title: Cj GC172  replicate 1

description: Campylobacter jejuni,  strain GC172,  genomic DNA

source_name: GC172  genomic DNA

tag: strain GC172


title: Cj GC182  replicate 1

status: Public on Oct 01 2007

type: genomic

city: Ottawa

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

country: Canada

institute: National Research Council

description: Campylobacter jejuni,  strain GC182,  genomic DNA

hyb_protocol: overnight hybridization at 37 deg in DIG-easy hyb solution (Roche). Washes performed as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

scan_protocol: scans acquired using Scanarray chipreader (BioRad) as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

data_processing: Features were extracted using ArrayPro Analyzer version 4.5 and imported into the BioArray Software Environment (BASE version 1.2). Spots flagged due to poor spot morphology or low signal intensity (less than 5 X local background) were filtered out. After print-tip Loess normalization, data was used to calculate the average log ratio [log2(Signal Tester / Signal Control)]

molecule: genomic DNA

organism: Campylobacter jejuni

source_name: GC182  genomic DNA

label_protocol: Approximately 2 µg of genomic DNA was labeled by chemical coupling to Label IT Cy dye as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

extract_protocol: Approximately 10^10 cells were harvested from cells grown overnight under microaerophilic conditions in Mueller Hinton plates. Genomic DNA extracted by modified lysis/phenol extraction protocol as described in Taboada et al (2004) J Clin Micro 42:4566-4576.

tag: strain GC182

source_name: NCTC11168 genomic DNA

tag: strain NCTC11168 (control)


title: Cj GC152  replicate 1

description: Campylobacter jejuni,  strain GC152,  genomic DNA

source_name: GC152  genomic DNA

tag: strain GC152


title: Cj GC160  replicate 1

description: Campylobacter jejuni,  strain GC160,  genomic DNA

source_name: GC160  genomic DNA

tag: strain GC160


title: Cj GC157  replicate 1

description: Campylobacter jejuni,  strain GC157,  genomic DNA

source_name: GC157  genomic DNA

tag: strain GC157


title: Cj GC156  replicate 1

description: Campylobacter jejuni,  strain GC156,  genomic DNA

source_name: GC156  genomic DNA

tag: strain GC156


title: Cj GC162  replicate 1

description: Campylobacter jejuni,  strain GC162,  genomic DNA

source_name: GC162  genomic DNA

tag: strain GC162


title: Cj GC150  replicate 1

description: Campylobacter jejuni,  strain GC150,  genomic DNA

source_name: GC150  genomic DNA

tag: strain GC150


title: Cj GC147  replicate 1

description: Campylobacter jejuni,  strain GC147,  genomic DNA

source_name: GC147  genomic DNA

tag: strain GC147


title: Cj GC175  replicate 1

description: Campylobacter jejuni,  strain GC175,  genomic DNA

source_name: GC175  genomic DNA

tag: strain GC175


title: Cj GC155  replicate 1

description: Campylobacter jejuni,  strain GC155,  genomic DNA

source_name: GC155  genomic DNA

tag: strain GC155


title: Cj GC124  replicate 1

description: Campylobacter jejuni,  strain GC124,  genomic DNA

source_name: GC124  genomic DNA

tag: strain GC124


title: Cj GC068  replicate 1

description: Campylobacter jejuni,  strain GC068,  genomic DNA

source_name: GC068  genomic DNA

tag: strain GC068


title: Cj GC114  replicate 1

description: Campylobacter jejuni,  strain GC114,  genomic DNA

source_name: GC114  genomic DNA

tag: strain GC114


title: Cj GC142  replicate 1

description: Campylobacter jejuni,  strain GC142,  genomic DNA

source_name: GC142  genomic DNA

tag: strain GC142


title: Cj GC125  replicate 1

description: Campylobacter jejuni,  strain GC125,  genomic DNA

source_name: GC125  genomic DNA

tag: strain GC125


title: Cj GC145  replicate 1

description: Campylobacter jejuni,  strain GC145,  genomic DNA

source_name: GC145  genomic DNA

tag: strain GC145


title: Cj GC165  replicate 1

description: Campylobacter jejuni,  strain GC165,  genomic DNA

source_name: GC165  genomic DNA

tag: strain GC165


title: Cj GC057  replicate 1

description: Campylobacter jejuni,  strain GC057,  genomic DNA

source_name: GC057  genomic DNA

tag: strain GC057

source_name: NCTC11168 genomic DNA

tag: strain NCTC11168 (control)


title: Cj GC060  replicate 1

description: Campylobacter jejuni,  strain GC060,  genomic DNA

source_name: GC060  genomic DNA

tag: strain GC060


title: Cj GC164  replicate 1

description: Campylobacter jejuni,  strain GC164,  genomic DNA

source_name: GC164  genomic DNA

tag: strain GC164


title: Cj GC005  replicate 1

description: Campylobacter jejuni,  strain GC005,  genomic DNA

source_name: GC005  genomic DNA

tag: strain GC005


title: Cj CURA084 replicate 1

description: Campylobacter jejuni,  strain CURA084, genomic DNA

source_name: CURA084 genomic DNA

tag: strain CURA084


title: Cj GC051  replicate 1

description: Campylobacter jejuni,  strain GC051,  genomic DNA

source_name: GC051  genomic DNA

tag: strain GC051


title: Cj GC020  replicate 1

description: Campylobacter jejuni,  strain GC020,  genomic DNA

source_name: GC020  genomic DNA

tag: strain GC020


title: Cj EC112  replicate 1

description: Campylobacter jejuni,  strain EC112,  genomic DNA

source_name: EC112  genomic DNA

tag: strain EC112


title: Cj EC110  replicate 1

description: Campylobacter jejuni,  strain EC110,  genomic DNA

source_name: EC110  genomic DNA

tag: strain EC110


title: Cj EC097  replicate 1

description: Campylobacter jejuni,  strain EC097,  genomic DNA

source_name: EC097  genomic DNA

tag: strain EC097


title: Cj GC021  replicate 1

description: Campylobacter jejuni,  strain GC021,  genomic DNA

source_name: GC021  genomic DNA

tag: strain GC021


title: Cj GC039  replicate 1

description: Campylobacter jejuni,  strain GC039,  genomic DNA

source_name: GC039  genomic DNA

tag: strain GC039


title: Cj EC056  replicate 1

description: Campylobacter jejuni,  strain EC056,  genomic DNA

source_name: EC056  genomic DNA

tag: strain EC056


title: Cj EC055  replicate 1

description: Campylobacter jejuni,  strain EC055,  genomic DNA

source_name: EC055  genomic DNA

tag: strain EC055


title: Cj EC043  replicate 1

description: Campylobacter jejuni,  strain EC043,  genomic DNA

source_name: EC043  genomic DNA

tag: strain EC043


title: Cj EC002  replicate 1

description: Campylobacter jejuni,  strain EC002,  genomic DNA

source_name: EC002  genomic DNA

tag: strain EC002


title: Cj EC027  replicate 1

description: Campylobacter jejuni,  strain EC027,  genomic DNA

source_name: EC027  genomic DNA

tag: strain EC027


title: Cj EC032  replicate 1

description: Campylobacter jejuni,  strain EC032,  genomic DNA

source_name: EC032  genomic DNA

tag: strain EC032

source_name: NCTC11168 genomic DNA

tag: strain NCTC11168 (control)


title: Cj EC007  replicate 1

description: Campylobacter jejuni,  strain EC007,  genomic DNA

source_name: EC007  genomic DNA

tag: strain EC007


title: Cj EC068  replicate 1

description: Campylobacter jejuni,  strain EC068,  genomic DNA

source_name: EC068  genomic DNA

tag: strain EC068


title: Cj EC083  replicate 1

description: Campylobacter jejuni,  strain EC083,  genomic DNA

source_name: EC083  genomic DNA

tag: strain EC083


title: Cj EC084  replicate 1

description: Campylobacter jejuni,  strain EC084,  genomic DNA

source_name: EC084  genomic DNA

tag: strain EC084


title: Cj EC026  replicate 1

description: Campylobacter jejuni,  strain EC026,  genomic DNA

source_name: EC026  genomic DNA

tag: strain EC026


title: Cj EC023  replicate 1

description: Campylobacter jejuni,  strain EC023,  genomic DNA

source_name: EC023  genomic DNA

tag: strain EC023


title: Cj EC082  replicate 1

description: Campylobacter jejuni,  strain EC082,  genomic DNA

source_name: EC082  genomic DNA

tag: strain EC082


title: Cj EC021  replicate 1

description: Campylobacter jejuni,  strain EC021,  genomic DNA

source_name: EC021  genomic DNA

tag: strain EC021


title: Cj CURA040 replicate 1

description: Campylobacter jejuni,  strain CURA040, genomic DNA

source_name: CURA040 genomic DNA

tag: strain CURA040


title: Cj EC073  replicate 1

description: Campylobacter jejuni,  strain EC073,  genomic DNA

source_name: EC073  genomic DNA

tag: strain EC073


title: SM, Uterus #3

status: Public on Sep 28 2007

type: RNA

city: Durham

first: Jen-Tsan Ashley

last: Chi

state: NC

address: 101 Science Drive

department: Duke Institute for Genome Sciences & Policy

country: USA

institute: Duke University

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34756.gif

hyb_protocol: not provided

scan_protocol: not provided

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

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene

label_protocol: not provided

extract_protocol: not provided

tag: Stratagene

tag: LabeledExtract

source_name: Uterus SM #3

tag: Uterus SM #3


title: SM, Colon #3

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34771.gif

source_name: SM, Colon #3

tag: SM, Colon #3


title: SM, Colon #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34770.gif

source_name: SM, Colon #2

tag: SM, Colon #2


title: SM, bladder #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34781.gif

source_name: SM, bladder #1

tag: SM, bladder #1


title: Coronary SM Serum St, T0a

description:
Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45335.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.94; Parameter Scan Time = 11:41:02; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125706; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.94; Parameter Scan Time = 11:41:02; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490807; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Strategene

tag: Strategene

source_name: Coronary SM Serum St, T0a

tag: Coronary SM Serum St, T0a


title: Coronary SM Serum St, T0b

description:
Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45336.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.01; Parameter Scan Time = 10:13:46; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125619; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.01; Parameter Scan Time = 10:13:46; Parameter PMT Volts = 640; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490720; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi


title: Coronary SM Serum St, T0c

description:
Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45337.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.22; Parameter Scan Time = 10:28:06; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125633; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.32; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.22; Parameter Scan Time = 10:28:06; Parameter PMT Volts = 620; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490734; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.88; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Coronary SM Serum St, T0c

tag: Coronary SM Serum St, T0c


title: Coronary SM Serum St, 12 hr

description:
Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45341.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.65; Parameter Scan Time = 11:13:22; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125678; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.65; Parameter Scan Time = 11:13:22; Parameter PMT Volts = 620; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490779; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.94; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Coronary SM Serum St, 12 hr

tag: Coronary SM Serum St, 12 hr


title: SM, Uterus #4

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34757.gif

source_name: Uterus SM #4

tag: Uterus SM #4


title: SM, coronary artery #3

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35890.gif

source_name: SM, coronary artery #3

tag: SM, coronary artery #3


title: SM, Brochial #4

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34768.gif

source_name: SM, Bronchial #4

tag: SM, Bronchial #4


title: SM, coronary artery #1, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35887.gif

source_name: SM, coronary artery #1, low

tag: SM, coronary artery #1, low


title: SM, coronary artery #2, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35889.gif

source_name: SM, coronary artery #2, low

tag: SM, coronary artery #2, low


title: Coronary SM Serum St, 3 hr

description:
Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45339.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.39; Parameter Scan Time = 10:49:16; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125655; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.39; Parameter Scan Time = 10:49:16; Parameter PMT Volts = 620; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490756; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.90; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Coronary SM Serum St, 3hr

tag: Coronary SM Serum St, 3hr


title: SM, Cervix #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34764.gif

source_name: SM, Cervix #2

tag: SM, Cervix #2


title: SM, Colon #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34769.gif

tag: Stratagene

source_name: SM, Colon #1

tag: SM, Colon #1


title: SM, bladder #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34783.gif

source_name: Stratagene

tag: LabeledExtract

source_name: SM, bladder #2

tag: SM, bladder #2


title: SM, coronary artery #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35888.gif

source_name: SM, coronary artery #2

tag: SM, coronary artery #2


title: Coronary SM Serum St, 6 hr

description:
Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45340.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.54; Parameter Scan Time = 11:00:58; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125666; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.54; Parameter Scan Time = 11:00:58; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490767; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.89; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Coronary SM Serum St, 6 hr

tag: Coronary SM Serum St, 6 hr


title: SM, Brochial #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34766.gif

source_name: SM, Bronchial #2

tag: SM, Bronchial #2


title: SM, Aorta Intima #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35885.gif

source_name: SM, Aorta Intima #1

tag: SM, Aorta Intima #1


title: Coronary SM Serum St, 24 hr

description:
Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45350.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.85; Parameter Scan Time = 11:30:26; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125696; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.85; Parameter Scan Time = 11:30:26; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490797; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Strategene

tag: Strategene

source_name: Coronary SM Serum St, 24 hr

tag: Coronary SM Serum St, 24 hr


title: SM, coronary artery #3, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35891.gif

source_name: SM, coronary artery #3, low

tag: SM, coronary artery #3, low


title: SM, Cervix #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34763.gif

source_name: SM, Cervix #1

tag: SM, Cervix #1


title: SM, Uterus #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34755.gif

source_name: Uterus SM #2

tag: Uterus SM #2


title: SM, ureter

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34785.gif

source_name: SM, ureter

tag: SM, ureter


title: SM, bladder #1, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36239.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi 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 = 30.75; Parameter Scan Time = 11:42:42; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41881; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.05; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi 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 = 30.75; Parameter Scan Time = 11:42:42; Parameter PMT Volts = 640; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260876; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.38; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: SM, bladder #1, low

tag: SM, bladder #1, low


title: SM, bronchial #4 , low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36012.gif

source_name: SM, bronchial #4 , low

tag: SM, bronchial #4 , low


title: SM, Aorta Intima #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35886.gif

source_name: SM, Aorta Intima #2

tag: SM, Aorta Intima #2


title: SM, urethra #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34788.gif

tag: Stratagene

source_name: SM, urethra #2

tag: SM, urethra #2


title: SM, uterus #2, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36004.gif

tag: LabeledExtract

source_name: SM, uterus #2, low

tag: SM, uterus #2, low


title: SM, uterus #4, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36006.gif

source_name: Stratagene

source_name: SM, uterus #4, low

tag: SM, uterus #4, low


title: SM, cervix #2, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36008.gif

source_name: SM, cervix #2, low

tag: SM, cervix #2, low


title: SM, Saphenous Vein #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34748.gif

source_name: Saphenous Vein SM #1

tag: Saphenous Vein SM #1


title: Coronary SM Serum St, 1 hr

description:
Simple annotation: Smooth muscle cells, Serum stimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45338.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.30; Parameter Scan Time = 10:38:41; Parameter PMT Volts = 600; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 125643; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.29; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.30; Parameter Scan Time = 10:38:41; Parameter PMT Volts = 620; Parameter Scan Date = 2003-09-27; Parameter Pixel Size = 10; Parameter Laser on time = 490744; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.92; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Coronary SM Serum St, 1hr

tag: Coronary SM Serum St, 1hr


title: SM, Brochial #3

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34767.gif

source_name: SM, Bronchial #3

tag: SM, Bronchial #3


title: SM, Hepatic artery

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34752.gif

source_name: Hepatic artery artery SM

tag: Hepatic artery artery SM


title: SM, PA #1, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35909.gif

source_name: SM, PA #1, low

tag: SM, PA #1, low


title: SM, urethra #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34786.gif

source_name: SM, urethra#1

tag: SM, urethra#1


title: SM, Saphenous Vein #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34749.gif

source_name: Saphenous Vein SM #2

tag: Saphenous Vein SM #2


title: SM, Tibial artery

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34750.gif

source_name: Tibial artery SM

tag: Tibial artery SM


title: SM, cervix #1, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36007.gif

source_name: SM, cervix #1, low

tag: SM, cervix #1, low


title: SM, PA #3, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35911.gif

source_name: SM, PA #3, low

tag: SM, PA #3, low


title: SM, bronchial #3 , low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36010.gif

source_name: SM, bronchial #3 , low

tag: SM, bronchial #3 , low


title: SM, Renal artery

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34753.gif

tag: Stratagene

source_name: Renal artery SM

tag: Renal artery SM


title: Quantitative proteomic analysis of anaerobic and aerobic yeast cultures

status: Public on Sep 26 2007

type: protein

city: Delft

first: Marco

middle: J.L de

last: Groot

state: Zuid Holland

address: Mekelweg 4

department: Mediamatics

country: Netherlands

institute: Delft University of Technology

description:
Protein separation and in-gel tryptic digestion - DTT was added to 125 ?g protein sample at a final concentration of 100 mM, after which the sample was boiled for 5 minutes prior to loading on gel. Equal amounts of protein from each sample (of the 14N labeled and of the 15N labeled culture) were mixed and 250 ?g of the protein mixture was separated through electrophoresis on a homemade 12 % SDS-PAGE gel of 13 cm long. Proteins were visualized using Gelcode Blue Stain Reagent (Pierce, USA) stain. The gel lane was cut into 40 slices. Each slice was cut into small pieces. The gel pieces were washed, in-gel reduced with DTT, followed by in-gel alkylation with iodoacetamide, and in-gel digested by adding trypsin to a final concentration of 10 ng/µl (overnight at 370C).
Nanoflow-LC-MS/MS analysis was performed by coupling an Agilent 1100 Series LC system (vacuum degasser, auto sampler, and one high-pressure-mixing binary pump without static mixer) to an LCQtm Classic Quadrupole Ion Trap mass spectrometer (Finnigan, San Jose, CA, USA). Peptides were delivered to a trap column (AquaTM C18RP (Phenomenex); 15 mm × 100 µm ID, packed in-house) at 5 ?l/min 100% buffer A (0.1 M acetic acid). After reducing the flow to approximately 150 nl/min using a splitter, the peptides were eluted over the analytical column (AquaTM C18RP (Phenomenex); 15 cm × 75 ?m ID, packed in-house) with a linear gradient from 0-50% buffer B (0.1 M acetic acid in 80 % v/v acetonitrile) in 120 minutes. The column eluent was sprayed directly into the ESI source of the mass spectrometer via a butt-connected nano-ESI emitter (New Objectives). The LCQ operated in positive ion mode, and peptides were fragmented in data-dependent mode. One MS survey scan was followed by one data-dependent MS/MS scan. Each digest was analyzed in triplicate using nanoflow-LC-MS/MS.
The SEQUEST algorithm was used to interpret the obtained MS/MS spectra against the complete non-redundant proteome database of S. cerevisiae in FASTA format, obtained from the European Bioinformatics Institute (EBI). The algorithm was run twice on each raw data file, firstly identifying proteins from the peptides containing 14N, and secondly from peptides containing 15N.

data_processing: Relative quantification of the proteins - Ion chromatograms from each peptide selected using DTAselect were extracted from the Xcalibur raw data file by a modified version of EXTRACT-CHRO. The relative protein levels  were determined by calculating peptide ion current ratios using RelEx software, which were also inspected manually. A number of proteins were solely detected in yeast samples from one growth condition, we defined these proteins and its peptides as ‘on-off’. The corresponding extracted ion chromatograms of these ‘on-off’ peptides were filtered from the dataset. The remaining peptide ratios were calculated by using the following settings: Peakshift = 1; Scans before and after = 2; Threshold factor = 0.55; Savitsky-Golay filter = 7 points; Min correlations at 1 and 10 are 0.75 and 0.85 respectively; S/N filter = 3. Peptide ratio outliers were removed and the relative protein ratios (Anaerobic/Aerobic) were calculated by the RelEx software. These protein ratios were manually corrected when the average deviation was more than 10%, based on correct peak detection or correlation within RelEx.

molecule: protein

organism: Saccharomyces cerevisiae

source_name: aerobic chemostat cultivation

label_protocol: Stable isotope labeling. Either 14N labeled nitrogen source (ammonium sulfate) or 98% 15N nitrogen source.

growth_protocol: Grown at 30°C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter. Aerobic cultures were sparged with air and the dissolved oxygen tension was measured online with an oxygen electrode (Ingold model 34 100 3002), and was above 60% of air saturation. The defined synthetic mineral medium composition was based on that described by Verduyn et al., the (NH)4SO4 concentration was however changed to 19 mM. The aerobic cultivations were fed with ca. 7.5 g.l-1 glucose.

extract_protocol: Samples for proteome analysis were sampled on ice and immediately centrifuged (5 min at 4 oC), washed twice with ice-cold water, and stored 5 times concentrated in water at minus 80 oC. Yeast cells were lyophilized prior to protein extraction. For protein extraction,  25 mg cellular dry-weight was mixed with 750 ?l of 2-fold concentrated SDS loading buffer (60 mM Tris-HCl, pH 6.8, 2.5 % (w/v) SDS, 10% v/v glycerol, protease inhibitors, i.e. Complete, Protease Inhibitor Cocktail Tablets; Roche Diagnostics). Glass beads (Sigma, acid washed, 425-600 ?m diameter) were added and the cells were disrupted by 5 times vortexing (60 s at 40C) alternated with cooling intervals (30 s on ice). The supernatant from the beads was collected after mild centrifugation. This extraction step was repeated for the pelleted cells, after which both supernatants were pooled. Lysates were further cleared by centrifugation at 3000 g for 10 minutes at 40C. Protein concentrations were determined using the 2D Quant Kit (Amersham Biosciences). The protein extracts were stored in aliquots of 125 ?g at -800C.

tag: haploid, prototrophic, strain CEN.PK113-7D (MATa, MAL2-8c, SUC2)

source_name: anaerobic chemostat cultivation

growth_protocol: Grown at 30°C in 2-liter chemostats (Applikon), with a working volume of 1.0 liter. For anaerobic chemostat cultivations, fermenters were equipped with Norprene tubing and O-rings to avoid oxygen diffusion and both the fermenter and medium vessel were continuously sparged with ultra-pure nitrogen gas containing less than 5 ppm oxygen. The defined synthetic mineral medium composition was based on that described by Verduyn et al., the (NH)4SO4 concentration was however changed to 19 mM. For anaerobic cultivations, glucose was ca. 25 g.l-1 and the medium was supplemented with the anaerobic growth factors Tween-80 and ergosterol (420 mg.l-1 and 10 mg.l-1 respectively)


title: SM, Hepatic Vein #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34746.gif

source_name: Stratagene

tag: LabeledExtract

source_name: HV #2 SM

tag: HV #2 SM


title: Embryonic Drosophila Kc cells PHO replicate 4

status: Public on Sep 25 2007

city: Basel

first: Christian

last: Beisel

address: Mattenstrasse 26

department: Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

description: Embryonic Drosophila cells, Kc cells

hyb_protocol: For each array, 3 µg of differentially labelled ChIP and input DNA were hybridized together with 15 µg sheared Hering sperm DNA (Invitrogen) in 40 µl 50% formamide, 6xSSC, 0,5% SDS, 5x Denhardt’s 16-18 h at 42°C.

scan_protocol: Microarrays were scanned in a Genepix 4100A Scanner from Axon Instruments equipped with the software GenePix Pro 5.1. Slides were scanned at a variable PMT for each channel (Cy3 or Cy5), a resolution of 10 µm per pixel and a suitable scan area.

data_processing: Spike-ins served to determine the normalization parameters which were subsequently used to normalize all intensity measurements on every microarray. All 8 spot replicates were averaged afterwards. All analyses were performed with R (www.r-project.org) and Bioconductor (www.bioonductor.org). The package arrayMagic (Buness, A., Huber, W., Steiner, K., Sultmann, H., & Poustka, A. (2005) Bioinformatics 21, 554-556) was used for processing and the package vsn for normalization (Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A., & Vingron, M. (2002) Bioinformatics 18 Suppl 1, S96-104).

organism: Drosophila melanogaster

source_name: Embryonic Drosophila cells, Kc cells, PHO ChIP

label_protocol: ChIPed and phenol/chloroform extracted DNA samples were amplified as described (Strutt, H., Cavalli, G., & Paro, R. (1997) Embo J 16, 3621-3632) except for a modification in the PCR protocol, in which a two step PCR was used. The ligation reaction was directly amplified in a 100 µl reaction using Taq polymerase (Qiagen) and 20 amplification cycles. 5 µl of this reaction were reamplified with 15 cycles under the same conditions. 2 µg of amplified and purified DNA were labelled with Cy-dye-CTP (Amersham) in a Klenow reaction. A defined mixture of non-Drosophila DNA fragments was added to the reaction as spike-in controls for array normalization. Labelled DNA was purified with a GFX PCR purification Kit (Amersham).

growth_protocol: Drosophila Kc cells were grown in Schneider’s Drosophila Medium (Gibco) supplemented with 10 % FBS (PAA Laboratories) at 25°C.

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described (Orlando, V., Strutt, H., & Paro, R. (1997) Methods 11, 205-214). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 500-1000 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. The PHO antibody was generated in the lab of J. Mueller at the EMBL, Heidelberg.

tag: PHO ChIP

source_name: Embryonic Drosophila cells, Kc cells, Input DNA

label_protocol: Phenol/chloroform extracted Input samples were amplified as described (Strutt, H., Cavalli, G., & Paro, R. (1997) Embo J 16, 3621-3632) except for a modification in the PCR protocol, in which a two step PCR was used. The ligation reaction was directly amplified in a 100 µl reaction using Taq polymerase (Qiagen) and 20 amplification cycles. 5 µl of this reaction were reamplified with 15 cycles under the same conditions. 2 µg of amplified and purified DNA were labelled with Cy-dye-CTP (Amersham) in a Klenow reaction. A defined mixture of non-Drosophila DNA fragments was added to the reaction as spike-in controls for array normalization. Labelled DNA was purified with a GFX PCR purification Kit (Amersham).

extract_protocol: Chromatin fixation was performed essentially as described (Orlando, V., Strutt, H., & Paro, R. (1997) Methods 11, 205-214). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 500-1000 bp. Soluble chromatin was separated from insoluble material by centrifugation. Supernatant was taken as Input control before immunoprecipitation.

tag: DNA purified from soluble chromatin as reference


title: SM, uterus #3, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36005.gif

source_name: SM, uterus #3, low

tag: SM, uterus #3, low


title: SM, bronchial #2 , low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36009.gif

source_name: SM, bronchial #2 , low

tag: SM, bronchial #2 , low


title: Embryonic Drosophila Kc cells PC replicate 4

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, PC ChIP

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described (Orlando, V., Strutt, H., & Paro, R. (1997) Methods 11, 205-214). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 500-1000 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. The PC antibody recognizing the C-terminal 199 amino acids of Polycomb was produced in rabbits and affinity purified.

tag: PC ChIP


title: Embryonic Drosophila Kc cells PHO replicate 1

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PHO replicate 2

description: Embryonic Drosophila cells, Kc cells


title: SM, PA #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34740.gif

source_name: SM, PA #1

tag: SM, PA #1


title: SM, PA #2, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35910.gif

source_name: SM, PA #2, low

tag: SM, PA #2, low


title: Embryonic Drosophila Kc cells PHO replicate 3

description: Embryonic Drosophila cells, Kc cells


title: SM, PA #3

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34742.gif

source_name: SM, PA #3

tag: SM, PA #3


title: SM, PA #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34741.gif

source_name: SM, PA #2

tag: SM, PA #2


title: SM, PA #4, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35912.gif

source_name: SM, PA #4, low

tag: SM, PA #4, low


title: SM, Popliteal Vein

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34747.gif

source_name: Popliteal Vein SM

tag: Popliteal Vein SM


title: Embryonic Drosophila Kc cells PC replicate 2

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PC replicate 1

description: Embryonic Drosophila cells, Kc cells


title: SM, colon #1, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36244.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi 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 = 31.27; Parameter Scan Time = 12:25:38; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41924; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi 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 = 31.27; Parameter Scan Time = 12:25:38; Parameter PMT Volts = 660; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260919; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: SM, colon #1, low

tag: SM, colon #1, low


title: Embryonic Drosophila Kc cells TRX replicate 5

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, TRX ChIP

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described (Orlando, V., Strutt, H., & Paro, R. (1997) Methods 11, 205-214). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 500-1000 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. The TRX antibody recognizing amino acids 2388-2674 of Trithorax was produced in rabbits and affinity purified.

tag: TRX ChIP


title: Embryonic Drosophila Kc cells TRX replicate 6

description: Embryonic Drosophila cells, Kc cells


title: SM, Coronary artery #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34751.gif

tag: Stratagene

source_name: Coronary artery SM

tag: Coronary artery SM


title: Embryonic Drosophila Kc cells TRX replicate 3

description: Embryonic Drosophila cells, Kc cells


title: SM, Renal Vein

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34744.gif

tag: LabeledExtract

source_name: RV SM

tag: RV SM


title: Embryonic Drosophila Kc cells TRX replicate 4

description: Embryonic Drosophila cells, Kc cells


title: SM, bladder #3

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34784.gif

source_name: Stratagene

source_name: SM, bladder #3

tag: SM, bladder #3


title: SM, Hepatic Vein #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34745.gif

source_name: HV #1 SM

tag: HV #1 SM


title: Embryonic Drosophila Kc cells TRX replicate 1

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, Input DNA

tag: DNA purified from soluble chromatin as reference


title: Embryonic Drosophila Kc cells TRX replicate 2

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila SF4 cells PSC ChIP replicate 2

description:
Embryonic Drosophila cells, SF4 cells.
The diploid SF4 cells show a higher degree of homogeneity regarding their karyotype compared to the heteroploid SL2 cells from which they originated (D. Arndt-Jovin, personal communication).

source_name: Embryonic Drosophila cells, SF4 cells, PSC ChIP

growth_protocol: Drosophila SF4 cells were grown in Schneider’s Drosophila Medium (Gibco) supplemented with 10 % FBS (PAA Laboratories) at 25°C.

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described (Orlando, V., Strutt, H., & Paro, R. (1997) Methods 11, 205-214). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 500-1000 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. The PSC antibody was described in Strutt & Paro (1997) Mol Cell Biol 17, 6773-6783

tag: PSC ChIP

source_name: Embryonic Drosophila cells, SF4 cells, Input DNA


title: Embryonic Drosophila SF4 cells PSC ChIP replicate 4


title: Embryonic Drosophila SF4 cells TRX ChIP replicate 3

source_name: Embryonic Drosophila cells, SF4 cells, TRX ChIP


title: Embryonic Drosophila SF4 cells TRX ChIP replicate 2


title: Embryonic Drosophila SF4 cells TRX ChIP replicate 1


title: Embryonic Drosophila SF4 cells TRX ChIP replicate 4


title: Embryonic Drosophila SF4 cells PC replicate 5

description:
Drosophila cells, SF4 cells.
The diploid SF4 cells show a higher degree of homogeneity regarding their karyotype compared to the heteroploid SL2 cells from which they originated (D. Arndt-Jovin, personal communication).

data_processing: Spike-ins served to determine the normalization parameters which were subsequently used to normalize all intensity measurements on every microarray. All 10 spot replicates were averaged afterwards. All analyses were performed with R (www.r-project.org) and Bioconductor (www.bioonductor.org). The package arrayMagic (Buness, A., Huber, W., Steiner, K., Sultmann, H., & Poustka, A. (2005) Bioinformatics 21, 554-556) was used for processing and the package vsn for normalization (Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A., & Vingron, M. (2002) Bioinformatics 18 Suppl 1, S96-104).

source_name: Embryonic Drosophila cells, SF4 cells, PC ChIP

tag: PC ChIP


title: Embryonic Drosophila SF4 cells PC replicate 8


title: Embryonic Drosophila Kc cells PC replicate 3

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, PC ChIP


title: Smooth Muscle, uterus #1

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32032.gif

source_name: Strategen reference

tag: Strategen reference

source_name: uterus smooth muscle 1

tag: uterus smooth muscle 1


title: Embryonic Drosophila SF4 cells PC replicate 3


title: Embryonic Drosophila SF4 cells PH ChIP replicate 3

source_name: Embryonic Drosophila cells, SF4 cells, PH ChIP

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described (Orlando, V., Strutt, H., & Paro, R. (1997) Methods 11, 205-214). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 500-1000 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. The PH antibody was described in Strutt & Paro (1997) Mol Cell Biol 17, 6773-6783

tag: PH ChIP


title: Embryonic Drosophila SF4 cells PHO ChIP replicate 1

source_name: Embryonic Drosophila cells, SF4 cells, PHO ChIP

tag: PHO ChIP


title: Embryonic Drosophila SF4 cells PHO ChIP replicate 3


title: Embryonic Drosophila SF4 cells PHO ChIP replicate 2


title: Embryonic Drosophila SF4 cells PSC ChIP replicate 1


title: Embryonic Drosophila SF4 cells PSC ChIP replicate 3


title: Embryonic Drosophila SF4 cells PHO ChIP replicate 4


title: Embryonic Drosophila SF4 cells PH ChIP replicate 1


title: Smooth Muscle, uterus #2

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32033.gif

source_name: uterus smooth muscle 2

tag: uterus smooth muscle 2


title: Embryonic Drosophila SF4 cells PH ChIP replicate 2


title: Embryonic Drosophila SF4 cells H3K27me3 ChIP replicate 4

source_name: Embryonic Drosophila cells, SF4 cells, H3K27me3 ChIP

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described (Orlando, V., Strutt, H., & Paro, R. (1997) Methods 11, 205-214). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 500-1000 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. The H3K27me3 antibody was generated in T. Jenuwein’s lab at the IMP, Vienna.

tag: H3K27me3 ChIP


title: Embryonic Drosophila SF4 cells PC replicate 6


title: SM, urethra#2, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36243.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.18; Parameter Scan Time = 12:14:39; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41914; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.18; Parameter Scan Time = 12:14:39; Parameter PMT Volts = 640; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260909; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.38; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: SM, urethra#2, low

tag: SM, urethra#2, low


title: Embryonic Drosophila SF4 cells PH ChIP replicate 4


title: Embryonic Drosophila SF4 cells PC replicate 4


title: Embryonic Drosophila SF4 cells PC replicate 7


title: Embryonic Drosophila Kc cells H3K27me3 ChIP replicate 4

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, H3K27me3 ChIP


title: Embryonic Drosophila SF4 cells H3K27me3 ChIP replicate 1


title: Embryonic Drosophila Kc cells H4ac replicate 3

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, H4ac ChIP

extract_protocol: Chromatin fixation and immunoprecipitation were performed essentially as described (Orlando, V., Strutt, H., & Paro, R. (1997) Methods 11, 205-214). 1x109 cells were fixed in 200 ml medium with 1% formaldehyde for 10 min at room temperature. Cross-linked cells were sonicated to produce chromatin fragments of an average size of 500-1000 bp. Soluble chromatin was separated from insoluble material by centrifugation. The supernatant containing chromatin of 5x107 cells was taken for immunoprecipitation. The Anti-acetyl-histone H4 antibody was purchased from Upstate (Cat# 06-866).

tag: Anti-acetyl histone H4 ChIP


title: Embryonic Drosophila Kc cells H4ac replicate 4

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila SF4 cells H4ac replicate 3

source_name: Embryonic Drosophila cells, SF4 cells, H4ac ChIP


title: Embryonic Drosophila SF4 cells H4ac replicate 4


title: Embryonic Drosophila Kc cells H4ac replicate 6

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila SF4 cells H4ac replicate 2


title: Embryonic Drosophila Kc cells H4ac replicate 5

description: Embryonic Drosophila cells, Kc cells

tag: Anti-acetyl histone H4


title: Embryonic Drosophila Kc cells H3K27me3 ChIP replicate 3

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PH replicate 6

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, PHO ChIP


title: Embryonic Drosophila Kc cells H4ac replicate 2

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, Input DNA


title: Embryonic Drosophila Kc cells PH replicate 5

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, PH ChIP


title: Embryonic Drosophila Kc cells H4ac replicate 1

description: Embryonic Drosophila cells, Kc cells


title: SM, colon #3, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36246.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 12:46:54; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41945; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.45; Parameter Scan Time = 12:46:54; Parameter PMT Volts = 660; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260940; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.40; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Stratagene

tag: Stratagene

source_name: SM, colon #3, low

tag: SM, colon #3, low


title: Embryonic Drosophila SF4 cells PC replicate 2

source_name: Embryonic Drosophila cells, SF4 cells, PC ChIP

source_name: Embryonic Drosophila cells, SF4 cells, Input DNA


title: Embryonic Drosophila Kc cells PSC replicate 5

description: Embryonic Drosophila cells, Kc cells

source_name: Embryonic Drosophila cells, Kc cells, PSC ChIP


title: Embryonic Drosophila SF4 cells PC replicate 1


title: Embryonic Drosophila Kc cells PSC replicate 4

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PSC replicate 1

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PSC replicate 3

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PSC replicate 2

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila SF4 cells H4ac replicate 6


title: Embryonic Drosophila Kc cells PSC replicate 6

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PH replicate 2

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PH replicate 3

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PH replicate 1

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells PH replicate 4

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila SF4 cells H4ac replicate 1


title: Embryonic Drosophila Kc cells H3K27me3 ChIP replicate 1

description: Embryonic Drosophila cells, Kc cells


title: Embryonic Drosophila Kc cells H3K27me3 ChIP replicate 2

description: Embryonic Drosophila cells, Kc cells

tag: H3K37me3 ChIP


title: Embryonic Drosophila SF4 cells H3K27me3 ChIP replicate 2


title: Embryonic Drosophila SF4 cells H3K27me3 ChIP replicate 3


title: Embryonic Drosophila SF4 cells H4ac replicate 5


title: 30minplus.3

status: Public on Sep 24 2007

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

description: Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and  exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP).

hyb_protocol: As recommended for Exon Array processing in “Gene Chip Whole Transcript (WT) Double- Stranded Assay Manual”

data_processing: We quantile normalized all 24 arrays, then used the Affymetrix Probe Logarithmic Intensity Error algorithm to generate both exon and transcript level expression estimates. To select actual signal, we discarded from further data analysis those transcripts and exons belonging to the lower quartile of their respective data sets. PLIER scores were generated with the command: $ apt-probset-summarize -a plier-gcbg version 1.55 2006/4/20. Exon-level data are provided in supplementary text file linked at foot of this record.

extract_protocol: All RNA processing, array hybridizations, and scanning were performed by the Dana- Farber Cancer Institute MicroArray Core. Total RNA was processed using a “Technology Access Gene Chip Eukaryotic Whole Transcript” protocol from Affymetrix (Santa Clara, CA). Except for three modifications this protocol the same as that currently recommended for Exon Array processing, “Gene Chip Whole Transcript (WT) Double- Stranded Assay Manual” . We performed the following three modifications: (1) 100ng of starting RNA, rather than 1ug, was used: (2) the rRNA reduction step was not carried out; and (3) in the second cycle of cDNA synthesis, a second cDNA strand was synthesized before the clean-up and labeling steps.

treatment_protocol: Human neuroblastoma IMR-32 cells (ATCC) were cultured at 37 °C in a humidified atmosphere with 5% CO2 in Eagle's Minimum Essential Media (EMEM, ATCC), modified to contain the following: Earle’s Balanced Salt Solution, non-essential amino acids, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1.5 g/L sodium bicarbonate, with 10% Fetal Bovine Serum (Invitrogen) and penicillin/streptomycin. Prior to membrane depolarization or ER stress studies, cells were grown in EMEM-serum to 70-90% confluency and were then serum-starved for 48 hours with two changes of serum-free EMEM. Stimulus treatments were performed as described [20] except that a HEPESKCl depolarization solution was prepared using tissue culture grade reagents (Sigma). IMR-32 cells were treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, or were exposed to 5?M thapsigargin (Tocris) for 24 hours.

tag: IMR-32 cells (ATCC)

tag: 50 mM KCl treatment for 0.5 hours


title: 30minplus.2

scan_protocol: As recommended for Exon Array processing in “Gene Chip Whole Transcript (WT) Double- Stranded Assay Manual”


title: plus_720_3

label: As recommended for Exon Array processing in “Gene Chip Whole Transcript (WT) Double- Stranded Assay Manual”

tag: 50 mM KCl treatment for 12 hours


title: SM, urethra#1, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36242.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.03; Parameter Scan Time = 12:04:08; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41902; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.01; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.03; Parameter Scan Time = 12:04:08; Parameter PMT Volts = 640; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260898; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.38; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

tag: LabeledExtract

source_name: SM, urethra#1, low

tag: SM, urethra#1, low


title: 90minplus.1

label_protocol: As recommended for Exon Array processing in “Gene Chip Whole Transcript (WT) Double- Stranded Assay Manual”

tag: 50 mM KCl treatment for 1.5 hours


title: how GLC embryos rep1

city: Rehovot

first: Talila

last: Volk

address: Hertzel street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description: Gene expression data from how GLC embryos 3-5 h AEL.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix 3000G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array  was arbitarily set to 250.

label: biotin

source_name: how GLC embryos 3-5 hrs AEL. Repetition1.

label_protocol: The probe Preparation, cDNA synthesis, cRNA reactions and hybridization with Affymetrix high-density oligonucleotide arrays for Drosophila melanogaster was carried out in the Weizmann Institute microarray unit.

growth_protocol: Two hour embryo collections were made from either YW or from how germline clone  mutant females on apple juice/yeast plates at 25°C. Plates were removed and the embryos were aged an additional 3 hr at 25°C.

extract_protocol: Total RNA was extracted from sufficient amounts of embryos ( 100 embryos) using the Macherey-Nagel's:Nucleospin RNA II Mini Kit following the protocol, and then kept in -70°C. Total RNA was prepared independently five times from embryos of each genetic background in order to better normalize the age of these embryo populations. The RNA samples were then collected and concentrated to give 1mg of total RNA using the RNA cleanup RNeasy Mini Kit (Qiagen).

treatment_protocol: . Homozygous how mutant embryos were separated from their siblings using a fluorescent microscope. Carefully staged embryos which had been aged 3–5 hr in this manner were collected and dechorionated.

tag: how GLC


title: how GLC embryos rep2

source_name: how GLC embryos 3-5 hrs AEL. Repetition2.


title: Wild type embryos rep2

description: Gene expression data from yw embryos 3-5 h AEL.

source_name: WT embryos 3-5 hrs AEL. Repetition2.

tag: yw


title: 14_360plus2

tag: 50 mM KCl treatment for 6 hours


title: 90minplus.2


title: 13_360plus1


title: 90minplus.3


title: zero_3

tag: untreated


title: 15_360plus3


title: THAP24_1

tag: 5µM thapsigargin (THAP) treatment for 24 hours


title: plus_720_2


title: SM, PA #4

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34743.gif

scan_protocol: not provided

source_name: SM, PA #4

tag: SM, PA #4


title: plus_720_1


title: THAP24_3


title: BW25113 W/T LBglu 24h biofilm cells

status: Public on Sep 21 2007

city: College Station

first: Jintae

last: Lee

state: TX

department: Chemical Engineering

institute: Texas A&M University

description: RNA extracted from biofilm cells of BW25113 wild type after 24h of growth in LBglu with glass wool

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli antisense array at 45°C for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The microarray was scanned at 570 nm to get an image file by the GeneChip Scanner 3000 (Affymetrix).  Using GeneChip® Operating Software, total cell intensity was scaled automatically in the software to an average value of 500.

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli

source_name: channel 1

label_protocol: The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process.  The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel.  The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181).

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the frozen bead beater tubes containing the cell pellets. The tubes were closed tightly and beat for 50 seconds at the maximum speed in a mini bead beater (cat. no. 3110BX, Biospec). The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen).


title: Wild type embryos rep1

source_name: WT embryos 3-5 hrs AEL.Repetition1.


title: 180minplus.2

tag: 50 mM KCl treatment for 3 hours


title: Escherichia coli strain VS94 + AI3; DMEM OD600=1.0

status: Public on Sep 20 2007

city: Dallas

first: David

middle: A

last: Rasko

address: 6000 Harry Hines Blvd. NA6.138

department: Microbiology

institute: University of Texas Southwestern Medical Center at Dallas

description:
All protocols were done according to manufacturers specifications:
 http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data included in file has not been processed other than those protocols within GCOSv1.4

source_name: Escherichia coli strain VS94

extract_protocol: Ambion RiboPure RNA Isolation

tag: Escherichia coli strain VS94 plus AI3 in the DMEM media grown to OD600=1.0


title: THAP24_2


title: 180minplus.1


title: Escherichia coli strain VS94 + epinephrine; DMEM OD600=1.0

hyb_protocol: All protocols were done according to manufacturers specifications:  http://www.affymetrix.com/support/technical/manual/expression_manual.affx

tag: Escherichia coli strain VS94 with epinephrine in the DMEM media grown to OD600=1.0


title: plus_1440_1

tag: 50 mM KCl treatment for 24 hours


title: Escherichia coli strain VS94 + dpd; DMEM OD600=1.0

scan_protocol: All protocols were done according to manufacturers specifications:  http://www.affymetrix.com/support/technical/manual/expression_manual.affx

tag: Escherichia coli strain VS94 with dpd in the media grown to an OD600=1.0


title: Acetaminophen  24hr  Rat  9537  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

status: Public on Sep 19 2007

city: RTP

first: Pierre

middle: Robert

last: Bushel

department: Biostatistics and Computational Biology Branch

institute: NIEHS

description: Liver Test (Blinded) Sample

data_processing: log base 2 ratio of Dye Normalized rProcessedSignal to gProcessedSignal

organism: Rattus norvegicus

tag: Strain

value: F344/N Gender:male Age:10-12 weeks Tissue:Liver


title: Acetaminophen  3hr  Rat  5339  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  8897  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: plus_1440_3

tag: IMR-32 cells (ATCC)


title: Acetaminophen  6hr  Rat  9203  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Escherichia coli strain VS94; DMEM OD600=1.0

label_protocol:
All protocols were done according to manufacturers specifications:
 http://www.affymetrix.com/support/technical/manual/expression_manual.affx

tag: Escherichia coli strain VS94 grown to OD600=1.0 in DMEM


title: Acetaminophen  24hr  Rat  8089  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  9100  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: plus_1440_2


title: Acetaminophen  24hr  Rat  9540  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  9476  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  7365  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  7077  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  7334  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  7763  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  8596  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  9934  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  7375  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  7198  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  7393  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  9388  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  7515  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  6930  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  8658  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  7743  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Escherichia coli strain 8624; DMEM OD600=1.0

source_name: Escherichia coli strain 8624

tag: Escherichia coli strain 8624; grown to OD600=1.0 in DMEM


title: Acetaminophen  6hr  Rat  9754  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  6071  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  5999  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  2730  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  5889  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  2652  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  3426  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  4550  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  2483  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  5924  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  7075  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  2197  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  2123  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  2330  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  2105  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  1457  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  1658  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  1376  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  1871  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  1045  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  1049  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  9398  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  0685  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  0613  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  1009  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  0504  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  5870  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  5557  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: BW25113 ymgB LBglu 24h biofilm cells

description: RNA extracted from biofilm cells of BW25113 ymgB mutant after 24h of growth in LBglu with glass wool

source_name: Channel 1


title: Acetaminophen  6hr  Rat  5396  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  4678  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  4623  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  4176  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  5389  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  8194  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  3942  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  7334  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  9754  left_liver_lobe

description: Liver Test (Blinded) Sample


title: zero_1


title: Acetaminophen  3hr  Rat  6474  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  9934  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  9203  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  7198  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  8128  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  8089  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  8918  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  7415  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  9388  left_liver_lobe

description: Liver Test (Blinded) Sample


title: 180minplus.3


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  7515  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  7415  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  7393  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  9398  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  5870  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  2015  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  9632  left_liver_lobe

description: Liver Test (Blinded) Sample


title: 30minplus.1

tag: 50 mM KCl treatment for 0.5 hours


title: zero_2


title: Acetaminophen  6hr  Rat  0644  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  6161  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  6071  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  5999  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  9476  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  9537  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  7077  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  8596  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  1277  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: SM, colon #2, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36245.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 12:36:21; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 12:36:21; Parameter PMT Volts = 660; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260930; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.37; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

tag: Stratagene

tag: LabeledExtract

source_name: SM, colon #2, low

tag: SM, colon #2, low


title: SM, bladder #3, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36241.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 11:53:34; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41892; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.01; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 11:53:34; Parameter PMT Volts = 640; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260887; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.38; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: SM, bladder #3, low

tag: SM, bladder #3, low


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  6161  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  5889  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  7743  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  6474  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  4550  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  7763  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  3hr  Rat  2698  left_liver_lobe vs. Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  7075  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  4176  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  5924  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  3420  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  2652  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  8128  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  2483  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  2730  left_liver_lobe

description: Liver Test (Blinded) Sample


title: SM, bladder #2, low

description:
Simple annotation: Smooth muscle cells, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36240.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 7800; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Jen-Tsan Ashley,,Chi 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 = 30.66; Parameter Scan Time = 11:31:33; Parameter PMT Volts = 600; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 41870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.79; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi 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 = 30.66; Parameter Scan Time = 11:31:33; Parameter PMT Volts = 650; Parameter Scan Date = 2002-12-04; Parameter Pixel Size = 10; Parameter Laser on time = 260865; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.36; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Jen-Tsan Ashley,,Chi

source_name: Stratagene

source_name: SM, bladder #2, low

tag: SM, bladder #2, low


title: Acetaminophen  6hr  Rat  5886  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  3hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  3hr  Rat  2105  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  6hr  Rat  5407  left_liver_lobe vs. Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  2197  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control  Acetaminophen  6hr  Rat  left_liver_lobe  Pool vs. Acetaminophen  6hr  Rat  1550  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Control Acetaminophen  24hr  Rat  left_liver_lobe Pool vs. Acetaminophen  24hr  Rat  2330  left_liver_lobe

description: Liver Test (Blinded) Sample


title: Acetaminophen  24hr  Rat  8194  left_liver_lobe vs. Control Acetaminophen  24hr  Rat  left_liver_lobe Pool

description: Liver Test (Blinded) Sample