title: gc 1-5 (4/22/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40594.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 13:41:03; Parameter PMT Volts = 570; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 29000; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.86; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 13:41:03; Parameter PMT Volts = 675; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 98831; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: gc 4-3 (11/24/02)

status: Public on Oct 04 2006

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35378.gif

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

molecule: total RNA

organism: Mus musculus


title: Control1

city: Chicago

first: yuanyuan

last: zha

state: IL

department: Department of Pathology

institute: University of Chicago

description: we are interested in which genes are upregulated during T cell anergy. Thus, RNA from normal quiescent T cell clones were extracted to be compared to RNA extracted from anergic T cell clones

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite 4.0

label: biotin

molecule: polyA RNA

source_name: Th1 T cell

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: total RNA was extracted using Trizol  method (Invitrogen)

tag: control CD4 T Cell clone


title: PM-5

status: Public on Oct 03 2006

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

description: unfertilized eggs, autumn-spawning strain

data_processing: The signal was normalized by the mean signal of the array

organism: Oncorhynchus mykiss

source_name: experimental group: photoperiod-advanced ovulation

tag: female

tag: year

tag: experimental group

value: photoperiod-advanced ovulation

tag: normalYSR-eyed-malfo

tag: % of eyed embryos (190degrees.day)

tag: % of malfomations at YSR (550degrees.day)

tag: % of normal alevins at YSR (550degrees.day)


title: pk 3-3 (2/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39175.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 840, 6520; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 13:54:22; Parameter PMT Volts = 490; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17157; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.68; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.48; Parameter Scan Time = 13:54:22; Parameter PMT Volts = 530; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87115; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden

source_name: MRB 2nd round (2/4/03)

tag: MRB 2nd round (2/4/03)


title: PM-4

description: unfertilized eggs, autumn spawning strain


title: N-2

source_name: experimental group: normal ovulation

value: normal ovulation


title: HI-4

source_name: experimental group: induced ovulation

value: induced ovulation


title: N-1


title: HI-9


title: gc 4-2 (9/23/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33684.gif

source_name: MRB 2nd round (9/23/02)

tag: MRB 2nd round (9/23/02)


title: gc 1-4 (2/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39177.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 7250; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 16:05:28; Parameter PMT Volts = 490; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17279; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 16:05:28; Parameter PMT Volts = 550; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87237; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.60; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: pk 4-2 (9/23/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33682.gif


title: pk 2-1 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35374.gif


title: pk 1 5 (4/22/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40599.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.21; Parameter Scan Time = 14:50:28; Parameter PMT Volts = 545; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 29070; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.21; Parameter Scan Time = 14:50:28; Parameter PMT Volts = 690; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 98900; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden

source_name: MRB 2nd round (4/22/03)

tag: MRB 2nd round (4/22/03)


title: gc 2-2 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35372.gif


title: HI-5


title: pk 2-4 (2/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39178.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 7250; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 14:31:15; Parameter PMT Volts = 490; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17184; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 14:31:15; Parameter PMT Volts = 560; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87142; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: pk 3-4 (2/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39179.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 6950; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 14:18:05; Parameter PMT Volts = 490; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17172; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 14:18:05; Parameter PMT Volts = 540; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87130; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.57; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: Control2


title: gc 4-4 (2/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39173.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 7250; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.31; Parameter Scan Time = 16:31:23; Parameter PMT Volts = 490; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17304; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.31; Parameter Scan Time = 16:31:23; Parameter PMT Volts = 570; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87263; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.61; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: gc 1-3 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36529.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 7840; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.13; Parameter Scan Time = 18:15:37; Parameter PMT Volts = 500; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 80718; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 4.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.5; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.13; Parameter Scan Time = 18:15:37; Parameter PMT Volts = 540; Parameter Scan Date = 2002-10-29; Parameter Pixel Size = 10; Parameter Laser on time = 77603; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.72; Parameter Scanning software version = 2.0.2.5; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: HI-3


title: HI-8


title: HI-10


title: HI-11


title: PM-2


title: pk 1-2 (11/24/02)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35370.gif


title: PM-3


title: PM-1


title: pk 4-4 (2/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39171.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 7250; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 16:18:07; Parameter PMT Volts = 490; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17291; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.25; Parameter Scan Time = 16:18:07; Parameter PMT Volts = 560; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87249; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.61; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: HI-7


title: PM-6


title: N-4


title: PM-13


title: pk 2-3 (2/4/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/39169.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 7250; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.06; Parameter Scan Time = 15:40:01; Parameter PMT Volts = 490; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 17253; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.06; Parameter Scan Time = 15:40:01; Parameter PMT Volts = 550; Parameter Scan Date = 2003-02-04; Parameter Pixel Size = 10; Parameter Laser on time = 87211; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: hES cells differentiated to an fibroblast-like cell type

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: The differentiated human embryonic fibroblast-like (HEF) cells did not express markers of the undifferentiated state but could instead be used for conditioning hES medium.

hyb_protocol: Employing materials and protocols by Illumina Inc.; hybridisation: 17h at 55 degC

scan_protocol: Using an Illumina scanner; gain factor: 2.5

data_processing: In BeadStudio 1.0 raw data were background subtracted and normalised using the "rank invariant" algorithm. Value = "null" denotes expression below background (p < 0.01).

organism: Homo sapiens

source_name: HEF cells derived from H9 hESCs

label_protocol: Linear amplification kit Ambion #IL1791 following the manufacturer's instructions. Input amount: 300ng of total RNA; IVT: 6h

growth_protocol: The differentiated cells were further selected by trypsinisation and expanded in serum-containing medium before RNA isolation.

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion following the manufacturer's instructions

treatment_protocol: Fibroblast-like differentiated cells were derived from differentiated H9 hES cells grown in MEF-conditioned medium prepared without FGF2 supplementation in the conditioning step. Fibroblast-like cells were enriched by mechanical removal of remaining undifferentiated colonies.

tag: Cells displayed fibroblast-like morphology and are capable of supporting the undifferentiated growth of parantal hES cells.


title: gc 2-5 (4/22/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40595.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 13:57:06; Parameter PMT Volts = 550; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 29016; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.84; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 13:57:06; Parameter PMT Volts = 675; Parameter Scan Date = 2003-04-22; Parameter Pixel Size = 10; Parameter Laser on time = 98847; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.55; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden


title: PM-11

description: unfertilized eggs, autumn-spawning strain


title: hESC FGF2-starved exp2

description: This sample presents the control for hESC FGF2 re-stimulated exp2

source_name: cell line H9

treatment_protocol: hES cells were grown in MEF-conditioned medium on matrigel for 2 days, starved in unconditioned medium without FGF2 and with 30uM of SU5402 (Calbiochem), followed by RNA isolation.

tag: human embryonic stem cell line H9, passage 55


title: NCCIT human embryonic carcinoma cells

description: Cells were > 90% undifferentiated as judged by immunocytochemistry using and OCT4 antibody. Data are average intensity values from three replicate cell cultures / hybridisations.

source_name: cell line NCCIT

growth_protocol: NCCIT cells were maintained undifferentiated in high-glucose DMEM supplemented with 10% FCS, 2mM L-glutamine, and penicillin-streptomycin.

tag: human embryonic carcinoma cell line NCCIT


title: hESC FGF2 re-stimulated exp2

description: The control for this sample is hESC FGF2-starved exp2

treatment_protocol: hES cells were grown in MEF-conditioned medium on matrigel for 2 days, starved in unconditioned medium without FGF2 and with 30uM of SU5402 (Calbiochem), and, after extensive washing, re-treated with 40 ng/ml of FGF2 in UM for 4h, followed by RNA isolation.


title: N-3


title: hESC FGF2-starved exp1

description: This sample presents the control for hESC FGF2 re-stimulated exp1

tag: human embryonic stem cell line H9, passage 54


title: PM-9


title: PM-7


title: hESC FGF2 re-stimulated exp1

description: The control for this sample is hESC FGF2-starved exp1


title: Staphylococcus aureus_UAMS-1_Post-Exponential_1

city: Pearl River

first: Ellen

last: Murphy

state: NY

address: 401 N. Middletown Road

department: Vaccines

institute: Wyeth Research

description: Gene expression data used to compare a clinical isolate of Staphylococcus aureus (UAMS-1) to a prototypic laboratory strain (RN6390) to assess the global differences in growth phase-dependent transcriptional profiles.

hyb_protocol: Hybridization was performed according to manufacturer's instructions for antisense prokaryotic arrays (Affymetrix expression analysis technical manual, Affymetrix, Inc., Santa Clara, Calif.)

scan_protocol: Scanning was performed as described in Beenken et al., Journal of Bacteriology, 2004 July, 186(14):4665-4684

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings; raw data were exported via the Metrics tab; no scaling was performed.

label: Biotin ddUTP

organism: Staphylococcus aureus

source_name: Staphylococcus strain UAMS-1, post-exponential phase cells

label_protocol: Conversion to cDNA and labeling was performed as described in Beenken et al., Journal of Bacteriology, 2004 July, 186(14):4665-4684

extract_protocol: Total bacterial RNA was isolated as described by Beenken et al., 2004 July, 186(14):4665-4684

tag: Staphylococcus aureus strain UAMS-1 cells grown to an optical density of 3.0 in tryptic soy broth with constant shaking


title: PM14


title: undifferentiated H9 hES cells

description: Data are average intensity values from three replicate cell cultures / hybridisations.

growth_protocol: hES cells grown in MEF-conditioned medium on Matrigel. Partially differentiated colonies were manually removed from the cultures prior to RNA isolation.

tag: human embryonic stem cell line H9, passage 47


title: Staphylococcus aureus_UAMS-1_Post-Exponential_2


title: PM-10


title: PM-8


title: HI-2


title: HI-1


title: PM-12


title: Staphylococcus aureus_UAMS-929_Post-Exponential_2

description: Gene expression data used to assess the Staphylococcus aureus genes regulated by the staphylococcal accessory regulator (SarA) in the clinical isolate UAMS-1

source_name: Staphylococcus strain UAMS-929, post-exponential phase cells

tag: Staphylococcus aureus strain UAMS-929 cells grown to an optical density of 3.0 in tryptic soy broth with constant shaking


title: Staphylococcus aureus_UAMS-1_Exponential_1

source_name: Staphylococcus strain UAMS-1, exponential phase cells

tag: Staphylococcus aureus strain UAMS-1 cells grown to an optical density of 1.0 in tryptic soy broth with constant shaking


title: Staphylococcus aureus_UAMS-1_Exponential_2


title: 55SD AIR_16

city: Research Triangle Park

first: Urmila

middle: P

last: Kodavanti

state: NC

address: 109 TW Alexander Drive

department: NHEERL, ETD

institute: USEPA

description:
Sprague Dawley rat air exposure.
Biological replicate #4

data_processing: GCOS derived values

label: biotin label

organism: Rattus norvegicus

source_name: Sprague Dawley rat air exposure

tag: Sprague Dawley rat air exposure.

tag: tissue

value: lung


title: 54SD AIR_15

description:
Sprague Dawley rat air exposure
biological replicate #3


title: 53SH SO2_14

description:
spontaneously hypertensive rat SO2 exposure.
Biological replicate #4


title: Staphylococcus aureus_UAMS-929_Post-Exponential_1


title: PIN_pool_vs_PIN4

city: Torino

first: Paolo

last: Provero

address: Via Nizza 52

department: Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Turin

hyb_protocol: Hybridization of labeled cDNA to microarrays was performed for 16 h at 64 °C in a humidified chamber (Corning Costar, Cambridge, MA).

scan_protocol: Microarrays were imaged using the ScanArray 4000 scanner (Perkin Elmer, Foster City, CA); Cy3 and Cy5 fluorescence intensities were extracted using the ScanAlyze software (http://rana.lbl.gov/EisenSoftware.htm).

data_processing: Gene expression was quantified with the SMA package using print tip group lowess normalization without background subtraction. For each array and each clone log2 ratios (M values) and the average log2 intensities (A value) of Cy3 and Cy5 signals were thus obtained.

source_name: laser-capture microdissected stroma derived from tissue sections of 10-weeks old mice bearing prostate intraepithelial neoplasia (PIN) - pool of 4 samples

label_protocol: Labeled cDNA was obtained by reverse transcription of 5 μg of aRNA and incorporation of Cy3-dCTP and Cy5-dCTP (Amersham Biosciences, Amersham, UK).

growth_protocol: standard mice maintenance in a specific pathogen-free facility according to Swiss guidelines for animal experimentation (authorization #1477).

extract_protocol: PicoPure RNA isolation kit (Arcturus, Mountain View, CA, www.arctur.com).

treatment_protocol: LCM slides were prepared from serial 8-μm-thick frozen tissues sections placed on a polyvinyl nuclease free membrane (Molecular Machines&Industries, Glattbrugg, CH). Tissue sections were fixed in ethanol 70% (30 sec), stained with haematoxylin and eosin (15 sec each), dehydrated in graded ethanol, treated with xylene and air-dried in a sterile laminar flow hood. Slides were microdissected immediately following staining using a μCut Laser Microdissection system (Nikon Eclipse TE200). All steps and solutions were performed under RNase free conditions.

tag: Strain

value: FVB

tag: Gender

value: male

tag: Age

value: 10-weeks old

tag: Tissue

value: prostate

tag: Tumor stage

source_name: laser-capture microdissected stroma derived from tissue sections of 10-weeks old mice bearing prostate intraepithelial neoplasia (PIN) - sample 4


title: Staphylococcus aureus_UAMS-929_Exponential_2

source_name: Staphylococcus strain UAMS-929, exponential phase cells

tag: Staphylococcus aureus strain UAMS-929 cells grown to an optical density of 1.0 in tryptic soy broth with constant shaking


title: pk 4-6 (5/7/03)

description:
Simple annotation: neurobiology, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/40728.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 740, 6910; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Edward,,Boyden Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.72; Parameter Scan Time = 13:23:50; Parameter PMT Volts = 525; Parameter Scan Date = 2003-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 32163; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.81; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.72; Parameter Scan Time = 13:23:50; Parameter PMT Volts = 645; Parameter Scan Date = 2003-05-07; Parameter Pixel Size = 10; Parameter Laser on time = 101963; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Edward,,Boyden

source_name: MRB 2nd round (5/7/03)

tag: MRB 2nd round (5/7/03)


title: Staphylococcus aureus_RN6390_Post-Exponential_1

source_name: Staphylococcus strain RN6390, post-exponential phase cells

tag: Staphylococcus aureus strain RN6390 cells grown to an optical density of 3.0 in tryptic soy broth with constant shaking


title: 52SH SO2_13

description:
spontaneously hypertensive rat SO2 exposure
Biological replicate #3


title: Staphylococcus aureus_RN6390_Post-Exponential_2


title: Staphylococcus aureus_RN6390_Exponential_2

source_name: Staphylococcus strain RN6390, exponential phase cells

tag: Staphylococcus aureus strain RN6390 cells grown to an optical density of 1.0 in tryptic soy broth with constant shaking


title: Staphylococcus aureus_UAMS-929_Exponential_1


title: PIN_pool_vs_PIN1

growth_protocol: standard mice maintenance in a specific pathogen-free facility according to Swiss guidelines for animal experimentation (authorization #1477)

source_name: laser-capture microdissected stroma derived from tissue sections of 10-weeks old mice bearing prostate intraepithelial neoplasia (PIN) - sample 1


title: PIN_pool_vs_PIN2

source_name: laser-capture microdissected stroma derived from tissue sections of 10-weeks old mice bearing prostate intraepithelial neoplasia (PIN) - sample 2


title: Staphylococcus aureus_RN6390_Exponential_1

extract_protocol: Total bacterial RNA was isolated as described by Beenken et al., Journal of Bacteriology 2004 July, 186(14):4665-4684


title: 51SH SO2_12

description:
spontaneously hypertensive rat SO2 exposure
Biological replicate #2


title: PIN_pool_vs_PT1

value: prostate intraepithelial neoplasia (PIN)

source_name: laser-capture microdissected stroma derived from from tissue sections of 24-weeks old mice bearing invasive prostate tumor (PT) - sample 1

value: 24-weeks old

value: invasive cancer stage (PT)


title: Staphylococcus aureus_UAMS-155_Post-Exponential_1

description: Gene expression data used to assess the Staphylococcus aureus genes regulated by the accessory gene regulator (agr) system in the clinical isolate UAMS-1

source_name: Staphylococcus strain UAMS-155, post-exponential phase cells

tag: Staphylococcus aureus strain UAMS-155 cells grown to an optical density of 3.0 in tryptic soy broth with constant shaking


title: 50SD SO2_11

description:
Sprague Dawley rat SO2 exposure
biolgical replicate #4

source_name: Sprague Dawley rat SO2 exposure

tag: Sprague Dawley rat SO2 exposure


title: 49SD SO2_10

description:
Sprague Dawley rat SO2 exposure
biological replicate #3


title: Staphylococcus aureus_UAMS-155_Post-Exponential_2


title: Staphylococcus aureus_UAMS-155_Exponential_1

source_name: Staphylococcus strain UAMS-155, exponential phase cells

tag: Staphylococcus aureus strain UAMS-155 cells grown to an optical density of 1.0 in tryptic soy broth with constant shaking


title: 48SD SO2_9

description:
Sprague Dawley rat SO2 exposure
biological replicate #2


title: Staphylococcus aureus_UAMS-155_Exponential_2


title: PIN_pool_vs_PIN3

source_name: laser-capture microdissected stroma derived from tissue sections of 10-weeks old mice bearing prostate intraepithelial neoplasia (PIN) - sample 3


title: BL41K3 plus replicate B

city: Munich

first: Joerg

last: Mages

address: Trogerstrasse 30

department: Institute of Medical Microbiology, Immunology and Hygiene

institute: Technical University Munich

description: BL41K3, EBNA-2 induced, replicate B

data_processing: rma normalized, linear values

tag: BL41K3, EBNA-2 induced


title: 47SD SO2_8

description:
Sprague Dawley rat SO2 exposure
biological replicate #1


title: BL41K3 minus replicate B

description: BL41K3 not induced, replicate B

tag: BL41K3 not induced


title: PIN_pool_vs_PT4

value: FVB.

value: male.

source_name: laser-capture microdissected stroma derived from from tissue sections of 24-weeks old mice bearing invasive prostate tumor (PT) - sample 4


title: 46SD AIR_7

description:
Sprague Dawley rat air exposure
biological replicate #2

tag: Sprague Dawley rat air exposure


title: BJABK3 plus replicate C

description: BJABK3, EBNA-2 induced, replicate C

tag: BJABK3, EBNA-2 induced


title: PIN_pool_vs_PT3

value: PIN = 10-weeks old.

value: prostate.

value: prostate intraepithelial neoplasia (PIN).

source_name: laser-capture microdissected stroma derived from from tissue sections of 24-weeks old mice bearing invasive prostate tumor (PT) - sample 3


title: BJABK3 plus replicate B

description: BJABK3, EBNA-2 induced, replicate B


title: PIN_pool_vs_PT6

source_name: laser-capture microdissected stroma derived from from tissue sections of 24-weeks old mice bearing invasive prostate tumor (PT) - sample 6


title: PIN_pool_vs_PT5

source_name: laser-capture microdissected stroma derived from from tissue sections of 24-weeks old mice bearing invasive prostate tumor (PT) - sample 5


title: 45SD AIR_6

description:
Sprague Dawley rat air exposure
biological replicate #1

source_name: Sprague Dawley rat air exposure

tag: tissue


title: PIN_pool_vs_PT2

source_name: laser-capture microdissected stroma derived from tissue sections of 10-weeks old mice bearing prostate intraepithelial neoplasia (PIN) - pool of 4 samples

tag: Strain

value: 10-weeks old.

source_name: laser-capture microdissected stroma derived from from tissue sections of 24-weeks old mice bearing invasive prostate tumor (PT) - sample 2

value: 24-weeks old.

value: invasive cancer stage (PT).


title: BJABK3 plus replicate A

description: BJABK3, EBNA-2 induced, replicate A


title: BL41K3 plus replicate A

description: BL41K3, EBNA-2 induced, replicate A


title: BL41K3 minus replicate A

description: BL41K3 not induced, replicate A


title: 43SH air_4

description:
spontaneously hypertensive rat
control air exposure
replicate #4

source_name: spontaneously hypertensive rat air exposure


title: BJABK3 minus replicate C

description: BJBK3 not induced, replicate C

tag: BJABK3 not induced


title: 44SH SO2_5

description:
spontaneously hypertensive rat
SO2 exposure
replicate #1


title: BJABK3 minus replicate B

description: BJBK3 not induced, replicate B


title: CF1 mouse embryonic fibroblasts treated with 40 ng/ml of FGF2

description: Non-stimulated CF1 mouse embryonic fibroblasts were used as control.

source_name: CF1 MEFs

growth_protocol: Cells were grown in FCS-containing medium, inactivated using mitomycin C, and replated onto gelatine-coated plates at 55,000 cells/sqcm. The next day, medium was changed to Serum Replacement-containing basic hES cell medium plus 40 ng/ml of FGF2. RNA was isolated one day later.

treatment_protocol: inactivated CF1 MEFs incubated with basic human embryonic stem cell medium plus 40 ng/ml of FGF2 for 24h

tag: primary mouse embryonic fibroblasts of strain CF1


title: CF1 mouse embryonic fibroblasts treated with 4 ng/ml of FGF2

growth_protocol: Cells were grown in FCS-containing medium, inactivated using mitomycin C, and replated onto gelatine-coated plates at 55,000 cells/sqcm. The next day, medium was changed to Serum Replacement-containing basic hES cell medium plus 4 ng/ml of FGF2. RNA was isolated one day later.

treatment_protocol: inactivated CF1 MEFs incubated with basic human embryonic stem cell medium plus 4 ng/ml of FGF2 for 24h


title: 42SH air_3

description:
spontaneously hypertensive rat
biological replicate #3

tag: spontaneously hypertensive rat air exposure.


title: 40SH air_1

description: control samples for spontaneously hypertensive rat (air exposure)

tag: spontaneously hypertensive (SH)


title: BJABK3 minus replicate A

description: BJBK3 not induced, replicate A


title: CF1 mouse embryonic fibroblasts

description: This sample presents the control for FGF2-treated CF1 mouse embryonic fibroblasts. Values are means of three biological replicates.

growth_protocol: Cells were grown in FCS-containing medium, inactivated using mitomycin C, and replated onto gelatine-coated plates at 55,000 cells/sqcm. The next day, medium was changed to Serum Replacement-containing basic hES cell medium without FGF2 supplementation. RNA was isolated one day later.

treatment_protocol: inactivated CF1 MEFs incubated with basic human embryonic stem cell medium for 24h


title: 41SH air_2

description:
spontaneously hypertensive rat
tissue: lung
biological replicate 2

tag: spontaneously hypertensive rat

tag: biological replicate 2


title: CF1 mouse embryonic fibroblasts treated with 13 ng/ml of FGF2

growth_protocol: Cells were grown in FCS-containing medium, inactivated using mitomycin C, and replated onto gelatine-coated plates at 55,000 cells/sqcm. The next day, medium was changed to Serum Replacement-containing basic hES cell medium plus 13 ng/ml of FGF2. RNA was isolated one day later.

treatment_protocol: inactivated CF1 MEFs incubated with basic human embryonic stem cell medium plus 13 ng/ml of FGF2 for 24h


title: human foreskin fibroblasts

source_name: ATCC line CRL-2429

growth_protocol: Cells were grown in high-glucose DMEM supplemented with 10% FCS, 2mM L-glutamine, and penicillin-streptomycin.

tag: exponentially growing human foreskin fibroblast line ATCC CRL-2429


title: KO - knock-out Treated - 0.5 hrs - repeat 1 - Cy5 - mAdbID:62538

status: Public on Oct 02 2006

city: Bethesda

first: Snorri

middle: S

last: Thorgeirsson

state: MD

address: 37 Convent Dr. # 4146

department: Laboratory of Experimental Carcinogenesis

institute: National Cancer institute/NIH

description: mAdb experiment ID: 62538

hyb_protocol: NCI Oligo Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42øC for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ul COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100øC for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42øC just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42øC in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

data_processing: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: WT Primary Hepatocytes - Pooled -Cy3

label_protocol: Cy3 Sample Labeling Protocol - generic

growth_protocol:
Cell Culture Protocol
Media: 1:1 DMEM and HAM's F12 supplemented with ITS
Other: Primary hepatocytes were seeded at 2x106 in 10 cm dishes in the plating medium supplemented with 10% FBS . After 4 hours, the plating medium was replaced to serum-free medium. The following day cells were treated with 50 ng/ml of rhHGF for 0.5, 2, 12 and 24 h. Triplicate cell cultures were established from three individual mice.

extract_protocol:
Extraction Protocol
Extraction method: Trizol protocol

tag: Gender

tag: Age

value: 9-10 weeks

tag: Tissue

value: liver

tag: Developmental stage

value: adult

tag: Cell type

value: Primary hepatocytes

source_name: KO - Met knock-out -treated 0.5 hr - Cy5

label_protocol: Cy5 Sample Labeling Protocol - generic

treatment_protocol:
Treatment type: compound
Agent: HGF (Hepatocyte Growth Factor)
Treatment dose: 50 nM
Treatment time: 0.5 hour

tag: Genotype/Genetic variation gene knock out

tag: Genotype/Genetic variation

value: Alb-Cre +/-; Met Fl/Fl


title: WT - Cre Treated - 0.5 hrs - repeat 3 - Cy5 - mAdbID:62546

description: mAdb experiment ID: 62546

value: male

source_name: WT - Cre Control - treated 0.5 hr - Cy5

tag: Genotype/Genetic variation Alb-Cre +/-


title: WT - Cre Treated - 0.5 hrs - repeat 1 - Cy5 - mAdbID:62544

description: mAdb experiment ID: 62544


title: WT - Cre Treated - 2 hrs - repeat 2 - Cy5 - mAdbID:62603

description: mAdb experiment ID: 62603

source_name: WT - Cre Control - treated 2 hr - Cy5

treatment_protocol:
Treatment type: compound
Agent: HGF (Hepatocyte Growth Factor)
Treatment dose: 50 nM
Treatment time: 2 hour


title: KO - knock-out Treated - 2 hrs - repeat 2 - Cy5 - mAdbID:62609

description: mAdb experiment ID: 62609

source_name: KO - Met knock-out -treated 2 hr - Cy5


title: KO - knock-out Treated - 2 hrs - repeat 1 - Cy5 - mAdbID:62608

description: mAdb experiment ID: 62608


title: KO - knock-out Treated - 0.5 hrs - repeat 2 - Cy5 - mAdbID:62539

description: mAdb experiment ID: 62539


title: KO - knock-out Treated - 0.5 hrs - repeat 3 - Cy5 - mAdbID:62540

description: mAdb experiment ID: 62540


title: WT - Cre Treated - 0.5 hrs - repeat 2 - Cy5 - mAdbID:62545

description: mAdb experiment ID: 62545


title: WT - Cre Treated - 2 hrs - repeat 3 - Cy5 - mAdbID:62604

description: mAdb experiment ID: 62604


title: WT - Cre Treated - 24 hrs - repeat 2 - Cy5 - mAdbID:61766

description: mAdb experiment ID: 61766

source_name: WT - Cre Control - treated 24 hr - Cy5

treatment_protocol:
Treatment type: compound
Agent: HGF (Hepatocyte Growth Factor)
Treatment dose: 50 nM
Treatment time: 24 hour


title: WT - Cre Treated - 2 hrs - repeat 1 - Cy5 - mAdbID:62602

description: mAdb experiment ID: 62602


title: KO - knock-out Treated - 24 hrs - repeat 2 - Cy5 - mAdbID:61773

description: mAdb experiment ID: 61773

source_name: KO - Met knock-out -treated 24 hr - Cy5


title: KO - knock-out Treated - 24 hrs - repeat 1 - Cy5 - mAdbID:61772

description: mAdb experiment ID: 61772


title: WT - Cre Treated - 24 hrs - repeat 1 - Cy5 - mAdbID:61765

description: mAdb experiment ID: 61765


title: WT - Cre Treated - 12 hrs - repeat 1 - Cy5 - mAdbID:61753

description: mAdb experiment ID: 61753

source_name: WT - Cre Control - treated 12 hr - Cy5


title: KO - knock-out Treated - 12 hrs - repeat 3 - Cy5 - mAdbID:61761

description: mAdb experiment ID: 61761

source_name: KO - Met knock-out -treated 12 hr - Cy5


title: KO - knock-out Treated - 24 hrs - repeat 3 - Cy5 - mAdbID:54820

description: mAdb experiment ID: 54820


title: KO - knock-out Treated - 12 hrs - repeat 1 - Cy5 - mAdbID:61759

description: mAdb experiment ID: 61759


title: KO - knock-out Untreated - 0 hrs - repeat 2 - Cy5 - mAdbID:61725

description: mAdb experiment ID: 61725

source_name: KO - Met knock-out - Untreated - Cy5


title: WT - Cre Treated - 12 hrs - repeat 2 - Cy5 - mAdbID:61754

description: mAdb experiment ID: 61754


title: Young vs. Old Dura 2

description:
Simple annotation: Development, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2003-04/39544.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1180, 7620; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Oliver,,Aalami Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 10:46:56; Parameter PMT Volts = 460; Parameter Scan Date = 2003-03-19; Parameter Pixel Size = 10; Parameter Laser on time = 24080; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.81; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.6; Parameter Scanning software = AxImageIO; Performer: Oliver,,Aalami Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.78; Parameter Scan Time = 10:46:56; Parameter PMT Volts = 690; Parameter Scan Date = 2003-03-19; Parameter Pixel Size = 10; Parameter Laser on time = 93984; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.2.6; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Oliver,,Aalami

source_name: AdultDura

tag: AdultDura

source_name: YoungDura

tag: YoungDura


title: Young vs. Old Dura 1

description:
Simple annotation: Development, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34792.gif


title: KO - knock-out Untreated - 0 hrs - repeat 1 - Cy5 - mAdbID:61724

description: mAdb experiment ID: 61724

tag: Strain


title: KO - knock-out Treated - 12 hrs - repeat 2 - Cy5 - mAdbID:61760

description: mAdb experiment ID: 61760


title: WT - Cre Treated - 24 hrs - repeat 3 - Cy5 - mAdbID:54724

description: mAdb experiment ID: 54724


title: WT - Cre Untreated - 0 hrs - repeat 1 - Cy5 - mAdbID:61713

description: mAdb experiment ID: 61713

source_name: WT - Cre Control - Untreated - Cy5

value: Transgenic-heterozygous for Cre recombinase


title: WT - Cre Untreated - 0 hrs - repeat 2 - Cy5 - mAdbID:61714

description: mAdb experiment ID: 61714


title: WT-1 control vs WT Ischemic - 1hr - repeat 1 - mAdbID:63125

status: Public on Oct 01 2006

first: Babru

middle: Bahan

last: Samal

address: 9000 Rockville Pike

department: SMN

institute: NIMH/NIH

description: mAdb experiment ID: 63125

hyb_protocol: Hybridization Protocol Other: Total RNA (15-50 ug in 15.5 ul) was incubated with amino-modified random primer (2 ug/ul, 2 ul) and RNase inhibitor (5 units/ul, 1 ul) at 70C for 10 min. Primer-RNA solution was then incubated at 42C for 2 h with the reverse transcriptase mix containing 5X first-strand buffer, 50X aadUTP/dNTPs (25 mM dATP, 25 mM dGTP, 25 mM dCTP, 15 mM dTTP and 10 mM aminoallyl dUTP), 0.1 M DDT, and Superscript II reverse transcriptase. The cDNAs were labeled with NHS-ester Cy3 and Cy5 dye in the presence of 1 M sodium bicarbinate. Array slides placed in a hybridization chamber (Corning, Corning, NY) were incubated at 42C for 16-24 h, and successively washed with 0.5x SSC, 0.01% SDS, and 0.06X SSC at room temperature for 10 min each.

source_name: WT Ischemic 1 hour - repeat 1

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was extracted with Trizol Reagent (Invitrogen) and purfied using RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol:
Treatment type: shock
Shock: oxygen deprivation
Treatment time: 1 hour
In-vivo treatment: Middle cerebral artery occlusion (MCAO) treatment. A 1.5-cm skin incision was placed between the left margin of the orbit and the tragus. The temporalis muscle was incised and retracted to expose the squamous portion of the temporal bone. A small burr hole (2 mm) was made with a high speed microdrill through the outer surface of the semitranslucent skull over the visibly identified middle cerebral artery at the level of the inferior cerebral vein. The inner layer of the skull was removed with fine forceps, and the dura was opened with a 30-gauge needle. The left MCA was electrocauterized between the olfactory tubercle and the distal segment of the MCA (unilateral occlusion) using a small vessel cauterizer. The olfactory branch of the MCA, which was consistently present, was preserved. The coagulated MCA segment was then transected with microscissors to verify that the occlusion was permanent. The surgical site was closed with 4-0 monofilament nylon sutures. 1 hour following MCAO, animals were killed by decapitation, and the brain was removed quickly. Approximately 10 mg of ipsilateral (left) cortex was dissected from the MCA territory (ischemic zone) and submerged completely under 100 microliters of RNAlater (Ambion, Austin, TX)for RNA isolation. The left cortex of normal (non-ischemic) mouse brain was used as a control for microarray labeling.

value: 129XC57BL6 PACAP +/+ F2

value: Brain

value: ipsilateral (left) cortex dissected from the MCA territory (ischemic zone)

source_name: WT Control-1

value: ipsilateral (left) cortex


title: WT - Cre Treated - 12 hrs - repeat 3 - Cy5 - mAdbID:61755

description: mAdb experiment ID: 61755


title: WT - Cre Untreated - 0 hrs - repeat 3 - Cy5 - mAdbID:54710

description: mAdb experiment ID: 54710


title: KO - knock-out Treated - 2 hrs - repeat 3 - Cy5 - mAdbID:51302

description: mAdb experiment ID: 51302


title: WT-2 control vs WT Ischemic -1hr - repeat 2 - mAdbID:63126

description: mAdb experiment ID: 63126

source_name: WT Control-2

source_name: WT Ischemic 1 hour - repeat 2


title: WT-6 control vs WT Ischemic -1hr - repeat 6 - mAdbID:63130

description: mAdb experiment ID: 63130

source_name: WT Control-6

source_name: WT Ischemic- 1 hr - repeat 6


title: WT-3 control vs WT Ischemic -1hr - repeat 3 - mAdbID:63127

description: mAdb experiment ID: 63127

source_name: WT Control-3

source_name: WT Ischemic - 1 hr - repeat 3


title: KO - knock-out Untreated - 0 hrs - repeat 3 - Cy5 - mAdbID:51300

description: mAdb experiment ID: 51300

source_name: WT Primary Hepatocytes - Pooled -Cy3


title: WT-4 control vs WT Ischemic -1hr - repeat 4 - mAdbID:63128

description: mAdb experiment ID: 63128

source_name: WT Control-4

source_name: WT Ischemic - 1hr - repeat 4


title: WT-5 control vs WT Ischemic -1hr - repeat 5 - mAdbID:63129

description: mAdb experiment ID: 63129

source_name: WT Control-5

source_name: WT Ischemic- 1hr - repeat 5


title: PD-5 control vs PD Ischemic - 24hr - repeat 5 - mAdbID:45875

description: mAdb experiment ID: 45875

source_name: PD Control-5

value: 129XC57BL6 PACAP -/- F2

source_name: PD Ischemic - 24hour- repeat 5

treatment_protocol:
Treatment type: shock
Shock: oxygen deprivation
Treatment time: 24 hours
In-vivo treatment: Middle cerebral artery occlusion (MCAO) treatment. A 1.5-cm skin incision was placed between the left margin of the orbit and the tragus. The temporalis muscle was incised and retracted to expose the squamous portion of the temporal bone. A small burr hole (2 mm) was made with a high speed microdrill through the outer surface of the semitranslucent skull over the visibly identified middle cerebral artery at the level of the inferior cerebral vein. The inner layer of the skull was removed with fine forceps, and the dura was opened with a 30-gauge needle. The left MCA was electrocauterized between the olfactory tubercle and the distal segment of the MCA (unilateral occlusion) using a small vessel cauterizer. The olfactory branch of the MCA, which was consistently present, was preserved. The coagulated MCA segment was then transected with microscissors to verify that the occlusion was permanent. The surgical site was closed with 4-0 monofilament nylon sutures. 24 hours following MCAO, animals were killed by decapitation, and the brain was removed quickly. Approximately 10 mg of ipsilateral (left) cortex was dissected from the MCA territory (ischemic zone) and submerged completely under 100 microliters of RNAlater (Ambion, Austin, TX)for RNA isolation. The left cortex of normal (non-ischemic) mouse brain was used as a control for microarray labeling.


title: PD-6 control vs PD Ischemic - 1hr - repeat 6 - mAdbID:45867

description: mAdb experiment ID: 45867

source_name: PD Control-6

source_name: PD Ischemic - 1 hour- repeat 6


title: PD-4 control vs PD Ischemic - 24hr - repeat 4 - mAdbID:45874

description: mAdb experiment ID: 45874

source_name: PD Control-4

source_name: PD Ischemic - 24hour- repeat 4


title: PD-2 control vs PD Ischemic - 24hr - repeat 2 - mAdbID:45872

description: mAdb experiment ID: 45872

source_name: PD Control-2

source_name: PD Ischemic-24hour- repeat 2


title: PD-4 control vs PD Ischemic - 1hr - repeat 4 - mAdbID:45862

description: mAdb experiment ID: 45862

source_name: PD Ischemic- 1 hour- repeat 4


title: WT-3 control vs WT Ischemic - 24 hr - repeat 3 - mAdbID:45778

description: mAdb experiment ID: 45778

source_name: WT Ischemic 24 hour - repeat 3


title: DIP of MBP.Leu3DB 40 nM 10/28. Cy3

status: Public on Sep 12 2006

type: genomic

city: Chapel Hill

first: Jason

middle: D

last: Lieb

address: CB# 3280, 202 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

description:
in vitro amylose resin precipitaion of mixture of MBP-Leu3DB/naked yeast genome
[MBP-Leu3DB] = 40 nM
done in 10/28/2003
*IPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysis

data_processing: lowess normalization

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: 40 nM MBP-Leu3DB DIP

extract_protocol: Genomic DNA is extracted and then sonicated

treatment_protocol: 40 nM MBP-Leu3DB DNA-ImmunoPrecipitation

tag: [MBP-Leu3DB] = 40 nM

source_name: input DNA

tag: naked yeast genomic DNA


title: PD-5 control vs PD Ischemic - 1hr - repeat 5 - mAdbID:45865

description: mAdb experiment ID: 45865

source_name: PD Ischemic- 1 hour - repeat 5


title: WT-5 control vs WT Ischemic - 24 hr - repeat 5 - mAdbID:45780

description: mAdb experiment ID: 45780

source_name: WT Ischemic 24 hour - repeat 5


title: DIP of MBP.Leu3DB 4 nM No.1. Cy3

description:
in vitro amylose resin precipitaion of mixture of MBP-Leu3DB/naked yeast genome
[MBP-Leu3DB] = 4 nM
done in Nov./2003 #1
*IPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.

source_name: 4 nM MBP-Leu3DB DIP

treatment_protocol: 4 nM MBP-Leu3DB DNA-ImmunoPrecipitation

tag: [MBP-Leu3DB] = 4 nM


title: DIP of MBP as negative control No.6

description:
in vitro amylose resin precipitaion of misture of MBP/naked yeast genome as negative control of MBP::Leu3DB DIP-chip
[MBP] = 4 nM
done in Nov./2003 #6
Flagged spots(low image quality) have been filtered.

source_name: 4 nM MBP DIP

treatment_protocol: 4 nM MBP DNA-ImmunoPrecipitation

tag: [MBP] = 4 nM


title: PD-2 control vs PD Ischemic - 1hr - repeat 2 - mAdbID:45859

description: mAdb experiment ID: 45859

source_name: PD Ischemic- 1 hour - repeat 2


title: PD-1 control vs PD Ischemic - 24hr - repeat 1 - mAdbID:45870

description: mAdb experiment ID: 45870

source_name: PD Control-1

source_name: PD Ischemic-24hour- repeat 1


title: DIP of MBP.Leu3DB 40 nM #1

description:
in vitro amylose resin precipitaion of mixture of MBP-Leu3DB/naked yeast genome
[MBP-Leu3DB] = 40 nM
done in Nov./2003
Flagged spots(low image quality) have been filtered.


title: DIP of MBP.Leu3DB 40 nM #5

tag: in vitro amylose resin precipitaion of mixture of MBP-Leu3DB/naked yeast genome


title: DIP of MBP as negative control No.2. Cy3

description:
in vitro amylose resin precipitaion of misture of MBP/naked yeast genome as negative control of MBP::Leu3DB DIP-chip
[MBP] = 4 nM
done in Nov./2003 #2
*IPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.

growth_protocol: Genomic DNA is extracted and then sonicated


title: DIP of MBP as negative control No.4. Cy3

description:
in vitro amylose resin precipitaion of misture of MBP/naked yeast genome as negative control of MBP::Leu3DB DIP-chip
[MBP] = 4 nM
done in Nov./2003 #4
*IPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.


title: DIP of MBP as negative control No.5. Cy3

description:
in vitro amylose resin precipitaion of misture of MBP/naked yeast genome as negative control of MBP::Leu3DB DIP-chip
[MBP] = 4 nM
done in Nov./2003 #5
*IPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.


title: PD-1 control vs PD Ischemic - 1hr - repeat 1 - mAdbID:45855

description: mAdb experiment ID: 45855

source_name: PD Ischemic-1hour- repeat 1


title: DIP of MBP.Leu3DB 4 nM No.2

description:
in vitro amylose resin precipitaion of mixture of MBP-Leu3DB/naked yeast genome
[MBP-Leu3DB] = 4 nM
done in Nov./2003 #2
Flagged spots(low image quality) have been filtered.


title: PD-3 control vs PD Ischemic - 24hr - repeat 3 - mAdbID:45873

description: mAdb experiment ID: 45873

source_name: PD Control-3

source_name: PD Ischemic - 24hour- repeat 3


title: DIP of MBP.Leu3DB 4 nM No.3. Cy3

description:
in vitro amylose resin precipitaion of mixture of MBP-Leu3DB/naked yeast genome
[MBP-Leu3DB] = 4 nM
done in Nov./2003 #3
*IPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.


title: WT-1 control vs WT Ischemic - 24 hr - repeat 1 - mAdbID:45775

description: mAdb experiment ID: 45775

source_name: WT Control-1

source_name: WT Ischemic 24 hour - repeat 1


title: WT-4 control vs WT Ischemic - 24 hr - repeat 4 - mAdbID:45779

description: mAdb experiment ID: 45779

source_name: WT Control-4

source_name: WT Ischemic 24 hour - repeat 4


title: PD-3 control vs PD Ischemic - 1hr - repeat 3 - mAdbID:45860

description: mAdb experiment ID: 45860

source_name: PD Ischemic- 1 hour - repeat 3


title: WT-2 control vs WT Ischemic - 24 hr - repeat 2 - mAdbID:45776

description: mAdb experiment ID: 45776

source_name: WT Control-2

source_name: WT Ischemic 24 hour - repeat 2


title: DIP of MBP as negative control No.3

description:
in vitro amylose resin precipitaion of misture of MBP/naked yeast genome as negative control of MBP::Leu3DB DIP-chip
[MBP] = 4 nM
done in Nov./2003 #3
Flagged spots(low image quality) have been filtered.

source_name: input DNA


title: ChIP of LEU3p-DB 6/14/03 No.2

description:
overexpressing LEU3p DNA-binding domain (1-147aa) under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3DB
anti-MBP(Abcam65)
done in 6/14/2003 #2
Flagged spots(low image quality) have been filtered.

source_name: input extract

growth_protocol: cells were grown to OD of 1

extract_protocol: Fixed cells were washed and lysed using bead beater and sonicated to get the extract

treatment_protocol: supernatant DNA as reference DNA

tag: Yeast strain

tag: expressing vector

value: pRS416-TEF1-MBPLeu3pDB, which overexpresses DNA-binding domain of Leu3(1-147aa).

tag: supernatant DNA as reference DNA

source_name: anti-MBP-Leu3DB ChIP

treatment_protocol: anti-MBP-Leu3DB ChIP

tag: anti-MBP-Leu3DB ChIPed DNA


title: ChIP of LEU3p-DB 7/19/03 No.2. Cy3

description:
overexpressing LEU3p DNA-binding domain (1-147aa) under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3DB
anti-MBP(Abcam65)
done in 7/19/2003 #2
*CHiPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.


title: ChIP of LEU3p-DB 7/19/03 No.1. Cy3

description:
overexpressing LEU3p DNA-binding domain (1-147aa) under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3DB
anti-MBP(Abcam65)
done in 6/14/2003 #1
*CHiPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.


title: DIP of MBP as negative control No.1. Cy3

description:
in vitro amylose resin precipitaion of misture of MBP/naked yeast genome as negative control of MBP::Leu3DB DIP-chip
[MBP] = 4 nM
done in Nov./2003 #1
*IPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.

source_name: 4 nM MBP DIP


title: ChIP of LEU3p-DB 11/4/03. Cy3

description:
overexpressing LEU3p DNA-binding domain (1-147aa) under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3DB
anti-MBP(Abcam65)
done in Nov./4/2003
*CHiPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.


title: ChIP of LEU3p AD as negative control 7/19/03

description:
overexpressing LEU3p activation domain alone under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3AD
anti-MBP(Abcam65)
done in 7/19/2003
Flagged spots(low image quality) have been filtered.

value: pRS416-TEF1-MBPLeu3pAD, in which DNA-binding domain of Leu3 is deleted.

source_name: anti-MBP-Leu3AD ChIP

treatment_protocol: anti-MBP-Leu3AD ChIP

tag: anti-MBP-Leu3AD ChIPed DNA


title: ChIP of LEU3p AD as negative control 7/31/03

description:
overexpressing LEU3p activation domain alone under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3AD
anti-MBP(Abcam65)
done in 7/31/2003
Flagged spots(low image quality) have been filtered.


title: ChIP of LEU3p AD as negative control 6/12/03

description:
overexpressing LEU3p activation domain alone under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3AD
anti-MBP(Abcam65)
done in 11/8/2003 #2
Flagged spots(low image quality) have been filtered.


title: ChIP of LEU3p AD as negative control 11/4/03. Cy3

description:
overexpressing LEU3p activation domain alone under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3AD
anti-MBP(Abcam65)
done in 11/8/2003 #2
ChIPed DNA is Cy3-labelled
Flagged spots(low image quality) have been filtered.


title: DIP of MBP.Leu3DB 40 nM 10/31No. Cy3

description:
in vitro amylose resin precipitaion of mixture of MBP-Leu3DB/naked yeast genome
[MBP-Leu3DB] = 40 nM
done in 10/28/2003
*IPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.

source_name: 40 nM MBP-Leu3DB DIP


title: ChIP of LEU3p AD as negative control 6/14/03 No.2. Cy3

description:
overexpressing LEU3p activation domain alone under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3AD
anti-MBP(Abcam65)
done in 6/14/2003 #2
ChIPed DNA is Cy3-labelled
Flagged spots(low image quality) have been filtered.


title: Anti-H3 ChIP-chip in Leu3-overexpressing strain ckl5129_LEU3antiH3_1

status: Public on Sep 08 2006

description:
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3R643G, which overexpresses constitutively active Leu3.
anti-Histone3 chiped DNA is Cy3-labeled
Flagged spots(low image quality) have been filtered.

source_name: anti-H3 ChIP

treatment_protocol: anti-H3 ChIPed DNA

tag: anti-H3 ChIPed DNA


title: ChIP of LEU3p AD as negative control 6/14/03 No.1. Cy3

description:
overexpressing LEU3p activation domain alone under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3AD
anti-MBP(Abcam65)
done in 6/14/2003 #1
ChIPed DNA is Cy3-labelled
Flagged spots(low image quality) have been filtered.


title: Anti-H3 ChIP-chip in Leu3-binding deficient strain ckl5077_LEU3ADantiH3_3

description:
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pAD, in which DNA-binding domain of Leu3 is deleted
anti-Histone3
Flagged spots(low image quality) have been filtered.

tag: ChIPed DNA


title: ChIP of LEU3p-DB 6/12/03

description:
overexpressing LEU3p DNA-binding domain (1-147aa) under TDH3 promoter in pRS416-TEF1-MBPLeu3pAD(DB-null-BspEI) vector.
yeast strain: BY4720, leu3null
MBP-tagged Leu3DB
anti-MBP(Abcam65)
done in 6/12/03
Flagged spots(low image quality) have been filtered.


title: Input/input negative control in Leu3-overexpressing strain ckl5013_LEU3input_4

description:
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3R643G, which overexpresses constitutively active Leu3.
input DNA/input DNA as negative control
Flagged spots(low image quality) have been filtered.

treatment_protocol: supernatant DNA

tag: supernatant DNA


title: Anti-H3 ChIP-chip in Leu3-binding deficient strain ckl5124_LEU3ADantiH3_2

description:
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pAD, in which DNA-binding domain of Leu3 is deleted
anti-Histone3 chiped DNA is Cy3-labeled
Flagged spots(low image quality) have been filtered.


title: Input/input negative control in Leu3-binding deficient strain ckl5073_LEU3ADinput_3

description:
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pAD, in which DNA-binding domain of Leu3 is deleted.
input DNA/input DNA as negative control
Flagged spots(low image quality) have been filtered.


title: Anti-H3 ChIP-chip in Leu3-overexpressing strain ckl5128_LEU3antiH3_2

value: pRS416-TEF1-MBPLeu3R643G, which overexpresses constitutively active Leu3.


title: ChIP of LEU3p AD as negative control 11/8/03 No.2


title: Anti-H3 ChIP-chip in Leu3-binding deficient strain ckl5127_LEU3ADantiH3_1


title: Input/input negative control in Leu3-overexpressing strain ckl5055_LEU3input_3

tag: east strain


title: Anti-H3 ChIP-chip in Leu3-overexpressing strain ckl5012_LEU3antiH3_4

description:
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3R643G, which overexpresses constitutively active Leu3.
anti-Histone3
Flagged spots(low image quality) have been filtered.


title: Anti-H3 ChIP-chip in Leu3-overexpressing strain ckl5070_LEU3antiH3_3


title: ChIP of full-length constitutively active LEU3p 7/19/03

description:
CHIP of full-length constitutively active MBP-tagged LEU3p under TDH3 promoter
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pR643G
MBP tagged
anti-MBP(Abcam65)
ChIP in 7/19/03
hybrid. in 8/4/03
Flagged spots(low image quality) have been filtered.

source_name: input extract: supernatant after IP

label_protocol: Direct Incorporation

extract_protocol:
Fixed cells were washed and lysed using bead beater and sonicated to get the extract
DNA was purified after reversing cross links using qiagen

treatment_protocol:
supernatant after IP
as reference DNA

tag: supernatant after IP

tag: as reference DNA

source_name: ChIP of full length constitutively active LEU3p

treatment_protocol: anti-MBP::Leu3 ChIP

tag: anti-MBP::Leu3 ChIPed DNA


title: Ma-Mel_86b

status: Public on Jun 27 2006

city: Zürich

first: Keith

last: Hoek

address: private

country: Switzerland

institute: Currently unaffilliated

description: Undescribed

source_name: culture of cutaneous metastasis of melanoma

tag: unknown


title: Input/input negative control in Leu3-binding deficient strain ckl5011_LEU3ADinput_4

description:
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pAD, in which DNA-binding domain of Leu3 is deleted.
as negative control
Flagged spots(low image quality) have been filtered.


title: Ma-Mel_82

description: Undescribed


title: ChIP of full-length constitutively active LEU3p 6/12/03

description:
CHIP of full-length constitutively active MBP-tagged LEU3p under TDH3 promoter
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pR643G
MBP-tagged Leu3
anti-MBP(Abcam65)
Flagged spots(low image quality) have been filtered.


title: Anti-H3 ChIP-chip in Leu3-binding deficient strain ckl5010_LEU3ADantiH3_4

description:
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pAD, in which DNA-binding domain of Leu3 is deleted.
anti-Histone3
Flagged spots(low image quality) have been filtered.


title: ChIP of full-length constitutively active LEU3p 11/4/03. Cy3

description:
CHIP of full-length constitutively active MBP-tagged LEU3p under TDH3 promoter
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pR643G
MBP-tagged Leu3
anti-MBP(Abcam65)
done in Nov./4/2003
*ChIPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.0 analysi


title: ChIP of full-length constitutively active LEU3p 6/14/03 #2

description:
CHIP of full-length constitutively active MBP-tagged LEU3p under TDH3 promoter
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pR643G
MBP-tagged Leu3
anti-MBP(Abcam65)
ChHiP in 6/14/03
hybrid. 8/4/03
Flagged spots(low image quality) have been filtered.


title: KNUD

description: Undescribed


title: ChIP of full-length constitutively active LEU3p 11/8 No.2. Cy3

description:
CHIP of full-length constitutively active MBP-tagged LEU3p under TDH3 promoter
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pR643G
MBP-tagged Leu3
anti-MBP(Abcam65)
done in Nov./8/2003
*ChIPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.


title: Ma-Mel_80a

description: Undescribed


title: Ma-Mel_74

description: Undescribed


title: Ma-Mel_79B

description: Undescribed


title: Ma-Mel_66b

description: Undescribed


title: Ma-Mel_65

description: Undescribed


title: Ma-Mel_59a

description: Undescribed


title: Ma-Mel_73a

description: Undescribed


title: Ma-Mel_57

description: Undescribed


title: ChIP of full-length constitutively active LEU3p 7/9/03

description:
CHIP of full-length constitutively active MBP-tagged LEU3p under TDH3 promoter
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pR643G
MBP-tagged Leu3
anti-MBP(Abcam65)
ChIP in 7/9/03
hybrid. in 7/31/03
Flagged spots(low image quality) have been filtered.


title: Ma-Mel_86a

description: Undescribed


title: ChIP of full-length constitutively active LEU3p 6/14/03 No.1. Cy3

description:
CHIP of full-length constitutively active MBP-tagged LEU3p under TDH3 promoter
Yeast strain: BY4720-LEU3null
expressing vector: pRS416-TEF1-MBPLeu3pR643G
MBP-tagged Leu3
anti-MBP(Abcam65)
ChHiP in 6/14/03
hybrid. 8/4/03
*CHiPed DNA is Cy3-labelled.
Flagged spots(low image quality) have been filtered.


title: Ma-Mel_54a

description: Undescribed


title: Ma-Mel_58

description: Undescribed


title: Ma-Mel_84

description: Undescribed


title: Ma-Mel_48A

description: Undescribed


title: Ma-Mel_45A

description: Undescribed


title: Ma-Mel_63A

description: Undescribed


title: Ma-Mel_42A

description: Undescribed


title: Ma-Mel_85

description: Undescribed


title: Ma-Mel_69

description: Undescribed


title: Ma-Mel_36

description: Undescribed


title: Ma-Mel_35

description: Undescribed


title: Ma-Mel_76

description: Undescribed


title: Ma-Mel_67

description: Undescribed


title: Ma-Mel_27

description: Undescribed


title: Ma-Mel_71

description: Undescribed


title: Ma-Mel_60

description: Undescribed


title: Ma-Mel_30

description: Undescribed


title: Ma-Mel_40

description: Undescribed


title: Ma-Mel_25

description: Undescribed


title: Ma-Mel_53a

description: Undescribed


title: Ma-Mel_50B

description: Undescribed


title: Ma-Mel_61A

description: Undescribed


title: Ma-Mel_52

description: Undescribed


title: Ma-Mel_07

description: Undescribed


title: Ma-Mel_46

description: Undescribed


title: Ma-Mel_39a

description: Undescribed


title: Ma-Mel_04

description: Undescribed


title: Ma-Mel_28

description: Undescribed


title: Ma-Mel_12

description: Undescribed


title: Ma-Mel_15

description: Undescribed


title: Ma-Mel_06

description: Undescribed


title: Ma-Mel_08b

description: Undescribed

source_name: culture of metastasis of melanoma


title: Ma-Mel_26A

description: Undescribed


title: Skeletal Muscle, biological rep1

status: Public on Jan 01 2007

city: Menlo Park

first: Tyson

middle: A

last: Clark

address: 1380 Willow Rd.

institute: Pacific Biosciences

description: Exon Level Gene Expression data from one of three biological replicates of normal adult skeletal muscle tissue

hyb_protocol: 20 ug of labeled ds cDNA was hybridized to the arrays for 16 hours at 50deg C in a hybridization solution containing 7% DMSO.  The same hybridization cocktail was hybridized to the 4 arrays in the set serially over 4 consecutive days.

scan_protocol: GeneChips were scanned using a GCS3000 scanner with 1.09um pixelation

data_processing: .CEL files were quantile normalized within tissues and median scaled across tissues using probesets from a set of housekeeping genes to a median value of 700.  Probeset values were summarized using SEA.

label: DLR-1a (biotin)

source_name: normal adult skeletal muscle tissue

label_protocol: ds cDNA was generated using the Affymetrix WT labeling reagents, cDNA was fragmented using DNase1 digestion, and end labeled with DLR-1a using terminal transferase

extract_protocol: unknown

tag: Gender

value: Male

tag: Age

tag: RNA Conc (ug/ul)

tag: Lot #