title: LN_MSM_10uM_48h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28402.gif

scan_protocol: not provided

source_name: 14.5 uM selenium LNCaP total RNA

tag: 14.5 uM selenium LNCaP total RNA

source_name: MSM 10 uM 48h LNCaP total RNA

tag: MSM 10 uM 48h LNCaP total RNA


title: E. coli vs PBS injection whole mosquitoes Rep3

status: Public on Aug 15 2007

type: RNA

city: Baltimore

first: George

last: Dimopoulos

state: MD

address: 615 N. Wolfe Street

department: Molecular Microbiology and Immunology

country: USA

institute: Johns Hopkins School of Public Health

description: AGILENT

hyb_protocol: AGILENT

scan_protocol: AXON

data_processing: GENEPIX

molecule: total RNA

organism: Anopheles gambiae

source_name: Intrathoracically injection of A. gambiae with E. coli, whole mosquitoes RNA collected at 4 hours after injection (Rep3)

label_protocol: AGILENT

extract_protocol: QIAGEN

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

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


title: PMBCL18

type: genomic

city: Vancouver

first: Lindsey

last: Kimm

state: British Columbia

address: 675 W10th Ave

department: Cancer Genetics

country: Canada

institute: BC Cancer Research Centre

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

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

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

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

label: Cyanine 3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Random prime reaction

tag: PMBCL tumor DNA

label: Cyanine 5

source_name: Female pooled genomic DNA

tag: Female pooled genomic reference DNA


title: S. aureus vs PBS injection whole mosquitoes Rep2

description: AGILENT

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


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

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46643.gif
Developmental Stage: Bradyzoite-infected, stress

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1600, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.18; Parameter Scan Time = 19:22:36; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 88547; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.18; Parameter Scan Time = 19:22:36; Parameter PMT Volts = 730; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 88483; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.92; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

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)

source_name: 400ng Reference

label_protocol: not provided

extract_protocol: not provided

tag: 400ng Reference

source_name: 400ng Bradyzoite Infected HFF, Stress Medium


title: 2wk J w2

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58011.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.09; Parameter Scan Time = 05:52:45; Parameter PMT Volts = 490; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 208324; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.09; Parameter Scan Time = 05:52:45; Parameter PMT Volts = 550; Parameter Scan Date = 2004-12-09; Parameter Pixel Size = 10; Parameter Laser on time = 427327; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.59; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

organism: Mus musculus

source_name: reference

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

tag: reference

source_name: wt

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

tag: wt


title: E. coli vs PBS injection whole mosquitoes Rep1

description: AGILENT

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


title: PMBCL19


title: Stress-Expt. 1, Rep. 1

description:
Simple annotation: Toxoplasma, development
Image: http://smd.stanford.edu/MicroArray/gifs/2003-11/46647.gif
Developmental Stage: Uninfected Stress

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ashley,,Fouts Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.52; Parameter Scan Time = 18:58:21; Parameter PMT Volts = 620; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 88523; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.11; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.52; Parameter Scan Time = 18:58:21; Parameter PMT Volts = 730; Parameter Scan Date = 2003-11-11; Parameter Pixel Size = 10; Parameter Laser on time = 88460; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.87; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ashley,,Fouts

source_name: 300ng Uninfected HFF, Stress Medium

tag: 300ng Uninfected HFF, Stress Medium


title: PMBCL20

source_name: Male pooled genomic DNA

tag: Male pooled genomic reference DNA


title: LN_MSM_10uM_4h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28388.gif

source_name: MSM 10 uM 4h LNCaP total RNA

tag: MSM 10 uM 4h LNCaP total RNA


title: S. aureus vs PBS injection whole mosquitoes Rep3

description: AGILENT

source_name: Intrathoracically injection of A. gambiae with S. aureus, whole mosquitoes RNA collected at 4 hours after injection (Rep3)


title: E. coli vs PBS injection whole mosquitoes Rep2

description: AGILENT

source_name: Intrathoracically injection of A. gambiae with E. coli, whole mosquitoes RNA collected at 4 hours after injection (Rep2)


title: 4wk J m1

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57297.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5320; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 22:13:33; Parameter PMT Volts = 600; Parameter Scan Date = 2004-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 204544; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.24; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 22:13:33; Parameter PMT Volts = 600; Parameter Scan Date = 2004-11-04; Parameter Pixel Size = 10; Parameter Laser on time = 423479; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.61; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: mutant - 195

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

tag: mutant - 195


title: LN_MSM_10uM_12h

description:
Simple annotation: prostate cancer, selenium
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/28392.gif

source_name: 14.5 uM selenium LNCaP total RNA

source_name: MSM 10 uM 18h LNCaP total RNA

tag: MSM 10 uM 18h LNCaP total RNA


title: PMBCL14

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

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


title: PfCTRP vs BLOOD GUT 3

description: AGILENT

source_name: Pf CTRP infected A. gambiae GUT at 24 hours rep 3

source_name: HUMAN BLOOD FED A. gambiae GUT at 24 hours


title: PfCTRP vs BLOOD CARC 2

description: AGILENT

source_name: Pf CTRP infected A. gambiae CARCASS at 24 hours rep 2

source_name: HUMAN BLOOD FED A. gambiae CARCASS at 24 hours


title: PfCTRP vs BLOOD CARC 1

description: AGILENT

source_name: Pf CTRP infected A. gambiae CARC at 24 hours rep 1

source_name: HUMAN BLOOD FED A. gambiae CARC at 24 hours


title: PfCTRP vs BLOOD GUT 2

description: AGILENT

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

tag: HUMAN BLOOD FED A. gambiae GUT at 24 hours


title: PfWT vs CTRP GUT 1

description: AGILENT

source_name: Pf WT infected A. gambiae GUT at 24 hours rep 1

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


title: PbWT vs CTRP GUT 3

description: AGILENT

source_name: Pb WT infected A. gambiae GUT at 24 hours rep 3

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


title: PfCTRP vs BLOOD GUT 1

description: AGILENT

source_name: Pf CTRP infected A. gambiae GUT at 24 hours rep 1


title: PfWT vs CTRP GUT 3

description: AGILENT

source_name: Pf WT infected A. gambiae GUT at 24 hours rep 3

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


title: PbWT vs CTRP GUT 2

description: AGILENT

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

tag: Pb CTRP infected A. gambiae GUT at 24 hours


title: PMBCL15

source_name: Male pooled genomic DNA


title: PMBCL17

source_name: Female pooled genomic DNA


title: PMBCL10


title: Niemann-Pick type C primary fibroblast 2 vs reference RNA

description:
Simple annotation: Transcription, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60730.gif

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

source_name: Amplified stratagene reference RNA

tag: Amplified stratagene reference RNA

source_name: Amplified 59413 Niemann-Pick type C primary fibroblasts


title: PbWT vs CTRP GUT 4

description: AGILENT

source_name: Pb WT infected A. gambiae GUT at 24 hours rep 4


title: PMBCL11


title: PbWT vs CTRP GUT 1

description: AGILENT

source_name: Pb WT infected A. gambiae GUT at 24 hours rep 1


title: PMBCL16


title: PMBCL12


title: PbWT vs CTRP CARC 3

description: AGILENT

source_name: Pb WT infected A. gambiae carcass at 24 hours rep 3

source_name: Pb CTRP infected A. gambiae carcass at 24 hours


title: PMBCL8


title: PMBCL9


title: PMBCL13


title: PMBCL5


title: PfWT vs CTRP CARC 2

description: AGILENT

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

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


title: PbWT vs CTRP CARC 1

description: AGILENT

source_name: Pb WT infected A. gambiae carcass at 24 hours rep 1

tag: Pb CTRP infected A. gambiae carcass at 24 hours


title: PbWT vs CTRP CARC 2

description: AGILENT

source_name: Pb WT infected A. gambiae carcass at 24 hours rep 2


title: PMBCL4


title: PfWT vs CTRP CARC 1

description: AGILENT

source_name: Pf WT infected A. gambiae carcass at 24 hours rep 1

tag: Pf CTRP infected A. gambiae carcass at 24 hours


title: PfWT vs CTRP CARC 3

description: AGILENT

source_name: Pf WT infected A. gambiae carcass at 24 hours rep 3


title: PMBCL3


title: PMBCL6


title: 8wk J w4

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60499.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 03:40:53; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221438; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.64; Parameter Scan Time = 03:40:53; Parameter PMT Volts = 670; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440444; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

source_name: reference

source_name: experimental

tag: experimental


title: SP HU syn Cds1 harvested at 240 min Bio_1

status: Public on Aug 14 2007

city: Singapore

first: Majid

last: Eshaghi

state: Singapore

address: Biopolis

department: Bilogical Investigation

country: Singapore

institute: Genome Institute of Singapore

description: Schizosaccharomyces pombe cells synchronized with 8 mM HU for 3 hrs and released in HU free media at 0 time points vs Schizosaccharomyces pombe cells synchronized with 8 mM HU for 3 hrs.

hyb_protocol: Samples were mixed with DIG Easy Hyb buffer (Roche) and Herring Sperm DNA (Invitrogen) before applying to MAUI mixer-slide assembly.  The slides were hybridized overnight for 16 hours at 42¡ãC under MAUI system (BioMicro). Hybridized slides were washed consecutively in 2¡Á SSC/0.1% SDS for 1 min, 1¡Á SSC for 4 min, 0.2¡Á SSC for 4 min, and 0.05¡Á SSC for 1 min, and then spin-dried before scanning.

data_processing: 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 4.0 analysis software.  After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed.  Meidans of log base 2 expression ratios were given in the data table.

organism: Schizosaccharomyces pombe

source_name: Fission yeast cells

label_protocol: Sheared DNA was random-priming labeled with amino-allyl-dUTP (aa-dUTP) using the BioPrime DNA Labeling kit (Invitrogen Corporation, Carlsbad, CA) according the manufacture¡¯s instruction.  Labeled DNA was extracted with phenol/chloroform/isoamyl alcohol and precipitated with ethanol or siopropanol. The labeled DNA was then coupled with cyanine dyes Cy5 (Amersham, Buckinghamshire, UK)

growth_protocol: Yeast cells were cultured at 30 degree centigrade.

extract_protocol: DNA of the cells were extracted as describled in materials and metholds.

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 240 min.

source_name: Fission yeast arrested cells with 8 mM Hydroxyurea  for 3 hrs.

label_protocol: Sheared DNA was random-priming labeled with amino-allyl-dUTP (aa-dUTP) using the BioPrime DNA Labeling kit (Invitrogen Corporation, Carlsbad, CA) according the manufacture¡¯s instruction.  Labeled DNA was extracted with phenol/chloroform/isoamyl alcohol and precipitated with ethanol or siopropanol. The labeled DNA was then coupled with cyanine dyes Cy3 (Amersham, Buckinghamshire, UK)

tag: Reference DNA was obtained by extracting the DNA from the cells treated with 8 mM HU for 3 hrs.


title: SP HU syn Cds1 harvested at 210 min Bio_1

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 4.0 analysis software.

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 210 min.


title: SP HU syn Cds1 harvested at 210 min Bio_2


title: 8wk J w3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60497.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 03:07:59; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221404; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.42; Parameter Scan Time = 03:07:59; Parameter PMT Volts = 680; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440411; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan

tag: reference


title: SP HU syn Cds1 harvested at 225 min Bio_2

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 225 min.


title: SP HU syn Cds1 harvested at 180 min Bio_2

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 180 min.


title: SP HU syn Cds1 harvested at 225 min Bio_1


title: SP HU syn Cds1 harvested at 195 min Bio_2

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 195 min.


title: SP HU syn Cds1 harvested at 180 min Bio_1


title: SP HU syn Cds1 harvested at 165 min Bio_2

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 165 min.


title: 8wk J m3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60498.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 03:28:58; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221426; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.56; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.61; Parameter Scan Time = 03:28:58; Parameter PMT Volts = 670; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440432; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 4wk J m2

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60503.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.00; Parameter Scan Time = 02:24:31; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221361; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.17; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.00; Parameter Scan Time = 02:24:31; Parameter PMT Volts = 650; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440367; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.46; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: PMBCL7

tag: PMBCL tumor DNA

source_name: Female pooled genomic DNA

tag: Female pooled genomic reference DNA


title: SP HU syn Cds1 harvested at 150 min Bio_2_R1

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 150 min.


title: 2wk B m3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60495.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.67; Parameter Scan Time = 04:23:51; Parameter PMT Volts = 540; Parameter Scan Date = 2005-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 222511; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.20; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.67; Parameter Scan Time = 04:23:51; Parameter PMT Volts = 640; Parameter Scan Date = 2005-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 441517; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: SP HU syn Cds1 harvested at 195 min Bio_1


title: 2wk B w3

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60496.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 04:54:04; Parameter PMT Volts = 540; Parameter Scan Date = 2005-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 222540; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.53; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 04:54:04; Parameter PMT Volts = 620; Parameter Scan Date = 2005-03-02; Parameter Pixel Size = 10; Parameter Laser on time = 441546; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: PMBCL2

source_name: Male pooled genomic DNA

tag: Male pooled genomic reference DNA


title: 4wk J m3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60502.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 02:10:02; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221346; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 02:10:02; Parameter PMT Volts = 640; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440353; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: SP HU syn Cds1 harvested at 165 min Bio_1


title: 8wk J m5

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60501.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1410, 5020; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 04:26:35; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221483; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.91; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.82; Parameter Scan Time = 04:26:35; Parameter PMT Volts = 640; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440489; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 8wk J m4

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60500.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 03:54:17; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221450; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.83; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 03:54:17; Parameter PMT Volts = 640; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440456; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.49; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 4wk J w3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60505.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5080; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 02:54:49; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221391; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.37; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 02:54:49; Parameter PMT Volts = 660; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440397; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.48; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: 4wk J w4

description:
Simple annotation: Mutant vs Wild-type, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60504.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5400; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Charandle,,Jordan Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 02:37:53; Parameter PMT Volts = 600; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 221374; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.29; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 02:37:53; Parameter PMT Volts = 660; Parameter Scan Date = 2005-02-27; Parameter Pixel Size = 10; Parameter Laser on time = 440380; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.47; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Charandle,,Jordan


title: SP HU syn Cds1 harvested at 120 min Bio_1

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 120 min.


title: SP HU syn Cds1 harvested at 135 min Bio_1_R1

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 135 min.


title: SP HU syn Cds1 harvested at 135 min Bio_2_R2


title: SP HU syn Cds1 harvested at 150 min Bio_1_R1


title: SP HU syn Cds1 harvested at 105 min Bio_2

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 105 min.


title: SP HU syn Cds1 harvested at 150 min Bio_1_R2


title: SP HU syn Cds1 harvested at 120 min Bio_2


title: SP HU syn Cds1 harvested at 240 min Bio_2


title: ChIP-chip examination of H3me2K4 in S. pombe jmj2-

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

institute: University of Texas at Austin

description: A reference design including a dye reversal was used to examine H3K4me3 localization in a genomic context in the jmj2 mutant. Genomic DNA was extracted after crosslinking from whole cell-extract and chromatin immunoprecipitated using an anti-H3K4me3 antibody

hyb_protocol: Hybridization performed by NimbleGen Systems, Inc.

scan_protocol: Scanning performed by NimbleGen Systems, Inc.

data_processing: Nimblegen-supplied data files were imported into the Bioconductor computing environment (http://bioconductor.org/). After performing quantile normalization, per-probe enrichments were estimated for each probe by fitting a fixed linear model accounting for array, dye, and treatment effects to the data using the limma package (Smyth 2004). Moderated t-statistics and the log-odds score for ChIP-chip enrichment were computed by empirical Bayes shrinkage of the standard errors with the False Discovery Rate controlled to 0.05 using the method of Benjamini and Hochberg.

label: Cy5 and Cy3

source_name: H3K4me3 immunoprecipitated DNA

label_protocol: Sample labeling performed by NimbleGen Systems, Inc.

extract_protocol: 7 ul of the immunoprecipitated DNA or a 1/100 dilution of input DNA were subjected to two rounds of sequenase primer extension with primer A, and later PCR amplified for 40 cycles with primer B. The PCR product was purified using Qiaquick PCR purification columns, eluted in water and concentrated by vacuum centrifugation to 0.5 ug/ul.

tag: jmj2-; h- strain

source_name: jmj2- control input DNA


title: SP HU syn Cds1 harvested at 135 min Bio_2_R1


title: SP HU syn Cds1 harvested at 090 min Bio_1

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 90 min.


title: SP HU syn Cds1 harvested at 105 min Bio_1


title: ChIP-chip examination of H3K4me3 in S. pombe wild-type

description: A reference design including a dye reversal was used to examine H3K4me3 localization in a genomic context in the wild-type. Genomic DNA was extracted after crosslinking from whole cell-extract and chromatin immunoprecipitated using an anti-H3K4me3 antibody

tag: Wild-type; h- strain

source_name: Wild-type control input DNA


title: 19 cy3_to 222 cy5

city: Columbia

first: Raja

middle: S

last: Settivari

state: MO

address: 920 E Campus Drive

department: ASRC

institute: University of Missouri

description: Rats (n=24) were fed ad libitum diets containing either ground endophyte-free (E-) seed or endophyte–infected (E+) seed for five days at thermoneutrality (21°C) or heat stress (32 C). Rats (n=24) with intraperitonial transmitters were used with core temperature (Tc) and general activity measured every 5 minutes during the study. At treatment end, the liver was removed, weighed and frozen in liquid nitrogen. Twelve rats were selected for microarray experiments, based on degree of sensitivity to fescue toxicosis. Degree of sensitivity was based on changes in relative liver weights, feed intake, average daily gain, and Tc from pretreatment levels. RNA was extracted from liver samples, converted to cDNA, and hybridized with the printed oligonucleotide slides. Treatments consisted of four treatment groups, E-TN, E+TN, E-HS, E+HS. E-TN IS control at thermoneutral for 26 days , E+TN toxin fed group at thermoneutral for 26 days; E-HS control at thermoneutral for 5 days and heat treatment for 21 days, E+HS is toxin fed group at thermoneutral for 5 days and heat stress for 21 days.

hyb_protocol: custom protocol

scan_protocol: genepix 6.0

data_processing: J-Maanova - intensity based LOWESS normalization

organism: Rattus norvegicus

source_name: RAT 222; MALE RAT LIVER TISSUE; E-HS

label_protocol: amersham kit protocol

extract_protocol: quiagen kit protocol

tag: E-HS

source_name: RAT 19; MALE RAT LIVER TISSUE; E+TN

label_protocol: amersham dye kit protocol

extract_protocol: quige kit protocol

tag: E+TN


title: SP HU syn Cds1 harvested at 075 min Bio_2

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 75 min.

tag: Reference DNA was obtained by extracting the DNA from the cells treated with 8 mM HU for 3 hrs.


title: 11 cy3_to 32 cy5

source_name: RAT 32; MALE RAT LIVER TISSUE; E-TN

tag: E-TN

source_name: RAT 11; MALE RAT LIVER TISSUE; E+HS

tag: E+HS


title: SP HU syn Cds1 harvested at 090 min Bio_2


title: 19 cy3_to 20 cy5.

source_name: RAT 20; MALE RAT LIVER TISSUE; E-HS


title: 24 cy3_to 28 cy5

source_name: RAT 28; MALE RAT LIVER TISSUE; E+TN

source_name: RAT 24; MALE RAT LIVER TISSUE; E-TN


title: 222 cy3_to 11 cy5


title: 222 cy3_to 23 cy5

source_name: RAT 23; MALE RAT LIVER TISSUE; E+HS


title: SP HU syn Cds1 harvested at 045 min Bio_1

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 45 min.


title: SP HU syn Cds1 harvested at 075 min Bio_1


title: SP HU syn Cds1harvested at 060 min Bio_1

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 60 min.


title: SP HU syn Cds1 harvested at 060 min Bio_2


title: 28 cy3_to 20 cy5


title: 20 cy3_to 23 cy5


title: 32 cy3_to 28 cy5


title: 32 cy3_to 25 cy5

source_name: RAT 25; MALE RAT LIVER TISSUE; E+TN


title: SP HU syn Cds1 harvested at 045 min Bio_2


title: 31 cy3_to 25 cy5

source_name: RAT 31; MALE RAT LIVER TISSUE; E-TN


title: SP HU syn Cds1 harvested at 030 min Bio_2_R2

source_name: Fission yeast cells

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 30 min.


title: 12 cy3_to 17 cy5

source_name: RAT 17; MALE RAT LIVER TISSUE; E+HS

source_name: RAT 12; MALE RAT LIVER TISSUE; E-HS


title: 37 cy3_to 29 cy5

source_name: RAT 29; MALE RAT LIVER TISSUE; E+TN

source_name: RAT 37; MALE RAT LIVER TISSUE; E-TN


title: 23 cy3_to 31 cy5


title: 11 cy3_to 31 cy5


title: 25 cy3_to 12 cy5


title: 12 cy3_to 34 cy5

source_name: RAT 34; MALE RAT LIVER TISSUE; E+HS


title: 17 cy3_to 37 cy5

source_name: RAT37; MALE RAT LIVER TISSUE; E-TN

source_name: RAT17; MALE RAT LIVER TISSUE; E+HS


title: SP HU syn Cds1 harvested at 015 min Bio_2

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 15 min.

source_name: Fission yeast arrested cells with 8 mM Hydroxyurea  for 3 hrs.


title: SP HU syn Cds1 harvested at 015 min Bio_1


title: SP HU syn Cds1 harvested at 030 min Bio_2_R1


title: 17 cy3_to 16 cy5

source_name: RAT 16; MALE RAT LIVER TISSUE; E-TN


title: 37 cy3_to 14 cy5.

source_name: RAT 14; MALE RAT LIVER TISSUE; E+TN


title: 30 cy3_to 35 cy5

source_name: RAT 35; MALE RAT LIVER TISSUE; E+HS

source_name: RAT 30; MALE RAT LIVER TISSUE; E-HS


title: SP HU syn WT harvested at 060 min Bio_2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 60 min.


title: 24 cy3_to 19 cy5

source_name: RAT 19; MALE RAT LIVER TISSUE; E+TN

source_name: RAT 24; MALE RAT LIVER TISSUE; E-TN


title: SP HU syn Cds1 harvested at 000 min Bio_2_R1

tag: Schizosaccharomyces pombe Cds1 cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 0 min.


title: SP HU syn Cds1 harvested at 030 min Bio_1_R1


title: SP HU syn Cds1 harvested at 000 min Bio_1_R2


title: 30 cy3_to 34 cy5


title: 14 cy3_to 30 cy5


title: SP HU syn Cds1 harvested at 000 min Bio_1_R1


title: 15 cy3_to 35 cy5

tag: MALE RAT LIVER TISSUE E +HS

source_name: RAT 15; MALE RAT LIVER TISSUE; E-HS

tag: MALE RAT LIVER TISSUE E-HS


title: SP HU syn WT  harvested at 055 min Bio_1

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 55 min.


title: SP HU syn WT harvested at 050 min Bio_2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 50 min.


title: SP HU syn WT  harvested at 055 min Bio_2


title: 14 cy3_to 15CY5


title: SP HU syn WT  harvested at 040 min Bio_2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 40 min.


title: SP HU syn WT  harvested at 050 min Bio_1


title: 16cy3_to 29 cy5

tag: MALE RAT LIVER TISSUE

tag: MALE RAT LIVER TISSUE E-TN


title: SP HU syn WT harvested at 060 min Bio_1


title: SP HU syn WT  harvested at 045 min Bio_2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 45 min.


title: SP HU syn WT  harvested at 045 min Bio_1

tag: Reference DNA was obtained by extracting the DNA from the cells treated with 8 mM HU for 3 hrs.


title: 34 cy3_to 16 cy5

tag: MALE RAT LIVER TISSUE E+ HS


title: 29 cy3_to 15 cy5

tag: MALE RAT LIVER E-HS

tag: MALE RAT LIVER TISSUE E+TN


title: SP HU syn WT  harvested at 040 min Bio_1


title: 35 cy3_to 24 cy5

tag: E-TN

tag: E+HS


title: SP HU syn WT  harvested at 035 min Bio_1_R2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 35 min.


title: SP HU syn WT  harvested at 035 min Bio_1_R1


title: SP HU syn WT  harvested at 020 min Bio_1

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 20 min.


title: SP HU syn WT  harvested at 035 min Bio_2_R1


title: SP HU syn WT  harvested at 030 min Bio_1_R2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 30 min.


title: SP HU syn WT  harvested at 030 min Bio_2_R1


title: SP HU syn WT  harvested at 035 min Bio_2_R2


title: SP HU syn WT  harvested at 030 min Bio_2_R2


title: SP HU syn WT  harvested at 025 min Bio_1

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 25 min.


title: SP HU syn WT  harvested at 005 min Bio_2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 5 min.


title: SP HU syn WT  harvested at 015 min Bio_1

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 15 min.


title: SP HU syn WT  harvested at 010 min Bio_2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 10 min.


title: SP HU syn WT  harvested at 010 min Bio_1


title: SP HU syn WT  harvested at 025 min Bio_2


title: SP HU syn WT  harvested at 020 min Bio_2


title: SP HU syn WT  harvested at 015 min Bio_2


title: SP HU syn WT harvested at 000 min Bio_2_R2

tag: Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 0 min.


title: SP HU syn WT  harvested at 000 min Bio_1_R2


title: SP HU syn WT  harvested at 005 min Bio_1


title: SP HU syn WT harvested at 000 min Bio_2_R1


title: SP HU syn WT  harvested at 030 min Bio_1_R1


title: SP HU syn WT harvested at 000 min Bio_1_R1


title: BC-M-044

status: Public on Aug 13 2007

city: Oslo

first: Therese

last: Sorlie

address: Montebello

department: Genetics

country: Norway

institute: The Norwegian Radium Hospital

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48077.gif; format: GIF
Datafile type: GenePix Results 3
name: 48077_Datafile type

source_name: Stratagene ref aRNA

tag: Stratagene ref aRNA


title: BC-M-031

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48075.gif; format: GIF
Datafile type: GenePix Results 3
name: 48075_Datafile type


title: BC-M-185

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48072.gif; format: GIF
Datafile type: GenePix Results 3
name: 48072_Datafile type


title: BC-M-067

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48080.gif; format: GIF
Datafile type: GenePix Results 3
name: 48080_Datafile type


title: BC-M-017

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48073.gif; format: GIF
Datafile type: GenePix Results 3
name: 48073_Datafile type


title: BC-M-150

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48262.gif; format: GIF
Datafile type: GenePix Results 3
name: 48262_Datafile type


title: BC-M-053

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48078.gif; format: GIF
Datafile type: GenePix Results 3
name: 48078_Datafile type


title: BC-M-355

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47878.gif; format: GIF
Datafile type: GenePix Results 3
name: 47878_Datafile type


title: BC-M-042

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48076.gif; format: GIF
Datafile type: GenePix Results 3
name: 48076_Datafile type


title: BC-M-088

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48082.gif; format: GIF
Datafile type: GenePix Results 3
name: 48082_Datafile type


title: BC-M-247

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47875.gif; format: GIF
Datafile type: GenePix Results 3
name: 47875_Datafile type


title: BC-M-079

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48081.gif; format: GIF
Datafile type: GenePix Results 3
name: 48081_Datafile type


title: BC-M-144

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48261.gif; format: GIF
Datafile type: GenePix Results 3
name: 48261_Datafile type


title: BC-M-300

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47876.gif; format: GIF
Datafile type: GenePix Results 3
name: 47876_Datafile type


title: BC-M-371

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47881.gif; format: GIF
Datafile type: GenePix Results 3
name: 47881_Datafile type


title: BC-M-222

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47873.gif; format: GIF
Datafile type: GenePix Results 3
name: 47873_Datafile type


title: BC-M-308

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47877.gif; format: GIF
Datafile type: GenePix Results 3
name: 47877_Datafile type


title: BC-M-022

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48074.gif; format: GIF
Datafile type: GenePix Results 3
name: 48074_Datafile type


title: BC-M-363

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47880.gif; format: GIF
Datafile type: GenePix Results 3
name: 47880_Datafile type


title: BC-M-240

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47959.gif; format: GIF
Datafile type: GenePix Results 3
name: 47959_Datafile type


title: BC-M-357

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47879.gif; format: GIF
Datafile type: GenePix Results 3
name: 47879_Datafile type


title: BC-M-341

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47872.gif; format: GIF
Datafile type: GenePix Results 3
name: 47872_Datafile type


title: BC-M-065

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48079.gif; format: GIF
Datafile type: GenePix Results 3
name: 48079_Datafile type


title: BC-M-201

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48264.gif; format: GIF
Datafile type: GenePix Results 3
name: 48264_Datafile type


title: Mouse Parotid-4

city: Rochester

first: Alaka

last: Srivastava

state: NY

address: 601 Elmwood Avenue

department: Oral Biology

institute: University of Rochester Medical Center

description: Fresh tissue was frozen in liquid N2 and then total RNA was extracted

data_processing: B-actin Normalized, see GSE6017 supplementary file background-final.xls for details

source_name: Parotid Gland

tag: Fresh Parotid Gland


title: BC-M-406

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47852.gif; format: GIF
Datafile type: GenePix Results 3
name: 47852_Datafile type


title: BC-M-234

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47874.gif; format: GIF
Datafile type: GenePix Results 3
name: 47874_Datafile type


title: BC-M-139

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48260.gif; format: GIF
Datafile type: GenePix Results 3
name: 48260_Datafile type


title: BC-M-163

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48263.gif; format: GIF
Datafile type: GenePix Results 3
name: 48263_Datafile type


title: BC-M-378

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47882.gif; format: GIF
Datafile type: GenePix Results 3
name: 47882_Datafile type


title: BC-M-391

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47851.gif; format: GIF
Datafile type: GenePix Results 3
name: 47851_Datafile type


title: BC-M-112

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48258.gif; format: GIF
Datafile type: GenePix Results 3
name: 48258_Datafile type


title: Mouse Parotid-1

description: Fresh tissue was frozen in Liquid N2 and then total RNA was isolated

tag: Fresh Mouse Parotid Gland


title: Human Parotid-4

description: Fresh tissue was frozen in liquid N2 and then total RNA was isolated


title: Human Parotid-2


title: BC-M-119

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48259.gif; format: GIF
Datafile type: GenePix Results 3
name: 48259_Datafile type


title: BC-M-338

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47853.gif; format: GIF
Datafile type: GenePix Results 3
name: 47853_Datafile type


title: Mouse Parotid-2


title: BC-M-373

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47855.gif; format: GIF
Datafile type: GenePix Results 3
name: 47855_Datafile type


title: Mouse Parotid-3


title: BC-M-086

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48255.gif; format: GIF
Datafile type: GenePix Results 3
name: 48255_Datafile type


title: BC-M-068

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49866.gif; format: GIF
Datafile type: GenePix Results 3
name: 49866_Datafile type


title: BC-M-066

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49865.gif; format: GIF
Datafile type: GenePix Results 3
name: 49865_Datafile type


title: BC-M-359

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47854.gif; format: GIF
Datafile type: GenePix Results 3
name: 47854_Datafile type


title: BC-M-388

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47856.gif; format: GIF
Datafile type: GenePix Results 3
name: 47856_Datafile type


title: Human Parotid-3


title: BC-M-064

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49864.gif; format: GIF
Datafile type: GenePix Results 3
name: 49864_Datafile type


title: BC-M-080

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48254.gif; format: GIF
Datafile type: GenePix Results 3
name: 48254_Datafile type


title: BC-M-069

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs//49867.gif; format: GIF
Datafile type: GenePix Results 3
name: 49867_Datafile type


title: BC-M-381

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47850.gif; format: GIF
Datafile type: GenePix Results 3
name: 47850_Datafile type


title: BC-M-098

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs//48257.gif; format: GIF
Datafile type: GenePix Results 3
name: 48257_Datafile type


title: BC-M-024

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49862.gif; format: GIF
Datafile type: GenePix Results 3
name: 49862_Datafile type


title: BC-M-089

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48256.gif; format: GIF
Datafile type: GenePix Results 3
name: 48256_Datafile type


title: BC-M-034

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49863.gif; format: GIF
Datafile type: GenePix Results 3
name: 49863_Datafile type


title: BC-M-023

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49861.gif; format: GIF
Datafile type: GenePix Results 3
name: 49861_Datafile type


title: BC-M-019

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49860.gif; format: GIF
Datafile type: GenePix Results 3
name: 49860_Datafile type


title: BC-M-018

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49859.gif; format: GIF
Datafile type: GenePix Results 3
name: 49859_Datafile type


title: BC-M-014

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49857.gif; format: GIF
Datafile type: GenePix Results 3
name: 49857_Datafile type


title: BC-M-085

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50744.gif; format: GIF
Datafile type: GenePix Results 3
name: 50744_Datafile type


title: BC-M-632

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49854.gif; format: GIF
Datafile type: GenePix Results 3
name: 49854_Datafile type


title: BC-M-709

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49855.gif; format: GIF
Datafile type: GenePix Results 3
name: 49855_Datafile type


title: BC-M-309

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49779.gif; format: GIF
Datafile type: GenePix Results 3
name: 49779_Datafile type


title: BC-M-630

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49853.gif; format: GIF
Datafile type: GenePix Results 3
name: 49853_Datafile type


title: BC-M-015

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49858.gif; format: GIF
Datafile type: GenePix Results 3
name: 49858_Datafile type


title: Human Parotid-1

description: Fresh tissue was frozen in Liquid N2 and then total RNA was isolated


title: BC-M-318

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50745.gif; format: GIF
Datafile type: GenePix Results 3
name: 50745_Datafile type


title: BC-M-016

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50743.gif; format: GIF
Datafile type: GenePix Results 3
name: 50743_Datafile type


title: BC-M-283

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49776.gif; format: GIF
Datafile type: GenePix Results 3
name: 49776_Datafile type


title: BC-M-003

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49856.gif; format: GIF
Datafile type: GenePix Results 3
name: 49856_Datafile type


title: BC-M-476

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50746.gif; format: GIF
Datafile type: GenePix Results 3
name: 50746_Datafile type


title: BC-M-298

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49778.gif; format: GIF
Datafile type: GenePix Results 3
name: 49778_Datafile type


title: BC-M-083

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50742.gif; format: GIF
Datafile type: GenePix Results 3
name: 50742_Datafile type


title: BC-M-285

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49573.gif; format: GIF
Datafile type: GenePix Results 3
name: 49573_Datafile type


title: BC-M-314

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49575.gif; format: GIF
Datafile type: GenePix Results 3
name: 49575_Datafile type


title: BC-M-071

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50741.gif; format: GIF
Datafile type: GenePix Results 3
name: 50741_Datafile type


title: BC-M-020

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50739.gif; format: GIF
Datafile type: GenePix Results 3
name: 50739_Datafile type


title: BC-M-057

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50740.gif; format: GIF
Datafile type: GenePix Results 3
name: 50740_Datafile type


title: BC-M-293

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49574.gif; format: GIF
Datafile type: GenePix Results 3
name: 49574_Datafile type


title: BC-M-275

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49774.gif; format: GIF
Datafile type: GenePix Results 3
name: 49774_Datafile type


title: BC-M-212

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49571.gif; format: GIF
Datafile type: GenePix Results 3
name: 49571_Datafile type


title: BC-M-267

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49773.gif; format: GIF
Datafile type: GenePix Results 3
name: 49773_Datafile type


title: BC-M-277

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49775.gif; format: GIF
Datafile type: GenePix Results 3
name: 49775_Datafile type


title: BC-M-246

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49771.gif; format: GIF
Datafile type: GenePix Results 3
name: 49771_Datafile type


title: BC-M-210

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49570.gif; format: GIF
Datafile type: GenePix Results 3
name: 49570_Datafile type


title: BC-M-512

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47682.gif; format: GIF
Datafile type: GenePix Results 3
name: 47682_Datafile type


title: BC-M-488

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47680.gif; format: GIF
Datafile type: GenePix Results 3
name: 47680_Datafile type


title: BC-M-263

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49772.gif; format: GIF
Datafile type: GenePix Results 3
name: 49772_Datafile type


title: BC-M-223

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47969.gif; format: GIF
Datafile type: GenePix Results 3
name: 47969_Datafile type


title: BC-M-493

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47681.gif; format: GIF
Datafile type: GenePix Results 3
name: 47681_Datafile type


title: BC-M-107

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50737.gif; format: GIF
Datafile type: GenePix Results 3
name: 50737_Datafile type


title: BC-M-245

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49769.gif; format: GIF
Datafile type: GenePix Results 3
name: 49769_Datafile type


title: BC-M-190

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47967.gif; format: GIF
Datafile type: GenePix Results 3
name: 47967_Datafile type


title: BC-M-570

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50738.gif; format: GIF
Datafile type: GenePix Results 3
name: 50738_Datafile type


title: BC-M-281

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49572.gif; format: GIF
Datafile type: GenePix Results 3
name: 49572_Datafile type


title: BC-M-100

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50735.gif; format: GIF
Datafile type: GenePix Results 3
name: 50735_Datafile type


title: BC-M-451

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50732.gif; format: GIF
Datafile type: GenePix Results 3
name: 50732_Datafile type


title: BC-M-167

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47965.gif; format: GIF
Datafile type: GenePix Results 3
name: 47965_Datafile type


title: BC-M-209

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47968.gif; format: GIF
Datafile type: GenePix Results 3
name: 47968_Datafile type


title: TG1 with pBS(Kan)Synhox hydrogen producing cells

city: College Station

first: Toshinari

last: Maeda

address: 220 Jack E. Brown Building

department: Department of Chemical Engineering

institute: Texas A&M University

description: RNA extracted from hydrogen producing cells of TG1 with pBS(Kan)Synhox after 6-hour cultivation in complex medium with fructose

data_processing: MAS 5.0 Expression Analysis Default Setting

label: biotin

organism: Escherichia coli

source_name: Channel 1


title: BC-M-171

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47966.gif; format: GIF
Datafile type: GenePix Results 3
name: 47966_Datafile type


title: BC-M-220

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49767.gif; format: GIF
Datafile type: GenePix Results 3
name: 49767_Datafile type


title: BC-M-055

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50733.gif; format: GIF
Datafile type: GenePix Results 3
name: 50733_Datafile type


title: BC-M-197

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49569.gif; format: GIF
Datafile type: GenePix Results 3
name: 49569_Datafile type


title: BC-M-087

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50734.gif; format: GIF
Datafile type: GenePix Results 3
name: 50734_Datafile type


title: BC-M-221

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49768.gif; format: GIF
Datafile type: GenePix Results 3
name: 49768_Datafile type


title: BC-M-146

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49765.gif; format: GIF
Datafile type: GenePix Results 3
name: 49765_Datafile type


title: BC-M-165

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49567.gif; format: GIF
Datafile type: GenePix Results 3
name: 49567_Datafile type


title: BC-M-722

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47964.gif; format: GIF
Datafile type: GenePix Results 3
name: 47964_Datafile type


title: BC-M-052

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47962.gif; format: GIF
Datafile type: GenePix Results 3
name: 47962_Datafile type


title: BC-M-191

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49568.gif; format: GIF
Datafile type: GenePix Results 3
name: 49568_Datafile type


title: TG1 with pBS(Kan) on hydrogen production

description: RNA extracted from hydrogen producing cells of TG1 with pBS(Kan) after 6-hour cultivation in complex medium with fructose


title: BC-M-122

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49763.gif; format: GIF
Datafile type: GenePix Results 3
name: 49763_Datafile type


title: BC-M-627

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47963.gif; format: GIF
Datafile type: GenePix Results 3
name: 47963_Datafile type


title: BC-M-132

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49764.gif; format: GIF
Datafile type: GenePix Results 3
name: 49764_Datafile type


title: BC-M-430

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50731.gif; format: GIF
Datafile type: GenePix Results 3
name: 50731_Datafile type


title: BC-M-334

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50727.gif; format: GIF
Datafile type: GenePix Results 3
name: 50727_Datafile type


title: BC-M-264

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49565.gif; format: GIF
Datafile type: GenePix Results 3
name: 49565_Datafile type


title: BC-M-539

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50719.gif; format: GIF
Datafile type: GenePix Results 3
name: 50719_Datafile type


title: 251a1 rep2

status: Public on Aug 09 2007

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32389.gif

scan_protocol: not provided

organism: Helicobacter pylori

source_name: 0.25 ug Tigr/Astra Reference

tag: 0.25 ug Tigr/Astra Reference


title: 249i5 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32388.gif


title: BC-M-130

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50716.gif; format: GIF
Datafile type: GenePix Results 3
name: 50716_Datafile type


title: 249f1 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32387.gif


title: 249c1 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32386.gif


title: 259i9

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32383.gif


title: BC-M-091

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49759.gif; format: GIF
Datafile type: GenePix Results 3
name: 49759_Datafile type


title: BC-M-457

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49560.gif; format: GIF
Datafile type: GenePix Results 3
name: 49560_Datafile type


title: BC-M-330

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50723.gif; format: GIF
Datafile type: GenePix Results 3
name: 50723_Datafile type


title: BC-M-101

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49760.gif; format: GIF
Datafile type: GenePix Results 3
name: 49760_Datafile type


title: BC-M-551

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47960.gif; format: GIF
Datafile type: GenePix Results 3
name: 47960_Datafile type


title: BC-M-232

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49564.gif; format: GIF
Datafile type: GenePix Results 3
name: 49564_Datafile type


title: BC-M-106

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49761.gif; format: GIF
Datafile type: GenePix Results 3
name: 49761_Datafile type


title: BC-M-157

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49566.gif; format: GIF
Datafile type: GenePix Results 3
name: 49566_Datafile type


title: 251c1 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32420.gif


title: 251a3 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32419.gif


title: 259a3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32380.gif


title: BC-M-148

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49766.gif; format: GIF
Datafile type: GenePix Results 3
name: 49766_Datafile type


title: BC-M-579

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/47961.gif; format: GIF
Datafile type: GenePix Results 3
name: 47961_Datafile type


title: 259c4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32381.gif


title: BC-M-075

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50715.gif; format: GIF
Datafile type: GenePix Results 3
name: 50715_Datafile type


title: 259i9 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32418.gif


title: 259f6

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32382.gif


title: 259a3 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32415.gif


title: 259c4 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32416.gif


title: BC-M-470

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49563.gif; format: GIF
Datafile type: GenePix Results 3
name: 49563_Datafile type


title: BC-M-335

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50714.gif; format: GIF
Datafile type: GenePix Results 3
name: 50714_Datafile type


title: 249i2 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32414.gif


title: 259i10 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32410.gif


title: 259f3 vs Tigr/Astra ref-2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36732.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 39740; Parameter Datafile type = GenePix Results 1.4; 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 Scan Temperature = 33.38; Parameter Scan Time = 10:17:52; Parameter PMT Volts = 500; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 62112; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; 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 Scan Temperature = 33.38; Parameter Scan Time = 10:17:52; Parameter PMT Volts = 550; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 59631; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama

source_name: 0.25 ug Tigr/Astra genomic DNA reference

source_name: 0.25 ug 259f3 genomic DNA

tag: 0.25 ug 259f3 genomic DNA


title: 259f3 vs Tigr/Astra ref

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36731.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 11520; Parameter Datafile type = GenePix Results 1.4; 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 Scan Temperature = 33.25; Parameter Scan Time = 10:12:09; Parameter PMT Volts = 480; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 62106; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; 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 Scan Temperature = 33.25; Parameter Scan Time = 10:12:09; Parameter PMT Volts = 580; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 59625; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama

tag: 0.25 ug Tigr/Astra genomic DNA reference


title: 249i2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32379.gif


title: BC-M-321

description:
Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49780.gif; format: GIF
Datafile type: GenePix Results 3
name: 49780_Datafile type


title: 249c3 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32412.gif


title: 249f4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32378.gif


title: 249a4 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32411.gif


title: 259c3 vs Tigr/Astra ref-2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36730.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 750, 39740; Parameter Datafile type = GenePix Results 1.4; 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 Scan Temperature = 33.47; Parameter Scan Time = 10:22:06; Parameter PMT Volts = 500; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 62115; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; 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 Scan Temperature = 33.47; Parameter Scan Time = 10:22:06; Parameter PMT Volts = 600; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 59634; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama

source_name: 0.25 ug 259c3 genomic DNA

tag: 0.25 ug 259c3 genomic DNA


title: 249c3

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32377.gif


title: 259c8

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32373.gif


title: 259i10

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32375.gif


title: 259a4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32372.gif


title: 249a4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32376.gif


title: 251f2 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32421.gif


title: 259f4

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32374.gif


title: 249i7

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32371.gif


title: 249f2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32370.gif


title: 259c8 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32408.gif


title: 259f4 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32409.gif


title: 259f6 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32417.gif


title: 259a4 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32407.gif


title: 259a5 vs Tigr/Astra ref-2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36728.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 830, 39820; Parameter Datafile type = GenePix Results 1.4; 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 Scan Temperature = 33.65; Parameter Scan Time = 10:33:23; Parameter PMT Volts = 500; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 62127; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; 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 Scan Temperature = 33.65; Parameter Scan Time = 10:33:23; Parameter PMT Volts = 600; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 59646; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama

source_name: 0.25 ug 259a5 genomic DNA

tag: 0.25 ug 259a5 genomic DNA


title: 259c3 vs Tigr/Astra ref

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36729.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1130, 11570; Parameter Datafile type = GenePix Results 1.4; 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 Scan Temperature = 33.53; Parameter Scan Time = 10:25:25; Parameter PMT Volts = 500; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 62119; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; 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 Scan Temperature = 33.53; Parameter Scan Time = 10:25:25; Parameter PMT Volts = 590; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 59637; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.67; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama


title: 259a5 vs Tigr/Astra ref

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/36727.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 650, 11800; Parameter Datafile type = GenePix Results 1.4; 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 Scan Temperature = 33.62; Parameter Scan Time = 10:30:04; Parameter PMT Volts = 500; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 62123; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; 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 Scan Temperature = 33.62; Parameter Scan Time = 10:30:04; Parameter PMT Volts = 590; Parameter Scan Date = 2002-11-07; Parameter Pixel Size = 10; Parameter Laser on time = 59642; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [83966]; Parameter Laser Power = 3.68; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama


title: 249i7 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32406.gif


title: 249f2 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32405.gif


title: 249c6 rep2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32404.gif