift (24 hrs) OD 1.897 in the absence of glucose. Strain - Rap1-Tap, BY4741661 in the absence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (168 hrs) culture #7

description: Rap1 ChIP-chip using Tap affinity tag on culture # 7 during post-diuaxic shift (168 hrs) OD 4.447 in the absence of glucose. Dye-Swap Strain - Rap1-Tap


title: Rap1-Tap IP during diauxic shift (24 hrs) culture #7

description: Rap1 ChIP-chip using Tap affinity tag on culture # 7 during diuaxic shift (24 hrs) OD 2.806 in the absence of glucose. Dye-Swap Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during stationary phase (336 hrs) culture #5

description: Rap1 ChIP-chip using Tap affinity tag on culture # 5 during stationary phase (336 hrs) OD 3.910 in the absence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741

growth_protocol: Stationary Phase 336 hrs


title: Rap1-Tap IP during post-diauxic shift (72 hrs) culture #5

description: Rap1 ChIP-chip using Tap affinity tag on culture # 5 during post-diuaxic shift (72 hrs) OD 4.900 in the absence of glucose. Dye-swap.Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during stationary phase (336 hrs) culture #7

description: Rap1 ChIP-chip using Tap affinity tag on culture # 7 during stationary phase (336 hrs) OD 3.728 in the absence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (168 hrs) culture #6

description: Rap1 ChIP-chip using Tap affinity tag on culture # 6 during post-diuaxic shift (168 hrs) OD 4.188 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (72 hrs) culture #4

description: Rap1 ChIP-chip using Tap affinity tag on culture # 4 during post-diuaxic shift (72 hrs) OD 4.974 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during diauxic shift (24 hrs) culture #8

description: Rap1 ChIP-chip using Tap affinity tag on culture # 8 during diuaxic shift (24 hrs) OD 2.600 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (72 hrs) culture #9

description: Rap1 ChIP-chip using Tap affinity tag on culture # 9 during post-diuaxic shift (72 hrs) OD 4.166 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (168 hrs) culture #11

description: Rap1 ChIP-chip using Tap affinity tag on culture # 11 during post-diuaxic shift (168 hrs) OD 4.966 in the absence of glucose.Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during stationary phase (336 hrs) culture #6

description: Rap1 ChIP-chip using Tap affinity tag on culture # 6 during stationary phase (336 hrs) OD 3.523 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during stationary phase (336 hrs) culture #4

description: Rap1 ChIP-chip using Tap affinity tag on culture # 4 during stationary phase (336 hrs) OD 3.987 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during stationary phase (504 hrs) culture #4

description: Rap1 ChIP-chip using Tap affinity tag on culture # 4 during stationary phase (504 hrs) OD 4.006 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (72 hrs) culture #6

description: Rap1 ChIP-chip using Tap affinity tag on culture # 6 during post-diuaxic shift (72 hrs) OD 4.675 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (72 hrs) culture #7

description: Rap1 ChIP-chip using Tap affinity tag on culture # 7 during post-diuaxic shift (72 hrs) OD 4.960 in the absence of glucose. Dye-swap Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (168 hrs) culture #9

description: Rap1 ChIP-chip using Tap affinity tag on culture # 9 during post-diuaxic shift (168 hrs) OD 3.821 in the absence of glucose.Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during expontential growth culture #5

description: Rap1 ChIP-chip using Tap affinity tag on culture # 5 during expontential growth OD 0.663 in the presence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during post-diauxic shift (72 hrs) culture #11

description: Rap1 ChIP-chip using Tap affinity tag on culture # 11 during post-diuaxic shift (72 hrs) OD 5.511 in the absence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during diauxic shift (24 hrs) culture #9

description: Rap1 ChIP-chip using Tap affinity tag on culture # 9 during diuaxic shift (24 hrs) OD 1.820 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during diauxic shift (24 hrs) culture #6

description: Rap1 ChIP-chip using Tap affinity tag on culture # 6 during diuaxic shift (24 hrs) OD 2.588 in the absence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during expontential growth culture #1 Dye-Swap Rep

description: Rap1 ChIP-chip using Tap affinity tag on culture # 1 during expontential growth OD 1.025 in the presence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741

source_name: S288C genomic DNA Reference

tag: S288C genomic DNA Reference


title: Rap1-Tap IP during expontential growth culture #2 Dye-Swap Rep

description: Rap1 ChIP-chip using Tap affinity tag on culture # 2 during expontential growth OD 0.676 in the presence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741

tag: Rap1-Tap Input DNA


title: Rap1-Tap IP during expontential growth culture #4

description: Rap1 ChIP-chip using Tap affinity tag on culture # 4 during expontential growth OD 0.600 in the presence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during expontential growth culture #3 Dye-Swap Rep

description: Rap1 ChIP-chip using Tap affinity tag on culture # 3 during expontential growth OD 0.729 in the presence of glucose. Dye-swap. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during expontential growth culture #3

description: Rap1 ChIP-chip using Tap affinity tag on culture # 3 during expontential growth OD 0.729 in the presence of glucose. Strain - Rap1-Tap, BY4741


title: Rap1-Tap IP during expontential growth culture #2

description: Rap1 ChIP-chip using Tap affinity tag on culture # 2 during expontential growth OD 0.676 in the presence of glucose. Strain - Rap1-Tap, BY4741


title: Stage 1, PT#5,Normal (HG-U133A)

status: Public on Nov 23 2006

type: RNA

city: Jacksonville

first: John

middle: A

last: Copland

state: FL

address: 4500 San Pablo Road

department: Biochemistry & Molecular Biology

institute: Mayo Clinic College of Medicine

description: Normal HRE

hyb_protocol: Follow fragmentation, 10ug of cRNA were hybridized for 16 hrs at 45C on HG U133A and HG U133B Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed with GCOS 1.2 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human Renal Epithelium

label_protocol: Biotinylated cRNA were prepared accordiing to the standard Affymetrix protocol from 8.4 ug of total RNA

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

tag: Normal, PT#5, STG1


title: Rap1-Tap IP during expontential growth culture #1

description: Rap1 ChIP-chip using Tap affinity tag on culture # 1 during expontential growth OD 1.025 in the presence of glucose. Strain - Rap1-Tap, BY4741


title: Cardia vs whole female midgut 2

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: 2-dye hybridization assay

hyb_protocol: agilent

scan_protocol: genepix

data_processing: genepix

organism: Anopheles gambiae

source_name: Cardia part 4 day old female unfed midgut 2

label_protocol: agilent

extract_protocol: qiagen

source_name: 4 day old female unfed midgut 2c

tag: 4 day old female unfed midgut 2c


title: Anterior-posterior vs whole female midgut 3

description: 2-dye hybridization assay

source_name: Anterior-posterior part 4 day old female unfed midgut 3

source_name: 4 day old female unfed midgut 3b

tag: 4 day old female unfed midgut 3b


title: Aerobic pH 7.0 rep4

status: Public on Mar 23 2006

city: Gambier

first: Joan

middle: Lyn

last: Slonczewski

state: OH

address: 202 N. College Rd

department: Biology Dept

institute: Kenyon College

description: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7. Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3. For each of the three pH conditions, RNA was isolated from five independent cultures.

hyb_protocol: Affymetrix standard procedures

scan_protocol: Affymetrix standard procedures

data_processing: Affymetrix GCOS software

organism: Escherichia coli K-12

source_name: Escherichia coli K-12 W3110

label_protocol: Labeled cDNA was prepared and hybridized to Affymetrix Antisense E. coli arrays by standard procedures.

growth_protocol: Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7. Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3. Five replicate cultures were grown at each pH.

extract_protocol: RNA was isolated using RNAprotect (Qiagen) and the RNeasy Kit.

treatment_protocol: Growth at pH 7.0

tag: Escherichia coli K-12 W3110


title: Aerobic pH 8.7 rep3

treatment_protocol: Growth at pH 8.7


title: Aerobic pH 7.0 rep5


title: Aerobic pH 7.0 rep2


title: Aerobic pH 5.0 rep5

treatment_protocol: Growth at pH 5.0


title: Aerobic pH 8.7 rep5


title: Aerobic pH 5.0 rep2


title: Aerobic pH 8.7 rep2


title: Aerobic pH 8.7 rep4


title: Aerobic pH 7.0 rep1


title: Aerobic pH 5.0 rep3


title: Stage 1, PT#5,Normal (HG-U133B)

description: Normal HRE


title: Aerobic pH 7.0 rep3


title: Aerobic pH 8.7 rep1


title: Aerobic pH 5.0 rep4


title: Aerobic pH 5.0 rep1

description: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7.  Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3.    For each of the three pH conditions, RNA was isolated from five independent cultures.

growth_protocol: Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7.  Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3.    Five replicate cultures were grown at each pH.


title: glucose pulse (0.2g/l) on  galactose chemostat (t=30min)

status: Public on Feb 03 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58959.gif

source_name: ref- t=0

tag: ref- t=0


title: glucose pulse (0.2g/l) on  galactose chemostat (t=15min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58957.gif


title: glucose pulse (0.2g/l) on  galactose chemostat (t=45min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58960.gif


title: glucose pulse (0.2g/l) on  galactose chemostat (t=2min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58952.gif


title: glucose pulse (0.2g/l) on  galactose chemostat (t=8min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58955.gif


title: glucose pulse (2g/l) on galactose chemostat (t=210min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58919.gif


title: glucose pulse (0.2g/l) on  galactose chemostat (t=4min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58953.gif


title: glucose pulse (0.2g/l) on  galactose chemostat (t=120min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58962.gif


title: glucose pulse (0.2g/l) on  galactose chemostat (t=6min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58954.gif


title: glucose pulse (0.2g/l) on  galactose chemostat (t=10min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58956.gif


title: glucose pulse (0.2g/l) on  galactose chemostat (t=150min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58963.gif


title: glucose pulse (2g/l) on galactose chemostat (t=7min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58909.gif


title: Surgical Sham Control Tail Skin 2

status: Public on Mar 04 2006

first: Roger

last: Wagner

department: Falk Cardiovascular Research Center

institute: Stanford University School of Medicine

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67347.gif; format: GIF

organism: Mus musculus

source_name: Reference RNA e17.5 embryo

tag: Reference RNA e17.5 embryo

source_name: Surgical Sham Tail skin

tag: Surgical Sham Tail skin


title: Surgical Sham Control Tail Skin 3

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67348.gif; format: GIF


title: glucose pulse (0.2g/l) on  galactose chemostat (t=20min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58958.gif


title: Lymphedema Tail Skin 1

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67343.gif; format: GIF

source_name: Lymphedema Tail skin

tag: Lymphedema Tail skin


title: Lymphedema Tail Skin 2

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67344.gif; format: GIF


title: glucose pulse (2g/l) on galactose chemostat (t=150min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58917.gif


title: Surgical Sham Control Tail Skin 1

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67346.gif; format: GIF


title: glucose pulse (0.2g/l) on  galactose chemostat (t=90min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58961.gif


title: Lymphedema Tail Skin 3

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67345.gif; format: GIF


title: Normal Tail Skin 1

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67340.gif; format: GIF

source_name: Normal Tail skin

tag: Normal Tail skin


title: Mammary gland R1 8 hr rep4

status: Public on Jan 01 2006

city: Houston

first: Kathryn

last: Schwertfeger

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: iFGFR1 mammary gland 8 hr AP20187

data_processing: MAS 5.0

label: Affymetrix

source_name: iFGFR1 mammary gland 8 hr AP20187

tag: Strain

value: FVB

tag: Genotype

tag: Gender

value: Female

tag: Age

value: 6 weeks

tag: Tissue

value: Mammary gland

tag: Treatment


title: Mammary gland R1 NT rep4

description: iFGFR1 mammary gland not treated

source_name: iFGFR1 mammary gland not treated

value: not treated


title: glucose pulse (2g/l) on galactose chemostat (t=20min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58912.gif


title: Normal Tail Skin 2

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67341.gif; format: GIF


title: Mammary gland R1 8 hr rep3

description: iFGFR1 mammary gland 8 hr AP20187

tag: Treament


title: glucose pulse (2g/l) on galactose chemostat (t=120min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58916.gif


title: glucose pulse (2g/l) on galactose chemostat (t=30min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58913.gif


title: glucose pulse (2g/l) on galactose chemostat (t=5min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58908.gif


title: glucose pulse (2g/l) on galactose chemostat (t=10min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58910.gif


title: Normal Tail Skin 3

description:
Simple annotation: Diseased tissue, Vascular injury
Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67342.gif; format: GIF


title: Mammary gland R1 16 hr rep3

description: iFGFR1 mammary gland 16 hr AP20187

source_name: iFGFR1 mammary gland 16 hr AP20187


title: Mammary gland R1 8 hr rep2

description: iFGFR2 mammary gland 8 hrs AP20187

source_name: iFGFR2 mammary gland 8 hrs AP20187


title: Mammary gland R1 24 hr rep2

description: iFGFR1 mammary gland 24 hr AP20187

source_name: iFGFR1 mammary gland 24 hr AP20187


title: Mammary gland R1 NT rep2

description: iFGFR1 mammary gland not treated


title: Mammary gland R1 24 hr rep1

description: iFGFR1 mammary gland 24 hrs AP20187

source_name: iFGFR1 mammary gland 24 hrs AP20187


title: Mammary gland R1 16 hr rep2

description: iFGFR1 mammary gland 16 hr AP20187


title: glucose pulse (2g/l) on galactose chemostat (t=3min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58907.gif


title: Mammary gland R1 16 hr rep4

description: iFGFR1 mammary gland 16 hr AP20187


title: glucose pulse (2g/l) on galactose chemostat (t=45min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58914.gif


title: glucose pulse (2g/l) on galactose chemostat (t=240min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58920.gif


title: glucose pulse (2g/l) on galactose chemostat (t=15min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58911.gif


title: Mammary gland R1 24 hr rep4

description: iFGFR1 mammary gland 24 hr AP20187


title: glucose pulse (2g/l) on galactose chemostat (t=90min)

description:
Simple annotation: Chemostat, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58915.gif


title: Rat fatty liver15

status: Public on Sep 16 2004

city: Cambridge

first: Julian

last: Griffin

address: Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
Rats (Charles River UK Ltd.) were fed either standard laboratory chow, or chow supplemented with 1% orotic acid (Sigma Aldrich, UK) ad libitum. Orotic acid feeding is a well-characterised method for inducing reversible fatty liver disease in rodents. Rats were killed by cervical dislocation and the left lateral lobe of the liver excised. Tissues were snap frozen and stored in liquid nitrogen and/or at –80oC.

Keywords = orotic acid
Lot batch = 1

hyb_protocol: Biotinylated cRNA was fragmented and hybridised to RGU34A Affymetrix GeneChips according to standard Affymetrix protocols.

scan_protocol: Performed according to standard Affymetrix protocols.

data_processing: Data were analysed with the Affymetrix Microarray Suite 5.0 algorithm to generate a “signal” value and a “detection” label. Prior to normalisation, probes that generated an absent call in all cells were removed. Normalisation was calculated using a Global Scaling method based on the entire data set. Globally scaled values <10 were rounded up to 10.

organism: Rattus norvegicus

source_name: Wistar rat liver tissue (control)

label_protocol: cDNA was generated from total RNA using SuperscriptTM Double-stranded cDNA Synthesis kit (Invitrogen, Life Technologies), cRNA was prepared by in vitro transcription (BioArray High Yield RNA transcript labelling kit Affymetrix, UK), and purified on an affinity resin column (RNeasy, Qiagen Ltd., UK).

extract_protocol: Total RNA was extracted by RNA Isolation Kit (Stratagene) from the livers of Wistar and Kyoto rats at day 0 (Wistar n=3, Kyoto n=2), day 1 and 3 (Wistar n=2, Kyoto n=2), and day 14 (Wistar n=3, Kyoto n=2).

tag: Kyoto rat liver tissue following animal exposure to orotic acid for 3 days


title: Mammary gland R1 24 hr rep3

description: iFGFR1 mammary gland 24 hr AP20187


title: Mammary gland R1 NT rep3

description: iFGFR1 mammary gland NT

source_name: iFGFR1 mammary gland NT


title: Rat fatty liver5

source_name: Kyoto Rat liver tissue following animal exposure to orotic acid for 14 days

tag: Kyoto rat liver tissue following animal exposure to orotic acid for 1 day


title: Rat fatty liver18

status: Public on Oct 08 2004

description:
Rats (Charles River UK Ltd.) were fed either standard laboratory chow, or chow supplemented with 1% orotic acid (Sigma Aldrich, UK) ad libitum. Orotic acid feeding is a well-characterised method for inducing reversible fatty liver disease in rodents. Rats were killed by cervical dislocation and the left lateral lobe of the liver excised. Tissues were snap frozen and stored in liquid nitrogen and/or at –80oC.

Keywords = orotic acid

source_name: Wistar rat liver following animal exposure to orotic acid for 14 days


title: Rat fatty liver13

source_name: Wistar rat liver tissue following animal exposure to orotic acid for 14 days


title: Mammary gland R1 16 hr rep1

description: iFGFR1 mammary gland 16 hrs AP20187

source_name: iFGFR1 mammary gland 16 hrs AP20187


title: Rat fatty liver2

source_name: Kyoto rat liver tissue following animal exposure to orotic acid for 1 day


title: Mammary gland R1 NT rep1

description: iFGFR1 mammary gland 0hr

source_name: iFGFR1 mammary gland 0hr

value: not treated (0 hour)


title: Rat fatty liver19

source_name: Wistar rat liver tissue following animal no exposure to orotic acid  (control)


title: Mammary gland R1 8 hr rep1

description: iFGFR1 mammary gland 8 hrs AP20187

source_name: iFGFR1 mammary gland 8 hrs AP20187