title: 2wk J w1

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57133.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.43; Parameter Scan Time = 18:54:01; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 202174; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.20; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.43; Parameter Scan Time = 18:54:01; Parameter PMT Volts = 640; Parameter Scan Date = 2004-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 421143; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.62; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 2wk B m2

status: Public on Aug 15 2007

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57128.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 33.04; Parameter Scan Time = 23:58:52; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-13; Parameter Pixel Size = 10; Parameter Laser on time = 198333; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 33.04; Parameter Scan Time = 23:58:52; Parameter PMT Volts = 690; Parameter Scan Date = 2004-10-13; Parameter Pixel Size = 10; Parameter Laser on time = 417301; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

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

molecule: total RNA

organism: Mus musculus

source_name: reference

label_protocol:
not provided
Extract preparation - Channel 1; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 1 (green); Protocol Type = Extract preparation; Parameter Channel 1 reference name = pooled mouse cerebellum RNA; Performer: Charandle,,Jordan
Labeling - Channel 1; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 1 (green).; Protocol Type = Labeling; Parameter Name = Cyscribe First Strand Labeling Kit (Amersham Biosciences); Performer: Charandle,,Jordan

extract_protocol: not provided

tag: reference

source_name: mutant

label_protocol:
not provided
Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Notebook page = Notebooks #5-6 pages 1-200; Performer: Charandle,,Jordan
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Cell Type = Prepared from Cerebellum; Performer: Charandle,,Jordan
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Date prepared = 2004-2005; Parameter Channel 2 reference name = mutant cerebellum cDNA; Parameter Extraction method = Trizol Reagent (Invitrogen/Gibco); Performer: Charandle,,Jordan
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Name = Cyscribe First Strand Labeling Kit (Amersham Biosciences); Performer: Charandle,,Jordan

tag: mutant


title: 4wk J w2

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57299.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.34; Parameter Scan Time = 22:30:25; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 204561; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.34; Parameter Scan Time = 22:30:25; Parameter PMT Volts = 610; Parameter Scan Date = 2004-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 423495; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.61; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

label_protocol:
not provided
Growth Conditions; Parameters that describe the conditions under which the biological sample was grown or propagated; Protocol Type = Growth Conditions; Parameter Notebook page = Notebooks #5-6 pages 1-200; Performer: Charandle,,Jordan
Biological Sample - Channel 2; Characteristics of the original biological sample used to generate the extract that was labeled and scanned in channel 2 (red).; Protocol Type = Biological Sample; Parameter Cell Type = Prepared from Cerebellum; Performer: Charandle,,Jordan
Extract preparation - Channel 2; Methods by which RNA/DNA/protein is prepared from a biological sample prior to amplification or labeling for channel 2 (red).; Protocol Type = Extract preparation; Parameter Date prepared = 2004-2005; Parameter Channel 2 reference name = wild-type cerebellum cDNA; Parameter Extraction method = Trizol Reagent (Invitrogen/Gibco); Performer: Charandle,,Jordan
Labeling - Channel 2; Methods for labeling extracted molecules that are used in hybridizations and scanned in Channel 2 (red); Protocol Type = Labeling; Parameter Name = Cyscribe First Strand Labeling Kit (Amersham Biosciences); Performer: Charandle,,Jordan


title: 8wk B m3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52754.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 4960; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 31.03; Parameter Scan Time = 01:26:11; Parameter PMT Volts = 520; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 167937; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.06; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 31.03; Parameter Scan Time = 01:26:11; Parameter PMT Volts = 720; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 386908; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.69; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: mut

tag: mut


title: 8wk B m2

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52752.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 00:30:09; Parameter PMT Volts = 520; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 167881; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.75; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 00:30:09; Parameter PMT Volts = 720; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 386852; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.68; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 4wk B m1

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54275.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 31.18; Parameter Scan Time = 07:59:43; Parameter PMT Volts = 540; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 183957; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.17; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 31.18; Parameter Scan Time = 07:59:43; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 402925; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: ref

tag: ref


title: 4wk B m2

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54273.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1640, 5120; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 31.61; Parameter Scan Time = 08:26:15; Parameter PMT Volts = 590; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 183983; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.55; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 31.61; Parameter Scan Time = 08:26:15; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 402951; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.68; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 8wk J m1

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55318.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 31.82; Parameter Scan Time = 00:06:43; Parameter PMT Volts = 530; Parameter Scan Date = 2004-09-03; Parameter Pixel Size = 10; Parameter Laser on time = 190074; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.63; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 31.82; Parameter Scan Time = 00:06:43; Parameter PMT Volts = 580; Parameter Scan Date = 2004-09-03; Parameter Pixel Size = 10; Parameter Laser on time = 409042; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: mutant - 57

tag: mutant - 57


title: 8wk J m2

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55320.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 01:23:09; Parameter PMT Volts = 540; Parameter Scan Date = 2004-09-03; Parameter Pixel Size = 10; Parameter Laser on time = 190149; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.25; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 01:23:09; Parameter PMT Volts = 560; Parameter Scan Date = 2004-09-03; Parameter Pixel Size = 10; Parameter Laser on time = 409117; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 8wk J w1

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55319.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 31.61; Parameter Scan Time = 23:48:20; Parameter PMT Volts = 550; Parameter Scan Date = 2004-09-02; Parameter Pixel Size = 10; Parameter Laser on time = 190055; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 31.61; Parameter Scan Time = 23:48:20; Parameter PMT Volts = 570; Parameter Scan Date = 2004-09-02; Parameter Pixel Size = 10; Parameter Laser on time = 409023; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 8wk B m6

description:
Simple annotation: Mutant vs Wild-type, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52760.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 4720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.22; Parameter Scan Time = 02:52:57; Parameter PMT Volts = 580; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 170660; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.10; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.22; Parameter Scan Time = 02:52:57; Parameter PMT Volts = 660; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 389630; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.69; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 2wk J m1

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57132.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.34; Parameter Scan Time = 18:44:50; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 202164; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.05; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.34; Parameter Scan Time = 18:44:50; Parameter PMT Volts = 640; Parameter Scan Date = 2004-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 421132; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.63; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: wt

tag: wt


title: 8wk B m4

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52757.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 4800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 31.03; Parameter Scan Time = 02:09:14; Parameter PMT Volts = 520; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 167981; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.17; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 31.03; Parameter Scan Time = 02:09:14; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 386951; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.69; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 2wk J m2

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57134.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.49; Parameter Scan Time = 19:01:56; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 202182; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.57; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.49; Parameter Scan Time = 19:01:56; Parameter PMT Volts = 640; Parameter Scan Date = 2004-10-30; Parameter Pixel Size = 10; Parameter Laser on time = 421150; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.62; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 8wk B w5

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52759.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 4880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 01:42:16; Parameter PMT Volts = 530; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 170589; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 01:42:16; Parameter PMT Volts = 680; Parameter Scan Date = 2004-05-28; Parameter Pixel Size = 10; Parameter Laser on time = 389560; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.73; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 8wk B w4

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52756.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 4960; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.97; Parameter Scan Time = 01:52:29; Parameter PMT Volts = 520; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 167964; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.97; Parameter Scan Time = 01:52:29; Parameter PMT Volts = 700; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 386935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.69; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 8wk B m1

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52751.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.84; Parameter Scan Time = 00:17:11; Parameter PMT Volts = 520; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 167869; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.84; Parameter Scan Time = 00:17:11; Parameter PMT Volts = 720; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 386840; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

label_protocol: not provided


title: 2wk B w1

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57130.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.52; Parameter Scan Time = 22:47:29; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-13; Parameter Pixel Size = 10; Parameter Laser on time = 198263; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.16; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.52; Parameter Scan Time = 22:47:29; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-13; Parameter Pixel Size = 10; Parameter Laser on time = 417231; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.64; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 2wk B m1

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57129.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.58; Parameter Scan Time = 19:46:27; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-13; Parameter Pixel Size = 10; Parameter Laser on time = 198082; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.58; Parameter Scan Time = 19:46:27; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-13; Parameter Pixel Size = 10; Parameter Laser on time = 417050; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.63; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: PrSC TGFb3/PrSC Ctrl reversed 51 20070327

city: Bethesda

first: Christopher

last: Pan

state: MD

address: Rm 5228, Bldg 50, South Dr.

department: NHGRI

institute: NIH

description: Human prostate stromal cells (PrSC)

hyb_protocol: The combined Cy3 and Cy5 labeled cDNAs are put in a total volume of 250 ul DEPC H20 and 250 ul of 2X Agilent hybridization buffer. The mixture is then denatured for 2 minutes and applied on the Agillent hybridization chamber/gasket slide in sandwich with the array slide. The hybridization is performed at 65 degre for 16 hours.

scan_protocol: Agilent Scanner

data_processing: IPLab/DeArray Linear Offset normalized

organism: Homo sapiens

source_name: Human prostate stromal cells (PrSC)

label_protocol: 15 microgram of total RNA was reverse transcribed with Anchor Oligo-dT and Aminoallyl dUTP, after NaOH RNA hydrolysis, the labeled Aminoallyl dUTP cDNA is purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104). The Aminoallyl dUTP cDNAs are then coupled with either Cy3 or Cy5 mono NHS Ester Dyes. The CyDyes labeled cDNAs are then purified with Qiagen, QIAQuick PCR Purification Kit (Cat. # 28104).

extract_protocol: RNA was extracted with Trizol/Chloroform method according to manifecturer protocol and the RNA is further purified by the Qiagen RNAeazy columns

tag: PrSC TGFb3

source_name: PrSC Ctrl

tag: Human prostate stromal cells (PrSC)


title: 8wk B w1

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52750.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.84; Parameter Scan Time = 00:03:07; Parameter PMT Volts = 550; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 167855; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.84; Parameter Scan Time = 00:03:07; Parameter PMT Volts = 720; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 386825; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.69; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 2wk B w2

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57131.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 33.01; Parameter Scan Time = 23:47:46; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-13; Parameter Pixel Size = 10; Parameter Laser on time = 198322; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 33.01; Parameter Scan Time = 23:47:46; Parameter PMT Volts = 690; Parameter Scan Date = 2004-10-13; Parameter Pixel Size = 10; Parameter Laser on time = 417290; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 8wk B w2

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52753.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 00:43:09; Parameter PMT Volts = 520; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 167895; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 00:43:09; Parameter PMT Volts = 720; Parameter Scan Date = 2004-05-15; Parameter Pixel Size = 10; Parameter Laser on time = 386865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: LN_MSM_10uM_6h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28390.gif

scan_protocol: not provided

source_name: 14.5 uM selenium LNCaP total RNA

tag: 14.5 uM selenium LNCaP total RNA

source_name: MSM 10 uM 6h LNCaP total RNA

tag: MSM 10 uM 6h LNCaP total RNA


title: LN_MSM_10uM_24h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28398.gif

source_name: MSM 10 uM 24h LNCaP total RNA

tag: MSM 10 uM 24h LNCaP total RNA


title: PrSC TGFb3/PrSC Ctrl reversed 52 20070327

description: Human prostate stromal cells (PrSC)


title: LN_MSM_10uM_18h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28395.gif

source_name: MSM 10 uM 18h LNCaP total RNA

tag: MSM 10 uM 18h LNCaP total RNA


title: K1106

type: genomic

city: Vancouver

first: Lindsey

last: Kimm

state: British Columbia

address: 675 W10th Ave

department: Cancer Genetics

country: Canada

institute: BC Cancer Research Centre

description: tumor DNA (cy3) hybridized against normal male pooled reference DNA (cy5)

hyb_protocol: Hybridization solution: 80% DIG-easy, 10% sheared herring sperm DNA, 10% yeast tRNA. Probe was blocked using 100ug human CoT-1 DNA and hybridized to the slide at 45C for ~36 hours under a 24x60mm coverslip in a hybrization cassette. Wash: 4X 0.1% SDS/0.1X SSC at 45C. Rinse: 4X 0.1X SSC, room temp. Dried with an oil-free air stream.

scan_protocol: Scanned at 10um resolution on a Applied Precision Instruments AutoE CCD-based scanner.

data_processing: Data was obtained from the scanned image files generated using SoftWoRx Tracker software from Applied Precision. Obtained data was normalized using a three-step normalization procedure; (Khojasteh et al BMC Bioinformatics 2005;6:274).

label: Cyanine 3

molecule: genomic DNA

label_protocol: Random prime reaction

tag: PMBCL tumor cell line

label: Cyanine 5

source_name: Male pooled genomic DNA

tag: Male pooled genomic reference DNA


title: LN_MSM_10uM_9h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28391.gif

source_name: MSM 10 uM 9h LNCaP total RNA

tag: MSM 10 uM 9h LNCaP total RNA


title: LN_MSM_10uM_1h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28383.gif

source_name: MSM 10 uM 1h LNCaP total RNA

tag: MSM 10 uM 1h LNCaP total RNA


title: LN_MSM_10uM_15h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28393.gif


title: PMBCL1

hyb_protocol: Hybridization solution: 80% DIG-easy, 10% sheared herring sperm DNA, 10% yeast tRNA.  Probe was blocked using 100ug human CoT-1 DNA and hybridized to the slide at 45C for ~36 hours under a 24x60mm coverslip in a hybrization cassette.  Wash: 4X 0.1% SDS/0.1X SSC at 45C.  Rinse: 4X 0.1X SSC, room temp.  Dried with an oil-free air stream.

data_processing: Data was obtained from the scanned image files generated using SoftWoRx Tracker software from Applied Precision.  Obtained data was normalized using a three-step normalization procedure; (Khojasteh et al BMC Bioinformatics 2005;6:274).

tag: PMBCL tumor DNA


title: Standard+TZ-Expt. 3, Rep. 3

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62752.gif
Developmental Stage: Tachyzoite-infected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 6960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.88; Parameter Scan Time = 17:11:20; Parameter PMT Volts = 760; Parameter Scan Date = 2005-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 38673; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.95; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.88; Parameter Scan Time = 17:11:20; Parameter PMT Volts = 850; Parameter Scan Date = 2005-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 111808; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.00; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 400ng Reference

tag: 400ng Reference

source_name: 400ng Tachyzoite Infected HFF

tag: 400ng Tachyzoite Infected HFF


title: Standard-Expt. 2a, Rep.1

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44329.gif
Developmental Stage: Uninfected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1720, 6120; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.30; Parameter Scan Time = 14:23:33; Parameter PMT Volts = 570; Parameter Scan Date = 2003-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 83537; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.82; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.30; Parameter Scan Time = 14:23:33; Parameter PMT Volts = 730; Parameter Scan Date = 2003-08-20; Parameter Pixel Size = 10; Parameter Laser on time = 83474; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.74; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 300ng HFF, Standard Medium

tag: 300ng HFF, Standard Medium


title: LN_MSM_10uM_2h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28385.gif

source_name: MSM 10 uM 2h LNCaP total RNA

tag: MSM 10 uM 2h LNCaP total RNA


title: Standard+TZ-Expt. 2a, Rep. 1

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44549.gif
Developmental Stage: Tachyzoite-infected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1960, 6760; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Ashley,,Fouts 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 = 36.03; Parameter Scan Time = 18:46:38; Parameter PMT Volts = 630; Parameter Scan Date = 2003-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 84191; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts 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 = 36.03; Parameter Scan Time = 18:46:38; Parameter PMT Volts = 780; Parameter Scan Date = 2003-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 84127; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.75; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 400ng Tachyzoite Infected HFF, Standard Medium


title: Stress+BZ-Expt. 3, Rep. 2

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47843.gif
Developmental Stage: Bradyzoite-infected, stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 6120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.67; Parameter Scan Time = 18:52:20; Parameter PMT Volts = 650; Parameter Scan Date = 2003-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 89542; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.99; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.67; Parameter Scan Time = 18:52:20; Parameter PMT Volts = 720; Parameter Scan Date = 2003-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 89478; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.82; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 400ng Bradyzoite Infected HFF, Stress Medium


title: Standard-Expt. 3, Rep. 3

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62827.gif
Developmental Stage: Uninfected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 7120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.45; Parameter Scan Time = 13:49:39; Parameter PMT Volts = 720; Parameter Scan Date = 2005-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 38944; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.81; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.45; Parameter Scan Time = 13:49:39; Parameter PMT Volts = 820; Parameter Scan Date = 2005-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 112079; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.73; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 300ng Uninfected HFF Standard Medium

tag: 300ng Uninfected HFF Standard Medium


title: Standard-Expt. 1, Rep. 1

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62826.gif
Developmental Stage: Uninfected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1130, 7150; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.91; Parameter Scan Time = 13:38:16; Parameter PMT Volts = 720; Parameter Scan Date = 2005-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 38933; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.77; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.91; Parameter Scan Time = 13:38:16; Parameter PMT Volts = 820; Parameter Scan Date = 2005-07-25; Parameter Pixel Size = 10; Parameter Laser on time = 112068; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.69; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 300ng Uninfected HFF, Standard Medium

tag: 300ng Uninfected HFF, Standard Medium


title: Standard-Expt. 3, Rep. 2

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47840.gif
Developmental Stage: Uninfected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.16; Parameter Scan Time = 18:09:55; Parameter PMT Volts = 640; Parameter Scan Date = 2003-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 89499; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.16; Parameter Scan Time = 18:09:55; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 89436; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.82; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: Reference 400ng

tag: Reference 400ng

source_name: 300ng Uninfected HFF, Standard medium

tag: 300ng Uninfected HFF, Standard medium


title: Standard+TZ-Expt. 3, Rep. 2

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47842.gif
Developmental Stage: Tachyzoite-infected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 6600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.55; Parameter Scan Time = 18:40:42; Parameter PMT Volts = 630; Parameter Scan Date = 2003-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 89530; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.90; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.55; Parameter Scan Time = 18:40:42; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 89467; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.82; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 400ng Tachyzoite infected HFF

tag: 400ng Tachyzoite infected HFF


title: Stress-Expt. 3, Rep. 2

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47841.gif
Developmental Stage: Uninfected Stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.39; Parameter Scan Time = 18:25:30; Parameter PMT Volts = 630; Parameter Scan Date = 2003-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 89515; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.39; Parameter Scan Time = 18:25:30; Parameter PMT Volts = 700; Parameter Scan Date = 2003-12-22; Parameter Pixel Size = 10; Parameter Laser on time = 89451; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.82; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 300ng Uninfected HFF, Stress Medium

tag: 300ng Uninfected HFF, Stress Medium


title: 4wk B w5

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59793.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 6160; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.07; Parameter Scan Time = 16:12:23; Parameter PMT Volts = 590; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 203159; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.07; Parameter Scan Time = 16:12:23; Parameter PMT Volts = 630; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 567963; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: Stress-Expt. 2a, Rep. 1

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44473.gif
Developmental Stage: Uninfected Stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1880, 7060; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Ashley,,Fouts 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 = 33.72; Parameter Scan Time = 12:34:26; Parameter PMT Volts = 640; Parameter Scan Date = 2003-08-26; Parameter Pixel Size = 10; Parameter Laser on time = 84001; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.81; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts 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 = 33.72; Parameter Scan Time = 12:34:26; Parameter PMT Volts = 780; Parameter Scan Date = 2003-08-26; Parameter Pixel Size = 10; Parameter Laser on time = 83937; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.74; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts


title: PrSC TGFb3/PrSC Ctrl 53 20070327

description: Human prostate stromal cells (PrSC)

scan_protocol: Agilent Scanner

source_name: Human prostate stromal cells (PrSC)

tag: PrSC TGFb3

source_name: PrSC Ctrl

tag: Human prostate stromal cells (PrSC)


title: 4wk B m4

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59798.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 6840; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.83; Parameter Scan Time = 15:47:01; Parameter PMT Volts = 590; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 203133; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.83; Parameter Scan Time = 15:47:01; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 567937; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.95; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 2wk J w3

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58013.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 6080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.43; Parameter Scan Time = 06:26:24; Parameter PMT Volts = 490; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 208354; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.43; Parameter Scan Time = 06:26:24; Parameter PMT Volts = 550; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 427357; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.59; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: reference

tag: reference

source_name: wt

tag: wt


title: 2wk J w4

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58015.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 480, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 05:53:38; Parameter PMT Volts = 490; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 196425; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.84; Parameter Scan Time = 05:53:38; Parameter PMT Volts = 520; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 561228; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 4wk B m5

description:
Simple annotation: Mutant vs Wild-type, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59792.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 6160; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.01; Parameter Scan Time = 16:03:55; Parameter PMT Volts = 590; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 203149; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.01; Parameter Scan Time = 16:03:55; Parameter PMT Volts = 640; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 567953; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.94; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 2wk J m3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58010.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 31.82; Parameter Scan Time = 05:32:54; Parameter PMT Volts = 490; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 208304; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 31.82; Parameter Scan Time = 05:32:54; Parameter PMT Volts = 550; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 427307; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.61; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: mutant

tag: mutant


title: 4wk B w4

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59797.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 6840; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.77; Parameter Scan Time = 15:38:50; Parameter PMT Volts = 570; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 203126; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.77; Parameter Scan Time = 15:38:50; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 567929; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: Stress+BZ-Expt. 2a, Rep. 2

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44474.gif
Developmental Stage: Bradyzoite-infected, stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 5880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Ashley,,Fouts 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 = 35.64; Parameter Scan Time = 12:19:14; Parameter PMT Volts = 640; Parameter Scan Date = 2003-08-26; Parameter Pixel Size = 10; Parameter Laser on time = 83985; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.83; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts 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 = 35.64; Parameter Scan Time = 12:19:14; Parameter PMT Volts = 770; Parameter Scan Date = 2003-08-26; Parameter Pixel Size = 10; Parameter Laser on time = 83921; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.75; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 400ng Reference

tag: 400ng Bradyzoite Infected HFF, Stress Medium


title: 4wk B m3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59795.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 6560; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.42; Parameter Scan Time = 15:16:24; Parameter PMT Volts = 570; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 203102; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.42; Parameter Scan Time = 15:16:24; Parameter PMT Volts = 660; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 567906; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.88; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: Stress+BZ-Expt. 2a, Rep. 1

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-08/44598.gif
Developmental Stage: Bradyzoite-infected, stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts 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 = 36.01; Parameter Scan Time = 18:59:16; Parameter PMT Volts = 630; Parameter Scan Date = 2003-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 84203; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts 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 = 36.01; Parameter Scan Time = 18:59:16; Parameter PMT Volts = 770; Parameter Scan Date = 2003-08-28; Parameter Pixel Size = 10; Parameter Laser on time = 84139; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.76; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts


title: 4wk B w3

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59796.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 760, 6840; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.60; Parameter Scan Time = 15:26:13; Parameter PMT Volts = 570; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 203112; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.60; Parameter Scan Time = 15:26:13; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 567916; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.88; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: Wild-type primary fibroblast 1 vs reference RNA

description:
Simple annotation: Transcription, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59826.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Jon,,Reddy

source_name: Amplified stratagene reference RNA

tag: Amplified stratagene reference RNA

source_name: Amplified AG10803 wild-type primary fibroblasts


title: 4wk J w1

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57298.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.25; Parameter Scan Time = 22:23:25; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 204554; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.96; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.25; Parameter Scan Time = 22:23:25; Parameter PMT Volts = 610; Parameter Scan Date = 2004-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 423489; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.61; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: Wild-type primary fibroblast 3 vs reference RNA

description:
Simple annotation: Transcription, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59827.gif

source_name: Amplified GM09503 wild-type primary fibroblasts


title: 4wk B w7

description:
Simple annotation: Mutant vs Wild-type, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59794.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 6640; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.20; Parameter Scan Time = 16:22:43; Parameter PMT Volts = 590; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 203169; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.20; Parameter Scan Time = 16:22:43; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-19; Parameter Pixel Size = 10; Parameter Laser on time = 567973; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: Standard+TZ-Expt. 2b, Rep. 2

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57146.gif
Developmental Stage: Tachyzoite-infected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.98; Parameter Scan Time = 14:35:32; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-03; Parameter Pixel Size = 10; Parameter Laser on time = 103779; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.98; Parameter Scan Time = 14:35:32; Parameter PMT Volts = 670; Parameter Scan Date = 2004-11-03; Parameter Pixel Size = 10; Parameter Laser on time = 103716; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.00; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

tag: 400ng Reference


title: Niemann-Pick type C primary fibroblast 4 vs reference RNA

description:
Simple annotation: Transcription, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59830.gif

source_name: Amplified GM18453 Niemann-Pick type C primary fibroblasts


title: Wild-type primary fibroblast 4 vs reference RNA

description:
Simple annotation: Transcription, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60731.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Jon,,Reddy

source_name: Amplified GM03726 wild-type primary fibroblasts


title: Niemann-Pick type C primary fibroblast 3 vs reference RNA

description:
Simple annotation: Transcription, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60729.gif

source_name: Amplified 83.16 Niemann-Pick type C primary fibroblasts


title: Stress-Expt. 2b, Rep. 2

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57145.gif
Developmental Stage: Uninfected Stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.86; Parameter Scan Time = 14:23:35; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-03; Parameter Pixel Size = 10; Parameter Laser on time = 103767; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.86; Parameter Scan Time = 14:23:35; Parameter PMT Volts = 670; Parameter Scan Date = 2004-11-03; Parameter Pixel Size = 10; Parameter Laser on time = 103703; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts


title: Niemann-Pick type C primary fibroblast 1 vs reference RNA

description:
Simple annotation: Transcription, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59831.gif

source_name: Amplified GM17909 Niemann-Pick type C primary fibroblasts


title: S. aureus vs PBS injection whole mosquitoes Rep1

city: Baltimore

first: George

last: Dimopoulos

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins School of Public Health

description: AGILENT

hyb_protocol: AGILENT

scan_protocol: AXON

data_processing: GENEPIX

organism: Anopheles gambiae

source_name: Intrathoracically injection of A. gambiae with S. aureus, whole mosquitoes RNA collected at 4 hours after injection (Rep1)

label_protocol: AGILENT

extract_protocol: QIAGEN

source_name: PBS injection whole A. gambiae mosquitoes at 4 hours

tag: Intrathoracically injection of A. gambiae with PBS, whole mosquitoes RNA collected at 4 hours after injection


title: Stress-Expt. 2b, Rep. 3

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57198.gif
Developmental Stage: Uninfected Stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 4480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts 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 = 32.37; Parameter Scan Time = 16:16:08; Parameter PMT Volts = 610; Parameter Scan Date = 2004-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 17023; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts 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 = 32.37; Parameter Scan Time = 16:16:08; Parameter PMT Volts = 690; Parameter Scan Date = 2004-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 190638; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.56; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts


title: Wild-type primary fibroblast 2 vs reference RNA

description:
Simple annotation: Transcription, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59829.gif

source_name: Amplified GM05659 wild-type primary fibroblasts


title: Standard+TZ-Expt. 1, Rep. 2

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46645.gif
Developmental Stage: Tachyzoite-infected Standard

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts 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 = 36.63; Parameter Scan Time = 19:10:53; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 88536; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts 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 = 36.63; Parameter Scan Time = 19:10:53; Parameter PMT Volts = 730; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 88472; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.90; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 400ng Tachyzoite Infected HFF Standard Medium


title: Stress+BZ-Expt. 2b, Rep. 3

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57196.gif
Developmental Stage: Bradyzoite-infected, stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1060, 4680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts 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 = 32.89; Parameter Scan Time = 16:51:06; Parameter PMT Volts = 610; Parameter Scan Date = 2004-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 17059; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts 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 = 32.89; Parameter Scan Time = 16:51:06; Parameter PMT Volts = 690; Parameter Scan Date = 2004-11-05; Parameter Pixel Size = 10; Parameter Laser on time = 190674; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.58; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 400ng Bradyzoite Infected HFF, Stress Medium


title: PfWT vs CTRP GUT 2

description: AGILENT

source_name: Pf WT infected A. gambiae GUT at 24 hours rep 2

source_name: Pf CTRP infected A. gambiae GUT at 24 hours


title: 2wk J m4

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58012.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan 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 = 32.28; Parameter Scan Time = 06:09:35; Parameter PMT Volts = 490; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 208340; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.01; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan 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 = 32.28; Parameter Scan Time = 06:09:35; Parameter PMT Volts = 550; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 427343; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.60; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: reference

source_name: mut

tag: mut