title: Em-38-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65816.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 530, 34970; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 460; Parameter Laser on time = 73157; Parameter Laser Power = 3.48; Parameter Scan Time = 13:30:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 73417; Parameter Laser Power = 3.76; Parameter Scan Time = 13:30:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.41; Performer: Nina,,Salama

tag: Emory strain Em-38-1


title: Em-4-3

status: Public on Nov 05 2009

type: genomic

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65828.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 860, 9200; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-14; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 460; Parameter Laser on time = 73127; Parameter Laser Power = 3.45; Parameter Scan Time = 13:00:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-14; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 73387; Parameter Laser Power = 3.75; Parameter Scan Time = 13:00:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Nina,,Salama

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

molecule: genomic DNA

organism: Helicobacter pylori

source_name: 500 ng 26695/J99 genomic DNA mix

label_protocol: 500 ng of genomic DNA of a reference sample (equimolar mix of 26695 and J99) was labeled with Cy3

extract_protocol: Genomic DNA extracted from reference strains 26695 and J99, and then mixed in equimolar concentrations.

tag: Equimolar mix of strains 26695/J99

tag: Reference DNA

label_protocol: 500 ng of genomic DNA of each test strain was labeled with Cy5

extract_protocol: Initial strain isolation from antral biopsies performed at Emory and culture sweeps sent to FHCRC (Seattle) for analysis. Single colony isolates (4) from each patient antral biopsy were isolated and profiled using RAPD. A single clone of each RAPD type detected in each patient (1-2) were analyzed. Genomic DNA was extracted and analyzed on duplicate arrays.

tag: Test Strain

tag: Emory strain Em-4-3


title: Em-42-3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65826.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1680, 8880; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 69444; Parameter Laser Power = 3.44; Parameter Scan Time = 09:33:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.90; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 630; Parameter Scan Power = 100; Parameter Laser on time = 69470; Parameter Laser Power = 3.64; Parameter Scan Time = 09:33:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.90; Performer: Nina,,Salama

tag: Emory strain Em-42-3


title: Em-20-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65777.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1160, 9510; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-05; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 74904; Parameter Laser Power = 3.48; Parameter Scan Time = 10:07:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 26.66; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-05; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 570; Parameter Scan Power = 100; Parameter Laser on time = 75295; Parameter Laser Power = 3.53; Parameter Scan Time = 10:07:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 26.66; Performer: Nina,,Salama

tag: Emory strain Em-20-1


title: Em-46-3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2008-10/81727.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1510, 8970; Software: type: feature extraction; Performer: Nina,,Salama 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 Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.78; Performer: Nina,,Salama 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 Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.78; Performer: Nina,,Salama

tag: Emory strain Em-46-3


title: Em-29-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65791.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1800, 8280; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 75993; Parameter Laser Power = 3.45; Parameter Scan Time = 11:08:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 76422; Parameter Laser Power = 3.74; Parameter Scan Time = 11:08:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.04; Performer: Nina,,Salama

tag: Emory strain Em-29-1


title: Em-7-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65854.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 480, 8640; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 73417; Parameter Laser Power = 3.46; Parameter Scan Time = 12:24:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.25; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 73677; Parameter Laser Power = 3.74; Parameter Scan Time = 12:24:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.25; Performer: Nina,,Salama

tag: Emory strain Em-7-1


title: Em-30-3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65795.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1640, 34440; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 700; Parameter Laser on time = 68887; Parameter Laser Power = 3.50; Parameter Scan Time = 12:48:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.76; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 810; Parameter Scan Power = 100; Parameter Laser on time = 68912; Parameter Laser Power = 3.68; Parameter Scan Time = 12:48:51; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.76; Performer: Nina,,Salama

tag: Emory strain Em-30-3


title: Em-9-2 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65859.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 35660; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 460; Parameter Laser on time = 67894; Parameter Laser Power = 3.61; Parameter Scan Time = 11:34:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.48; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 67952; Parameter Laser Power = 3.71; Parameter Scan Time = 11:34:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.48; Performer: Nina,,Salama

tag: Emory strain Em-9-2


title: Em-15-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65765.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 680, 9120; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-05; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 74884; Parameter Laser Power = 3.43; Parameter Scan Time = 09:48:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.95; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-05; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 75275; Parameter Laser Power = 3.49; Parameter Scan Time = 09:48:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.95; Performer: Nina,,Salama

tag: Emory strain Em-15-3


title: Em-29-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65790.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1350, 9510; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 75860; Parameter Laser Power = 3.45; Parameter Scan Time = 15:46:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.10; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 76289; Parameter Laser Power = 3.75; Parameter Scan Time = 15:46:46; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.10; Performer: Nina,,Salama


title: Em-6-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65853.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1510, 8520; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 480; Parameter Laser on time = 67647; Parameter Laser Power = 3.49; Parameter Scan Time = 11:54:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.94; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-06-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 67705; Parameter Laser Power = 3.73; Parameter Scan Time = 11:54:40; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.94; Performer: Nina,,Salama

tag: Emory strain Em-6-1


title: Em-48-3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65841.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 600, 6880; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-08-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 510; Parameter Laser on time = 71593; Parameter Laser Power = 3.45; Parameter Scan Time = 12:25:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.48; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-08-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 71731; Parameter Laser Power = 3.67; Parameter Scan Time = 12:25:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.48; Performer: Nina,,Salama

tag: Emory strain Em-48-3


title: Em-49-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65844.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2100, 35220; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-23; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 76162; Parameter Laser Power = 3.44; Parameter Scan Time = 11:56:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.83; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-23; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 560; Parameter Scan Power = 100; Parameter Laser on time = 76591; Parameter Laser Power = 3.76; Parameter Scan Time = 11:56:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.83; Performer: Nina,,Salama

tag: Emory strain Em-49-1


title: Em-34-3 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65807.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1350, 34530; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-16; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 590; Parameter Laser on time = 75873; Parameter Laser Power = 3.45; Parameter Scan Time = 15:59:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-11-16; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 76301; Parameter Laser Power = 3.76; Parameter Scan Time = 15:59:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.19; Performer: Nina,,Salama

tag: Emory strain Em-34-3


title: Em-38-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65817.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1870, 9190; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 530; Parameter Laser on time = 75242; Parameter Laser Power = 3.46; Parameter Scan Time = 09:11:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.38; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 640; Parameter Scan Power = 100; Parameter Laser on time = 75670; Parameter Laser Power = 3.76; Parameter Scan Time = 09:11:23; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 33.38; Performer: Nina,,Salama

tag: Emory strain Em-38-1


title: Em-13-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65761.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1330, 35470; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 500; Parameter Laser on time = 74646; Parameter Laser Power = 3.46; Parameter Scan Time = 15:29:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.20; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-09-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 580; Parameter Scan Power = 100; Parameter Laser on time = 75037; Parameter Laser Power = 3.82; Parameter Scan Time = 15:29:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 34.20; Performer: Nina,,Salama

tag: Equimolar mix of strains 26695/J99

tag: Emory strain Em-13-1


title: WT3 21d testis

type: RNA

city: Philadelphia

first: Jieyan

last: Pan

state: PA

address: 3800 Spruce Street

department: Department of Animal Biology

institute: University of Pennsylvania

description: gene expression data from 21d mouse testis

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: Affymetrix Microarray Suite 5.0 was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of 16 microarray sectors was set as background and subtracted from all features in that sector. Probe pairs were scored positive or negative for detection of the targeted sequence by comparing signals from the perfect match and mismatch probe features.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mouse  testis

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP

growth_protocol: Mice were housed under normal barrier condition

extract_protocol: Total RNA was extracted using Trizol reagent followed by purification using an RNeasy kit.

treatment_protocol: Testes were collected from juvenile mice at post-natal day 21. The testes were weighted and stored at -80°C.


title: Landrace_jejunum_day 28-A

status: Public on Nov 03 2009

city: Yaan

first: yunzi

last: sun

state: Sichuan

address: No36,Xingkang Road

department: Institute of Animal Nutrition,

country: China

institute: Sichuan Agricultural University

description: Landrace_jejunum_day 28-A

hyb_protocol: Follow manufacture’s  instructions, see at manufacture’s web site www.affymetrix.com

data_processing: The .dat image is analyzed for probe intensities; results are reported in tabular and graphical formats. Information on data analysis is provided in the enclosed GeneChip® Expression Analysis: Data Analysis Fundamentals booklet (P/N 701190).

organism: Sus scrofa

source_name: jejunum_total RNA_Landrace_day 28-A

extract_protocol: The porcine jejunum total RNA isolated by using TRIzol Reagent (invitrogen, Cat. No. 15596-018).

tag: The total RNA pool of porcine jejunum from 2 Landrace pigs

tag: Landrace Tissue

value: jejunum

tag: 28 days of birth

tag: A

value: animal protein diet


title: Landrace_jejunum_day 28-B

description: Landrace_jejunum_day 28-B

scan_protocol: Follow manufacture’s  instructions, see at manufacture’s web site www.affymetrix.com

source_name: jejunum_total RNA_Landrace_day 28-B

tag: B

value: vegetable protein diet


title: Nxf2 KO3 21d testis

source_name: mouse testis


title: Em-41-2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65822.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 35000; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 69109; Parameter Laser Power = 3.45; Parameter Scan Time = 10:26:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.06; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-07-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 69135; Parameter Laser Power = 3.63; Parameter Scan Time = 10:26:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.06; Performer: Nina,,Salama

tag: Reference DNA

tag: Test Strain

tag: Emory strain Em-41-2


title: Nxf2 KO2 21d testis


title: WT1 21d testis


title: Nxf2 KO1 21d testis


title: WT2 21d testis


title: Landrace_jejunum_day 35-B

description: Landrace_jejunum_day 35-B

label: Follow manufacture’s  instructions, see at manufacture’s web site www.affymetrix.com

source_name: jejunum_total RNA_Landrace_day 35-B

tag: 35 days of birth


title: Ecoli_wildtype_1%_butanol_Sample2_TechRep1

status: Public on Nov 01 2009

city: Princeton

first: Mark

last: Brynildsen

state: NJ

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

description: Cells were grown in MOPS media/0.2% glucose and aerobic conditions.

hyb_protocol: Samples were hybridized as specified in the Corning UltraGAPS manual.  Slides were blocked and washed as specified in the Corning UltraGAPS manual.

scan_protocol: Slides were scanned immediately after washing with a Virtek/BioRad scanner.

data_processing: Quantification of the scans were performed with ImaGene (Version 6.0.1; BioDiscovery; El Segundo, CA; www.biodiscovery.com); with the results presented in the associated text files.  The normalized data VALUE was generated using LOWESS normalization with rank invariant selection, as implemented in lcDNA (receptor.seas.ucla.edu/lcDNA; Hyduke DR, Rohlin L, Kao KC, Liao JC. 2003 A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7(3):227-234.)

organism: Escherichia coli

source_name: Ecoli wildtype grown in MOPS

label_protocol: Indirect labeling with amino-allyl dUTP

extract_protocol: Qiagen RNeasy Midikit

tag: Strain

source_name: Ecoli wildtype grown in MOPS, 10 minutes after 1% butanol treatment

treatment_protocol: Treated with 1% vol/vol butanol 10 minutes prior to harvest


title: Landrace_jejunum_day 24-A

description: Landrace_jejunum_day 24-A

source_name: jejunum_total RNA_Landrace_day 24-A

label_protocol: Follow manufacture’s  instructions, see at manufacture’s web site www.affymetrix.com

tag: 24 days of birth


title: Landrace_jejunum_day 35-A

description: Landrace_jejunum_day 35-A

source_name: jejunum_total RNA_Landrace_day 35-A


title: Landrace_jejunum_day 21

description: Landrace_jejunum_day 21

source_name: jejunum_total RNA_Landrace_day 21

tag: 21 days of birth


title: Landrace_jejunum_day 24-B

description: Landrace_jejunum_day 24-B

source_name: jejunum_total RNA_Landrace_day 24-B


title: Landrace_jejunum_day 8

description: Landrace_jejunum_day 8

source_name: jejunum_total RNA_Landrace_day 8

tag: 8 days of birth


title: Landrace_jejunum_day 0

description: Landrace_jejunum_day 0

source_name: jejunum_total RNA_Landrace_day 0

tag: 0 days (piglet was just born)


title: Ecoli_wildtype_1%_butanol_Sample2_TechRep2


title: Ecoli_wildtype_1%_butanol_Sample3_TechRep2


title: Em-40-1 dupl

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/65821.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1560, 8320; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-21; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 75215; Parameter Laser Power = 3.45; Parameter Scan Time = 08:44:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-10-21; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 75644; Parameter Laser Power = 3.73; Parameter Scan Time = 08:44:12; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.95; Performer: Nina,,Salama

tag: Emory strain Em-40-1


title: Landrace_jejunum_day 3

description: Landrace_jejunum_day 3

source_name: jejunum_total RNA_Landrace_day 3

tag: 3 days of birth


title: Ecoli_wildtype_3%_ethanol_Sample4_TechRep2

source_name: Ecoli wildtype grown in MOPS, 10 minutes after 3% ethanol treatment

treatment_protocol: Treated with 3% vol/vol ethanol 10 minutes prior to harvest


title: Ecoli_wildtype_3%_ethanol_Sample4_TechRep1


title: Ecoli_wildtype_1%_butanol_Sample3_TechRep1


title: Landrace_jejunum_day 14

description: Landrace_jejunum_day 14

source_name: jejunum_total RNA_Landrace_day 14

tag: 14 days of birth


title: Ecoli_wildtype_3%_ethanol_Sample3_TechRep1


title: Ecoli_ko_ihfA_1%_isobutanol_Sample2_TechRep2

source_name: Ecoli ko-ihfA grown in MOPS

source_name: Ecoli ko-ihfA grown in MOPS, 10 minutes after 1% isobutanol treatment

treatment_protocol: Treated with 1% vol/vol isobutanol 10 minutes prior to harvest


title: Ecoli_wildtype_1%_isobutanol_Sample3_TechRep2

source_name: Ecoli wildtype grown in MOPS, 10 minutes after 1% isobutanol treatment


title: Ecoli_ko_ihfA_1%_isobutanol_Sample2_TechRep1


title: Ecoli_wildtype_3%_ethanol_Sample2_TechRep2


title: Ecoli_ko_arcA_1%_isobutanol_Sample2_TechRep2

source_name: Ecoli ko-arcA grown in MOPS

source_name: Ecoli ko-arcA grown in MOPS, 10 minutes after 1% isobutanol treatment


title: Ecoli_wildtype_3%_ethanol_Sample2_TechRep1


title: Ecoli_wildtype_3%_ethanol_Sample3_TechRep2


title: Ecoli_ko_fur_1%_isobutanol_Sample2_TechRep1

source_name: Ecoli ko-fur grown in MOPS

source_name: Ecoli ko-fur grown in MOPS, 10 minutes after 1% isobutanol treatment


title: Ecoli_ko_ihfA_1%_isobutanol_Sample3_TechRep2


title: Ecoli_ko_arcA_1%_isobutanol_Sample4_TechRep2


title: Ecoli_ko_ihfA_1%_isobutanol_Sample3_TechRep1


title: Ecoli_wildtype_3%_ethanol_Sample1_TechRep2

source_name: Ecoli wildtype grown in MOPS


title: Ecoli_ko_arcA_1%_isobutanol_Sample2_TechRep1


title: Ecoli_wildtype_1%_butanol_Sample4_TechRep2

source_name: Ecoli wildtype grown in MOPS, 10 minutes after 1% butanol treatment


title: Ecoli_wildtype_1%_isobutanol_Sample3_TechRep1


title: Ecoli_wildtype_3%_ethanol_Sample1_TechRep1


title: Ecoli_ko_phoB_1%_isobutanol_Sample2_TechRep2

source_name: Ecoli ko-phoB grown in MOPS

source_name: Ecoli ko-phoB grown in MOPS, 10 minutes after 1% isobutanol treatment


title: Ecoli_ko_arcA_1%_isobutanol_Sample4_TechRep1


title: Ecoli_ko_phoB_1%_isobutanol_Sample2_TechRep1


title: Ecoli_ko_phoB_1%_isobutanol_Sample1_TechRep2


title: Ecoli_ko_phoB_1%_isobutanol_Sample4_TechRep2


title: Ecoli_wildtype_1%_butanol_Sample4_TechRep1


title: Ecoli_wildtype_calibration_Sample2_TechRep2

treatment_protocol: RNA from 1% isobutanol treated sample and untreated sample were mixed after RNA purification


title: Ecoli_ko_fur_1%_isobutanol_Sample2_TechRep2


title: Ecoli_ko_arcA_1%_isobutanol_Sample3_TechRep2


title: Ecoli_ko_arcA_1%_isobutanol_Sample1_TechRep2


title: Ecoli_wildtype_1%_isobutanol_Sample2_TechRep2


title: Ecoli_ko_phoB_1%_isobutanol_Sample4_TechRep1


title: Ecoli_wildtype_1%_butanol_Sample1_TechRep2


title: Ecoli_ko_arcA_1%_isobutanol_Sample1_TechRep1


title: Ecoli_wildtype_1%_butanol_Sample1_TechRep1


title: Ecoli_wildtype_1%_isobutanol_Sample2_TechRep1


title: Ecoli_ko_phoB_1%_isobutanol_Sample1_TechRep1


title: Ecoli_ko_ihfA_1%_isobutanol_Sample1_TechRep2


title: Ecoli_wildtype_1%_isobutanol_Sample5_TechRep1


title: Ecoli_wildtype_1%_isobutanol_Sample5_TechRep2


title: Ecoli_wildtype_calibration_Sample1_TechRep1


title: Ecoli_wildtype_calibration_Sample1_TechRep2


title: Ecoli_wildtype_1%_isobutanol_Sample1_TechRep1


title: Ecoli_ko_phoB_1%_isobutanol_Sample3_TechRep2


title: Ecoli_wildtype_1%_isobutanol_Sample4_TechRep2


title: Ecoli_ko_arcA_1%_isobutanol_Sample3_TechRep1


title: Ecoli_ko_phoB_1%_isobutanol_Sample3_TechRep1


title: Ecoli_ko_fur_1%_isobutanol_Sample1_TechRep1

source_name: Ecoli ko-furgrown in MOPS, 10 minutes after 1% isobutanol treatment


title: Ecoli_ko_fur_1%_isobutanol_Sample1_TechRep2


title: Ecoli_ko_fur_1%_isobutanol_Sample3_TechRep2


title: Ecoli_ko_fur_1%_isobutanol_Sample3_TechRep1


title: Ecoli_wildtype_1%_isobutanol_Sample4_TechRep1


title: Ecoli_wildtype_1%_isobutanol_Sample1_TechRep2


title: Third replicate D. sechellia testes RNA  / D. melanogaster whole fly RNA

city: Hamilton

first: Rama

middle: S.

last: Singh

state: Ontario

address: 1280 Main Street West

department: Biology Department

country: Canada

institute: McMaster University

description: Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to the CDMC protocols http://www.flyarrays.com/downloads.html

data_processing: Data procesing was performed using GeneTraffic Duo (Iobion Informatics). Spots presenting a ratio probe intensity / backgroung intensity lower than 2 were removed, as spots with a probe intensity lower than 2 times the local background. Spots from the three replicates with a covariance greater than 150% were rejected. Before statistical analysis genes with less than 2/3 of valid spots were removed.

organism: Drosophila melanogaster

source_name: 4 days old whole D. melanogaster male

growth_protocol: temperature 25°C, 12 h light/dark cycle. Flies were bred on cornmeal and molasses medium

extract_protocol: Trizol extraction on whole D. melanogaster males

tag: strain

value: 14021-0231.00, Gender:male, Age:4 days old, whole fly

organism: Drosophila sechellia

source_name: D. sechellia testes

extract_protocol: Extraction using the RiboPure Kit (Ambion) was performed on a pool of 200 testes. A one round of RNA amplification was performed using the MessageIIAmp aRNA kit (Ambion) according to the specifications of the manufacturer

treatment_protocol: Testes of 4 days old males were dissected in PBS buffer and kept in RNAlater.

tag: Gender

value: male, Age:4 days old, tissue:testes without accessory glands


title: First replicate Hybrid sechellia x simulans testes / D. melanogaster whole fly

hyb_protocol: CDMC protocol

scan_protocol: CDMC protocol

source_name: 4 day old whole D. melanogaster male

label_protocol: CDMC protocol

organism: Drosophila sechellia x Drosophila simulans

source_name: Hybrid D. sechellia x D. simulans testes

tag: Hybrids were obtained by crossing 10 females D. sechellia (Jean David, CNRS, Gif sur Yvette) with 15 males D. simulans (strain 14021-0251.2) per vial. Gender

value: male, Age:4 days old, tissue:testes without accessory glands.


title: Third replicate D. simulans testes RNA  / D. melanogaster whole fly RNA

description:
Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to the CDMC protocols

http://www.flyarrays.com/downloads.html

growth_protocol:
temperature 25°C
12 h light/dark cycle
Flies were bred on cornmeal and molasses medium

treatment_protocol:
temperature 25°C
12 h light/dark cycle
Flies were bred on cornmeal and molasse medium

value: male

tag: Age

value: 4 days old

tag: whole fly

organism: Drosophila simulans

source_name: D. simulans testes

tag: tissue

value: testes without accessory glands


title: Second replicate Hybrid simulans x sechellia testes  / D. melanogaster whole fly

source_name: Hybrid D. simulans x D. sechellia testes

tag: Hybrids were obtained by crossing 10 females D. simulans (strain 14021-0251.2) with 15 males D. sechellia (Jean David, CNRS, Gif sur Yvette)  per vial. Gender


title: Ecoli_ko_ihfA_1%_isobutanol_Sample4_TechRep2

source_name: Ecoli ko-ihfA grown in MOPS

source_name: Ecoli ko-ihfA grown in MOPS, 10 minutes after 1% isobutanol treatment


title: Third replicate Hybrid sechellia x simulans testes / D. melanogaster whole fly


title: First replicate Hybrid simulans x sechellia testes  / D. melanogaster whole fly


title: Ecoli_wildtype_calibration_Sample2_TechRep1


title: Second replicate Hybrid sechellia x simulans testes / D. melanogaster whole fly


title: Ecoli_ko_fur_1%_isobutanol_Sample4_TechRep2


title: Ecoli_ko_fur_1%_isobutanol_Sample4_TechRep1


title: Ecoli_ko_ihfA_1%_isobutanol_Sample1_TechRep1


title: Ecoli_ko_ihfA_1%_isobutanol_Sample4_TechRep1


title: Second replicate D. sechellia testes RNA  / D. melanogaster whole fly RNA

value: #12, Gender:male, Age:4 days old, tissue:testes without accessory glands


title: UCB-MSC M02 differentiated state Rep2

status: Public on Oct 31 2009

city: Seoul

first: Hyo-Soo

last: Kim

address: 28 Yongon-dong, Chongno-gu

country: South Korea

institute: Seoul National University Hospital

description: Gene expression data from UCB-MSC M02 under 3 days differentiation condition

hyb_protocol: Fragmented cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 Array.

scan_protocol: After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with wash buffer. After washing, the arrays were stained with a streptavidin-phycoerythrin complex. After staining, intensities were determined with a GeneChip scanner 3000, controlled by GCOS Affymetrix software.

data_processing: As a normalization process, RMA (Robust Multi-Array Average) normalization was applied to remove systematic variance. By applying RMA, the raw intensity values are background corrected, log2 transformed and then quantile normalized.

organism: Homo sapiens

source_name: UCB-MSCs under 3 days differentiation conditions

label_protocol: cDNA was synthesized from total RNA using the One-Cycle cDNA Synthesis Kit. After clean up with a Sample Cleanup Module, double strand cDNA was used for in vitro transcription (IVT). cDNA was transcribed using the GeneChip IVT Labeling Kit, in the presence of biotin-labeled CTP and UTP. After clean up with a Sample Cleanup Module, labeled cRNA was fragmented by fragmentation buffer.

growth_protocol: mononuclear cells were isolated by centrifugation (400G, 50 min) in a Ficoll hypaque gradient (density 1.077 g/cm3, Sigma). And these cells were cultured in α-minimum essential medium (α-MEM, Gibco BRL, Carlsbad), supplemented with 10% FBS (Gibco BRL, Carlsbad), 10,000 units/ml penicillin G sodium, 10,000 ug/ml streptomycin sulfate, and 25 ug/ml amphotericin B (Invitrogen Co.) at a concentration 5.0 x 106 cells/cm2. Cultures were maintained in a humidified 37℃ cell incubator with 5% CO2 with a change of culture medium twice a week. Three weeks later, monolayer of fibroblast-like adherent cells were trypsinized (0.25% trypsin, HyClone), washed, resuspended in culture medium and subcultured at a concentration of 1.0 x 106 cells/cm2

extract_protocol: Total RNAs from UCB-MSCs were isolated using TRIzol (Invitrogen, Carlsbad) and the RNeasy Mini kit (Qiagen, Valencia) as described previously

treatment_protocol: Proteins extracted from myocardium with AMI (MI proteins) were added to culture media with concentration of 25 ug/ml. Additionally, oscillating pressure was applied with specially designed oscillating pressure chamber to simulate intra-cardiac pressure change. Cells were harvested after three days of exposure to MI protein and one day in oscillating pressure chamber.

tag: female, cord blood


title: UCB-MSC M02 differentiated state Rep3


title: First replicate D. sechellia testes  / D. melanogaster whole fly

description: Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to their protocols http://www.flyarrays.com/downloads.html


title: UCB-MSC M02 Naïve state Rep2

description: Gene expression data from UCB-MSC M02 naïve state

source_name: UCB-MSCs in naïve state


title: UCB-MSC M01 differentiated state Rep1

description: Gene expression data from UCB-MSC M01 under 3 days differentiation condition


title: UCB-MSC M02 Naïve state Rep1


title: Second replicate D. simulans testes RNA  / D. melanogaster whole fly RNA

description: Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to the CDMC protocols. http://www.flyarrays.com/downloads.html


title: UCB-MSC M01 Naïve state Rep2

description: Gene expression data from UCB-MSC M01 naïve state


title: UCB-MSC M01 differentiated state Rep2


title: UCB-MSC M02 Naïve state Rep3


title: Acb_Water_only-rep7

status: Public on Sep 01 2009

city: Westfield

middle: William

last: Kimpel

state: IN

address: 15032 Hunter Court

department: Psychiatry

institute: Indiana University

description: Gene expression data from brain nucleus accumbens shell

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on RGU34A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with RMA

organism: Rattus norvegicus

source_name: Nucleus accumbens shell from P rat with no ethanol

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: RNA was extracted using Trizol followed by Qiagen RNeasy mini kit.

tag: P rat

tag: no ethanol


title: UCB-MSC M01 Naïve state Rep1


title: First replicate D. simulans testes RNA  / D. melanogaster whole fly RNA

description:
Labelling and hybridizations were performed at the Canadian Drosophila Microarray Centre according to the CDMC protocols
http://www.flyarrays.com/downloads.html

extract_protocol:
Extraction using the RiboPure Kit (Ambion) was performed on a pool of 200 testes.
A one round of RNA amplification was performed using the MessageIIAmp aRNA kit (Ambion) according to the specifications of the manufacturer

value: testes without accessory gland


title: Acb_Water_only-rep4


title: UCB-MSC M01 Naïve state Rep3


title: Acb_Water_only-rep6


title: Acb_Water_only-rep8


title: UCB-MSC M01 differentiated state Rep3


title: UCB-MSC M02 differentiated state Rep1


title: Third replicate Hybrid simulans x sechellia testes  / D. melanogaster whole fly


title: Acb_Water_only-rep5


title: Acb_Water_only-rep2


title: Acb_Water_only-rep3


title: Acb_Limited_Ethanol-rep7

source_name: Nucleus accumbens shell from P rat with access to limited ethanol

tag: access to limited ethanol


title: Acb_Limited_Ethanol-rep10


title: Acb_Water_only-rep1


title: Acb_Limited_Ethanol-rep6


title: Acb_Limited_Ethanol-rep3


title: Acb_Limited_Ethanol-rep9


title: Acb_Limited_Ethanol-rep5


title: Acb_Limited_Ethanol-rep8


title: Acb_Continuous_ethanol-rep6

source_name: Nucleus accumbens shell from P rat exposed to continuous ethanol

tag: exposed to continuous ethanol


title: Acb_Water_only-rep9


title: Acb_Limited_Ethanol-rep2


title: Acb_Limited_Ethanol-rep1


title: Acb_Continuous_ethanol-rep8


title: Acb_Continuous_ethanol-rep9


title: Acb_Continuous_ethanol-rep10


title: Acb_Continuous_ethanol-rep7


title: Acb_Continuous_ethanol-rep3


title: Acb_Continuous_ethanol-rep5


title: Acb_Limited_Ethanol-rep4


title: Acb_Continuous_ethanol-rep4


title: Liver at Zeitgeber time zt48 3

status: Public on Aug 31 2009

first: YoungJi

address: 28 Yongon-dong Chongno-gu

institute: Seoul National University Biomedical Informatics

description: entrainment: 12-hour light and 12-hour dark cycle (LD12:12) for four weeks under constant temperature

hyb_protocol: Hybridizations were carried out by using the Illumina gene expression system according to the manufacturer's instructions.

scan_protocol: Illumina scanner

data_processing: Raw data were were normalized by ''chip-wise'' method using the rank invariant algorithm

label: Biotin

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit following the manufacturer's instructions. Input amount: 100ng of total RNA

extract_protocol: Total RNA from frozen liver tissues was isolated by using the mirVana RNA Isolation kit (Ambion, Austin, TX) according to the manufacturer's protocol.

tag: gender

tag: age

value: 12 weeks

value: liver


title: Liver at Zeitgeber time zt44 1


title: Liver at Zeitgeber time zt44 2


title: Liver at Zeitgeber time zt48 1


title: Liver at Zeitgeber time zt44 3


title: Acb_Continuous_ethanol-rep1


title: Liver at Zeitgeber time zt48 2


title: Liver at Zeitgeber time zt40 3


title: Liver at Zeitgeber time zt32 1


title: Liver at Zeitgeber time zt32 2


title: Liver at Zeitgeber time zt36 2


title: Liver at Zeitgeber time zt36 3


title: Liver at Zeitgeber time zt32 3


title: Liver at Zeitgeber time zt24 2


title: Liver at Zeitgeber time zt28 1


title: Liver at Zeitgeber time zt40 1


title: Acb_Continuous_ethanol-rep2


title: Liver at Zeitgeber time zt28 2


title: Liver at Zeitgeber time zt40 2


title: Liver at Zeitgeber time zt24 1


title: Liver at Zeitgeber time zt16 1


title: Liver at Zeitgeber time zt20 3


title: Liver at Zeitgeber time zt16 3


title: Liver at Zeitgeber time zt20 2


title: Liver at Zeitgeber time zt36 1


title: Liver at Zeitgeber time zt28 3


title: Liver at Zeitgeber time zt20 1


title: moDC 16h_rep4

status: Public on Jul 27 2009

city: Aveiro

first: Patrícia

middle: Matos

last: Pereira

address: Campus Universitário de Santiago

department: Biology

country: Portugal

institute: University of Aveiro

hyb_protocol: PREHYBRIDIZATION: 1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS. 2. Heat the prehybridization solution to 50 ºC in a 100 ml Coplin Jar. 3. Place slides to be analyzed into the pre-heated pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible. 4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water. 5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization.  HYBRIDIZATION: Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine target (moDC 0h- and 16h-post LPS stimulation labelled RNA) with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature.  Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions: 1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber. 2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber. 3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place. 4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.

scan_protocol: Scanning of slides using the Agilent G2565AA DNA microarray scanner: Resolution: 10 um Red laser PMT= 100%, Green laser PMT= 100%

data_processing:
Pre-processing of the data was performed using BRB-ArrayTools v3.4.0 software. Manually flagged bad spots were eliminated and the local background was subtracted, followed by the averaging of replicate features on the array. Data points were removed when intensities values for both dyes were below 200% of background.
Feature extraction was performed with QuantArray v3.0 software, using the adaptative circle method for measuring the Median signal intensity and Median background intensity.For background calculations were considered the 5-20 percentile of least intense pixels and for signal calculations the 80-95 percentile of most intense pixels. The feature extraction grid was adjusted manually and visually bad spots were flagged using the software flag tool.
A global median normalization of microarray data was applied and log2 intensity ratios (M values) were obtained.

source_name: moDCs 0h-post LPS stimulation

label_protocol:
The 0h- and 16h-post LPS stimulation total RNA was labelled using the miRacULS II miRNA labelling kit (Kreatech) according manufacture’s instructions. Briefly, 3 ug of total RNA were incubated with Cy5- or Cy3-ULS for 15 min at 85ºC. The labelled RNAs were purified to remove non-reacted Cy-ULS followed by isolation of the labelled small RNA fraction, to produce a fluorescently-labelled small RNA sample for microarray analysis.
Dye incorporation was monitored by UV-visible spectroscopy and DoL (Degree of Labeling) number was calculated.
Amount of probe (ng/ul):
(OD 260nm - (OD dye * corr. factor)) * dilution factor * 40) / cuvette lenght (cm)
pmol of dye incorporated (pmol/ul):
Cy3 OD 550nm x dilution factor/ (cuvette length (cm) * edye * 1 * 10^-6)= pmol of Cy3 dye incorporatede
Cy5 OD 649nm x dilution factor/ (cuvette length (cm) * edye * 1 * 10^-6)= pmol of Cy5 dye incorporatede
DoL Calculation (%):
(340 * (Conc. of dye (pmol/ul) * 100%) / (Conc. of probe (ng/ul) * 1000)
Note: the DoL value should be inside the recommended range, i.e. between 1.0-3.6.

growth_protocol: Fresh human leukapheresis products were obtained from the EFS (Marseille, France). Human peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-PaqueTM PLUS (Amersham Biosciences), washed four times with RPMI 1640 medium and CD14+ cells were immunomagnetically purified with AutoMACS system following the protocol of the manufacturer (Miltenyi Biotech). Purified CD14+ monocytes were analyzed using a FACSCalibur (Becton Dickinson), confirming the purity of CD14+ cells to be 95%. To promote differentiation into immature dendritic cells, the purified CD14+ cells (0.5x106cells/ml) were plated in 6-well plates (2x106 cells/well) and cultured in RPMI 1640 medium supplemented with 10% FCS, non essential amino acids, penicillin/streptomycin 100 ng/mL (>1000U/ml), recombinant human GM-CSF and 20 ng/mL (>100U/ml) IL-4 for 5 days (both from PeproTech). At days 2 and 4, half of the volume of the medium was replaced by fresh medium supplemented with GM-CSF and IL-4. For DC maturation, 100 ng/mL LPS (Escherichia coli type 026:B6; Sigma-Aldrich) was added to the cells at day 5, for 4h or 16h, followed by cell harvesting.

extract_protocol: Human monocyte-derived dendritic cells were grown in culture for 5 days. Total RNA was isolated from untreated (0h) and 4h or 16h LPS-treated dendritic cells, using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was always assessed with the an Agilent 2100 Bioanalyzer (Agilent).

tag: Cell

value: Human monocyte-derived dendritic cells

source_name: moDCs 16h-post LPS stimulation


title: Liver at Zeitgeber time zt24 3


title: Liver at Zeitgeber time zt16 2


title: moDC 4h_rep4

hyb_protocol: PREHYBRIDIZATION: 1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS. 2. Heat the prehybridization solution to 50 ºC in a 100 ml Coplin Jar. 3. Place slides to be analyzed into the pre-heated pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible. 4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water. 5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization.  HYBRIDIZATION: Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine target (moDC 0h- and 4h-post LPS stimulation labelled RNA) with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature.  Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions: 1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber. 2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber. 3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place. 4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.

label_protocol:
The 0h-and 4h-post LPS stimulation total RNA was labelled using the miRacULS II miRNA labelling kit (Kreatech) according manufacture’s instructions. Briefly, 3 ug of total RNA were incubated with Cy5- or Cy3-ULS for 15 min at 85ºC. The labelled RNAs were purified to remove non-reacted Cy-ULS followed by isolation of the labelled small RNA fraction, to produce a fluorescently-labelled small RNA sample for microarray analysis.
Dye incorporation was monitored by UV-visible spectroscopy and DoL (Degree of Labeling) number was calculated.
Amount of probe (ng/ul):
(OD 260nm - (OD dye * corr. factor)) * dilution factor * 40) / cuvette lenght (cm)
pmol of dye incorporated (pmol/ul):
Cy3 OD 550nm x dilution factor/ (cuvette length (cm) * edye * 1 * 10^-6)= pmol of Cy3 dye incorporatede
Cy5 OD 649nm x dilution factor/ (cuvette length (cm) * edye * 1 * 10^-6)= pmol of Cy5 dye incorporatede
DoL Calculation (%):
(340 * (Conc. of dye (pmol/ul) * 100%) / (Conc. of probe (ng/ul) * 1000)
Note: the DoL value should be inside the recommended range, i.e. between 1.0-3.6.

source_name: moDCs 4h-post LPS stimulation


title: moDC 16h_rep1

label_protocol:
The 0h-and 16h-post LPS stimulation total RNA was labelled using the miRacULS II miRNA labelling kit (Kreatech) according manufacture’s instructions. Briefly, 3 ug of total RNA were incubated with Cy5- or Cy3-ULS for 15 min at 85ºC. The labelled RNAs were purified to remove non-reacted Cy-ULS followed by isolation of the labelled small RNA fraction, to produce a fluorescently-labelled small RNA sample for microarray analysis.
Dye incorporation was monitored by UV-visible spectroscopy and DoL (Degree of Labeling) number was calculated.
Amount of probe (ng/ul):
(OD 260nm - (OD dye * corr. factor)) * dilution factor * 40) / cuvette lenght (cm)
pmol of dye incorporated (pmol/ul):
Cy3 OD 550nm x dilution factor/ (cuvette length (cm) * edye * 1 * 10^-6)= pmol of Cy3 dye incorporatede
Cy5 OD 649nm x dilution factor/ (cuvette length (cm) * edye * 1 * 10^-6)= pmol of Cy5 dye incorporatede
DoL Calculation (%):
(340 * (Conc. of dye (pmol/ul) * 100%) / (Conc. of probe (ng/ul) * 1000)
Note: the DoL value should be inside the recommended range, i.e. between 1.0-3.6.

value: Human monocyte-derived dencritic cells


title: Liver at Zeitgeber time zt08 3


title: moDC 4h_rep1

hyb_protocol: PREHYBRIDIZATION: 1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS. 2. Heat the prehybridization solution to 50 ºC in a 100 ml Coplin Jar. 3. Place slides to be analyzed into the pre-heated pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible. 4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water. 5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization.  HYBRIDIZATION: Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine target (0h- and 4h-post LPS stimulation labelled RNA) with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature.   Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions: 1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber. 2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber. 3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place. 4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.

label_protocol:
The 0h- and 4h-post LPS stimulation total RNA was labelled using the miRacULS II miRNA labelling kit (Kreatech) according manufacture’s instructions. Briefly, 3 ug of total RNA were incubated with Cy5- or Cy3-ULS for 15 min at 85ºC. The labelled RNAs were purified to remove non-reacted Cy-ULS followed by isolation of the labelled small RNA fraction, to produce a fluorescently-labelled small RNA sample for microarray analysis.
Dye incorporation was monitored by UV-visible spectroscopy and DoL (Degree of Labeling) number was calculated.
Amount of probe (ng/ul):
(OD 260nm - (OD dye * corr. factor)) * dilution factor * 40) / cuvette lenght (cm)
pmol of dye incorporated (pmol/ul):
Cy3 OD 550nm x dilution factor/ (cuvette length (cm) * edye * 1 * 10^-6)= pmol of Cy3 dye incorporatede
Cy5 OD 649nm x dilution factor/ (cuvette length (cm) * edye * 1 * 10^-6)= pmol of Cy5 dye incorporatede
DoL Calculation (%):
(340 * (Conc. of dye (pmol/ul) * 100%) / (Conc. of probe (ng/ul) * 1000)
Note: the DoL value should be inside the recommended range, i.e. between 1.0-3.6.

value: Human Monocyte-derived dendritic cells


title: moDC 4h_rep2

hyb_protocol: PREHYBRIDIZATION: 1. Make 100 ml prehybridization buffer (for a maximum of 4 slides) containing 1M Tris-HCL pH=9 pre-heated at 50ºC, 100mM ethanolamide and 0.1% SDS. 2. Heat the prehybridization solution to 50 ºC in a 100 ml Coplin Jar. 3. Place slides to be analyzed into the pre-heated pre-hybridization buffer. Incubate for 20 minutes at 50 ºC with constant agitation, if possible. 4. Wash thoroughly by inverting or gently shaking the container with nuclease-free water constantly for 1 minute. Decant the water and repeat this rising step with fresh nuclease-free water. 5. Allow the slides to dry by centrifuging 3 minute 800 rpm. Slides should be used immediately following prehybridization.  HYBRIDIZATION: Pre-heat 3x hybridization solution (Ambion) to 65 ºC for at least 5 min to overcome SDS precipitation. Combine target (moDC 0h- and 4h-Post LPS stimulation labelled RNA) with hybridization buffer (preheated to 65 ºC). Heat at 95 ºC for 3 minutes. Immediately put on ice for at least 1 min. Spin-down briefly. Add 4x blocking reagent (Kreatech). Incubate on dark for 1 minute at room temperature. Using Agilent gasket slides (G2534-60003), Agilent SureHyb hybridization chambers (G2534A) and hybridization oven (G2545A), see Agilent User Manual for instructions: 1. For each array, put a gasket slide onto a SureHyb chamber and add a total of 250 ul target as 1 dot in the center of the chamber. 2. Put a microarray slide on the gasket slide by holding it in place with your fingertips, towards the top edge of the gasket chamber. 3. Gently (!) allow the microarray slide to drop onto the gasket chamber by lowering it with the aid of your other hand. Do not move the microarray slide after it is in place. 4. Place the SureHyb chamber into the hybridization oven at 42 ºC for 16 hours.


title: Liver at Zeitgeber time zt12 3


title: Liver at Zeitgeber time zt12 1


title: Liver at Zeitgeber time zt08 1


title: moDC 16h_rep3


title: Liver at Zeitgeber time zt12 2


title: moDC 16h_rep2


title: moDC 4h_rep3


title: Liver at Zeitgeber time zt04 2


title: legs A vs abdomen A3

status: Public on Jun 01 2009

city: Bloomington

first: Justen

last: Andrews

address: 915 East Third Street

description: To compare the gene expression levels during horn development of dung beetle Onthophagus taurus, head horns, thoracic horn, legs, and abdominal epithelium from pupae were used. Samples from abdomen were used as common reference for three other tissues.

hyb_protocol: Labeled aRNAs from test and reference samples (adjusted to a total of 50pmol dye for each) were mixed with KREAblock (ULS aRNA Fluorescent Labeling kit, Kreatech, Amsterdam, Netherlands) and 2x enhanced cDNA hybridization buffer (Genisphere), and then heated at 80°C for 10 min. Microarrays were pre-treated for one hour at 55°C in pre-hybridization buffer consisting of 5xSSC, 0.1%SDS, and 1% I-block (Applied Biosystems, CA). Both mixed sample and the microarrays were kept at 55°C until hybridization. Hybridization was performed in a dark humidified chamber at 55°C overnight. Microarrays were rinsed in buffer A (2xSSC/0.2%SDS) at 55°C and then incubated in buffer A at 65°C for 10min. Arrays were then transferred to 2xSSC (room temperature) for 10 min, followed by incubation in 0.2x SSC for 10min (room temperature). Arrays were then dried by centrifugation at 500rcf for 4 min.

scan_protocol: Microarrays were scanned using a GenePix scanner 4200 (Molecular Devices).

data_processing: Data were filtered and extracted using GenePix v.5.0 and imported into Bioconductor. Normalization for M-values was performed using spatial and intensity dependant Lowess smoothing in OLIN and differential expression was assessed using Limma.

organism: Onthophagus taurus

source_name: Onthophagus taurus large male legs A

label_protocol: RNA was amplified using a T7-based RNA amplification method (Klebes et al. 2002) as follows. One microgram of RNA was reverse transcribed using Oligo(dT)-T7 primer (Ambion) and SuperScriptIII reverse transcriptase (Invitrogen). Second strand synthesis was performed using DNA polymerase (Invitrogen) and RNase H (Invitrogen). In-vitro transcription was performed using the MEGAscript T7 kit (Ambion). Amplified RNA (aRNA) was labeled with Cy3 using the ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands).

growth_protocol: All animals were raised in laboratory colony.

extract_protocol: Total RNA was extracted from dissected tissue using Qiagen RNeasy kit according to the manufacturers protocol.

tag: Species

value: Onthophagus taurus

tag: Sex

value: male (large)

tag: Stage

value: pupae within 24hrs after pupation

tag: Tissue

value: dissected legs

source_name: Onthophagus taurus large male abdominal epithlium A3

label_protocol: RNA was amplified using a T7-based RNA amplification method (Klebes et al. 2002) as follows. One microgram of RNA was reverse transcribed using Oligo(dT)-T7 primer (Ambion) and SuperScriptIII reverse transcriptase (Invitrogen). Second strand synthesis was performed using DNA polymerase (Invitrogen) and RNase H (Invitrogen). In-vitro transcription was performed using the MEGAscript T7 kit (Ambion). Amplified RNA (aRNA) was labeled with Cy5 using the ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands).

value: dissected dorsal abdominal epithelium


title: Liver at Zeitgeber time zt04 3

tag: strain


title: Liver at Zeitgeber time zt04 1


title: legs D vs abdomen D3

source_name: Onthophagus taurus large male legs D

source_name: Onthophagus taurus large male abdominal epithlium D3


title: legs C vs abdomen C3

source_name: Onthophagus taurus large male legs C

source_name: Onthophagus taurus large male abdominal epithlium C3


title: legs E vs abdomen E3

source_name: Onthophagus taurus large male legs E

source_name: Onthophagus taurus large male abdominal epithlium E3


title: legs B vs abdomen B3

source_name: Onthophagus taurus large male legs B

source_name: Onthophagus taurus large male abdominal epithlium B3


title: Liver at Zeitgeber time zt08 2


title: thoracic horn B vs abdomen B2

source_name: Onthophagus taurus large male thoracic horn B

value: dissected thoracic horns

source_name: Onthophagus taurus large male abdominal epithlium B2


title: thoracic horn A vs abdomen A2

source_name: Onthophagus taurus large male thoracic horn A

source_name: Onthophagus taurus large male abdominal epithlium A2


title: thoracic horn D vs abdomen D2

source_name: Onthophagus taurus large male thoracic horn D

source_name: Onthophagus taurus large male abdominal epithlium D2


title: head horn B vs abdomen B1

source_name: Onthophagus taurus large male head horn B

value: dissected head horns

source_name: Onthophagus taurus large male abdominal epithlium B1


title: thoracic horn E vs abdomen E2

source_name: Onthophagus taurus large male thoracic horn E

source_name: Onthophagus taurus large male abdominal epithlium E2


title: head horn D vs abdomen D1

source_name: Onthophagus taurus large male head horn D

source_name: Onthophagus taurus large male abdominal epithlium D1


title: thoracic horn C vs abdomen C2

source_name: Onthophagus taurus large male thoracic horn C

source_name: Onthophagus taurus large male abdominal epithlium C2


title: head horn C vs abdomen C1

source_name: Onthophagus taurus large male head horn C

source_name: Onthophagus taurus large male abdominal epithlium C1


title: head horn E vs abdomen E1

source_name: Onthophagus taurus large male head horn E

source_name: Onthophagus taurus large male abdominal epithlium E1


title: Lens epithelium, WT, #2L

status: Public on May 01 2009

first: Teri

last: Greiling

department: Biological Structure

institute: University of Washington

description: Each data set was taken from one lens only.  All lens data sets were from one litter of animals.

hyb_protocol: GeneChip Hybridization Oven at 45ºC with rotation, washing on GeneChip Fulidics Station_450 using EukGE-Ws2v4_450 washing/staining protocol with Antibody Amplification Staining Protocol

scan_protocol: 7G GeneChip Scanner, single scan, 570 nm filter, software GCOS1.4

data_processing: Global scaling in GCOS1.4 using all probsets and TGT value of 500

source_name: Lens epithelium, wild-type mouse

label_protocol: Two cycle amplification using Ambion MessageAmp II aRNA amplification kit and MessageAmp II-biotin enhanced amplification kits

growth_protocol: Normal housing

extract_protocol: RNeasy micro kit (Qiagen)

treatment_protocol: Lens was cryosectioned, stained with Cressyl Violet, and dehydrated. Laser capture microdissection (Arcturus PixCell2e) was used to remove epithelial cells from each section.

tag: Strain

value: Wild-type, C57Bl/6 background

tag: Gender

value: female

tag: Age

value: 28 days

tag: Eye

value: Left


title: head horn A vs abdomen A1

hyb_protocol: Labeled aRNAs from test and reference samples (adjusted to a total of 50pmol dye for each) were mixed with KREAblock (ULS aRNA Fluorescent Labeling kit, Kreatech, Amsterdam, Netherlands) and 2x enhanced cDNA hybridization buffer (Genisphere), and then heated at 80°C for 10 min.  Microarrays were pre-treated for one hour at 55°C in pre-hybridization buffer consisting of 5xSSC, 0.1%SDS, and 1% I-block (Applied Biosystems, CA).  Both mixed sample and the microarrays were kept at 55°C until hybridization.  Hybridization was performed in a dark humidified chamber at 55°C overnight.  Microarrays were rinsed in buffer A (2xSSC/0.2%SDS) at 55°C and then incubated in buffer A at 65°C for 10min. Arrays were then transferred to 2xSSC (room temperature) for 10 min, followed by incubation in 0.2x SSC for 10min (room temperature). Arrays were then dried by centrifugation at 500rcf for 4 min.

data_processing: Data were filtered and extracted using GenePix v.5.0 and imported into Bioconductor.  Normalization for M-values was performed using spatial and intensity dependant Lowess smoothing in OLIN and differential expression was assessed using Limma.

source_name: Onthophagus taurus large male head horn A

label_protocol: RNA was amplified using a T7-based RNA amplification method (Klebes et al. 2002) as follows.  One microgram of RNA was reverse transcribed using Oligo(dT)-T7 primer (Ambion) and SuperScriptIII reverse transcriptase (Invitrogen).  Second strand synthesis was performed using DNA polymerase (Invitrogen) and RNase H (Invitrogen). In-vitro transcription was performed using the MEGAscript T7 kit (Ambion).  Amplified RNA (aRNA) was labeled with Cy3 using the ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands).

source_name: Onthophagus taurus large male abdominal epithlium A1

label_protocol: RNA was amplified using a T7-based RNA amplification method (Klebes et al. 2002) as follows.  One microgram of RNA was reverse transcribed using Oligo(dT)-T7 primer (Ambion) and SuperScriptIII reverse transcriptase (Invitrogen).  Second strand synthesis was performed using DNA polymerase (Invitrogen) and RNase H (Invitrogen). In-vitro transcription was performed using the MEGAscript T7 kit (Ambion).  Amplified RNA (aRNA) was labeled with Cy5 using the ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands).


title: Lens epithelium, WT, #6L


title: Lens epithelium, SPARC KO, #4L

source_name: Lens epithelium, SPARC knock-out mouse

value: SPARC-null, C57Bl/6 background


title: Lens epithelium, WT, #5L


title: CB14VIN4

city: Stellenbosch

first: Debra

last: Rossouw

state: Western Cape

address: Cnr Neethling and Victoria rd

department: Institute for Wine Biotechnology

country: South Africa

institute: University of Stellenbosch

hyb_protocol: Standard Affymetrix operating procedure

scan_protocol: Standard Affymetrix operating procedure

data_processing: Expression Console with Plier algorithm.

label: Biotin-streptavidin

organism: Saccharomyces cerevisiae

source_name: day14, VIN13 strain

label_protocol: Standard Affymetrix operating procedure

extract_protocol: Standard Affymetrix operating procedure

tag: Colombar must

tag: fermentation day14

tag: VIN13 strain

tag: replicate #3


title: Lens epithelium, SPARC KO, #1R

value: Right


title: Lens epithelium, SPARC KO, #1L


title: CB14B2

source_name: day14, BM45 strain

tag: BM45 strain

tag: replicate #2


title: CB14B1

tag: replicate #1


title: CB5VIN2

source_name: day5, VIN13 strain

tag: fermentation day5


title: CB5VIN3


title: CB14B3


title: Lens epithelium, SPARC KO, #7L

value: male


title: CB14VIN1


title: CB2VIN2

source_name: day2, VIN13 strain

tag: fermentation day2


title: CB2VIN3


title: CB2B2

source_name: day2, BM45 strain

tag: day2 of fermentation


title: Liver

city: Baltimore

first: Andrew

middle: P.

last: Feinberg

state: MD

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

description: Liver

hyb_protocol: Performed by NimbleGen using standard protocol

data_processing: Briefly, we first quantile normalized Cy3 (Input) intensities from all arrays to a common target. We used a smoothing procedure to improve the signal to noise ratio of the M (log2 ratio Cy5/Cy3) values and fitted a function of M values to the chromosomal location using loess. We then picked the genomic regions with the lowest 20% fitted values as the reference region. The Cy5 intensities in the reference regions should have similar distributions in each sample. We therefore quantile normalized them to the same distribution target. The quantile procedure was used to construct a function to map pre-normalization Cy5 intensities to post-normalization Cy5 intensities. This map was then applied to all the Cy5 intensities. This procedure made the M values comparable from array to array.

source_name: Chromatin immunoprecipitated DNA from liver cells using H3K9Me2 antibody

tag: Liver

source_name: Input DNA


title: CB5B2

source_name: day5, BM45 strain


title: CB2VIN1


title: CB2B4


title: CB5VIN1


title: CB5B1


title: CB14VIN3


title: EC 354 (BII)

status: Public on Apr 01 2009

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: HUVEC infected with S. aureus from blood of septic patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 37 degree, 5% CO2

extract_protocol: Rneasy

treatment_protocol: Endothelial cells (ECs) were prepared from human umbilical cord veins by digestion with 0.5 mg ml-1 collagenase type I (Sigma, St. Louis, MO) for 15 min at 37 C as previously described, cells were used within 3 passages. S. aureus were harvested after overnight incubation at 37 ºC on blood agar plates and suspended to 0.5 McFarland in PBS (pH 7.4), corresponding to approximately 1 x 108 cfu ml-1. The infection of HUVEC with S. aureus was performed as previously described. After 4 h of incubation, supernatants were collected and 350 ul RLT-buffer (Qiagen GmbH, Hilden, Germany) was added to each well.

tag: tissue

value: primary endothelial cells from umbilical cord


title: EC ZB1164 (CIV)

source_name: HUVEC infected with S. aureus from healthy nasal carrier


title: EC pos control

source_name: EC pos control

treatment_protocol: infected


title: EC ZB1100 (CI)


title: EC 566 (BIV)


title: EC 41 (BI)


title: EC ZB1105 (CII)


title: EC ZB1241 (CV)


title: EC 744 (BV)


title: EC 399 (BIII)


title: Planktonic_Stationary_rep2

city: Sapporo

first: Akinobu

last: Ito

address: North-13, West-8, Kitaku

department: Graduate School of Engineering

country: Japan

institute: Hokkaido University

description: Planktonic sample

hyb_protocol: Affymetrix protocols

scan_protocol: Affymetrix protocols

data_processing: Normalization was performed with dchip software using the Invariant Set Normalization method. Sample Planktonic_Stationary_rep2 was used as the baseline array.

source_name: Planktonic stationary phase in MOPS media with 0.2% glucose

label_protocol: The isolated RNA was converted to cDNA, and the synthesized cDNA was fragmented and labeled with GeneChip DNA Labeling Reagent according to Affymetrix protocols.

growth_protocol: Samples were grown in MOPS minimal media with 0.2% glucose.

extract_protocol: Samples were RNA-stabilized with Qiagen RNAProtect Bacterial Reagent, and total RNA was isolated with Qiagen RNeasy mini kit (Qiagen).

value: Escherichia coli MG1655 pOX38Km


title: Planktonic_Stationary_rep1

description: Planktonic sample


title: Planktonic_Stationary_rep3

description: Planktonic sample


title: Planktonic_Exponential_rep3

description: Planktonic sample

source_name: Planktonic exponential phase in MOPS media with 0.2% glucose


title: Planktonic_Exponential_rep1

description: Planktonic sample


title: EC ZB1160 (CIII)


title: Planktonic_Exponential_rep2

description: Planktonic sample


title: Biofilm_Outside_rep3

description: Biofilm sample on glass surface

source_name: Outside of biofilm in MOPS media with 0.2% glucose


title: Biofilm_Inside_rep3

description: Biofilm sample on glass surface

source_name: Inside of biofilm in MOPS media with 0.2% glucose


title: Biofilm_Outside_rep1

description: Biofilm sample on glass surface


title: Biofilm_Outside_rep2

description: Biofilm sample on glass surface


title: EC neg control

source_name: EC neg control

treatment_protocol: uninfected


title: Biofilm_Inside_rep2

description: Biofilm sample on glass surface


title: Biofilm_Inside_rep1

description: Biofilm sample on glass surface


title: DP thymocytes 2

status: Public on Mar 31 2009

city: Boston

first: Young

middle: IL

last: Choi

state: MA

address: 77 Avenue Louis Pasteur

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from N15TCR+/+Rag2-/- DP thymocytes

hyb_protocol: The hybridization cocktail containing 15 mg adjusted fragmented cRNA mixed with eukaryotic hybridization controls (contains control cRNA and chip control oligonucleotide B2) was hybridized with pre-equilibrated MOUSE430 2.0 Affymetrix chips at 45°C for 16 h.  After the hybridization cocktails were removed, the chips were washed and stained with normal goat IgG and biotinylated mouse anti-streptavidin antibody and restained with streptavidin-PE.

scan_protocol: The chips were scanned in an HIP chip scanner (Affymetrix)

data_processing:
the scanned results were analyzed by dChip
cut-off critera after dChip: lower confidence bound (LCB) of the fold change (FC) between the experiment and the baseline

source_name: CD4+CD8+ immature thymocytes

label_protocol: Two microgram of total RNA were used in the first-strand cDNA synthesis with T7-d(T)24 primer (GCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24) and Superscript II using the CodeLink expression assay reagent kit (Amersham, Piscataway, NJ) following the manufacturer's protocol. The purified cDNA was incubated at 37°C for 5 h in an in vitro transcription reaction to produce cRNA labeled with biotin.

growth_protocol: Mice at the specific age were kept in DanaFarber Cancer Institute animal facility

extract_protocol: Total RNA was purified using Qiagne RNA purification column accoridng to the manufacturer's guide

treatment_protocol: Sort the indicated populations using a MoFlo cell sorter from six age and sex matched 5-6 week old N15 TCR tg+/+ RAG-2-/- H-2b mice after staining single cell suspension with anti-CD4 (L3T4) and anti-CD8 (Ly-2) antibodies

value: 5-6 weeks old


title: CD8SP thymocytes 2

description: Gene expression data from N15TCR+/+Rag2-/- CD8SP thymocytes

source_name: CD4-CD8+ mature thymocytes


title: CD8SP thymocytes 1


title: Young rep6

status: Public on Mar 30 2009

city: St. Louis

first: Sheila

last: Stewart

state: MO

address: 660 S Euclid

institute: Cell Biology & Physiology

description: Early passage BJ fibroblasts, grown in serum-free media for 72hrs at 3% O2

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard scanning protocol

data_processing: Normalized and modeled using dChip

source_name: Human Foreskin BJ fibroblasts

label_protocol: Standard Affymetrix labeling protocol

extract_protocol: Standard TRIZOL extraction

tag: Early passage human foreskin BJ fibroblasts


title: 72 Hours Resistant

status: Public on Jun 13 2009

type: SAGE

anchor: NlaIII

city: Bogota

first: Silvia

last: Restrepo

department: Biological Science

country: Colombia

institute: Universidad de los Andes

description: No of unique tags: 1158776

data_processing: The SAGE tags were counted, and catalogued using SAGE2000 (http://www.invitrogen.com/sage). Tags were then normalized for each library and calculated according to the formula of Audic and Claverie (Audic and Claverie, 1997). SAGE tags were identified in two ways (Lee et al., 2002). First we used Identitag (http://pbil.univ-lyon1.fr/software/identitag/) (Keime et al. 2004) to identify tags from our SAGE libraries using the TCs and singleton we obtained from S. phureja and using the S. tuberosum and S. lycopersicum TIGR TCs and singletons (release April, 2008), (http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=potato and http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=tomato). Tags that could not be identified using ours or TIGR transcripts were mapped to a virtual Tag library constructed from the NCBI tomato (http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=4081) and potato (http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=4113) UniGene build (release April, 2008).

organism: Solanum phureja

source_name: 72 hpi leaves

growth_protocol: Four-week-old Solanum phureja plants (cv. Col3 and Col2) were selected for inoculations. One day prior to inoculation, all plants (S. phureja and S. tuberosum Tuquerreña and Diacol Capiro cultivars used as susceptible controls of inoculations) were placed into a humid chamber with a 12-h light period, 100% relative humidity, and a average temperature of 15ºC.

extract_protocol: Frozen plant tissues were ground, using a cold mortar and a pestle. Total potato leaf RNA was extracted using the SV RNA Total Isolation kit (Promega). The RNA was precipitated, pooled, and stored at –80°C.

treatment_protocol: Plants were inoculated with a mixture of P. infestans isolates collected from S. phureja and S. tuberosum diseased tissues. Isolates 2011, 2021, 2031, 2041 and 2061 were isolated from S. phureja and previously described (Vargas et al., 2008) and isolates A07, A13 and A15 (S. tuberosum), A08 and A09 (S. phureja) were characterized in this study. Inoculations were made with a sporangial suspension (32,000/ml), and plants were sprayed until run-off, as previously described (Smart et al.1998).

tag: four-week-old S. phureja cv. Col3


title: CD4intCD8+ thymocytes 2

description: Gene expression data from N15TCR+/+Rag2-/- CD4intCD8+ thymocytes

source_name: CD4intCD8+ maturing thymocytes


title: CD4intCD8+ thymocytes 1


title: CB5B3


title: Young rep4


title: 12 Hours Susceptible

description: No of unique tags: 1099531

source_name: 12 hpi leaves

tag: four-week-old S. phureja cv. Col2


title: Young rep5


title: Replicative Senescent rep5

description: BJ fibroblasts passaged in culture till they reached senescence (population doubling >85) as assessed by SA-Bgal. 72h starved in serum-free media and incubated at 3% O2

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard protocol

label_protocol: Affymetrix standard labeling protocol

extract_protocol: TRIZOL standard extraction procedure

tag: Late passage BJ fibroblasts


title: Young rep1


title: 0 Hours Resistant

description: No of unique tags: 2738110

source_name: mock inoculated leaves


title: Replicative Senescent rep3


title: Bleomycin-treated rep4

description: BJ fibroblasts artificially-aged

hyb_protocol: Affymetrix standard hybridization procedure

label_protocol: Affymetrix standard labeling procedure

tag: Human foreskin BJ fibroblasts

tag: 100ug/ml of bleomycin sulfate for 24hr, 72 serum-free incubation in 3% O2


title: 72 Hours Susceptible

description: No of unique tags: 1244455


title: Replicative Senescent rep1


title: Young rep3


title: Replicative Senescent rep2


title: Replicative Senescent rep4


title: Bleomycin-treated rep1

description: BJ fibroblasts artificially-aged


title: Bleomycin-treated rep2

description: BJ fibroblasts artificially-aged


title: Young rep2


title: Bleomycin-treated rep3

description: BJ fibroblasts artificially-aged


title: Replicative Senescent rep6


title: Tibialis anterior muscle from MLC-SOCS-3/C57Bl6J mice rep2

status: Public on Mar 01 2009

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Gene expression data from tibialis muscle extracted from 11 week-old mouse

hyb_protocol: Following fragmentation and labeling, 3ug of DNA were hybridized for 17 hr at 45C on Mouse gene 1.0ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and Gene Level-RMA sketch  as normalization method.

source_name: Tibialis anterior muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA.

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

treatment_protocol: Tibialis muscle was extracted from 6h starved mice and quickly frozen in liquid nitrogen.

tag: C57Bl6J mice

tag: transgenic animals expressing constitutively SOCS-3 specifically in skeletal muscle (under the control of MLC-1 promoter)


title: Tibialis anterior muscle from MLC-SOCS-3/C57Bl6J mice rep3


title: Tibialis anterior muscle from control C57Bl6J mice rep2

tag: control animals (not modified genetically)


title: 25_blood_post

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 5ug of Cy3 labelled amplified sample was mixed with Cy5 labelled amplified human reference RNA, concentrated & amersham hyb buffer added. Slides were incubated at 42C for 3 days

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 μl hybridisation mix (19 μl Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150μl aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000B-2. Voltage: 500,350. Resolution (micrometers): 10.

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.

source_name: 25_blood_post(Blood taken post treatment, ES-285 dose 256mg/2.)

label_protocol: Total RNA (5 ug) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (GE, UK) using the Cyscribe Indirect cDNA Labelling Kit protocol (GE, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 ug Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: RNA was extracted from whole blood using the PreAnalytiX PAXGene system according to the manufacturers instructions. The total RNA samples were then further purified using Qiagen RNeasy Cleanup, as manufacturers instructions.

tag: treatment

value: post treatment

tag: sample tissue type

value: blood

source_name: Amplified Stratagene Human Reference(Stratagene Human Reference RNA amplified with Ambion MessageAmp II kit.)

extract_protocol: Universal Human total RNA Supplied By Stratagene    Centrifuge @ 12000g for 20min at 4C, Pipette out supernatant, add 200ul of 70% Ethanol, vortex and centrifuge @ 12000g for 20min. Pipette out supernatant and leave to air dry for 30 min. Add 200ul of RNAse free water.

value: Mixed Pool of Human Cell Lines


title: 12 Hours Resistant

description: No of unique tags: 1607776


title: 0 Hours Susceptible

description: No of unique tags: 1355986


title: Tibialis anterior muscle from MLC-SOCS-3/C57Bl6J mice rep1


title: Tibialis anterior muscle from control C57Bl6J mice rep3


title: Tibialis anterior muscle from control C57Bl6J mice rep1