title: T47D monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59148.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 5970; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.19; Parameter Scan Time = 17:33:41; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215798; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.98; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.19; Parameter Scan Time = 17:33:41; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434804; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/HMEC co-culture 2

status: Public on Nov 14 2007

type: RNA

city: Basel

first: Martin

last: Buess

state: CH

address: Petersgraben 4

department: Medizinische Onkologie

country: Switzerland

institute: University Hospital Basel

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59623.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.30; Parameter Scan Time = 10:51:33; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220089; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 30.36; Parameter Scan Time = 09:16:47; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439000; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.50; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

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: Homo sapiens

source_name: stratagene human reference

label_protocol:
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess
amplified RNA dircect inocorporaton; The protocol was modified for amplified RNA: 1. 6ug of amplified RNA and 10ug of random hexamer primer were mixed in a total volume of 15.4 ul. Then the described protocol was followed.; Protocol Type = Labeling; Performer: Martin,,Buess

extract_protocol: not provided

tag: StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer

value: Martin,,Buess

label_protocol:
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess
amplified RNA direct incorporation method; The protocol was modified for amplified RNA:  6ug of amplified RNA was mixed with 10ug of random hexamer primer pd(N)6( Procuct number 27-2166-01, Amersham Biosciences) in a total volume of 15.4 ul. Then the protocol was followed as described; Protocol Type = Labeling; Performer: Martin,,Buess

growth_protocol: Co-culture conditions; Human mammary epithelial cells (HMEC) (Cambrex Bio Science Walkersville, Inc) were expanded in mammary epithelial basal medium supplemented with bovine pituitary extract, human EGF, insulin and antibiotics (Clonetics, Cambrex Bio Science Walkersville, Inc). MCF-7, T47D, MDA-MB231, MDA-MB436, SKBR-3,  Hs578T, BT549, CCL-171, HTB-125 (ATTC) and HDF (Cambrex Bio Science Walkersville, Inc) were propagated in DMEM supplemented with 10% FBS (HyClone, Logan UT), glutamine, 100U/ml penicillin and 100 μg/ml streptomycin (GIBCO, Grand Island, N.Y.). For co-culture experiments the cells were cultivated for 48 hours at 50,000 cells/cm2 in endothelial basal media (CAMBREX Bio Science Rockland, Inc Rockland, Maine) with 0.2% FBS, which was a good universal media for all cells involved. Separated co-cultures were kept in Transwell? chambers 0.4μm pore size (Costar, Corning Inc. Corning, NY). Cells negatively tested for mycoplasma infection using MycoAlert Tm (CAMBREX Bio Science Rocland, Inc Rockland, Maine) and VenorGem? (SIGMA, Saint Louis, Missouri) mycoplasma detection kits according to the manufacturer?s instructions.; Protocol Type = Biological Sample; Performer: Martin,,Buess

extract_protocol: RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Martin,,Buess

tag: LabeledExtract


title: BT549 monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59150.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1350, 5770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 15:34:05; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215679; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 15:34:05; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434685; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: MDA-MB436 monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59147.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1350, 5770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.24; Parameter Scan Time = 15:12:32; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215658; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.24; Parameter Scan Time = 15:12:32; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434664; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.50; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125 monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59620.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5500; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.21; Parameter Scan Time = 10:40:08; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220078; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.93; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.21; Parameter Scan Time = 10:40:08; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439084; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: HTB

tag: HTB


title: CCL-171/MCF-7 co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57141.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5590; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.98; Parameter Scan Time = 11:32:55; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 203490; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.63; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.98; Parameter Scan Time = 11:32:55; Parameter PMT Volts = 600; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 422424; 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: Martin,,Buess


title: Hs578T monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59143.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 5070; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.06; Parameter Scan Time = 16:58:51; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215764; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.06; Parameter Scan Time = 16:58:51; Parameter PMT Volts = 630; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434770; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: Hs578 T

tag: Hs578 T


title: CCL-171/MCF-7 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57140.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5590; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 33.07; Parameter Scan Time = 11:45:30; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 203502; 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: Martin,,Buess 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 = 33.07; Parameter Scan Time = 11:45:30; Parameter PMT Volts = 570; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 422437; 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: Martin,,Buess


title: HDF/MCF-7 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57142.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1500, 5970; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.92; Parameter Scan Time = 11:21:54; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 203480; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.92; Parameter Scan Time = 11:21:54; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 422414; 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: Martin,,Buess


title: CCL-171 /BT549 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59142.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 4880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 15:00:52; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215646; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 15:00:52; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434652; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.50; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

label_protocol: not provided

tag: stratagene human reference


title: CCL-171/SKBR3 co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56882.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1610, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 10:49:16; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 201514; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.91; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 10:49:16; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 420483; 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: Martin,,Buess

source_name: stratagene common reference

source_name: CCL-171 /SKBR3

tag: CCL-171 /SKBR3


title: HDF/SKBR3 co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56884.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1610, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 30.78; Parameter Scan Time = 10:13:17; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 201479; 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: Martin,,Buess 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 = 30.78; Parameter Scan Time = 10:13:17; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 420447; 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: Martin,,Buess


title: MCF-7 monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53651.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 30.94; Parameter Scan Time = 09:13:04; Parameter PMT Volts = 550; Parameter Scan Date = 2004-07-10; Parameter Pixel Size = 10; Parameter Laser on time = 179281; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 30.94; Parameter Scan Time = 09:13:04; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-10; Parameter Pixel Size = 10; Parameter Laser on time = 398250; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.74; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: BT549 monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59145.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 6020; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 16:07:43; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215713; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.76; Parameter Scan Time = 16:07:43; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434719; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171/ MCF-7 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53509.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 5640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.31; Parameter Scan Time = 14:00:31; Parameter PMT Volts = 570; Parameter Scan Date = 2004-07-03; Parameter Pixel Size = 10; Parameter Laser on time = 177256; 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: Martin,,Buess 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 = 32.31; Parameter Scan Time = 14:00:31; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-03; Parameter Pixel Size = 10; Parameter Laser on time = 396224; 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: Martin,,Buess


title: CCL-171 /Hs578T co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59140.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 5210; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 15:46:03; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215691; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.16; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 15:46:03; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434698; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: HTB-125/MCF-7 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59624.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1100, 5750; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.70; Parameter Scan Time = 11:52:37; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 220150; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.04; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.70; Parameter Scan Time = 11:52:37; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-24; Parameter Pixel Size = 10; Parameter Laser on time = 439157; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: T47D monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59149.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 5070; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 16:47:31; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215753; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 16:47:31; Parameter PMT Volts = 630; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434759; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171/SKBR3 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56881.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1610, 5560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.45; Parameter Scan Time = 10:59:55; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 201524; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.89; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.45; Parameter Scan Time = 10:59:55; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 420493; 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: Martin,,Buess

source_name: CCL 171 /SKBR3

tag: CCL 171 /SKBR3


title: CCL-171/ MDA-MB231 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53507.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 13:25:19; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-03; Parameter Pixel Size = 10; Parameter Laser on time = 177221; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.81; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 13:25:19; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-03; Parameter Pixel Size = 10; Parameter Laser on time = 396189; 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: Martin,,Buess


title: CCL-171/SKBR3 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53508.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.19; Parameter Scan Time = 13:36:37; Parameter PMT Volts = 580; Parameter Scan Date = 2004-07-03; Parameter Pixel Size = 10; Parameter Laser on time = 177232; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.92; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.19; Parameter Scan Time = 13:36:37; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-03; Parameter Pixel Size = 10; Parameter Laser on time = 396201; 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: Martin,,Buess


title: HDF/SKBR3 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56883.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1540, 5620; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 11:44:23; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 201569; 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: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 11:44:23; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 420537; 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: Martin,,Buess


title: HMEC monoculture 4

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56557.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.92; Parameter Scan Time = 12:28:32; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199448; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.92; Parameter Scan Time = 12:28:32; Parameter PMT Volts = 610; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418417; 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: Martin,,Buess

source_name: HMEC

tag: HMEC


title: MDA-MB231 monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56555.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 5290; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.19; Parameter Scan Time = 10:23:38; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199325; 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: Martin,,Buess 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 = 32.19; Parameter Scan Time = 10:23:38; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418293; 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: Martin,,Buess


title: MDA-MB231 monoculture 3

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56556.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 33.25; Parameter Scan Time = 13:02:35; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199482; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 33.25; Parameter Scan Time = 13:02:35; Parameter PMT Volts = 640; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418450; 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: Martin,,Buess


title: CCL-171/MDA-MB231 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56559.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 6000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.70; Parameter Scan Time = 09:38:33; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199279; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.70; Parameter Scan Time = 09:38:33; Parameter PMT Volts = 620; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418247; 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: Martin,,Buess

source_name: MDA MB231/CCL 171

tag: MDA MB231/CCL 171


title: Hs578T monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59144.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1300, 5750; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 17:55:55; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215820; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.06; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 17:55:55; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434826; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171 monoculture 5

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56552.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 33.16; Parameter Scan Time = 12:50:54; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199471; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.92; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 33.16; Parameter Scan Time = 12:50:54; Parameter PMT Volts = 620; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418439; 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: Martin,,Buess


title: HDF monoculture 3

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56554.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6060; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 33.50; Parameter Scan Time = 13:28:08; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199508; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.75; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 33.50; Parameter Scan Time = 13:28:08; Parameter PMT Volts = 750; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418476; 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: Martin,,Buess

source_name: HDF

tag: HDF


title: HDF monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56553.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1540, 5620; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 33.35; Parameter Scan Time = 17:00:12; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199719; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 33.35; Parameter Scan Time = 17:00:12; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418687; 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: Martin,,Buess


title: HMEC monoculture 5

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56558.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1540, 5620; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 33.10; Parameter Scan Time = 16:35:50; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199695; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 33.10; Parameter Scan Time = 16:35:50; Parameter PMT Volts = 720; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418664; 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: Martin,,Buess


title: MDA-MB436 monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59146.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1380, 5520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 16:19:48; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 215725; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 16:19:48; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 434731; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: CCL-171 monoculture 4

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56551.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 11:10:29; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199371; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 11:10:29; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418340; 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: Martin,,Buess


title: CCL-171 monoculture 3

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56191.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 30.57; Parameter Scan Time = 09:10:39; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 196142; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 30.57; Parameter Scan Time = 09:10:39; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 415110; 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: Martin,,Buess


title: HDF/MCF-7 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53896.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 09:09:23; Parameter PMT Volts = 570; Parameter Scan Date = 2004-07-15; Parameter Pixel Size = 10; Parameter Laser on time = 182012; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.08; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 09:09:23; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-15; Parameter Pixel Size = 10; Parameter Laser on time = 400980; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.72; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: stratagen human reference


title: MCF-7 monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57135.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1390, 5590; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 33.32; Parameter Scan Time = 12:32:20; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 203549; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 33.32; Parameter Scan Time = 12:32:20; Parameter PMT Volts = 570; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 422484; 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: Martin,,Buess


title: HTB-125/SKBR3 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53891.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.79; Parameter Scan Time = 09:23:41; Parameter PMT Volts = 570; Parameter Scan Date = 2004-07-15; Parameter Pixel Size = 10; Parameter Laser on time = 182026; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.79; Parameter Scan Time = 09:23:41; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-15; Parameter Pixel Size = 10; Parameter Laser on time = 400995; 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: Martin,,Buess

source_name: HTB-125 /SKBR3

tag: HTB-125 /SKBR3


title: MDA-MB231 monoculture 4

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54252.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1740, 5950; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 09:19:57; Parameter PMT Volts = 590; Parameter Scan Date = 2004-07-28; Parameter Pixel Size = 10; Parameter Laser on time = 183854; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.94; Parameter Scan Time = 09:19:57; Parameter PMT Volts = 590; Parameter Scan Date = 2004-07-28; Parameter Pixel Size = 10; Parameter Laser on time = 402822; 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: Martin,,Buess


title: SKBR3 monoculture 3

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56878.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1540, 5620; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.70; Parameter Scan Time = 11:33:56; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 201559; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.73; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.70; Parameter Scan Time = 11:33:56; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 420527; 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: Martin,,Buess


title: SKBR3 monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53310.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1540, 5350; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.67; Parameter Scan Time = 13:04:37; Parameter PMT Volts = 570; Parameter Scan Date = 2004-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 176034; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.97; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.67; Parameter Scan Time = 13:04:37; Parameter PMT Volts = 640; Parameter Scan Date = 2004-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 395002; 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: Martin,,Buess

source_name: stragene human reference


title: MCF-7 monoculture 3

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57136.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1390, 5590; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 33.38; Parameter Scan Time = 12:43:38; Parameter PMT Volts = 580; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 203560; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 33.38; Parameter Scan Time = 12:43:38; Parameter PMT Volts = 590; Parameter Scan Date = 2004-11-02; Parameter Pixel Size = 10; Parameter Laser on time = 422495; 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: Martin,,Buess


title: Muscle HRT baseline 1216

status: Public on Nov 12 2007

city: Jyväskylä

first: Eija

last: Pöllänen

address: PO Box 35/Viveca

department: Department of Health Sciences

country: Finland

institute: University of Jyväskylä

description: This sample presents baseline sample of ID_1216 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

hyb_protocol: Employing protocols by Illumina Inc.; hybridization: 17 h at 55 degC

scan_protocol: Using an Illumina BeadReader containin two lasers: 532 nm and 635 nm and performing with 0.8 microns resolution. The data was acquired by the BeadStudio Direct Hybridization V.1.5.0.34

data_processing: The raw data was acquired by the BeadStudio Direct Hybridization V.1.5.0.34 (Illumina inc) and quantile normalized with Inforsense KDE 3.1 (InforSense Inc.) software

source_name: vastus lateralis muscle, HRT user, baseline

label_protocol: Illumina RNA amplification kit (Ambion Inc., #I1755) was used according to manufacturer’s instructions. Input amount: 500 ng of total RNA.

extract_protocol: Frozen muscle biopsy samples were homogenized in Trizol-reagent (Invitrogen Inc.) with aid of FastPrep FP120 -apparatus (MP Biomedicals). Manufacturer’s protocol was followed through the isolation procedure.

treatment_protocol: needle muscle biopsy, immediately frozen in liquid nitrogen after extrication from biobsy needle, stored at - 70 degC until RNA extraction

tag: Gender

value: female

tag: Age

value: 55 at onset of intervention

tag: menopausal status

value: early postmenopausal


title: Muscle HRT follow-up 1216

description: This sample presents follow-up sample of ID_1216 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, HRT user, follow-up


title: HTB-125/MCF-7 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54177.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 08:57:11; Parameter PMT Volts = 570; Parameter Scan Date = 2004-07-15; Parameter Pixel Size = 10; Parameter Laser on time = 182001; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.68; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.55; Parameter Scan Time = 08:57:11; Parameter PMT Volts = 610; Parameter Scan Date = 2004-07-15; Parameter Pixel Size = 10; Parameter Laser on time = 400969; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.72; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: HTB 125/MCF7

tag: HTB 125/MCF7


title: Muscle HRT follow-up 1092

description: This sample presents follow-up sample of ID_1092 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

value: 52.5 at onset of intervention


title: CCL-171 /HMEC co-culture 5

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56570.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 12:39:03; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199459; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 12:39:03; Parameter PMT Volts = 610; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418427; 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: Martin,,Buess

tag: stratagene common reference


title: HDF/SKBR3 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54178.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1310, 5580; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 09:48:56; Parameter PMT Volts = 580; Parameter Scan Date = 2004-06-27; Parameter Pixel Size = 10; Parameter Laser on time = 176585; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 09:48:56; Parameter PMT Volts = 640; Parameter Scan Date = 2004-06-27; Parameter Pixel Size = 10; Parameter Laser on time = 395553; 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: Martin,,Buess


title: SKBR3 monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56877.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1540, 5620; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 11:23:30; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 201548; 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: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 11:23:30; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-28; Parameter Pixel Size = 10; Parameter Laser on time = 420516; 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: Martin,,Buess


title: HMEC monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53258.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1700, 5660; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.16; Parameter Scan Time = 13:39:42; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-23; Parameter Pixel Size = 10; Parameter Laser on time = 175832; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.16; Parameter Scan Time = 13:39:42; Parameter PMT Volts = 680; Parameter Scan Date = 2004-06-23; Parameter Pixel Size = 10; Parameter Laser on time = 394800; 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: Martin,,Buess


title: CCL-171/HMEC co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55987.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5870; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 30.81; Parameter Scan Time = 09:22:17; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 196153; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 30.81; Parameter Scan Time = 09:22:17; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 415121; 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: Martin,,Buess


title: HDF/HMEC co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53257.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1770, 5590; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.09; Parameter Scan Time = 13:52:37; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-23; Parameter Pixel Size = 10; Parameter Laser on time = 175845; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.09; Parameter Scan Time = 13:52:37; Parameter PMT Volts = 680; Parameter Scan Date = 2004-06-23; Parameter Pixel Size = 10; Parameter Laser on time = 394814; 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: Martin,,Buess

source_name: HDF/HMEC

tag: HDF/HMEC


title: Muscle HRT baseline 1092

description: This sample presents baseline sample of ID_1092 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: Muscle non-HRT follow-up 94

description: This sample presents follow-up sample of ID_94 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, non-HRT user, baseline

value: 51.5 at onset of intervention


title: HMEC monoculture 3

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55986.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1430, 5250; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 10:43:31; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 196235; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 10:43:31; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 415203; 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: Martin,,Buess

source_name: stratagene human reference

label_protocol: amplified RNA dircect inocorporaton; The protocol was modified for amplified RNA: 1. 6ug of amplified RNA and 10ug of random hexamer primer were mixed in a total volume of 15.4 ul. Then the described protocol was followed.; Protocol Type = Labeling; Performer: Martin,,Buess

tag: StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer

label_protocol: amplified RNA direct incorporation method; The protocol was modified for amplified RNA:  6ug of amplified RNA was mixed with 10ug of random hexamer primer pd(N)6( Procuct number 27-2166-01, Amersham Biosciences) in a total volume of 15.4 ul. Then the protocol was followed as described; Protocol Type = Labeling; Performer: Martin,,Buess


title: MDA-MB231 monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53095.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.06; Parameter Scan Time = 09:19:56; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-16; Parameter Pixel Size = 10; Parameter Laser on time = 173767; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.06; Parameter Scan Time = 09:19:56; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-16; Parameter Pixel Size = 10; Parameter Laser on time = 392738; 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: Martin,,Buess

tag: LabeledExtract


title: HDF/HMEC co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56569.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.71; Parameter Scan Time = 11:23:20; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199384; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.71; Parameter Scan Time = 11:23:20; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418352; 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: Martin,,Buess

source_name: HMEC/HDF

tag: HMEC/HDF


title: HDF/MDA-MB 231 co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56566.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 5960; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 10:12:02; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199313; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.31; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.03; Parameter Scan Time = 10:12:02; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418282; 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: Martin,,Buess


title: mouse_fasted-gut_72h_5-6

city: Amsterdam

first: Milka

last: Sokolovic

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: AMC

description: Gene-expression profiling, pathway analysis, and immunohistochemistry were carried out on mouse small intestine after 0, 12, 24, and 72 hours of fasting to look at the gut's adaptive response to fasting.

hyb_protocol: Hybridization protocol that acompanies the Agilent's 60-mer Mouse Development (22K) Oligo Microarray G4120A was strictly followed

scan_protocol: Agilent’s dual-laser microarray slide scanner was used. The data were retrieved with Agilent’s Feature Extraction software 6.1.1.

data_processing: Value column represents Log(REDsignal/GREENsignal) per feature. Processed signals from Agilent feature extraction file were used.

organism: Mus musculus

source_name: 72h fasted gut, 5&6

label_protocol: 20 μg mRNA, pooled from 2 intestines (5&6), was reverse transcribed with Cy3-labelled dCTP (Perkin Elmer, Boston, USA), using the Agilent Fluorescent Direct Label Kit.

extract_protocol: Total intestinal RNA was extracted from frozen tissue with guanidiniumthiocyanate, followed by cesium-chloride centrifugation to avoid contamination with mucus. The quality of RNA was assessed with the RNA 6000 Nano LabChip® Kit in an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Mice were housed at 20-22°C, 50-60% humidity, a 12 hours light/dark cycle, and food and water ad libitum. At 6 weeks of age, mice were fasted by removing chow for up to 72 hours before sacrifice (n = 6 per group). The animals were kept in metabolic cages to prevent the consumption of beddings and were kept warm with an infrared lamp starting at 24h. All animals were sacrificed between 9:00 and 10:00 a.m. by cervical dislocation. The small intestine was removed quickly in such a way that adherent tissue remained behind, it was opened longitudinally, rinsed in phosphate-buffered saline, blotted, weighed, snap-frozen in liquid N2, and stored at -80°C.

tag: Male FVB mice, at 6 weeks of age, 72h fasted

source_name: fed gut, 1-6

label_protocol: Cy5-labeled cDNA produced from RNA pooled from 6 fed animals served as the common reference across all arrays

tag: Male FVB mice, at 6 weeks of age, fed


title: CCL-171 monoculture 2

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55983.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.21; Parameter Scan Time = 16:26:55; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 196439; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.87; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.21; Parameter Scan Time = 16:26:55; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 415407; 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: Martin,,Buess


title: HDF monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53093.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 09:48:17; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-16; Parameter Pixel Size = 10; Parameter Laser on time = 173798; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.85; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 09:48:17; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-16; Parameter Pixel Size = 10; Parameter Laser on time = 392768; 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: Martin,,Buess