title: DS-2, ARD682b, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57664.gif
Cell Line: labia majora
Disease State: CAIS
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 29.53; Parameter Scan Time = 12:03:48; Parameter PMT Volts = 700; Parameter Scan Date = 2004-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 9888; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 29.53; Parameter Scan Time = 12:03:48; Parameter PMT Volts = 820; Parameter Scan Date = 2004-11-23; Parameter Pixel Size = 10; Parameter Laser on time = 9870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.34; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus


title: DS-2, ARD75, CAIS/Mosaik, lGSF

status: Public on Oct 20 2007

type: RNA

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58457.gif
Disease State: CAIS, somatic mosaicism
Cell Line: labia majora
Sex/Mating type: 46,XY

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 4780; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 13:06:13; Parameter PMT Volts = 730; Parameter Scan Date = 2004-12-21; Parameter Pixel Size = 10; Parameter Laser on time = 11727; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.63; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 13:06:13; Parameter PMT Volts = 820; Parameter Scan Date = 2004-12-21; Parameter Pixel Size = 10; Parameter Laser on time = 11709; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.35; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

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 Reference Lot: 1130623

label_protocol: not provided

extract_protocol: not provided

tag: Stratagene Reference Lot

tag: LabeledExtract

source_name: RNA 126

tag: RNA 126


title: DS-2, N-11, NORM, nsGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-12/58030.gif
Cell Line: scrotum
Disease State: normal male
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.72; Parameter Scan Time = 13:59:28; Parameter PMT Volts = 640; Parameter Scan Date = 2004-10-26; Parameter Pixel Size = 10; Parameter Laser on time = 9442; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.72; Parameter Scan Time = 13:59:28; Parameter PMT Volts = 700; Parameter Scan Date = 2004-10-26; Parameter Pixel Size = 10; Parameter Laser on time = 9424; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.36; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Ref. Lot.: 1130623

tag: Stratagene Ref. Lot.


title: DS-2, N-56, NORM, nfGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61260.gif
Cell Line: foreskin
Disease State: normal male
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 30.08; Parameter Scan Time = 09:26:36; Parameter PMT Volts = 700; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 8862; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 30.08; Parameter Scan Time = 09:26:36; Parameter PMT Volts = 800; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 8845; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.42; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Ref. Lot.-Nr. 1130623

tag: Stratagene Ref. Lot.-Nr. 1130623

source_name: RNA 073

tag: RNA 073


title: DS-3, ARD527a, AIS2, sGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60390.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1840, 5880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 26.88; Parameter Scan Time = 10:16:24; Parameter PMT Volts = 700; Parameter Scan Date = 2005-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 12694; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 26.88; Parameter Scan Time = 10:16:24; Parameter PMT Volts = 840; Parameter Scan Date = 2005-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 12676; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.30; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Ref. Lot-Nr. 1130623

tag: Stratagene Ref. Lot-Nr. 1130623

source_name: RNA 133

tag: RNA 133


title: DS-2, N-40, NORM, nfGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-04/60756.gif
Disease State: normal male
Cell Line: foreskin
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1670, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 30.14; Parameter Scan Time = 10:59:30; Parameter PMT Volts = 640; Parameter Scan Date = 2004-07-15; Parameter Pixel Size = 10; Parameter Laser on time = 8548; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.61; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 30.14; Parameter Scan Time = 10:59:30; Parameter PMT Volts = 750; Parameter Scan Date = 2004-07-15; Parameter Pixel Size = 10; Parameter Laser on time = 8530; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.43; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: RNA 044

tag: RNA 044


title: DS-2, N-4, NORM, nsGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59168.gif
Disease State: normal male
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.71; Parameter Scan Time = 13:47:39; Parameter PMT Volts = 690; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 9053; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.71; Parameter Scan Time = 13:47:39; Parameter PMT Volts = 750; Parameter Scan Date = 2004-10-05; Parameter Pixel Size = 10; Parameter Laser on time = 9036; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.37; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus


title: DS-3, ARD1144, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63402.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1180, 5220; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 30.42; Parameter Scan Time = 10:57:53; Parameter PMT Volts = 640; Parameter Scan Date = 2005-06-28; Parameter Pixel Size = 10; Parameter Laser on time = 14135; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 30.42; Parameter Scan Time = 10:57:53; Parameter PMT Volts = 700; Parameter Scan Date = 2005-06-28; Parameter Pixel Size = 10; Parameter Laser on time = 14118; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.25; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: RNA 171

tag: RNA 171


title: FEC100_0150_A

status: Public on Oct 18 2007

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: Patients included in clinical trials (PACS01 / PEGASE01).

hyb_protocol: Labelled cDNAs were then hybridized in 0.3 ml hybridization mix in scintillation vials for 48 h at 68° C. After hybridization filters were washed twice in 0.1x SSC, 0.1% SDS at 68° C for 90 min.

scan_protocol: DNA microarrays were scanned at 25-µm resolution using a Fuji BAS 5000 image plate system (Raytest, Paris, France). The hybridization signals were quantified using ArrayGauge software v.1.3 (Fuji, Ltd, Tokyo, Japan).

data_processing: Data were background noise subtracted (negative controls ± 6 SD), then normalized by original global intensity of hybridization and finally log2-transformed. Only genes well measured for 70% of patients were retained. Data have been normalized with an expression data correction by the amount of PCR product spotted onto the membrane (ratio : Patient probe / Testing probe).

source_name: FEC100_0150_A Breast tumor tissue

label_protocol: Between 0.4 and one µg of total RNA was used as template to generate cDNA bearing T7 promoter, then antisense RNA (aRNA) was generated by in vitro transcription using MEGAscript technology according to the Ambion protocol (Ambion Inc., Austin TX). An aliquot of 2µg of labelled aRNA was then primed with random hexaprimers and reverse transcribed with a mix of cold dNTPs and [a-33P]dCTP.

extract_protocol: All RNA was prepared on the same platform by the CsCl-cushion, as described (Chirgwin, 1979, Biochemistry, 18, 5294-5299.). The quality and the quantity of RNA samples were evaluated by Agilent 2100 Bioanalyser RNA LabChip kit (Agilent Technologies, Palo Alto, CA, USA).

tag: Breast tumor tissue


title: DS-2, N-59, NORM, nfGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/61887.gif
Cell Line: foreskin
Disease State: normal male
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 31.51; Parameter Scan Time = 09:54:25; Parameter PMT Volts = 660; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 8890; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 31.51; Parameter Scan Time = 09:54:25; Parameter PMT Volts = 750; Parameter Scan Date = 2004-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 8873; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.41; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: RNA 045

tag: RNA 045


title: DS-2, N-12, NORM, nsGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58710.gif
Cell Line: scrotum
Disease State: normal male
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.86; Parameter Scan Time = 13:12:17; Parameter PMT Volts = 730; Parameter Scan Date = 2005-01-13; Parameter Pixel Size = 10; Parameter Laser on time = 12054; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.86; Parameter Scan Time = 13:12:17; Parameter PMT Volts = 830; Parameter Scan Date = 2005-01-13; Parameter Pixel Size = 10; Parameter Laser on time = 12036; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.33; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratengene Reference Lot: 1130623

tag: Stratengene Reference Lot

source_name: RNA 136

tag: RNA 136


title: FEC100_0149_A

source_name: FEC100_0149_A Breast tumor tissue


title: FEC100_0148_A

source_name: FEC100_0148_A Breast tumor tissue


title: DS-3, GS641-7, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63148.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 4400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 11:28:13; Parameter PMT Volts = 640; Parameter Scan Date = 2005-06-28; Parameter Pixel Size = 10; Parameter Laser on time = 14164; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.22; Parameter Scan Time = 11:28:13; Parameter PMT Volts = 700; Parameter Scan Date = 2005-06-28; Parameter Pixel Size = 10; Parameter Laser on time = 14147; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.23; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: RNA 190

tag: RNA 190


title: ARD183

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17352.gif
Disease State: AIS-3
Cell Line: foreskin
Sex/Mating type: 46,XY

scan_protocol: not provided

source_name: mixed reference (FR + CRG)

tag: mixed reference (FR + CRG)

source_name: ARD183, G0, DMEM F12, 15% FCS

tag: ARD183, G0, DMEM F12, 15% FCS


title: FEC100_0147_A

source_name: FEC100_0147_A Breast tumor tissue


title: ARD534

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17391.gif
Cell Line: labioscrotal skin
Disease State: AIS-3
Sex/Mating type: 46,XY

source_name: ARD534, 14 days DMEM F12, 15% FCS, G0

tag: ARD534, 14 days DMEM F12, 15% FCS, G0


title: DS-2, ARD402b, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59180.gif
Disease State: CAIS
Cell Line: labia majora
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.09; Parameter Scan Time = 12:52:01; Parameter PMT Volts = 740; Parameter Scan Date = 2005-01-13; Parameter Pixel Size = 10; Parameter Laser on time = 12033; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.64; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.09; Parameter Scan Time = 12:52:01; Parameter PMT Volts = 820; Parameter Scan Date = 2005-01-13; Parameter Pixel Size = 10; Parameter Laser on time = 12015; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.33; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Ref. Lot: 1130623

tag: Stratagene Ref. Lot

tag: LabeledExtract


title: ARD208

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17592.gif
Disease State: AIS-3
Cell Line: labioscrotal skin
Sex/Mating type: 46,XY

source_name: ARD208, 14 days DMEM F12, 15% FCS, Go

tag: ARD208, 14 days DMEM F12, 15% FCS, Go


title: DS-3, N-2, AGS, nlGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-09/63754.gif
Cell Line: labia minora
Disease State: "AIS-3", partially virilized individual with congenital adrenal hyperplasia
Sex/Mating type: 46,XX

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 11:36:46; Parameter PMT Volts = 640; Parameter Scan Date = 2005-06-23; Parameter Pixel Size = 10; Parameter Laser on time = 13941; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 11:36:46; Parameter PMT Volts = 730; Parameter Scan Date = 2005-06-23; Parameter Pixel Size = 10; Parameter Laser on time = 13923; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.24; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Ref. Lot.-Nr. 1130623

tag: Stratagene Ref. Lot.-Nr. 1130623


title: FEC100_0146_A

source_name: FEC100_0146_A Breast tumor tissue


title: ARD407

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17430.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY

source_name: ARD407, 14 days DMEM F12, 15% FCS, G0

tag: ARD407, 14 days DMEM F12, 15% FCS, G0


title: ARD557, CAIS, F, GOF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18145.gif
Disease State: CAIS
Cell Line: gonadal fibroblasts
Sex/Mating type: 46,XY

source_name: ARD557, 14 days DMEM F12, 12.9% FCS, Go

tag: ARD557, 14 days DMEM F12, 12.9% FCS, Go


title: ARD709

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17365.gif
Disease State: AIS-3
Cell Line: gonadal fibroblasts
Sex/Mating type: 46,XY

source_name: mixed reference (CRG + FR)

tag: mixed reference (CRG + FR)

source_name: ARD709, 14 days DMEM F12, 15% FCS, Go

tag: ARD709, 14 days DMEM F12, 15% FCS, Go


title: N-LS12, NORM, M, FSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18313.gif
Disease State: normal male
Cell Line: forearm skin
Sex/Mating type: 46,XY

source_name: Forearm skin fibroblasts LS12, 14 days DMEM F12, 12.9% FCS, G0


title: FEC100_0145_A

source_name: FEC100_0145_A Breast tumor tissue


title: DS-2, ARD411c, CAIS, lGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59221.gif
Cell Line: labia majora
Disease State: CAIS
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 28.46; Parameter Scan Time = 11:39:05; Parameter PMT Volts = 720; Parameter Scan Date = 2005-01-13; Parameter Pixel Size = 10; Parameter Laser on time = 11961; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.67; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 28.46; Parameter Scan Time = 11:39:05; Parameter PMT Volts = 830; Parameter Scan Date = 2005-01-13; Parameter Pixel Size = 10; Parameter Laser on time = 11943; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.31; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference Lot: 1130623

tag: Stratagene Reference Lot

source_name: RNA 077

tag: RNA 077


title: FEC100_0143_A

source_name: FEC100_0143_A Breast tumor tissue

tag: Breast tumor tissue


title: FEC100_0140_A

source_name: FEC100_0140_A Breast tumor tissue


title: FEC100_0141_A

source_name: FEC100_0141_A Breast tumor tissue


title: FEC100_0139_A

source_name: FEC100_0139_A Breast tumor tissue


title: DS-2, ARD407, AIS2, sGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-01/58709.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 4920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.46; Parameter Scan Time = 13:16:45; Parameter PMT Volts = 730; Parameter Scan Date = 2004-12-21; Parameter Pixel Size = 10; Parameter Laser on time = 11738; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.46; Parameter Scan Time = 13:16:45; Parameter PMT Volts = 820; Parameter Scan Date = 2004-12-21; Parameter Pixel Size = 10; Parameter Laser on time = 11720; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.34; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: RNA 136


title: FEC100_0142_A

source_name: FEC100_0142_A Breast tumor tissue


title: FEC100_0137_A

source_name: FEC100_0137_A Breast tumor tissue


title: ARD001, AIS-3

description:
Simple annotation: Development, Anatomical comparisons
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17379.gif
Disease State: AIS-3
Cell Line: labioscrotal skin
Sex/Mating type: 46,XY

source_name: mixed reference (FR + CRG)

source_name: ARD1, 14 days DMEM F12, 15% FCS, G0

tag: ARD1, 14 days DMEM F12, 15% FCS, G0


title: FEC100_0138_A

source_name: FEC100_0138_A Breast tumor tissue


title: FEC100_0136_A

source_name: FEC100_0136_A Breast tumor tissue


title: ARD306

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17428.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY

source_name: ARD 306, 14 days DMEM F12, 15% FCS, G0

tag: ARD 306, 14 days DMEM F12, 15% FCS, G0


title: FEC100_0135_A

description: Patients included in clinical trials (PACS01 / PEGASE01).

source_name: FEC100_0135_A Breast tumor tissue


title: ARD075

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17463.gif
Disease State: CAIS, somatic mosaicism
Cell Line: labia majora
Sex/Mating type: 46,XY

source_name: ARD075, 14 days DMEM F12, 15% FCS, Go

tag: ARD075, 14 days DMEM F12, 15% FCS, Go


title: FEC100_0144_A

source_name: FEC100_0144_A Breast tumor tissue


title: DS-3, N-3, NORM, nlGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-08/63082.gif
Cell Line: labia majora
Disease State: normal female
Sex/Mating type: 46,XX

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 29.07; Parameter Scan Time = 10:43:26; Parameter PMT Volts = 640; Parameter Scan Date = 2005-06-28; Parameter Pixel Size = 10; Parameter Laser on time = 14121; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.69; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 29.07; Parameter Scan Time = 10:43:26; Parameter PMT Volts = 700; Parameter Scan Date = 2005-06-28; Parameter Pixel Size = 10; Parameter Laser on time = 14103; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.25; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Strategene Ref. Lot-Nr. 1130623

tag: Strategene Ref. Lot-Nr. 1130623

source_name: RNA 191

tag: RNA 191


title: FEC100_0134_A

source_name: FEC100_0134_A Breast tumor tissue


title: FEC100_0133_A

source_name: FEC100_0133_A Breast tumor tissue


title: DS-3, ARD527b, AIS2, sGSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60440.gif
Disease State: AIS-2
Cell Line: scrotum
Sex/Mating type: 46,XY

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1840, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Paul-Martin,,Holterhus 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 = 29.10; Parameter Scan Time = 10:52:18; Parameter PMT Volts = 640; Parameter Scan Date = 2005-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 12730; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.0; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus 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 = 29.10; Parameter Scan Time = 10:52:18; Parameter PMT Volts = 770; Parameter Scan Date = 2005-03-18; Parameter Pixel Size = 10; Parameter Laser on time = 12712; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [86228]; Parameter Laser Power = 3.30; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Paul-Martin,,Holterhus

source_name: Stratagene Reference Lot.-Nr. 1130623

tag: Stratagene Reference Lot.-Nr. 1130623

source_name: RNA 133

tag: RNA 133


title: FEC100_0131_A

source_name: FEC100_0131_A Breast tumor tissue


title: FEC100_0132_A

source_name: FEC100_0132_A Breast tumor tissue


title: N-ST4, NORM, M, ASF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18015.gif
Disease State: normal male
Cell Line: abdomen skin
Sex/Mating type: 46,XY

source_name: mixed reference (CRG + FR)

tag: LabeledExtract

source_name: Abdominal skin fibroblast ST4, 14 days DMEM F12, 12.9% FCS, Go


title: ARD291, CAIS, F, GOF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18101.gif
Disease State: CAIS
Cell Line: gonadal fibroblasts
Sex/Mating type: 46,XY

source_name: mixed reference (FR + CRG)

tag: mixed reference (FR + CRG)

source_name: ARD291, 14 days DMEM F12, 12.9% FCS, G0

tag: ARD291, 14 days DMEM F12, 12.9% FCS, G0


title: FEC100_0130_A

source_name: FEC100_0130_A Breast tumor tissue


title: FEC100_0129_A

source_name: FEC100_0129_A Breast tumor tissue


title: FEC100_0124_A

source_name: FEC100_0124_A Breast tumor tissue


title: FEC100_0120_A

source_name: FEC100_0120_A Breast tumor tissue


title: FEC100_0128_A

source_name: FEC100_0128_A Breast tumor tissue


title: FEC100_0123_A

source_name: FEC100_0123_A Breast tumor tissue


title: FEC100_0126_A

source_name: FEC100_0126_A Breast tumor tissue


title: FEC100_0121_A

source_name: FEC100_0121_A Breast tumor tissue


title: FEC100_0127_A

source_name: FEC100_0127_A Breast tumor tissue


title: FEC100_0122_A

source_name: FEC100_0122_A Breast tumor tissue


title: FEC100_0112_A

source_name: FEC100_0112_A Breast tumor tissue


title: FEC100_0117_A

source_name: FEC100_0117_A Breast tumor tissue


title: FEC100_0118_A

source_name: FEC100_0118_A Breast tumor tissue


title: FEC100_0119_A

source_name: FEC100_0119_A Breast tumor tissue


title: FEC100_0113_A

source_name: FEC100_0113_A Breast tumor tissue


title: FEC100_0115_A

source_name: FEC100_0115_A Breast tumor tissue


title: FEC100_0114_A

source_name: FEC100_0114_A Breast tumor tissue


title: FEC100_0116_A

source_name: FEC100_0116_A Breast tumor tissue


title: FEC100_0107_A

source_name: FEC100_0107_A Breast tumor tissue


title: FEC100_0106_A

source_name: FEC100_0106_A Breast tumor tissue


title: FEC100_0111_A

source_name: FEC100_0111_A Breast tumor tissue


title: FEC100_0105_A

source_name: FEC100_0105_A Breast tumor tissue


title: FEC100_0109_A

source_name: FEC100_0109_A Breast tumor tissue


title: FEC100_0110_A

source_name: FEC100_0110_A Breast tumor tissue


title: FEC100_0108_A

source_name: FEC100_0108_A Breast tumor tissue


title: FEC100_0103_A

source_name: FEC100_0103_A Breast tumor tissue


title: FEC100_0104_A

source_name: FEC100_0104_A Breast tumor tissue


title: FEC100_0102_A

source_name: FEC100_0102_A Breast tumor tissue


title: FEC100_0099_A

source_name: FEC100_0099_A Breast tumor tissue


title: FEC100_0100_A

source_name: FEC100_0100_A Breast tumor tissue


title: FEC100_0098_A

source_name: FEC100_0098_A Breast tumor tissue


title: FEC100_0095_A

source_name: FEC100_0095_A Breast tumor tissue


title: FEC100_0101_A

source_name: FEC100_0101_A Breast tumor tissue


title: FEC100_0096_A

source_name: FEC100_0096_A Breast tumor tissue


title: FEC100_0094_A

source_name: FEC100_0094_A Breast tumor tissue


title: FEC100_0085_A

source_name: FEC100_0085_A Breast tumor tissue


title: FEC100_0092_A

source_name: FEC100_0092_A Breast tumor tissue


title: FEC100_0090_A

source_name: FEC100_0090_A Breast tumor tissue


title: FEC100_0086_A

source_name: FEC100_0086_A Breast tumor tissue


title: FEC100_0084_A

source_name: FEC100_0084_A Breast tumor tissue


title: FEC100_0097_A

source_name: FEC100_0097_A Breast tumor tissue


title: FEC100_0093_A

source_name: FEC100_0093_A Breast tumor tissue


title: FEC100_0083_A

source_name: FEC100_0083_A Breast tumor tissue


title: FEC100_0091_A

source_name: FEC100_0091_A Breast tumor tissue


title: FEC100_0087_A

source_name: FEC100_0087_A Breast tumor tissue


title: FEC100_0089_A

source_name: FEC100_0089_A Breast tumor tissue


title: FEC100_0125_A

source_name: FEC100_0125_A Breast tumor tissue


title: FEC100_0082_A

source_name: FEC100_0082_A Breast tumor tissue


title: FEC100_0088_A

source_name: FEC100_0088_A Breast tumor tissue


title: FEC100_0081_A

source_name: FEC100_0081_A Breast tumor tissue


title: FEC100_0079_A

source_name: FEC100_0079_A Breast tumor tissue


title: Colon mucosa noninfected, day3, duplo 01

city: Wageningen

first: Wendy

last: Rodenburg

address: Bornsesteeg 45

department: Food Bioactives Group

country: Netherlands

institute: RIKILT-Institute of food safety

description: Rat Colon Mucosa

hyb_protocol: Equal volumes of Cy5 target sample and Cy3 reference sample were combined, mixed with 2x hybridisation buffer (Agilent Technoloiges) and 10x control targets (Agilent Technologies) and hybridized to a Whole Rat Genome ologo array (G4131A, Agilent Technologies), for 17 hours at 60°C in an Agilent hybridization oven with rotation (Agilent Technologies). After hybridization the arrays were washed with an SSPE wash procedure (Agilent Technologies) according to manufacturers protocol.

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner (Agilent Technologies).

data_processing: The signals were extracted using Feature Extraction 8.1 (Agilent Technologies), Protocol 44K, FE grid 0131-D-20050217. The signal intensity and the background of each spot was measured as median signal values. Data was exported into GeneMaths XT (Applied Maths, Sint-Martens-Latem, Belgium) for analysis. Spots with an average Cy5 signal intensity, over all arrays, lower than 2-fold average Cy5 local background were discarded. Subsequently, the remaining Cy5 signal intensities were normalized against the Cy3 reference using RIKILT normalization protocol (Pellis L, et al. (2003) Physiol Genomics 16: 99-106).

organism: Rattus norvegicus

source_name: Colon mucosa,  noninfected, day3, duplo 01

label_protocol: 20 µg of total RNA was mixed with 4 µg T21 primer, heated at 65C for 3 min (RNA denaturation) followed by 25C for 10 min (primer annealing). cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy5-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42 degrees C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of 96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37 degrees C for 10 minutes. The reaction was neutralized with 2.5 µl 1 M Tris-HCl, pH 6.8 and 2µl 1M HCl. The Cy5 and Cy3 reactions were purified with the Qiaquick PCR purification kit (Westburg) and precipitated overnight at -20 degrees C using NaAc/ EtOH. The cDNAs were resolved in 100 µl RNase free H2O.

extract_protocol: Total RNA was isolated from the colon homogenates using TRIzol reagent (Invitrogen, San Diego, CA) according to the manufacturer’s instructions. Total RNA was purified using Rneasy columns (Qiagen, Chatsworth, CA).

treatment_protocol: Colon scrapings were homogenized in liquid N2 using a mortar and pestle cooled with liquid N2.(Fisher Emergo, Landsmeer, The Netherlands).

tag: Wistar, Gender

value: Male, Age:10 weeks, Tissue:Colon Mucosa.

source_name: Reference RNA. This consists of a pool of equal molar total RNA samples of all groups analyzed.

label_protocol: 20 µg of total RNA was mixed with 4 µg T21 primer, heated at 65C for 3 min (RNA denaturation) followed by 25C for 10 min (primer annealing). cDNA was synthesized by adding 5x first strand buffer (Invitrogen), 10 mM DTT, 0.5mM dATP, 0.5 mM dGTP, 0.5 mM dTTP, 0.04 mM dCTP, 0.04 mM Cy3-dCTP, 1.2U RnaseOUT and 6U SuperScript II Reverse Transcriptase to a total volume of 62.5 µl. The reaction was incubated at 42 degrees C for 2 h. The reaction was precipitated using 1/10 volume of 3 M sodium-acetate (pH 5.2) and 2.5 volumes of 96% ethanol and RNA was broken down by 2.5 µl 1 M NaOH and incubation at 37 degrees C for 10 minutes. The reaction was neutralized with 2.5 µl 1 M Tris-HCl, pH 6.8 and 2µl 1M HCl. The Cy5 and Cy3 reactions were purified with the Qiaquick PCR purification kit (Westburg) and precipitated overnight at -20 degrees C using NaAc/ EtOH. The cDNAs were resolved in 100 µl RNase free H2O.


title: FEC100_0080_A

source_name: FEC100_0080_A Breast tumor tissue


title: Colon mucosa noninfected, day3, duplo 02

description: Rat Colon Mucosa

source_name: Colon mucosa,  noninfected, day3, duplo 02


title: Colon mucosa noninfected, day1, duplo 01

description: Rat Colon Mucosa

source_name: Colon mucosa,  noninfected, day1, duplo 01


title: Colon mucosa noninfected, day1, duplo 02

description: Rat Colon Mucosa

source_name: Colon mucosa,  noninfected, day1, duplo 02


title: FEC100_0076_A

source_name: FEC100_0076_A Breast tumor tissue


title: FEC100_0072_A

source_name: FEC100_0072_A Breast tumor tissue


title: FEC100_0078_A

source_name: FEC100_0078_A Breast tumor tissue


title: FEC100_0073_A

source_name: FEC100_0073_A Breast tumor tissue


title: FEC100_0075_A

source_name: FEC100_0075_A Breast tumor tissue


title: FEC100_0074_A

source_name: FEC100_0074_A Breast tumor tissue


title: FEC100_0066_A

source_name: FEC100_0066_A Breast tumor tissue


title: FEC100_0071_A

source_name: FEC100_0071_A Breast tumor tissue


title: FEC100_0068_A

source_name: FEC100_0068_A Breast tumor tissue


title: FEC100_0070_A

source_name: FEC100_0070_A Breast tumor tissue


title: Colon mucosa salmonella, day3, duplo 02

description: Rat Colon Mucosa

source_name: Colon mucosa,  salmonella, day3, duplo 02


title: FEC100_0063_A

source_name: FEC100_0063_A Breast tumor tissue


title: Colon mucosa salmonella, day1, duplo 02

description: Rat Colon Mucosa

source_name: Colon mucosa,  salmonella, day1, duplo 02

source_name: Reference RNA. This consists of a pool of equal molar total RNA samples of all groups analyzed.


title: FEC100_0077_A

source_name: FEC100_0077_A Breast tumor tissue


title: FEC100_0062_A

source_name: FEC100_0062_A Breast tumor tissue


title: FEC100_0064_A

source_name: FEC100_0064_A Breast tumor tissue


title: FEC100_0060_A

source_name: FEC100_0060_A Breast tumor tissue


title: FEC100_0067_A

source_name: FEC100_0067_A Breast tumor tissue


title: FEC100_0065_A

source_name: FEC100_0065_A Breast tumor tissue


title: Colon mucosa salmonella, day6, duplo 02

description: Rat Colon Mucosa

source_name: Colon mucosa,  salmonella, day6, duplo 02


title: FEC100_0069_A

source_name: FEC100_0069_A Breast tumor tissue


title: Colon mucosa salmonella, day3, duplo 01

description: Rat Colon Mucosa

source_name: Colon mucosa,  salmonella, day3, duplo 01


title: FEC100_0061_A

source_name: FEC100_0061_A Breast tumor tissue


title: Colon mucosa salmonella, day6, duplo 01

description: Rat Colon Mucosa

source_name: Colon mucosa,  salmonella, day6, duplo 01


title: FEC100_0057_A

source_name: FEC100_0057_A Breast tumor tissue


title: FEC100_0056_A

source_name: FEC100_0056_A Breast tumor tissue


title: FEC100_0059_A

source_name: FEC100_0059_A Breast tumor tissue


title: FEC100_0058_A

source_name: FEC100_0058_A Breast tumor tissue


title: Colon mucosa noninfected, day6, duplo 01

description: Rat Colon Mucosa

source_name: Colon mucosa,  noninfected, day6, duplo 01


title: Colon mucosa salmonella, day1, duplo 01

description: Rat Colon Mucosa

source_name: Colon mucosa,  salmonella, day1, duplo 01

source_name: Reference RNA. This consists of a pool of equal molar total RNA samples of all groups analyzed.


title: FOS diet, salmonella infected, rep02

description: Rat Colon Mucosa

hyb_protocol: Equal volumes of Cy5 target samples and Cy3 reference sample were combined, mixed with 2x hybridisation buffer (Agilent Technoloiges) and 10x control targets (Agilent Technologies) and hybridized to a Whole Rat Genome ologo array (G4131A, Agilent Technologies), for 17 hours at 60°C in an Agilent hybridization oven with rotation (Agilent Technologies). After hybridization the arrays were washed with an SSPE wash procedure (Agilent Technologies) according to manufacturers protocol.

scan_protocol: Arrays were scanned using the Scanarray Express HT (Perkin Elmer, Wellesley, MA) at a laserpower of 90% and a photomultiplier tube voltage of 55% for Cy5 and 60% for Cy3.

data_processing:
The signals were extracted using ArrayVision (version 7.0, Imaging Research, Ontario, Canada). The signal intensity of each spot was measured as median density. Data was exported into GeneMaths XT (Applied Maths, Sint-Martens-Latem, Belgium) for analysis. Spots with an average Cy5 signal intensity, over all arrays, lower than 2-fold average Cy5 local background were discarded. Subsequently, the remaining Cy5 signal intensities were normalized against the Cy3 reference using RIKILT normalization protocol (Pellis L, et al. (2003) Physiol Genomics 16: 99-106).

In the VALUE column for this particular dataset 24440 genes of the total 44K array had a Cy5 spot signal intensity 2 times above the background. Only these spots are normalized and have a normalized value. I further clarified the data processing text.

source_name: Colon mucosa, FOS diet, salmonella infected, duplo 02

source_name: Reference RNA

tag: Reference RNA consisted of a pool of equal molar total RNA samples of all groups analyzed.


title: FOS diet, salmonella infected, rep01

description: Rat Colon Mucosa

source_name: Colon mucosa, FOS diet, salmonella infected, duplo 01


title: FEC100_0054_A

source_name: FEC100_0054_A Breast tumor tissue


title: FEC100_0055_A

source_name: FEC100_0055_A Breast tumor tissue


title: cellulose diet, salmonella infected, rep01

description: Rat Colon Mucosa

source_name: Colon mucosa, cellulose diet, salmonella infected, duplo 01


title: cellulose diet, salmonella infected, rep02

description: Rat Colon Mucosa

source_name: Colon mucosa, cellulose diet, salmonella infected, duplo 02


title: FEC100_0048_A

source_name: FEC100_0048_A Breast tumor tissue


title: cellulose diet, rep02

description: Rat Colon Mucosa

source_name: Colon mucosa, cellulose diet, duplo 02


title: FEC100_0052_A

source_name: FEC100_0052_A Breast tumor tissue


title: FEC100_0049_A

source_name: FEC100_0049_A Breast tumor tissue


title: FEC100_0051_A

source_name: FEC100_0051_A Breast tumor tissue


title: FEC100_0047_A

source_name: FEC100_0047_A Breast tumor tissue


title: FEC100_0053_A

source_name: FEC100_0053_A Breast tumor tissue


title: FEC100_0042_A

source_name: FEC100_0042_A Breast tumor tissue


title: FEC100_0045_A

source_name: FEC100_0045_A Breast tumor tissue


title: FEC100_0044_A

source_name: FEC100_0044_A Breast tumor tissue


title: FEC100_0046_A

source_name: FEC100_0046_A Breast tumor tissue


title: FEC100_0050_A

source_name: FEC100_0050_A Breast tumor tissue


title: FEC100_0040_A

source_name: FEC100_0040_A Breast tumor tissue


title: FEC100_0043_A

source_name: FEC100_0043_A Breast tumor tissue


title: FEC100_0041_A

source_name: FEC100_0041_A Breast tumor tissue


title: cellulose diet, rep01

description: Rat Colon Mucosa

source_name: Colon mucosa, cellulose diet, duplo 01

source_name: Reference RNA


title: FEC100_0037_A

source_name: FEC100_0037_A Breast tumor tissue


title: FEC100_0039_A

source_name: FEC100_0039_A Breast tumor tissue


title: FEC100_0038_A

source_name: FEC100_0038_A Breast tumor tissue


title: Monocyte_NoStimulation_16H

city: San Diego

first: Heng

last: Dai

state: CA

address: 3210 Merryfield Row

department: Bioinformatics

country: USA

institute: Johnson & Johnson PRD

description: human primary monocytes, no stimulation at 16 hour.

hyb_protocol: Each cRNA was applied to duplicate Codelink  microarrays (GE Healthcare) according to the manufacturer’s protocol, and hybridized at 37°C overnight. Slides were washed and stained with an Alexa555-streptavidin conjugate (Invitrogen).

scan_protocol: The slides were scanned at 532 nm with an Agilent G2565BA Microarray Scanner (Agilent Technologies, Palo Alto, CA) according to manufacture instructions.

data_processing: Fluorescence intensity for each feature of the array was obtained by using Codelink EXP v4.1 software (GE Healthcare). For each sample, intensities from duplicate chips (when available) are averaged and quantile-quantile normalized cross all chips. The value field in result table holds the normalized intensity.

label: biotin

source_name: primary monocytes, not stimulated, 16h

label_protocol: One round of T7 polymerase-based linear RNA amplification was performed by reverse transcription of RNA with a T7 promoter oligo(dT) primer, followed by in-vitro transcription using the RiboBeast 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre, Madison, WI) as specified in the manufacturer’s protocol with the following modifications: SuperscriptII (Invitrogen, Carlsbad, CA) was used as the reverse transcriptase, and the RNeasy 96 block was used for purification (Qiagen, Valencia, CA). Following purification, the cRNA target was conjugated with biotin-ester (Biotium, Hayward, CA), purified again with the Qiagen RNeasy 96 block, and concentrated by Speed-Vac (Thermosavant, Waltham, MA).  Biotin-labeled cRNA was fragmented at 94°C for 20 minutes and added to Codelink hybridization buffer A and B (GE Healthcare).

growth_protocol: Human blood from healthy donors was obtained through Normal Blood Donor Service of The Scripps Research Institute.  Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation using Ficoll-Paque Plus (GE Healthcare, Chandler, AZ). Briefly, peripheral human blood was diluted 1:1 with cold PBS containing 2 mM EDTA and 30 ml was then loaded carefully on top of 15 ml of Ficoll-Paque Plus in a 50-ml tube.  After centrifugation at 2000 rpm for 30 min in a Sorvall RTH-750 tabletop centrifuge, the PBMC layer was carefully transferred and washed 1 ´ with cold PBS containing 2 mM EDTA. The cells were washed two additional times, and centrifuged at 1100 rpm to remove platelets in the supernatant.   Primary monocytes were then isolated from PBMCs using the Monocyte Isolation Kit II (Miltenyi Biotec) according to the manufacturer’s protocols.

extract_protocol: Cells were harvested at various time points and total RNA was isolated using the RNeasy Mini Plus Kit (Qiagen, Valencia, CA).

treatment_protocol: For LTB4 treatment, cells were seeded in 12-well plates at 2 ´ 106 /well in 2 ml Hank’s buffered salt solution (HBSS) containing 1% FBS, 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were incubated at 37°C for 1 hour before being stimulated with 60 nM LTB4 (final ethanol concentration 0.019%) or 0.019% ethanol as vehicle control.

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells), harvested at 16 hour without LTB4 stimulation.


title: FEC100_0036_A

source_name: FEC100_0036_A Breast tumor tissue


title: Monocyte_NoStimulation_3H

description: human primary monocytes, no stimulation at 3 hour.

source_name: primary monocytes, not stimulated, 3 hour

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells), harvested at 3 hour without LTB4 stimulation.


title: Monocyte_NoStimulation_6H

description: human primary monocytes, no stimulation at 6 hour.

source_name: primary monocytes, not stimulated, 6h

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells), harvested at 6 hour without LTB4 stimulation.


title: Monocyte_LTB4_16h

description: human primary monocytes, LTB4 stimulation at 16 hour.

source_name: human primary monocytes, treated with LTB4, 16h

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells), harvested at 16 hour after LTB4 stimulation


title: Monocyte_LTB4_6H

description: human primary monocytes, LTB4 stimulation at 6 hour.

source_name: human primary monocytes, treated with LTB4, 6h

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells), harvested at 6 hour after LTB4 stimulation.


title: Monocyte_LTB4_3H

description: human primary monocytes, LTB4 stimulation at 3 hour.

source_name: human primary monocytes, treated with LTB4, 3h

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells), harvested at 3 hour after LTB4 stimulation


title: Monocyte_NoStimulation_1H

description: human primary monocytes, no stimulation at 1 hour.

source_name: primary monocytes, not stimulated, 1h

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells), harvested at 1 hour without LTB4 stimulation.


title: Monocyte_Control_0H

description: human primary monocytes, control w no treatment, time zero

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells)


title: Monocyte_LTB4_1H

description: human primary monocytes, treated with LTB4 for 1 hour.

source_name: human primary monocytes, treated with LTB4, 1h

tag: Primary monocytes isolated from normal PBMC (Peripheral Blood Mononuclear Cells). Treated with LTB4 for 1 hour.


title: FEC100_0031_A

source_name: FEC100_0031_A Breast tumor tissue

tag: Breast tumor tissue


title: FEC100_0035_A

source_name: FEC100_0035_A Breast tumor tissue


title: FEC100_0027_A

source_name: FEC100_0027_A Breast tumor tissue


title: FEC100_0032_A

source_name: FEC100_0032_A Breast tumor tissue


title: FEC100_0029_A

source_name: FEC100_0029_A Breast tumor tissue


title: FEC100_0033_A

source_name: FEC100_0033_A Breast tumor tissue


title: FEC100_0025_A

source_name: FEC100_0025_A Breast tumor tissue


title: FEC100_0024_A

source_name: FEC100_0024_A Breast tumor tissue


title: FEC100_0030_A

source_name: FEC100_0030_A Breast tumor tissue


title: FEC100_0023_A

source_name: FEC100_0023_A Breast tumor tissue


title: FEC100_0028_A

source_name: FEC100_0028_A Breast tumor tissue


title: FEC100_0021_A

source_name: FEC100_0021_A Breast tumor tissue


title: FEC100_0026_A

source_name: FEC100_0026_A Breast tumor tissue


title: FEC100_0022_A

source_name: FEC100_0022_A Breast tumor tissue


title: FEC100_0018_A

source_name: FEC100_0018_A Breast tumor tissue


title: FEC100_0019_A

source_name: FEC100_0019_A Breast tumor tissue


title: FEC100_0017_A

source_name: FEC100_0017_A Breast tumor tissue


title: FEC100_0015_A

source_name: FEC100_0015_A Breast tumor tissue


title: FEC100_0014_A

source_name: FEC100_0014_A Breast tumor tissue


title: FEC100_0016_A

source_name: FEC100_0016_A Breast tumor tissue


title: Liver antiangiogenic-treatment rep4

city: Barcelona

first: Manuel

last: Morales-Ruiz

address: Villarroel 170

department: Biochemistry and Molecular Genetics

country: Spain

institute: Hospital Clinic

hyb_protocol: The fragmented cRNA was hybridized to the oligonucleotide microarray, which was washed and stained with streptavidin-phycoerythrin  as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Santa Clara, CA)

scan_protocol: Scanning was performed with an Agilent Microarray Scanner (Agilent Technologies)

data_processing: GeneChip analysis was performed with libraries from the Bioconductor project. The starting point for all the analysis was the CEL files generated by the Affymetrix software. Each CEL file contains data on the intensity at each probe on the GeneChip. To import CEL file data into the Bioconductor system, we used the ReadAffy function of the “affy” package. Next, we used the RMA approximation for background adjustment, normalization, and summarization using the median polish algorithm . The RMA measures were computed using the RMA function from the affy package.

label: Biotin

source_name: cirrhotic liver, antiangiogenic treatment

label_protocol: Twenty µg of total RNA was used to synthesize double-strand cDNA with SuperScript II reverse transcriptase (Life Technologies) and a T7-(dT)24 primer (Metabion, Germany). Then, biotinylated cRNA was synthesized from the double-stranded cDNA using the RNA Transcript Labeling kit (Enzo Life Sciences) and was purified and fragmented.

extract_protocol: Total RNA was extracted from frozen liver with Trizol reagent (Life Technologies, Rockville, MD). The extracted total RNA was purified with the RNeasy kit (Qiagen).

treatment_protocol: Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid

tag: Strain:Wistar, Gender

value: male, Tissue:cirrhotic liver, Induction of cirrhosis:CCl4


title: FEC100_0013_A

source_name: FEC100_0013_A Breast tumor tissue


title: Liver antiangiogenic-treatment rep3


title: FEC100_0034_A

source_name: FEC100_0034_A Breast tumor tissue


title: FEC100_0012_A

source_name: FEC100_0012_A Breast tumor tissue


title: Liver vehicle rep2

source_name: cirrhotic liver, vehicle treatment


title: FEC100_0010_A

source_name: FEC100_0010_A Breast tumor tissue


title: FEC100_0006_A

source_name: FEC100_0006_A Breast tumor tissue


title: FEC100_0008_A

source_name: FEC100_0008_A Breast tumor tissue


title: FEC100_0011_A

source_name: FEC100_0011_A Breast tumor tissue


title: FEC100_0001_A

source_name: FEC100_0001_A Breast tumor tissue


title: FEC100_0007_A

source_name: FEC100_0007_A Breast tumor tissue


title: FEC100_0002_A

source_name: FEC100_0002_A Breast tumor tissue


title: FEC100_0005_A

source_name: FEC100_0005_A Breast tumor tissue


title: FEC100_0009_A

source_name: FEC100_0009_A Breast tumor tissue


title: Liver vehicle rep3


title: FEC100_0004_A

source_name: FEC100_0004_A Breast tumor tissue


title: FEC100_0003_A

source_name: FEC100_0003_A Breast tumor tissue


title: Liver vehicle rep4


title: Small RNAs from Dictyostelium discoideum: 5' independent ligation

status: Public on Oct 17 2007

type: MPSS

city: Uppsala

first: Johan

last: Reimegård

address: Biomedical Center

department: Department of cell and molecular biology

country: Sweden

institute: Uppsala University

description: cDNA library of small RNAs from Dictyostelium discoideum

data_processing: The total count of the different small RNAs

organism: Dictyostelium discoideum

source_name: Dictyostelium discoideum

growth_protocol: Cells were grown axenically in HL5 medium and synchronously developed on nitrocellulose membranes (Sussman, M. 1987, Methods Cell Biol, 28, 9-29).

extract_protocol: cDNA libraries of small D. discoideum RNAs were constructed. Briefly, total RNA was isolated by the TRIzol method (Invitrogen) from growing D. discoideum AX4 strain cells as well as from cells developed for 16 hours and 24 hours, and the fractions were subsequently pooled. The RNA was subjected to size fractionation (18-26 nt RNAs) and ligation of a 3’ linker, followed by reverse transcription (Lee, R.C. and Ambros, V., 2001, Science). Apart from synthesizing a complementary DNA strand, the reverse transcriptase adds a few non-templated C residues at the 3’ end. These C:s were then hybridized to a DNA oligo with three 3’ G:s followed by RT-PCR, cloning and sequencing.

treatment_protocol: RNA pooled from growing cells and cells developed for 16 and 24 hours

tag: Strain

value: AX4, medium:HL5


title: Small RNAs from Dictyostelium discoideum: 5' dependent ligation

extract_protocol: cDNA libraries of small D. discoideum RNAs were constructed. Briefly, total RNA was isolated by the TRIzol method (Invitrogen) from growing D. discoideum AX4 strain cells as well as from cells developed for 16 hours and 24 hours, and the fractions were subsequently pooled. After size fractionation (18-26 nt RNAs) and ligation of a 3’ linker, the RNA was directly ligated to a 5’ linker, thus selecting for small RNAs with 5’ monophosphates (Lau, N.C.et al, 2001, Science). Following RT-PCR, the PCR fragments were cloned and sequenced.


title: Tobacco NtDC1B overexpressor 4 days slide2 rep1

status: Public on Oct 16 2007

city: Yokohama

first: Ken

last: Matsuoka

state: Kanagawa

address: 1-7-22 Suehirocho, Tsurumi-ku,

department: Plant Science Center

country: Japan

institute: RIKEN

description: Tobacco microarray consists of 4 slides. Modification of single channel label data was used. For hybridizations, we used Cy5-labeled cDNA and Cy3-labeled vector sequence. All DNA spots on array contain flanking vector sequence that was introduced by amplification of cDNA inserts by PCR with universal primers (clones in pGEM Te - M13 universal primers, clones in pBKSII - M13 FWD/KS reverse). Using Cy5 (signal) and Cy3 (control), data can be normalized by creating Cy5/Cy3 ratio, thus allowing normalization for amount of spotted DNA on individual slides by microarray spotter.

hyb_protocol: Before use, the DNA on the spotted microarray slides was immobilized by cross-linking the slides under UV light (energy 50 mJ cm2) and slides were prehybridized for 1 h at 55°C in prehybridization buffer [1% bovine serum albumin (BSA), 5× saline sodium citrate (SSC) and 0.1% sodium dodecyl sulfate (SDS)] as described previously [1,2]. Hybridization of microarrays with Cy-5-labeled sample cDNA and Cy-3-labeled DNA sequence as control was performed in ExpressHyb hybridization solution (Clontech, Palo Alto, CA, USA) at 60°C for 4 h as described previously [1]. The protocol described in [1] was later modified with the use of a Cy-3-labeled polylinker DNA fragment located between the M13 forward/reverse or M13 forward/KS reverse primer sites of the respective vectors (pGEM-Teasy and pBII KS+), instead of the labeled oligo-DNA that was used previously [2]. The hybridized slides were washed in SSC/SDS buffer solutions at 55°C (final wash in 0.1× SSC and 0.1% SDS) and briefly rinsed in water. Slides were dried by centrifugation. [1]Demura, T., Tashiro, G., Horiguchi, G. et al. (2002) Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proc. Natl Acad. Sci. USA, 99, 15794–15799. [2]Matsuoka, K., Demura, T., Galis, I., Horiguchi, T., Sasaki, M., Tashiro, G. and Fukuda, H. (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol. 45, 1280–1289.

scan_protocol: The Cy-5 (sample signal) and Cy-3 (control signal) were obtained by scanning with a GenePix 4000A microarray scanner (Molecular Dynamics). The scans were subsequently analyzed by the MicroArray Suite iplab program (Scananalytics, BD Biosciences, Rockville, MD, USA).

data_processing: Raw signal data were first modified by subtraction of respective background values. Ratio of VALUE means (Cy-5-labeled cDNA signal)/(Cy-3-labeled vector control signal) after background correction are listed in result table.

molecule: polyA RNA

organism: Nicotiana tabacum

source_name: NtDC1B overexpressor, tobacco cells, 4 days

label_protocol: polyA mRNA quality was estimated by Bioanalyzer. 1 μg of mRNA was labeled and used for single-slide hybridizations. Samples were spiked with control Kanamycin mRNA (Promega). Labeling was performed using SuperScript II reverse transcriptase (Invitrogen), random 9-mer primers, poly(A)-specific poly (dT) primers, and Cy-3/Cy-5-labeled dCTP nucleotides (Amersham Biosciences) for first-strand cDNA synthesis. Quality of probe was estimated by gel electrophoresis and subsequent fluoroimaging analysis.

extract_protocol: The cells were collected by filtration and snap-frozen in liquid nitrogen. Total RNA was prepared using TRIzol reagent (Invitrogen) as described in the manufacturer’s protocols. The poly(A)-rich RNA fraction was isolated from total RNA using a GenElute mRNA Miniprep Kit (Sigma) in two subsequent runs of purification following the Miniprep Kit protocol.

tag: NtDC1B overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 2 of 4, replicate 1


title: Liver antiangiogenic-treatment rep1

source_name: cirrhotic liver, antiangiogenic treatment

treatment_protocol: Cirrhosis was induced by inhalation of CCl4 administered twice weekly. Control and cirrhotic rats were fed ad libitum with standard feed and water containing Phenobarbital (0.3 g/L) as drinking fluid .


title: Liver antiangiogenic-treatment rep2


title: Tobacco NtDC1B overexpressor 4 days slide4 rep1

tag: NtDC1B overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 4 of 4, replicate 1


title: Tobacco NtMYBGR1 overexpressor 4 days slide2 rep1

source_name: NtMYBGR1 overexpressor, tobacco cells, 4 days

tag: NtMYBGR1 overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 2 of 4, replicate 1


title: Tobacco NtDC1B overexpressor 4 days slide4 rep2

tag: NtDC1B overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 4 of 4, replicate 2


title: Tobacco NtDC1B overexpressor 4 days slide2 rep2

tag: NtDC1B overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 2 of 4, replicate 2


title: Liver vehicle rep1


title: Tobacco pMAT137 vector control 4 days slide2 rep1

source_name: PMAT137 vector control, tobacco cells, 4 days, control sample

tag: PMAT137 vector [1] transformed (control) tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 2 of 4, replicate 1

tag: [1] Yuasa K, Toyooka K, Fukuda H & Matsuoka K (2005) Membrane-anchored prolyl hydroxylase with an export signal from the endoplasmic reticulum. Plant J 41, 81-94.


title: Tobacco pMAT137 vector control 4 days slide2 rep2

tag: PMAT137 vector [1] transformed (control) tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 2 of 4, replicate 2


title: ERRa ko baseline heart, sample 1

city: Duarte

first: Janice

last: Huss

address: 1450 E. Duarte Rd.

department: Gene Regulation and Drug Discovery

institute: Beckman Research Institute, City of Hope National Medical Center

description:
For the test chip, the levels of bioB, bioC, bioD, cre, phe, trp, lys, and thr will be assessed. All transcripts should be called 'present' and the average difference values of each should be in approximate
proportion to their absolute copy number. Successful signal from bioB, bioC, bioD, and cre, but suboptimal signal from phe, trp, lys, and thr suggests that cDNA synthesis and in vitro transcription was
inefficient. Poor signal from all controls suggests a hybridization, washing, or staining failure. Normally, the bioB hybridization control (representing 2x108 transcript copies) will be at or slightly above the level of background noise. The relative expression level of GAPDH and b-actin will also be assessed. The test chip contains probes directed at the 5' and 3' end of these genes for human, mouse, and rat species.
In general, the signals from 5' directed probe sets should be no lower than 50% of those from 3' directed probe sets. A 5'/3' ratio of less than 0.5 suggests that cDNA synthesis may have been less than efficient.

hyb_protocol: Fifteen micrograms of fragmented cRNA is delivered to the core facility. A hybridization 'cocktail' is constructed containing the cRNA, 50 pM of control oligonucleotide B2 (Geneset), 1X control cRNA mix, 0.1 mg/ml herring sperm DNA, and 1X MES hybridization buffer in a volume of 300 ml, The control oligonucleotide B2 (5'-biotin:GTCGTCAAGATGCTACCGTTCAGGA-3') is designed to hybridize to structural features on the chip to allow for proper scanning and grid alignment. The control cRNA mix is provided by the core facility and is composed of a second set of four, biotinylated, in vitro antisense transcripts of cDNAs encoding the E. coli biotin synthesis genes bioB, bioC, bioD, and the P1 bacteriophage cre recombinase gene. Probes corresponding to these bacterial transcripts are also represented on all Affymetrix GeneChips (including test chips). Each synthetic transcript is quantitated and represented at a copy number of 2x108 to 2x1010, corresponding roughly to the expected dynamic range of detection for the GeneChip. This set of control cRNAs allows for the monitoring of hybridization, washing, and staining conditions and also provides a second set of reference samples for normalizing between experiments. One hundred microliters of the hybridization cocktail is heated to 95°C, 45°C, and then applied to the a Test2 GeneChip array. The remainder of the cocktail is stored at -70°C and the test chip is hybridized at 45°C for 16 hours. After hybridization, the hybridization cocktail is removed from the chip and stored at -70°C. The chip is immediately placed in the Affymetrix GeneChip Fluidics Station 400 and washed using the preprogrammed steps "mini_euk2". This wash program involves a low stringency wash, high stringency wash, steptavidin/phycoerythrin stain, low stringency wash, anti-streptavidin antibody stain, a secondsteptavidin/phycoerythrin stain, and a final low stringency wash. If the labeled cRNA target passes all metrics of the Test2 chip, it is again heated to 95°C, 45°C,and hybridized to the GeneChip of interest. Hybridization, washing, staining, and scanning is repeated as described above except the automated fluids program "euk2" is used. The labeled cRNA target maybe repeatedly hybridized on 4-6 chips.

scan_protocol: After washing and staining, the test chip is placed in the Affymetrix GeneChip array scanner and image data is captured and converted to numerical output using the Microarray Analysis Suite version 4.0.

data_processing:
Acquired experimental data from the chip is analyzed using the GeneChip Microarray Suite version 4.0. For comparison between two chips, the 'baseline chip' intensity values are measured and
normalized to the average signal intensity. Intensity values of the 'experimental chip' are then compared to the baseline chip and a 'difference change' is calculated. Alternatively, hybridization signals may be normalized using the specific expression signals from the set of bacterial control transcripts. The output of the GeneChip software provides a qualitative call: 'increase', 'marginal increase', 'no change',
'decrease', and 'marginal decrease' as well as discrete numerical metrics used to make the call. Expression elements may be ranked based on absolute level of expression or relative change in
expression between a two chip comparison. All numerical data may be exported to a Microsoft Excel spreadsheet for further analysis. Expression elements are identified by a GenBank accession number
and the GeneChip analysis software allows for immediate hyperlink to the GenBank entry for full sequence annotation.

organism: Mus musculus

source_name: ERRA KO ventricle, baseline

label_protocol:
At least ten micrograms of total RNA is isolated from indicated tissues or cell lines using Trizol reagent (Life Technologies) following the supplier's protocol. RNA is then treated with RNase-free, DNase (Life Technologies) and further purified using the RNeasy total RNA clean up protocol (Qiagen). Purified, DNA-free RNA is assessed for integrity by formaldehyde / agarose gel electrophoresis and quantitated by 260 nm absorbence. An aliquot of cRNA control mix is added to ten micrograms of purified total RNA. The cRNA control mix is provided by the core facility and is composed of a set of four, in vitro transcripts generated
by T3 RNA polymerase. These polyadenylated transcripts encode the B. subtilis genes thr, trp, phe, and lys. Probes corresponding to these bacterial transcripts are represented on all Affymetrix GeneChips
(including test chips). Each synthetic transcript is quantitated and represented at a copy number of 5x106 to 5x108, corresponding roughly to the expected dynamic range of detection for the GeneChip
system. This set of control transcripts allows for the monitoring of cDNA synthesis and in vitro transcription of biotinylated targets and also provides a reference sample for normalizing between
experiments. RNA is converted to double stranded cDNA using the SuperScript Choice system (Life Technologies) following the supplier's protocol except that an HPLC-purified T7-dT24 primer (Geneset) is
utilized for first strand synthesis. After synthesis, the double stranded cDNA is purified by phenol/chloroform extraction and ethanol precipitation. The purified cDNA is used to generate the biotinylated cRNA target using the Bioarray High Yield RNA transcript labeling kit (Enzo) and following the supplier's protocol. The labeled cRNA is then
purified using the RNeasy total RNA clean up protocol (Qiagen) and quantitated by 260nm absorbence. Twenty micrograms of cRNA is fragmented by heating at 94°C for 35 minutes in fragmentation
buffer (40 mM Tris-acetate pH 8.1; 125 mM KOAc; 30 mM MgOAc). An aliquot of fragmented and nfragmented cRNA is analyzed by formaldehyde/agarose gel electrophoresis to ensure appropriate size
distribution (average size: 700 bp unfragmented and 100 bp after fragmentation).

extract_protocol: Tissue homogenization in RNAzol B, followed by organic clean-up and isopropanol precipitation.

tag: Sv129/C57B6 intercrossed hybrid line, 12 week old male


title: ERRa ko baseline heart, sample 2

source_name: ERRa ko ventricle, baseline

tag: Sv129/C57B6 hybrid strain, 12 week old male


title: Tobacco glucan elicitor Laminarin 1h slide2 rep2

source_name: Laminarin treatment, tobacco cells, 1h

treatment_protocol: Four days old tobacco BY-2 cells after subculture were treated with 500 microg/ml Laminarin for 1h.

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 2


title: Tobacco pMAT137 vector control 4 days slide4 rep2

tag: PMAT137 vector [1] transformed (control) tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 4 of 4, replicate 2


title: Tobacco NtMYBGR1 overexpressor 4 days slide2 rep2

tag: NtMYBGR1 overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 2 of 4, replicate 2


title: Tobacco pMAT137 vector control 4 days slide4 rep1

tag: PMAT137 vector [1] transformed (control) tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 4 of 4, replicate 1


title: Tobacco NtMYBGR1 overexpressor 4 days slide4 rep2

tag: NtMYBGR1 overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 4 of 4, replicate 2


title: Tobacco glucan elicitor Laminarin 1h slide2 rep3

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 3


title: Tobacco NtMYBGR1 overexpressor 4 days slide4 rep1

tag: NtMYBGR1 overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 4 of 4, replicate 1


title: Tobacco glucan elicitor Laminarin 1h slide2 rep1

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 1


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide2 rep2

source_name: AaGlucan enrich-Fr. treatment, tobacco cells, 1h

treatment_protocol:
Four days old tobacco BY-2 cells after subculture were treated with 10 microg/ml AaGlucan enrich-Fr. for 1h. AaGlucan was purified from Alternaria alternata 102 as a potent elicitor for tobacco [3].
[3] Shinya, T., Menard, R., Kozone, I., Matsuoka, H., Shibuya, N., Kauffmann, S., Matsuoka, K. and Saito, M. (2006) Novel b-1,3-, 1,6-oligoglucan elicitor from Alternaria alternata 102 for defense responses in tobacco. FEBS J. 273: 2421-2431.

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 2


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide2 rep3

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 3


title: Tobacco glucan elicitor Laminarin 1h slide4 rep3

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 3


title: ERRa wt baseline heart, sample 2

source_name: ERRa wt ventricle, baseline


title: ERRa wt baseline heart, sample 1

source_name: ERRA WT ventricle, baseline

tag: Sv129/C57B6 intercrossed hybrid strain, 12 week old male


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide2 rep1

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 1


title: Tobacco glucan elicitor cont 1h slide2 rep3

source_name: Water treatment, tobacco cells, 1h, control sample

treatment_protocol: Four days old tobacco BY-2 cells after subculture were treated with water for 1h.

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 3


title: Tobacco glucan elicitor Laminarin 1h slide4 rep1

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 1


title: Tobacco glucan elicitor Laminarin 1h slide4 rep2

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 2


title: Tobacco glucan elicitor cont 1h slide2 rep2

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 2


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide4 rep3

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 3


title: Tobacco glucan elicitor cont 1h slide2 rep1

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 2 of 4, replicate 1


title: Tobacco glucan elicitor cont 1h slide4 rep2

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 2


title: Tobacco NtDC1B overexpressor 4 days slide3 rep2

tag: NtDC1B overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 3 of 4, replicate 2


title: Tobacco NtMYBGR1 overexpressor 4 days slide3 rep2

tag: NtMYBGR1 overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 3 of 4, replicate 2


title: Tobacco NtMYBGR1 overexpressor 4 days slide3 rep1

tag: NtMYBGR1 overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 3 of 4, replicate 1


title: Tobacco NtDC1B overexpressor 4 days slide3 rep1

tag: NtDC1B overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 3 of 4, replicate 1


title: Tobacco NtDC1B overexpressor 4 days slide1 rep1

tag: NtDC1B overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 1 of 4, replicate 1


title: Tobacco glucan elicitor cont 1h slide4 rep1

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 1


title: Tobacco glucan elicitor cont 1h slide4 rep3

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 3


title: Tobacco pMAT137 vector control 4 days slide3 rep2

tag: PMAT137 vector [1] transformed (control) tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 3 of 4, replicate 2

tag: [1] Yuasa K, Toyooka K, Fukuda H & Matsuoka K (2005) Membrane-anchored prolyl hydroxylase with an export signal from the endoplasmic reticulum. Plant J 41, 81-94.


title: Tobacco pMAT137 vector control 4 days slide1 rep2

tag: PMAT137 vector [1] transformed (control) tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 1 of 4, replicate 2


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide4 rep2

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 2


title: Tobacco NtMYBGR1 overexpressor 4 days slide1 rep2

tag: NtMYBGR1 overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 1 of 4, replicate 2


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide4 rep1

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 4 of 4, replicate 1


title: Tobacco pMAT137 vector control 4 days slide1 rep1

tag: PMAT137 vector [1] transformed (control) tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 1 of 4, replicate 1


title: Tobacco NtMYBGR1 overexpressor 4 days slide1 rep1

tag: NtMYBGR1 overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 1 of 4, replicate 1


title: Tobacco NtDC1B overexpressor 4 days slide1 rep2

tag: NtDC1B overexpressed tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 1 of 4, replicate 2


title: Tobacco pMAT137 vector control 4 days slide3 rep1

tag: PMAT137 vector [1] transformed (control) tobacco cells in NtMYBGR1 or NtDC1B overexpression experiment, 4 days after subculture, slide 3 of 4, replicate 1


title: Tobacco glucan elicitor Laminarin 1h slide1 rep3

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 3


title: Tobacco glucan elicitor Laminarin 1h slide3 rep2

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 3 of 4, replicate 2


title: Tobacco glucan elicitor Laminarin 1h slide3 rep3

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 3 of 4, replicate 3


title: Tobacco glucan elicitor Laminarin 1h slide1 rep2

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 2


title: Tobacco glucan elicitor Laminarin 1h slide1 rep1

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 1


title: Tobacco glucan elicitor Laminarin 1h slide3 rep1

tag: Laminarin treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 3 of 4, replicate 1


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide1 rep1

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 1


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide1 rep2

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 2


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide1 rep3

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 3


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide3 rep1

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 3 of 4, replicate 1


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide3 rep2

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 3 of 4, replicate 2


title: Tobacco glucan elicitor AaGlucan enrich-Fr. 1h slide3 rep3

tag: AaGlucan enrich-Fr., treated tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 3 of 4, replicate 3


title: Tobacco glucan elicitor cont 1h slide3 rep3

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 3 of 4, replicate 3


title: Tobacco glucan elicitor cont 1h slide3 rep2

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 3 of 4, replicate 2


title: Tobacco glucan elicitor cont 1h slide1 rep2

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 2


title: Tobacco glucan elicitor cont 1h slide3 rep1

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 3, replicate 1


title: TNT_7ppm_Rep5 vs TNT_139ppm_Rep5

status: Public on Oct 15 2007

city: Vicksburg

first: Ping

last: Gong

state: MS

address: 3909 Halls Ferry Road

department: Environmental Laboratory

institute: US Army ERDC

description: A RNAlater-ICE fixed worm was chopped into 8-10 pieces in equal length. Total RNA was isolated using Qiagen RNeasy Mini Kit from each of the 8-10 pieces and was pooled as one biological replicate representing each individual earthworm. The pooled total RNA was purified to obtain mRNA using NucleoTrap Nucleic Acid Purification Kit (BD Biosciences).

hyb_protocol: Labeled cDNA probes for both channels (Genisphere) were added to the array, covered with a glass cover slip, which was then placed in a 50-ml tube. A few drops of water was also added into the tube to keep the air moisture. The capped tube was incubated at 55oC in a hybridization oven without rotation overnight (ca. 16 hr). Arrays were post-hyb washed according to manufacture's instruction (Genisphere).

scan_protocol: Arrays were scanned at 5-um resolution using VersArray ChipReader (Bio-Rad).

data_processing: A spot was flagged out if (1) its raw signal intensity was below its background level, (2) it overlapped with other spots, or (3) it was stained or over-saturated. The filtered spot intensity data were normalized by (1) subtraction of background intensity, (2) cross-channel LOWESS (local regression), and (3) centering to each channel's median spot intensity.

organism: Eisenia fetida

source_name: mRNA from worm (Rep#5) treated with 7 ppm of TNT labeled with Cyanine-3 (green)

label_protocol: 30 ng mRNA was reverse-transcribed into cDNA and labeled using Genisphere 3DNA 900 Expression Array Detection Cy3 kit.

extract_protocol: RNeasy kit (Qiagen)

tag: Adult earthowrms exposed in soil for 28 days.

tag: Worms were snap frozen in liquid nitrogen.

tag: Worm tissue was fixed in RNAlater-ICE (Ambion).

source_name: mRNA from worm (Rep#5) treated with 139 ppm of TNT labeled with Alex Fluor 647 (red)

label_protocol: 30 ng mRNA was reverse transcribed into cDNA and labeled using Genisphere 3DNA 900 Expression Array Detection Alex Fluor 647 kit.

tag: Worm tissue was fixed in RNAlater-ICe (Ambion).


title: TNT_0ppm_Rep5 vs TNT_35ppm_Rep5

source_name: mRNA from worm (Rep#5) treated with 0 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#5) treated with 35 ppm of TNT labeled with Alex Fluor 647 (red)


title: Tobacco glucan elicitor cont 1h slide1 rep1

scan_protocol: The Cy-5 (sample signal) and Cy-3 (control signal) were obtained by scanning  with a GenePix 4000A microarray scanner (Molecular Dynamics). The scans were subsequently analyzed by the MicroArray Suite iplab program (Scananalytics, BD Biosciences, Rockville, MD, USA).

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 1


title: TNT_139ppm_Rep1 vs TNT_0ppm_Rep2

source_name: mRNA from worm (Rep#1) treated with 139 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#2) treated with 0 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_0ppm_Rep1 vs TNT_35ppm_Rep2

source_name: mRNA from worm (Rep#1) treated with 0 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#2) treated with 35 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_0ppm_Rep4 vs TNT_35ppm_Rep5

source_name: mRNA from worm (Rep#4) treated with 0 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_35ppm_Rep1 vs TNT_7ppm_Rep2

source_name: mRNA from worm (Rep#1) treated with 35 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#2) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_139ppm_Rep5 vs TNT_0ppm_Rep2

source_name: mRNA from worm (Rep#5) treated with 139 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_139ppm_Rep4 vs TNT_0ppm_Rep5

source_name: mRNA from worm (Rep#4) treated with 139 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#5) treated with 0 ppm of TNT labeled with Alex Fluor 647 (red)


title: Tobacco glucan elicitor cont 1h slide1 rep3

tag: Water treated (control) tobacco cells in glucan elicitor treatment experiment, 1h time point, slide 1 of 4, replicate 3


title: TNT_0ppm_Rep2 vs TNT_35ppm_Rep2

source_name: mRNA from worm (Rep#2) treated with 0 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_35ppm_Rep3 vs TNT_7ppm_Rep3

source_name: mRNA from worm (Rep#3) treated with 35 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#3) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_35ppm_Rep5 vs TNT_7ppm_Rep5

source_name: mRNA from worm (Rep#5) treated with 35 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#5) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_7ppm_Rep2 vs TNT_139ppm_Rep2

source_name: mRNA from worm (Rep#2) treated with 7 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#2) treated with 139 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_139ppm_Rep2 vs TNT_0ppm_Rep4

source_name: mRNA from worm (Rep#2) treated with 139 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#4) treated with 0 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_139ppm_Rep4 vs TNT_0ppm_Rep1

source_name: mRNA from worm (Rep#1) treated with 0 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_7ppm_Rep1 vs TNT_139ppm_Rep2

source_name: mRNA from worm (Rep#1) treated with 7 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_7ppm_Rep4 vs TNT_139ppm_Rep5

source_name: mRNA from worm (Rep#4) treated with 7 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#5) treated with 139 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_7ppm_Rep2 vs TNT_139ppm_Rep3

source_name: mRNA from worm (Rep#3) treated with 139 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_7ppm_Rep5 vs TNT_139ppm_Rep1

source_name: mRNA from worm (Rep#5) treated with 7 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#1) treated with 139 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_0ppm_Rep3 vs TNT_35ppm_Rep3

source_name: mRNA from worm (Rep#3) treated with 0 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#3) treated with 35 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_139ppm_Rep2 vs TNT_0ppm_Rep3

source_name: mRNA from worm (Rep#3) treated with 0 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_139ppm_Rep1 vs TNT_0ppm_Rep3

source_name: mRNA from worm (Rep#1) treated with 139 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_7ppm_Rep3 vs TNT_139ppm_Rep3

source_name: mRNA from worm (Rep#3) treated with 7 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_7ppm_Rep4 vs TNT_139ppm_Rep4

source_name: mRNA from worm (Rep#4) treated with 139 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_139ppm_Rep3 vs TNT_0ppm_Rep4

source_name: mRNA from worm (Rep#3) treated with 139 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_0ppm_Rep1 vs TNT_35ppm_Rep1

source_name: mRNA from worm (Rep#1) treated with 0 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#1) treated with 35 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_139ppm_Rep3 vs TNT_0ppm_Rep5

source_name: mRNA from worm (Rep#5) treated with 0 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_0ppm_Rep2 vs TNT_35ppm_Rep3

source_name: mRNA from worm (Rep#2) treated with 0 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_0ppm_Rep3 vs TNT_35ppm_Rep4

source_name: mRNA from worm (Rep#4) treated with 35 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_35ppm_Rep4 vs TNT_7ppm_Rep4

source_name: mRNA from worm (Rep#4) treated with 35 ppm of TNT labeled with Cyanine-3 (green)

source_name: mRNA from worm (Rep#4) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)


title: TNT_0ppm_Rep4 vs TNT_35ppm_Rep4

source_name: mRNA from worm (Rep#4) treated with 0 ppm of TNT labeled with Cyanine-3 (green)


title: TNT_35ppm_Rep4 vs TNT_7ppm_Rep5

source_name: mRNA from worm (Rep#5) treated with 7 ppm of TNT labeled with Alex Fluor 647 (red)