title: HDF/MDA-MB231 co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54180.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1760, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 09:35:04; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-16; Parameter Pixel Size = 10; Parameter Laser on time = 173784; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.16; Parameter Scan Time = 09:35:04; Parameter PMT Volts = 600; Parameter Scan Date = 2004-06-16; Parameter Pixel Size = 10; Parameter Laser on time = 392755; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.64; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: HDF/ MDA-MB231

tag: HDF/ MDA-MB231


title: HMEC monoculture 2

status: Public on Nov 14 2007

type: RNA

city: Basel

first: Martin

last: Buess

state: CH

address: Petersgraben 4

department: Medizinische Onkologie

country: Switzerland

institute: University Hospital Basel

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55985.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1430, 5250; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.06; Parameter Scan Time = 10:05:50; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 196197; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.04; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.06; Parameter Scan Time = 10:05:50; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 415165; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

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 human reference

label_protocol:
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess
amplified RNA dircect inocorporaton; The protocol was modified for amplified RNA: 1. 6ug of amplified RNA and 10ug of random hexamer primer were mixed in a total volume of 15.4 ul. Then the described protocol was followed.; Protocol Type = Labeling; Performer: Martin,,Buess

extract_protocol: not provided

tag: StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer

value: Martin,,Buess

source_name: HMEC

label_protocol:
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Martin,,Buess
amplified RNA direct incorporation method; The protocol was modified for amplified RNA:  6ug of amplified RNA was mixed with 10ug of random hexamer primer pd(N)6( Procuct number 27-2166-01, Amersham Biosciences) in a total volume of 15.4 ul. Then the protocol was followed as described; Protocol Type = Labeling; Performer: Martin,,Buess

growth_protocol: Co-culture conditions; Human mammary epithelial cells (HMEC) (Cambrex Bio Science Walkersville, Inc) were expanded in mammary epithelial basal medium supplemented with bovine pituitary extract, human EGF, insulin and antibiotics (Clonetics, Cambrex Bio Science Walkersville, Inc). MCF-7, T47D, MDA-MB231, MDA-MB436, SKBR-3,  Hs578T, BT549, CCL-171, HTB-125 (ATTC) and HDF (Cambrex Bio Science Walkersville, Inc) were propagated in DMEM supplemented with 10% FBS (HyClone, Logan UT), glutamine, 100U/ml penicillin and 100 μg/ml streptomycin (GIBCO, Grand Island, N.Y.). For co-culture experiments the cells were cultivated for 48 hours at 50,000 cells/cm2 in endothelial basal media (CAMBREX Bio Science Rockland, Inc Rockland, Maine) with 0.2% FBS, which was a good universal media for all cells involved. Separated co-cultures were kept in Transwell? chambers 0.4μm pore size (Costar, Corning Inc. Corning, NY). Cells negatively tested for mycoplasma infection using MycoAlert Tm (CAMBREX Bio Science Rocland, Inc Rockland, Maine) and VenorGem? (SIGMA, Saint Louis, Missouri) mycoplasma detection kits according to the manufacturer?s instructions.; Protocol Type = Biological Sample; Performer: Martin,,Buess

extract_protocol: RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Martin,,Buess

tag: HMEC

tag: LabeledExtract


title: HDF/HMEC co-culture 2

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56568.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1640, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.40; Parameter Scan Time = 10:47:18; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199348; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.40; Parameter Scan Time = 10:47:18; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418316; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.63; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: stratagene common reference

source_name: HMEC/HDF

tag: HMEC/HDF


title: CCL-171 monoculture 1

description:
Simple annotation: Cell-line, Controls
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53408.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.28; Parameter Scan Time = 10:17:56; Parameter PMT Volts = 560; Parameter Scan Date = 2004-07-01; Parameter Pixel Size = 10; Parameter Laser on time = 177048; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 1.95; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.28; Parameter Scan Time = 10:17:56; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-01; Parameter Pixel Size = 10; Parameter Laser on time = 396016; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: CCL 171 coculture

tag: CCL 171 coculture


title: CCL-171/HMEC co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/55988.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1430, 5250; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.18; Parameter Scan Time = 10:29:33; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 196221; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.20; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.18; Parameter Scan Time = 10:29:33; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 415190; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.64; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

label_protocol: not provided

tag: stratagene human reference


title: Muscle HRT baseline 13

status: Public on Nov 12 2007

city: Jyväskylä

first: Eija

last: Pöllänen

address: PO Box 35/Viveca

department: Department of Health Sciences

country: Finland

institute: University of Jyväskylä

description: This sample presents baseline sample of ID_13 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

hyb_protocol: Employing protocols by Illumina Inc.; hybridization: 17 h at 55 degC

scan_protocol: Using an Illumina BeadReader containin two lasers: 532 nm and 635 nm and performing with 0.8 microns resolution. The data was acquired by the BeadStudio Direct Hybridization V.1.5.0.34

data_processing: The raw data was acquired by the BeadStudio Direct Hybridization V.1.5.0.34 (Illumina inc) and quantile normalized with Inforsense KDE 3.1 (InforSense Inc.) software

source_name: vastus lateralis muscle, HRT user, baseline

label_protocol: Illumina RNA amplification kit (Ambion Inc., #I1755) was used according to manufacturer’s instructions. Input amount: 500 ng of total RNA.

extract_protocol: Frozen muscle biopsy samples were homogenized in Trizol-reagent (Invitrogen Inc.) with aid of FastPrep FP120 -apparatus (MP Biomedicals). Manufacturer’s protocol was followed through the isolation procedure.

treatment_protocol: needle muscle biopsy, immediately frozen in liquid nitrogen after extrication from biobsy needle, stored at - 70 degC until RNA extraction

tag: Gender

value: female

tag: Age

value: 51.5 at onset of intervention

tag: menopausal status

value: early postmenopausal


title: Muscle HRT baseline 551

description: This sample presents baseline sample of ID_551 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

value: 53 at onset of intervention


title: Muscle HRT follow-up 13

description: This sample presents follow-up sample of ID_13 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, HRT user, follow-up


title: Muscle non-HRT baseline 94

description: This sample presents baseline sample of ID_94 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, non-HRT user, baseline


title: HDF/MDA-MB231 co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56567.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 5570; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 31.91; Parameter Scan Time = 10:00:12; Parameter PMT Volts = 570; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199301; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.71; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 31.91; Parameter Scan Time = 10:00:12; Parameter PMT Volts = 620; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418269; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.63; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess


title: Muscle HRT follow-up 551

description: This sample presents follow-uo sample of ID_551 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: CCL-171/HMEC co-culture 4

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56563.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1570, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.89; Parameter Scan Time = 12:17:43; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199438; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.59; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.89; Parameter Scan Time = 12:17:43; Parameter PMT Volts = 610; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418407; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.63; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

tag: stratagene common reference


title: Muscle HRT follow-up 145

description: This sample presents follow-up sample of ID_145 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

value: 52 at onset of intervention


title: Muscle non-HRT follow-up 268

description: This sample presents follow-up sample of ID_268 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, non-HRT user, follow-up

value: 53.5 at onset of intervention


title: mouse_fasted-gut_24h_5-6

city: Amsterdam

first: Milka

last: Sokolovic

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: AMC

description: Gene-expression profiling, pathway analysis, and immunohistochemistry were carried out on mouse small intestine after 0, 12, 24, and 72 hours of fasting to look at the gut's adaptive response to fasting.

hyb_protocol: Hybridization protocol that acompanies the Agilent's 60-mer Mouse Development (22K) Oligo Microarray G4120A was strictly followed

scan_protocol: Agilent’s dual-laser microarray slide scanner was used. The data were retrieved with Agilent’s Feature Extraction software 6.1.1.

data_processing: Value column represents Log(REDsignal/GREENsignal) per feature. Processed signals from Agilent feature extraction file were used.

organism: Mus musculus

source_name: 24h fasted gut, 5&6

label_protocol: 20 μg mRNA, pooled from 2 intestines (5&6), was reverse transcribed with Cy3-labelled dCTP (Perkin Elmer, Boston, USA), using the Agilent Fluorescent Direct Label Kit.

extract_protocol: Total intestinal RNA was extracted from frozen tissue with guanidiniumthiocyanate, followed by cesium-chloride centrifugation to avoid contamination with mucus. The quality of RNA was assessed with the RNA 6000 Nano LabChip® Kit in an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Mice were housed at 20-22°C, 50-60% humidity, a 12 hours light/dark cycle, and food and water ad libitum. At 6 weeks of age, mice were fasted by removing chow for up to 72 hours before sacrifice (n = 6 per group). The animals were kept in metabolic cages to prevent the consumption of beddings and were kept warm with an infrared lamp starting at 24h. All animals were sacrificed between 9:00 and 10:00 a.m. by cervical dislocation. The small intestine was removed quickly in such a way that adherent tissue remained behind, it was opened longitudinally, rinsed in phosphate-buffered saline, blotted, weighed, snap-frozen in liquid N2, and stored at -80°C.

tag: Male FVB mice, at 6 weeks of age, 24h fasted

source_name: fed gut, 1-6

label_protocol: Cy5-labeled cDNA produced from RNA pooled from 6 fed animals served as the common reference across all arrays

tag: Male FVB mice, at 6 weeks of age, fed


title: mouse_fasted-gut_24h_3-4

source_name: 24h fasted gut, 3&4


title: Muscle non-HRT baseline 268

description: This sample presents baseline sample of ID_268 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention


title: mouse_fasted-gut_24h_1-2

source_name: 24h fasted gut, 1&2


title: Muscle HRT follow-up 937

description: This sample presents follow-up sample of ID_937 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-interventionc

value: 55.5 at onset of intervention


title: Muscle HRT baseline 1057

description: This sample presents baseline sample of ID_1057 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: Muscle non-HRT follow-up 1302

description: This sample presents follow-up sample of ID_1302 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-interventionc

source_name: vastus lateralis muscle,non-HRT user,follow-up

value: 57 at onset of intervention


title: Muscle HRT follow-up 1057

description: This sample presents follow-up sample of ID_1057 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: Muscle HRT follow-up 824

description: This sample presents follow-up sample of ID_824 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

value: 54 at onset of intervention


title: mouse_gut_0h_5-6

source_name: fed gut, 5&6

source_name: fed gut, 5-6


title: Muscle HRT follow-up 941

description: This sample presents follow-up sample of ID_941 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: Muscle non-HRT baseline 1302

description: This sample presents baseline sample of ID_1302 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention


title: mouse_fasted_gut_12h_1-2

source_name: 12h fasted gut, 1&2

tag: Male FVB mice, at 6 weeks of age, 12h fasted


title: Muscle HRT baseline 941

description: This sample presents baseline sample of ID_941 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-interventionc


title: Muscle HRT baseline 937

description: This sample presents baseline sample of ID_937 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-interventionc


title: mouse_fasted-gut_12h_5-6

source_name: 12h fasted gut, 5&6


title: CCL-171/HMEC co-culture 1

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/53411.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess 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 = 32.19; Parameter Scan Time = 10:06:33; Parameter PMT Volts = 560; Parameter Scan Date = 2004-07-01; Parameter Pixel Size = 10; Parameter Laser on time = 177037; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess 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 = 32.19; Parameter Scan Time = 10:06:33; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-01; Parameter Pixel Size = 10; Parameter Laser on time = 396005; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.66; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: stratagen human reference

tag: stratagen human reference


title: Muscle HRT baseline 824

description: This sample presents baseline sample of ID_824 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: mouse_gut_0h_3-4

source_name: fed gut, 3&4

label_protocol: 20 μg mRNA, pooled from 2 intestines (1&2), was reverse transcribed with Cy3-labelled dCTP (Perkin Elmer, Boston, USA), using the Agilent Fluorescent Direct Label Kit.


title: CCL-171/MDA-MB231 co-culture 3

description:
Simple annotation: Cell-line, co-culture
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56560.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1640, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Martin,,Buess Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.31; Parameter Scan Time = 10:36:14; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 199337; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 1.83; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.31; Parameter Scan Time = 10:36:14; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 418305; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.63; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Martin,,Buess

source_name: stratagene common reference


title: Muscle non-HRT follow-up 440

description: This sample presents follow-up sample of ID_440 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention


title: mouse_fasted-gut_72h_3-4

source_name: 72h fasted gut, 3&4

tag: Male FVB mice, at 6 weeks of age, 72h fasted


title: mouse_gut_0h_1-2

source_name: fed gut, 1&2


title: Muscle non-HRT baseline 440

description: This sample presents baseline sample of ID_440 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention


title: sfp1 delta Glu-lim2

status: Public on Nov 10 2007

city: Delft

first: Chiara

last: Cipollina

address: Julianalaan 67

department: Biotechnology

institute: Delft University of Technology

description: The Saccharomyces cerevisiae sfp1 null mutant strain CEN.PK111.32D (MATa MAL2-8c SUC2 leu2-3,112 SFP1::KlLEU2) was used in this study. Cells were grown at 30?C in 2-L chemostats (Applikon), with a working volume of 1.0 L. Cultures were fed with a defined mineral medium (the medium composition was based on that described by Verduyn et al, Yeast 8:501-17, 1992) that limited growth by glucose at dilution rate of 0.05 h-1 under anaerobic conditions (maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas at 0.5 l min-1). Furthermore, Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. The stirrer speed was 800 rpm. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The working volume of the cultures was kept constant by means of an electrical level sensor. The off-gas was cooled by a condenser connected to a cryostat set at 2?C and analysed as previously described (van Maris et al, Appl. Environ. Microbiol. 69:2094-99, 1993). Chemostat cultures were assumed to be in steady-state when, after at least five volume changes, the culture dry-weight, specific carbon-dioxide production rate, changed by less than 2% during 24 hours. Steady state samples were taken from cultures below 18 generations in chemostat. Dry weight, extra-cellular metabolites, dissolved oxygen and gas profiles had to be constant over at least three volume changes prior to sampling for RNA extraction. Probe preparation and hybridization to Affymetrix Genechip? microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

data_processing: GeneChip? Operating Software (GCOS), version 1.2. Samples scaled to 150.

label: Biotin-labeled cRNA

organism: Saccharomyces cerevisiae

source_name: chemostat sampled cells

tag: Strain

value: CEN.PK111.32D; Genotype:MATa MAL2-8c SUC2 leu2-3,112 SFP1::KlLEU2


title: sfp1 delta EtOH-lim3

description: The Saccharomyces cerevisiae sfp1 null mutant strain CEN.PK111.32D (MATa MAL2-8c SUC2 leu2-3,112 SFP1::KlLEU2) was used in this study. Cells were grown at 30°C in 2-L chemostats (Applikon), with a working volume of 1.0 L. Cultures were fed with a defined mineral medium (the medium composition was based on that described by Verduyn et al, Yeast 8:501-17, 1992) that limited growth by ethanol at dilution rate of 0.1 h-1 under aerobic conditions setting the airflow at 0.5 l min-1. The stirrer speed was 800 rpm. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The working volume of the cultures was kept constant by means of an electrical level sensor. The off-gas was cooled by a condenser connected to a cryostat set at 2°C and analysed as previously described (van Maris et al, Appl. Environ. Microbiol. 69:2094-99, 1993). Chemostat cultures were assumed to be in steady-state when, after at least five volume changes, the culture dry-weight, specific carbon-dioxide production rate, changed by less than 2% during 24 hours. Steady state samples were taken from cultures below 18 generations in chemostat. Dry weight, extra-cellular metabolites, dissolved oxygen and gas profiles had to be constant over at least three volume changes prior to sampling for RNA extraction. Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

data_processing: GeneChip® Operating Software (GCOS), version 1.2. Samples scaled to 150.


title: CENPK113.7D Glu-lim1

description: The prototrophic reference Saccharomyces cerevisiae strain CEN.PK113.7D (MATa MAL2-8c SUC2) was used in this study. Cells were grown at 30°C in 2-L chemostats (Applikon), with a working volume of 1.0 L. Cultures were fed with a defined mineral medium (the medium composition was based on that described by Verduyn et al, Yeast 8:501-17, 1992) that limited growth by glucose at dilution rate of 0.05 h-1 under anaerobic conditions (maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas at 0.5 l min-1). Furthermore, Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. The stirrer speed was 800 rpm. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The working volume of the cultures was kept constant by means of an electrical level sensor. The off-gas was cooled by a condenser connected to a cryostat set at 2°C and analysed as previously described (van Maris et al, Appl. Environ. Microbiol. 69:2094-99, 1993). Chemostat cultures were assumed to be in steady-state when, after at least five volume changes, the culture dry-weight, specific carbon-dioxide production rate, changed by less than 2% during 24 hours. Steady state samples were taken from cultures below 18 generations in chemostat. Dry weight, extra-cellular metabolites, dissolved oxygen and gas profiles had to be constant over at least three volume changes prior to sampling for RNA extraction. Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

data_processing: GeneChip Operating Software (GCOS), version 1.2. Samples scaled to 150.

value: CENPK113.7D; Genotype:MATa MAL2-8c SUC2


title: sfp1 delta EtOH-lim1


title: sfp1 delta Glu-lim3


title: CENPK113.7D EtOH-lim3

description: The prototrophic reference Saccharomyces cerevisiae strain CEN.PK113.7D (MATa MAL2-8c SUC2) was used in this study. Cells were grown at 30?C in 2-L chemostats (Applikon), with a working volume of 1.0 L. Cultures were fed with a defined mineral medium (the medium composition was based on that described by Verduyn et al, Yeast 8:501-17, 1992) that limited growth by ethanol at dilution rate of 0.1 h-1 under aerobic conditions setting the airflow at 0.5 l min-1. The stirrer speed was 800 rpm. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The working volume of the cultures was kept constant by means of an electrical level sensor. The off-gas was cooled by a condenser connected to a cryostat set at 2?C and analysed as previously described (van Maris et al, Appl. Environ. Microbiol. 69:2094-99, 1993). Chemostat cultures were assumed to be in steady-state when, after at least five volume changes, the culture dry-weight, specific carbon-dioxide production rate, changed by less than 2% during 24 hours. Steady state samples were taken from cultures below 18 generations in chemostat. Dry weight, extra-cellular metabolites, dissolved oxygen and gas profiles had to be constant over at least three volume changes prior to sampling for RNA extraction. Probe preparation and hybridization to Affymetrix Genechip? microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).


title: CENPK113.7D Glu-lim2

description: The prototrophic reference Saccharomyces cerevisiae strain CEN.PK113.7D (MATa MAL2-8c SUC2) was used in this study. Cells were grown at 30?C in 2-L chemostats (Applikon), with a working volume of 1.0 L. Cultures were fed with a defined mineral medium (the medium composition was based on that described by Verduyn et al, Yeast 8:501-17, 1992) that limited growth by glucose at dilution rate of 0.05 h-1 under anaerobic conditions (maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas at 0.5 l min-1). Furthermore, Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. The stirrer speed was 800 rpm. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The working volume of the cultures was kept constant by means of an electrical level sensor. The off-gas was cooled by a condenser connected to a cryostat set at 2?C and analysed as previously described (van Maris et al, Appl. Environ. Microbiol. 69:2094-99, 1993). Chemostat cultures were assumed to be in steady-state when, after at least five volume changes, the culture dry-weight, specific carbon-dioxide production rate, changed by less than 2% during 24 hours. Steady state samples were taken from cultures below 18 generations in chemostat. Dry weight, extra-cellular metabolites, dissolved oxygen and gas profiles had to be constant over at least three volume changes prior to sampling for RNA extraction. Probe preparation and hybridization to Affymetrix Genechip? microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).


title: sfp1 delta EtOH-lim2

label: Biotin-labeld cRNA


title: CENPK113.7D Glu-lim3


title: CENPK113.7D EtOH-lim2


title: Muscle HRT follow-up 370

description: This sample presents baseline sample of ID_370 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, HRT user, follow-up

value: 52.5 at onset of intervention


title: CENPK113.7D EtOH-lim1

description: The prototrophic reference Saccharomyces cerevisiae strain CEN.PK113.7D (MATa MAL2-8c SUC2) was used in this study. Cells were grown at 30°C in 2-L chemostats (Applikon), with a working volume of 1.0 L. Cultures were fed with a defined mineral medium (the medium composition was based on that described by Verduyn et al, Yeast 8:501-17, 1992) that limited growth by ethanol at dilution rate of 0.1 h-1 under aerobic conditions setting the airflow at 0.5 l min-1. The stirrer speed was 800 rpm. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The working volume of the cultures was kept constant by means of an electrical level sensor. The off-gas was cooled by a condenser connected to a cryostat set at 2°C and analysed as previously described (van Maris et al, Appl. Environ. Microbiol. 69:2094-99, 1993). Chemostat cultures were assumed to be in steady-state when, after at least five volume changes, the culture dry-weight, specific carbon-dioxide production rate, changed by less than 2% during 24 hours. Steady state samples were taken from cultures below 18 generations in chemostat. Dry weight, extra-cellular metabolites, dissolved oxygen and gas profiles had to be constant over at least three volume changes prior to sampling for RNA extraction. Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).

data_processing: :  GeneChip® Operating Software (GCOS), version 1.2. Samples scaled to 150.


title: Human Glioblastoma Case GB94

status: Public on Nov 09 2007

type: genomic

city: Cambridge

first: Koichi

last: Ichimura

address: Addenbrooke's Hospital Box 231

department: Pathology

country: United Kingdom

institute: University of Cambridge

description: Normalised aginst median of the 5Mb clones

hyb_protocol: The purified DNA from test and reference were pooled and mixed with 45µg of Cot1 DNA and ethanol precipitated. The precipitated DNA was dissolved in 30µl of hybridisation buffer, incubated at 37˚C for 2 hours and applied to the prehybridised microarray. Hybridisation was performed in a humidified Micro Array Hybridisation Chamber (Camlab, Cambridge, UK) at 37˚C for 48 hours under a coverslip. The arrays were then washed successively in 1x PBS/0.05% Tween20 at room temperature for 15 min twice, 50% formamide/2xSSC at 42˚C for 30 min once, 1x PBS/0.05% Tween20 at room temperature for 15min and 1x PBS for 5min twice.

scan_protocol: Scanned on an Axon GenePix 4100A personal scanner. Images were quantified using GenePix Pro version 5.1.

data_processing: The median of the ratio of test/reference spot intensity, after subtraction of local background, of the 5Mb-clones in each subarray was used as the normalization factor. The chromosomal arm on which most microsatellite markers showed allelic balance was chosen for normalization. The test/reference ratio of each clone was divided by the normalization factor for each subarray, an average of the duplicate calculated and log2-transformed.

molecule: genomic DNA

source_name: Genomic DNA from a human glioblastoma labeled with Cyanine-5 (red).

label_protocol: 400ng of tumour and reference genomic DNA were labelled with Cy5-dCTP and Cy3-dCTP (GE Healthcare), respectively, using BioPrime kit (Invitrogen) according to the manufacturer’s instruction, except that custom-prepared dNTP (dCTP 1mM, dATP 2mM, dGTP 2mM and dTTP 2mM) was used. After overnight incubation at 37°C, the labelled DNA were purified using a G-50 spin column (GE Healthcare).

extract_protocol: Proteinase K digestion followed by phenol:chloroform extraction

treatment_protocol: Proteinase K digestion followed by phenol:chlorform extraction

tag: Brain tumor tissue

tag: Male

source_name: Pooled genomic DNA from 20 normal human female blood labeled with Cyanine-3 (green).

tag: Blood

tag: Female


title: Human Glioblastoma Case GB99

source_name: Pooled genomic DNA from 20 normal human male blood labeled with Cyanine-3 (green).


title: Human Glioblastoma Case GB64


title: Human Glioblastoma Case GB76


title: Human Glioblastoma Case GB63


title: Human Glioblastoma Case GB56


title: Human Glioblastoma Case GB84


title: Human Glioblastoma Case GB69


title: Human Glioblastoma Case GB47


title: Human Glioblastoma Case GB52


title: Human Glioblastoma Case GB35


title: Human Glioblastoma Case GB30


title: Human Glioblastoma Case GB3


title: mouse_fasted-gut_12h_3-4

description: Gene-expression profiling, pathway analysis, and immunohistochemistry were carried out on mouse small intestine after 0, 12, 24, and 72 hours of fasting to look at the gut's adaptive response to fasting.

source_name: 12h fasted gut, 3&4

source_name: fed gut, 1-6


title: Human Glioblastoma Case GB294


title: Human Glioblastoma Case GB291


title: Muscle non-HRT follow-up 1296

description: This sample presents follow-up sample of ID_1296 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, non-HRT user, follow-up


title: Muscle HRT baseline 370

source_name: vastus lateralis muscle, HRT user, baseline


title: Human Glioblastoma Case GB268


title: sfp1 delta Glu-lim1

description: The Saccharomyces cerevisiae sfp1 null mutant strain CEN.PK111.32D (MATa MAL2-8c SUC2 leu2-3,112 SFP1::KlLEU2) was used in this study. Cells were grown at 30°C in 2-L chemostats (Applikon), with a working volume of 1.0 L. Cultures were fed with a defined mineral medium (the medium composition was based on that described by Verduyn et al, Yeast 8:501-17, 1992) that limited growth by glucose at dilution rate of 0.05 h-1 under anaerobic conditions (maintained by sparging the medium reservoir and the fermentor with pure nitrogen gas at 0.5 l min-1). Furthermore, Norprene tubing and butyl septa were used to minimize oxygen diffusion into the anaerobic cultures. The stirrer speed was 800 rpm. The pH was measured on-line and kept constant at 5.0 by the automatic addition of 2 M KOH using an Applikon ADI 1030 Biocontroller. The working volume of the cultures was kept constant by means of an electrical level sensor. The off-gas was cooled by a condenser connected to a cryostat set at 2°C and analysed as previously described (van Maris et al, Appl. Environ. Microbiol. 69:2094-99, 1993). Chemostat cultures were assumed to be in steady-state when, after at least five volume changes, the culture dry-weight, specific carbon-dioxide production rate, changed by less than 2% during 24 hours. Steady state samples were taken from cultures below 18 generations in chemostat. Dry weight, extra-cellular metabolites, dissolved oxygen and gas profiles had to be constant over at least three volume changes prior to sampling for RNA extraction. Probe preparation and hybridization to Affymetrix Genechip® microarrays were performed following Affymetrix instructions. The one-cycle eukaryotic target labelling assay was used, starting with 15 mg total RNA. The quality of total RNA, cDNA, cRNA and fragmented cRNA were checked using the Agilent Bioanalyzer 2100 (Agilent Technologies).


title: Muscle HRT baseline 145

description: This sample presents baseline sample of ID_145 individual, who belonged to hormone replacement therapy group (HRT) of "HRT and excercise"-intervention


title: Human Glioblastoma Case GB33


title: Human Glioblastoma Case GB267


title: Human Glioblastoma Case GB264


title: Human Glioblastoma Case GB266


title: Muscle non-HRT baseline 1296

description: This sample presents baseline sample of ID_1296 individual, who belonged to non-hormone replacement therapy group (non-HRT) of "HRT and excercise"-intervention

source_name: vastus lateralis muscle, non-HRT user, baseline


title: Human Glioblastoma Case GB263


title: Human Glioblastoma Case GB251


title: Human Glioblastoma Case GB262


title: Human Glioblastoma Case GB260


title: Human Glioblastoma Case GB261


title: Human Glioblastoma Case GB257


title: Human Glioblastoma Case GB255


title: Human Glioblastoma Case GB250


title: Human Glioblastoma Case GB225


title: Human Glioblastoma Case GB219


title: Human Glioblastoma Case GB214


title: Human Glioblastoma Case GB222


title: Human Glioblastoma Case GB211


title: Human Glioblastoma Case GB212


title: Human Glioblastoma Case GB248


title: Human Glioblastoma Case GB18


title: Human Glioblastoma Case GB183


title: Human Glioblastoma Case GB182


title: Human Glioblastoma Case GB197


title: Human Glioblastoma Case GB204


title: Human Glioblastoma Case GB177


title: Human Glioblastoma Case GB205


title: Human Glioblastoma Case GB195


title: Human Glioblastoma Case GB201


title: Human Glioblastoma Case GB157


title: Human Glioblastoma Case GB153


title: Human Glioblastoma Case GB21


title: Human Glioblastoma Case GB208


title: Human Glioblastoma Case GB207


title: Human Glioblastoma Case GB194


title: Human Glioblastoma Case GB193


title: Human Glioblastoma Case GB206


title: Human Glioblastoma Case GB185


title: Human Glioblastoma Case GB191


title: Human Glioblastoma Case GB189


title: Human Glioblastoma Case GB161


title: Human Glioblastoma Case GB176


title: Human Glioblastoma Case GB147


title: Human Glioblastoma Case GB152


title: Human Glioblastoma Case GB168


title: Human Glioblastoma Case GB141


title: Human Glioblastoma Case GB139


title: Human Glioblastoma Case GB159


title: mouse_fasted-gut_72h_1-2

source_name: 72h fasted gut, 1&2


title: Human Glioblastoma Case GB140


title: Human Glioblastoma Case GB136


title: Human Glioblastoma Case GB131


title: Human Glioblastoma Case GB129


title: Human Glioblastoma Case GB149


title: Human Glioblastoma Case GB127


title: Human Anaplastic Astrocytoma Case AA99

source_name: Genomic DNA from a human anaplastic astrocytoma labeled with Cyanine-5 (red).


title: Human Anaplastic Astrocytoma Case AA75


title: Human Anaplastic Astrocytoma Case AA65


title: Human Anaplastic Astrocytoma Case AA90


title: Human Glioblastoma Case GB105


title: Human Anaplastic Astrocytoma Case AA83


title: Human Anaplastic Astrocytoma Case AA93


title: Human Anaplastic Astrocytoma Case AA42


title: Human Anaplastic Astrocytoma Case AA53


title: Human Anaplastic Astrocytoma Case AA24


title: Human Glioblastoma Case GB216

description: Normalised aginst median of all 1q clones

data_processing: The median of the ratio of test/reference spot intensity, after subtraction of local background, of all clones on either 1p or 1q in each subarray was used as the normalization factor. The chromosomal arm on which most microsatellite markers showed allelic balance was chosen for normalization. The test/reference ratio of each clone was divided by the normalization factor for each subarray, an average of the duplicate calculated and log2-transformed.


title: Human Anaplastic Astrocytoma Case AA14


title: Human Anaplastic Astrocytoma Case AA68


title: Human Glioblastoma Case GB198


title: Human Astrocytoma Grade II Case A54

source_name: Genomic DNA from a human astrocytoma WHO grade II labeled with Cyanine-5 (red).


title: Human Glioblastoma Case GB126


title: Human Anaplastic Astrocytoma Case AA101


title: Human Anaplastic Astrocytoma Case AA29


title: Human Anaplastic Astrocytoma Case AA22


title: Human Glioblastoma Case GB190


title: Human Glioblastoma Case GB164


title: Human Glioblastoma Case GB181


title: Human Anaplastic Astrocytoma Case AA107


title: Human Anaplastic Astrocytoma Case AA49


title: Human Astrocytoma Grade II Case A49


title: Human Anaplastic Astrocytoma Case AA54


title: Human Anaplastic Astrocytoma Case AA34


title: Human Anaplastic Astrocytoma Case AA73


title: Human Anaplastic Astrocytoma Case AA115


title: Human Astrocytoma Grade II Case A56


title: Human Anaplastic Astrocytoma Case AA111


title: Human Astrocytoma Grade II Case A48


title: Human Astrocytoma Grade II Case A23


title: Human Astrocytoma Grade II Case A12


title: Human Astrocytoma Grade II Case A35


title: Human Glioblastoma Case GB160


title: Human Astrocytoma Grade II Case A34


title: Human Astrocytoma Grade II Case A25


title: Human Anaplastic Astrocytoma Case AA108


title: Viro3P10-086

status: Public on Nov 07 2007

city: San Francisco

first: Amy

last: Kistler

state: CA

department: Biochemistry and Biophysics

country: USA

institute: UCSF

hyb_protocol: Cy3 labeled sample was hybridized to the microarray in 3 × SSC at 65°C overnight (Eisen MB and Brown PO, 1999.  Methods in Enzymology 303, 179-205).

scan_protocol: Microarrays were scanned with an Axon 4000B scanner (Axon Instruments, Union City, CA, USA) and gridded using the bundled GenePix 3.0 software.

data_processing: Spot analysis was performed with GenePix v3.0 and stored in a relational database (NOMAD). Data was sum-normalized and filtered to remove poor performing spots. We then analyzed our results using a computational tool, E-predict, to identify virus positive specimens as described in Urisman, A, et al., 2005.  Genome Biology 6(9): R78.

organism: Viruses

source_name: Amplified RNA from nasal lavage of outpatient cold specimen

label_protocol: RNA extracted from the samples was amplified using a modified Round A-B random PCR method Bohlander SK et al., 1992. Genomics 13, 1322-1324), as previously described (Urisman A et al., 2005.  Genome Biology 6(9), R78; protocol S1 in Wang D et al., 2003.  PLoS Biology 1:2, E2). Briefly, random-primed reverse transcription and second strand synthesis were carried out using primer A (5'-GTT TCC CAG TCA CGA TCN NNN NNN NN-3'). The resulting material was then amplified with 40 cycles of PCR using primer B (5'-GTT TCC CAG TCA CGA TC-3'). This was followed by an additional 20 cycles of PCR with primer B to incorporate aminoallyl-dUTP. The amplified material was then labeled with Cy3.

extract_protocol: 1ml of homogenized nasal lavage sample was mixed with 3.5ml of RLT buffer (Qiagen USA, Valencia, CA) with 2-mercaptoethanol and frozen at bedside on dry ice and stored at –80ºC.  Total RNA was extracted from these specimens using the RNeasy Mini Kit (Qiagen USA, Valencia, CA,USA) as follows. The nasal lavage-RLT mixture was thawed and 1mL of this mixture was diluted with 1mL of 70% ethanol RNA.  The resulting 2mLs were applied to an RNeasy column in three 650 µl aliquots. The remaining steps were carried out in accordance with the manufacturer's protocol, including on-column DNase digest. RNA was eluted from the columns with 30 µl nuclease-free water, and 9 µl was used for amplification and hybridization.


title: Viro3P10-105

tag: Amplified RNA from nasal lavage of outpatient cold specimen


title: Viro3P10-104


title: Viro3P10-260


title: Viro3P10-106


title: Viro3P10-085


title: Viro3P10-107


title: Viro3P10-108


title: Viro3P10-118


title: Viro3P10-103


title: Viro3P10-101


title: Viro3P10-112


title: Viro3P10-116


title: Viro3P10-158


title: Viro3P10-113


title: Viro3P10-111


title: Viro3P10-157


title: Viro3P10-152


title: Viro3P10-153


title: Viro3P10-114


title: Viro3P10-155


title: Viro3P10-109


title: Viro3P10-115


title: Viro3P10-156


title: Viro3P10-117


title: Viro3P10-154


title: MegaViroP3-250

hyb_protocol: Cy5 labeled sample was hybridized to the microarray in 3 × SSC at 65°C overnight (Eisen MB and Brown PO, 1999.  Methods in Enzymology 303, 179-205).

label_protocol: RNA extracted from the samples was amplified using a modified Round A-B random PCR method Bohlander SK et al., 1992. Genomics 13, 1322-1324), as previously described (Urisman A et al., 2005.  Genome Biology 6(9), R78; protocol S1 in Wang D et al., 2003.  PLoS Biology 1:2, E2). Briefly, random-primed reverse transcription and second strand synthesis were carried out using primer A (5'-GTT TCC CAG TCA CGA TCN NNN NNN NN-3'). The resulting material was then amplified with 40 cycles of PCR using primer B (5'-GTT TCC CAG TCA CGA TC-3'). This was followed by an additional 20 cycles of PCR with primer B to incorporate aminoallyl-dUTP. The amplified material was then labeled with Cy5.


title: MegaViroP1-211


title: MegaViroP3-251


title: MegaViroP3-254


title: Viro3P10-089


title: MegaViroP3-253


title: MegaViroP3-257


title: MegaViroP3-259


title: MegaViroP3-252


title: MegaViroP3-258


title: MegaViroP4-040


title: Viro3P10-151


title: MegaViroP3-256


title: Viro3P10-159


title: MegaViroP1-183


title: MegaViroP4-029


title: MegaviroP1-210


title: MegaViroP3-247


title: MegaViroP1-206


title: MegaViroP1-137


title: MegaViroP3-260


title: MegaViroP1-151


title: TS ets2 flox7 DMd4+SB rep 2 Grp E

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description: SB treated DM cells f_f; medium DM; Adeno SB; TS_ets2_flox7_DMd4+SB rep2

hyb_protocol: As recommended by illumina.

scan_protocol: As suggested by Illumina using the Illumina scanner.

data_processing: None: raw data from Beadstudio

label: Streptavidin Cy3

source_name: TS_ets2_flox7_DMd4+SB rep2

label_protocol: As described in the illumina Mouse-6 chip processing protocol. Briefly, generation of biotin labelled cRNA from the product of RT cDNA synthesis and 2nd strand cDNA synthesis.

growth_protocol: TS cells were isolated from blastocysts and grown as previously described (Tanaka et al., 1998). Briefly, Growth medium (GM) was RPMI 1640 supplemented with 20% FBS, 1 mM sodium pyruvate, 100 μM b-mercaptoethanol, 100 U/ml penicillin, 100μg/ml streptomycin, 2 mM L-glutamine, 25 ng/ml human recombinant FGF4 (Sigma), 1 μg/ml heparin, and 70% EFCM. TS cell differentiation was induced by withdrawal of FGF4 and EFCM after trypsinization and replating at appropriate density. For TS colony formation assay, optimally growing TS cells were trypsinized and replated at 500-2000 cells per 6-cm dish onto feeder cells, and fed with fresh GM every 2-3 days for 1-2 weeks.

extract_protocol: Illumina TotalPrep RNA amplification kit (Ambion Catalog#IL1791)


title: MegaViroP10-036


title: MegaViroP1-136


title: TS differ AdenoEmpty DM Grp D

description: TS differ f_f; medium DM; Adeno Empty

source_name: TSdiffer_AdenoEmpty DM

tag: TS differ f_f; medium DM; Adeno Empty


title: TS ets2 flox7 DMd4+SB rep 1 Grp E

description: SB treated DM cells f_f; medium DM; Adeno SB; TS_ets2_flox7_DMd4+SB rep1

source_name: TS_ets2_flox7_DMd4+SB rep1


title: MegaViroP3-249


title: MegaViroP3-248


title: MegaViroP8-244


title: TS ets2 flox7 GMd4  rep 1 Grp C

description: #1 biological replicate TS_ets2_flox7_GMd4  rep1 in GM media.

source_name: TS_ets2_flox7_GMd4  rep1

tag: TScells f_f medium GM; AdenoEMPTY


title: MegaViroP8-241


title: MegaViroP8-240


title: MegaViroP8-242


title: TS7 AdCreGFP Day 3 rep 1 Grp B

description: #1 biological replicate from two for the transfected TS7_AdCreGFP Day 3 rep1 cell line on day 3 in GM media.

source_name: TS7_AdCreGFP Day 3 rep1

tag: f_f; medium GM; Adeno Cre; TS7_AdCreGFP Day 3 rep1


title: MegaViroP8-245


title: MegaViroP8-243


title: MegaViroP4-033


title: MegaViroP8-246


title: TS ets2 flox7 DMd4  rep 1 Grp D

description: TS differ f_f; medium DM; Adeno Empty; TS_ets2_flox7_DMd4  rep1

source_name: TS_ets2_flox7_DMd4  rep1

tag: f_f TS differ; medium DM; Adeno EMPTY ; TS_ets2_flox7_DMd4  rep1


title: TS7 AdCreGFP Day 3 rep 2 Grp B

description: #2 biological replicate from two for the transfected TS7_AdCreGFP Day 3 rep1 cell line on day 3 in GM media.

source_name: TS7_AdCreGFP Day 3 rep2

tag: f_f; medium GM; AdenoCre; TS7_AdCreGFP Day 3 rep2


title: TS9 AdGFP Day 3 rep 4 Grp A

description: #4 biological replicate from four for the transfected TS9_AdGFP cell line on day 3 in GM media.

source_name: TS9_AdGFP Day 3 rep4

tag: f_f; medium GM; Adeno GFP; TS9_AdGFP Day 3 rep4


title: TS7 AdGFP Day 3 rep 3 Grp A

description: Third biological replicate from three for the transfected TS7_AdGFP cell line on day 3 in GM media.

source_name: TS7_AdGFP Day 3 rep3

tag: f_f; medium GM; Adeno GFP; TS7_AdGFP Day 3 rep3


title: MegaViroP4-037


title: TS7 AdGFP Day 3 rep 1 Grp A

description: First biological replicate from three for the transfected TS7_AdGFP cell line on day 3 in GM media.

source_name: TS7_AdGFP Day 3 rep1

tag: f_f; medium GM; AdenoGFP;  TS7_AdGFP Day 3 rep1


title: MegaViroP4-036


title: MegaViroP1-164


title: MegaViroP4-030


title: MegaViroP4-038


title: MegaViroP4-035


title: MegaViroP4-032


title: MegaViroP4-039


title: MegaViroP8-239


title: MegaViroP4-034


title: TS7 AdGFP Day 3 rep 2 Grp A

description: Second biological replicate from three for the transfected TS7_AdGFP cell line on day 3 in GM media.

source_name: TS7_AdGFP Day 3 rep2

tag: f_f; medium GM; Adeno GFP; TS7_AdGFP Day 3 rep2


title: MegaViroP4-221


title: TS9 AdCreGFP Day 3 rep 3 Grp B

description: Third biological replicate from three for the transfected TS9_AdCreGFP cell line on day 3 in GM media.

source_name: TS9_AdCreGFP cell line day 3 in GM

tag: f_f; medium GM; AdenoCre; TS9_AdCreGFP cell line day 3 in GM


title: MegaViroP10-034


title: MegaViroP10-035


title: MegaViroP1-140


title: MegaViroP10-033


title: TS9 AdGFP Day 3 rep 3 Grp A

description: Third biological replicate from three for the transfected TS9_AdGFP cell line on day 3 in GM media.

source_name: TS9_AdGFP day3 in GM

tag: f_f; GM medium; AdenoGFP; TS9_AdGFP day3 in GM


title: MegaViroP3-261


title: TS9 AdCreGFP Day 3 rep 1 Grp B

description: Second biological replicate from three for the transfected TS9_AdCreGFP cell line on day 3 in GM media.

tag: f_f; medium GM; Adeno CRE; TS9_AdCREGFP day 3 in GM


title: MegaViroP1-141


title: TS9 AdGFP Day 3 rep 2 Grp A

source_name: TS9_AdGFP cell line day 3 in GM

tag: f_f; medium GM; AdenoGFP; TS9AdGFP day3 in GM


title: MegaViroP4-195


title: MegaViroP1-145


title: Atypical follicular adenoma, sample 95

status: Public on Nov 06 2007

city: angers

first: Jean-Fred

last: Fontaine

address: 4 rue Larrey

country: France

institute: INSERM

description: gene expression data from thyroid tissue diagnosed as Atypical follicular adenoma

hyb_protocol: the array was hybridized with a complex target prepared from 5 ?g total RNA by simultaneous RT and [alpha-33P]deoxy-CTP labelling as described by the manufacturer.

scan_protocol: hybridization images were obtained by scanning with an imaging plate device (Fuji BAS 5000, Raytest, Paris, France). Signal intensities were quantified using ArrayGauge software (Fujifilm Medical Systems, Stanford, CT, USA).

data_processing: data were subjected to print-tip Lowess normalization and median normalization

source_name: Homo sapiens thyroid, Atypical follicular adenoma

extract_protocol: Total RNA was extracted from tissue samples using a standard guanidium isothiocyanate protocol (TRIzol reagent, Life Technologies, Inc., Gaithersburg, MD, USA)

tag: Gender

tag: Age

value: 78 years

tag: Thyroïditis

value: yes

tag: Metastasis:

tag: Nucleus type

value: Follicular

tag: Nodule type

value: Begining

tag: Vesicle type

value: Microfollicular

tag: Connective tissue type

value: Trabecular

tag: Filter ID


title: Wild type, sample 96

description: gene expression data from thyroid tissue diagnosed as Wild type

source_name: Homo sapiens thyroid, Wild type

label_protocol: the array was hybridized with a complex target prepared from 5 ?g total RNA by simultaneous RT and [alpha-33P]deoxy-CTP labelling as described by the manufacturer.

value: female

value: 77 years

value: Normal


title: B-CPAP cell line, sample 89

description: gene expression data from thyroid tissue diagnosed as B-CPAP cell line

source_name: Homo sapiens thyroid, B-CPAP cell line

tag: Gender:

tag: Age:

tag: Thyroïditis:

value: Papillary

tag: Nodule type:

tag: Vesicle type:

tag: Connective tissue type:


title: B-CPAP cell line, sample 87


title: B-CPAP cell line, sample 85


title: B-CPAP cell line, sample 86


title: Oncocytic adenoma, sample 93

description: gene expression data from thyroid tissue diagnosed as Oncocytic adenoma

source_name: Homo sapiens thyroid, Oncocytic adenoma

value: 51 years

value: Alone


title: Viro3P10-160

source_name: Amplified RNA from nasal lavage of outpatient cold specimen


title: B-CPAP cell line, sample 88


title: Oncocytic adenoma, sample 90

value: male

value: 62 years

value: medium

value: Multiple

value: Macrofollicular


title: B-CPAP cell line, sample 84


title: B-CPAP cell line, sample 83


title: XTC.UC1 cell line , sample 78

description: gene expression data from thyroid tissue diagnosed as XTC.UC1 cell line

source_name: Homo sapiens thyroid, XTC.UC1 cell line

tag: Nucleus type:


title: Wild type, sample 94


title: XTC.UC1 cell line , sample 77


title: Atypical follicular adenoma, sample 91

value: 59 years

value: no


title: XTC.UC1 cell line , sample 81


title: XTC.UC1 cell line , sample 79


title: Wild type, sample 92

value: yes

value: Follicular


title: B-CPAP cell line, sample 82


title: XTC.UC1 cell line , sample 80


title: XTC.UC1 cell line , sample 76


title: Multinodular goiter, sample 66

description: gene expression data from thyroid tissue diagnosed as Multinodular goiter

source_name: Homo sapiens thyroid, Multinodular goiter

value: 60 years

tag: Metastasis

value: Anisonucleosis


title: Multinodular goiter, sample 72

tag: Gender

value: female

value: 65 years


title: Oncocytic adenoma, sample 70

tag: Age

value: 57 years

value: Microfollicular

value: Normal


title: MegaViroP1-194

tag: Amplified RNA from nasal lavage of outpatient cold specimen


title: Multinodular goiter, sample 65

value: 48 years

tag: Thyroïditis

value: Begining


title: Oncocytic adenoma, sample 71

value: 51 years

tag: Metastasis:

tag: Nucleus type

value: Alone

value: Trabecular


title: E8.0b_rep2

city: Stanford

first: Nesanet

last: Mitiku

address: 300 Pasteur Drive Alway M313

department: Genetics

institute: Stanford University

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59856.gif
Developmental Stage: E8.25

hyb_protocol: see channel 2 labeling protocol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku 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 = 30.94; Parameter Scan Time = 18:47:27; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 24271; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.76; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku

source_name: REF

label_protocol: see channel 2 labeling protocol

extract_protocol: Reference RNA extraction: The common reference used in this work was comprised of a mixture of maternal brain, E17.5 embryo, E17.5 placenta, and CGR8 ES cells.  All tissues used in the reference RNA pool, with the exception of CGR8 ES cells, were ground via mortar and pestle in the presence of liquid nitrogen.  The resulting powder was put through one acid phenol extraction, two Trizol (Invitrogen) extractions, DNAse I (Ambion) treated, and then re-purified over RNAqueous Midi columns (Ambion).  The ES cell component of the reference pool was purified similarly beginning with the acid phenol extraction.  In lieu of mortar and pestle grinding, ES cells were spun down and directly resuspended in solution D.  Total RNA from all four sources was combined at a proportion of 1:1.5:2:2.5 (brain:placenta:ES cells:E17.5 embryos, according to mass) and linearly amplified (mMessageAmp, Ambion).  All reference amplification reactions were then pooled. This reference aRNA pool was used for all hybridizations.; Protocol Type = Extract preparation; Performer: Nesanet,,Mitiku

tag: REF

source_name: EXP

label_protocol: Microarray Methods: Labeling and Hybridization  Each labeling reaction was carried out using 4 mcg of aRNA , 10 mcg of pDN6 (Amersham), 0.6 mcL 50X dNTPs (Invitrogen), 3 mcL 0.1M DTT, 3 mcL Cy3 or Cy5 dUTP and 2mcL Superscript II (Invitrogen) reverse transcriptase in the supplied buffer.  Samples were incubated at 42°C for 2 hours in an Eppendorf cycler with the lid heated to 47°C.  Each labeling reaction was stopped via the addition of 15 mcL of 0.1N NaOH + 2mM EDTA followed by incubation at 70°C for 10 min.  15 mcL of 0.1N HCL was added to neutralize each sample.  Cy3 and Cy5 samples for a single hybridization were combined.  Labeled aRNA samples were then purified over Microcon YM-30 columns (Millipore); samples were washed 5X with TE buffer and suspended in a volume of 10.14 mcl TE by the end of purification.; Protocol Type = Labeling; Performer: Nesanet,,Mitiku

extract_protocol:
Embryonic RNA extraction/preparation (experimental sample):  Total RNA was prepared using a variation on the acid phenol method of Chomczynski et al(Chomczynski and N. 1987).  The method of sample homogenization in solution D (4M guanidinium thiocyanate, 100mM NaOAc, 0.5% Sarkosyl, 0.1M beta-mercaptoethanol)  varied according to the composition of the sample from which RNA was being extracted. Early post-implantation embryos were transferred into microfuge tubes containing solution D immediately following dissection and staging; homogenization was achieved by flicking until complete dissolution.  Homogenized samples were stored at -80degC until RNA isolation.   On the day of RNA isolation, solution D-homogenized samples were defrosted and vortexed to ensure complete mixing.  As the initial volume of lysate was in accordance to the initial sample quantity, lysate volumes were variable, and solution volumes throughout the RNA isolation were adjusted for the initial lysate volume.  Initial lysate volumes were one of the following: 650 mcL/400 mcL/300 mcL/100 mcL.  Lysates were stored at -80degC.  65 mcL/40 mcL/30 mcL/10mcL NaOAc pH 4.0 was added to each defrosted sample, followed by 650 mcL/400 mcL/300 mcL/100 mcL H20-saturated phenols.  130 mcL/80 mcL/60 mcL/20 mcL of chloroform:isoamyl alcohol was added to each sample.  Samples were mixed via inversion then incubated on ice for 15 minutes.  After this incubation, samples were centrifuged at 20817g for 15 minutes at room temperature.  The top phase of each sample was removed carefully, so as not to disturb the cloudy interphase layer, and deposited in a fresh nuclease-free tube.  In order to precipitate the RNA, the following were added to each sample: 65 mcL/40 mcL/30 mcL/10 mcL NaOAc, 5 mcL linear acrylamide (Ambion), and 650 mcL/400 mcL/300 mcL/100 mcL isopropanol.   After the first round of RNA purification, all samples were stored at -80degC.  Prior to starting the second round of purifications, the samples were first defrosted on ice, and then centrifuged at 20817g for 30 minutes at room temperature.  The isopropanol was carefully aspirated, and the remaining pellet was resuspended in sample lysis buffer (RNAqueous Mini kit, Ambion).  During this step, the provided silica-based filter cartridges were assembled in microfuge tubes.  Following dissolution of the pellet, 400mcL of 64% ethanol was added.  Mixing was achieved through pipeting 2-3 times.  The resulting mixture was immediately applied to the previously prepared filter cartridges.  After centrifugation at 13000g for 1 minute, the flow-through was discarded.  Subsequently, each cartridge was washed once with 700mcL of Wash Solution #1 and twice with 500 mcL of Wash Solution #2.  Cartridges were spun for 1 minute in the absence of wash solution in order to remove any residual ethanol.  Purified RNA was eluted into a fresh nuclease free tube with nuclease-free H20 preheated to 75degC.  RNA integrity was assessed by examining 5mcL of each sample by gel electrophoresis. RNA was quantified using Ribogreen reagent (Molecular Probes).  Experimental samples were diluted 1:10 or 1:20, as needed to avoid signal saturation, prior to quantification.  RNA dilutions for standard curve generation were freshly prepared from the manufacturer supplied stock.  Each sample was prepared for measurement as follows: 2 mcL diluted experimental sample + 98 mcL nuclease-free TE + 100 mcL of freshly diluted Ribogreen reagent.  All measurements were conducted in 96 well format.  All embryonic samples were linearly amplified.; Protocol Type = Extract preparation; Performer: Nesanet,,Mitiku
embryo samples; Outbred timed pregnant Swiss Webster mice were used for all experiments. Mice were sacrificed by cervical dislocation and uteri removed by caesarian section.  Uteri were washed in PBS and then transferred into Petri dishes containing fresh cold PBS.  Individual decidua were removed from each uterus and then transferred to fresh PBS with 10% Fetal Bovine Serum (FBS).  Embryos were dissected out of their implantation decidual tissue with fine watchmakers forceps under a light microscope.  Embryonic stage was determined by coupling gestational age to morphologic landmarks. After staging, embryos were either transferred into solution D (see sample extraction).; Protocol Type = Amplification; Performer: Nesanet,,Mitiku

tag: EXP


title: E8.75_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59857.gif
Developmental Stage: E8.75

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 7240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku 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 = 30.32; Parameter Scan Time = 18:15:57; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 24240; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.00; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: Microfollicular adenoma , sample 68

description: gene expression data from thyroid tissue diagnosed as Microfollicular adenoma

source_name: Homo sapiens thyroid, Microfollicular adenoma

value: 54 years

tag: Nodule type

tag: Vesicle type

tag: Connective tissue type

tag: Filter ID


title: Microfollicular adenoma , sample 61

value: 53 years

value: Polymorphic


title: XTC.UC1 cell line , sample 74

tag: Gender:

tag: Age:

tag: Thyroïditis:

tag: Nodule type:


title: Graves’s disease, sample 57

description: gene expression data from thyroid tissue diagnosed as Graves’s disease

source_name: Homo sapiens thyroid, Graves’s disease

value: male

value: 55 years

value: no

tag: Nucleus type:

tag: Vesicle type:


title: Microfollicular adenoma , sample 67

tag: Gender

tag: Age

tag: Metastasis

value: Follicular


title: XTC.UC1 cell line , sample 75

tag: Metastasis:

tag: Connective tissue type:


title: Multinodular goiter, sample 69

value: female

value: 42 years

tag: Thyroïditis

tag: Nucleus type

value: Multiple

value: Macrofollicular


title: Macrofollicular adenoma, sample 64

description: gene expression data from thyroid tissue diagnosed as Macrofollicular adenoma

source_name: Homo sapiens thyroid, Macrofollicular adenoma

value: 30 years

tag: Nodule type

value: Normal


title: Multinodular goiter, sample 63

value: 62 years

tag: Vesicle type


title: Atypical follicular adenoma, sample 59

value: 39 years

value: Anisonucleosis

value: Begining

value: Microfollicular

tag: Connective tissue type


title: Microfollicular adenoma , sample 73

value: 56 years

value: Alone

tag: Filter ID


title: Multinodular goiter, sample 62

value: 54 years


title: Graves’s disease, sample 56

value: 55 years

value: yes


title: Autoimmune thyroiditis, sample 60

description: gene expression data from thyroid tissue diagnosed as Autoimmune thyroiditis

source_name: Homo sapiens thyroid, Autoimmune thyroiditis

value: 40 years

value: Follicular


title: MegaViroP10-037

tag: Amplified RNA from nasal lavage of outpatient cold specimen


title: Macrofollicular adenoma, sample 55

value: male

value: 46 years

value: no


title: Autoimmune thyroiditis, sample 58

value: female


title: E7.75_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/59855.gif
Developmental Stage: E7.75

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 7000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku 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 = 29.96; Parameter Scan Time = 17:54:57; Parameter PMT Volts = 540; Parameter Scan Date = 2004-06-03; Parameter Pixel Size = 10; Parameter Laser on time = 24213; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.72; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku

tag: REF

tag: EXP


title: Macrofollicular adenoma, sample 54

value: 63 years

value: Polymorphic

value: Normal


title: Microfollicular adenoma , sample 52

value: 57 years


title: Graves’s disease, sample 51

tag: Nodule type:


title: Multinodular goiter, sample 53

value: 68 years

value: Anisonucleosis

value: Multiple

value: Macrofollicular


title: Graves’s disease, sample 45

value: 78 years

tag: Nucleus type:


title: Macrofollicular adenoma, sample 42

value: 62 years

value: Trabecular


title: Macrofollicular adenoma, sample 48

value: 73 years

value: yes

value: Alone


title: Macrofollicular adenoma, sample 49

value: male

value: 38 years

value: Follicular


title: Macrofollicular adenoma, sample 43

value: female

value: 56 years

value: no


title: Multinodular goiter, sample 40

value: Normal


title: Microfollicular adenoma , sample 44

value: 69 years

value: Microfollicular


title: Microfollicular adenoma , sample 35

value: 91 years

value: Polymorphic


title: Multinodular goiter, sample 33

value: 39 years

value: Multiple

value: Macrofollicular


title: Macrofollicular adenoma, sample 39

value: 52 years


title: Multinodular goiter, sample 32

value: 58 years


title: Multinodular goiter, sample 31

value: 71 years

value: yes


title: Multinodular goiter, sample 37

value: 45 years

value: medium


title: Macrofollicular adenoma, sample 30

value: male

value: 59 years

value: Follicular

value: Alone


title: Macrofollicular adenoma, sample 36

value: female

value: 60 years

value: no

value: Begining

value: Normal


title: Macrofollicular adenoma, sample 34

value: 56 years


title: Multinodular goiter, sample 46

value: 48 years

value: Macrofollicular


title: Macrofollicular adenoma, sample 29

value: 49 years

value: Trabecular


title: Microfollicular adenoma , sample 38

value: 87 years

value: Microfollicular


title: Macrofollicular adenoma, sample 26

value: 55 years


title: Macrofollicular adenoma, sample 28

value: 69 years

value: Multiple


title: Macrofollicular adenoma, sample 27

value: 30 years

value: Follicular


title: Microfollicular adenoma , sample 25

value: female

value: 70 years


title: Multinodular goiter, sample 24

value: 54 years

value: yes

value: no

value: Anisonucleosis


title: Macrofollicular adenoma, sample 41

value: male

value: 61 years

value: Begining

value: Normal


title: Multinodular goiter, sample 23

value: 68 years

value: Macrofollicular


title: Wild type, sample 17

value: 37 years

value: Microfollicular


title: Wild type, sample 18

value: 64 years


title: Macrofollicular adenoma, sample 19

value: Multiple

value: Polymorphic


title: Macrofollicular adenoma, sample 21

value: female

value: 51 years

value: medium

value: Follicular


title: Macrofollicular adenoma, sample 50

value: 34 years

value: no

value: Alone


title: Multinodular goiter, sample 22

value: 59 years


title: Oncocytic carcinoma, sample 13

description: gene expression data from thyroid tissue diagnosed as Oncocytic carcinoma

source_name: Homo sapiens thyroid, Oncocytic carcinoma

value: 57 years

tag: Vesicle type:

value: Trabecular


title: Oncocytic adenoma, sample 10

tag: Gender

value: male

value: 44 years

value: Begining

value: Normal


title: Wild type, sample 9

tag: Age

value: 45 years

value: Microfollicular


title: Wild type, sample 14

value: 69 years


title: Oncocytic adenoma, sample 12

value: female

value: 54 years

value: Multiple

value: Macrofollicular


title: Atypical follicular adenoma, sample 16

value: Papillary


title: Atypical follicular adenoma, sample 15

value: 58 years

value: yes

value: Follicular


title: Wild type, sample 11

value: 28 years

value: no


title: Oncocytic adenoma, sample 7

value: 64 years


title: Follicular carcinoma, sample 6

description: gene expression data from thyroid tissue diagnosed as Follicular carcinoma

source_name: Homo sapiens thyroid, Follicular carcinoma

value: Alone


title: Atypical follicular adenoma, sample 4

value: 78 years

value: Begining

value: Trabecular


title: Wild type, sample 5

value: Microfollicular

value: Normal


title: Wild type, sample 8

value: female

value: 57 years


title: Atypical follicular adenoma, sample 3

value: 77 years

value: Multiple

value: Polymorphic


title: Oncocytic adenoma, sample 189

value: male

value: 65 years


title: Macrofollicular adenoma, sample 20

value: 54 years

tag: Metastasis

value: Follicular

value: Macrofollicular


title: Atypical follicular adenoma, sample 188

value: 37 years

value: no

tag: Metastasis:

value: Papillary


title: XTC.UC1 cell line , sample 190

tag: Gender:

tag: Age:

tag: Thyroïditis:

tag: Connective tissue type:


title: Atypical oncocytic adenoma, sample 186

description: gene expression data from thyroid tissue diagnosed as Atypical oncocytic adenoma

source_name: Homo sapiens thyroid, Atypical oncocytic adenoma

value: 73 years

tag: Thyroïditis

value: yes

tag: Nucleus type

tag: Nodule type

tag: Vesicle type


title: Atypical follicular adenoma, sample 1

value: 39 years

value: Alone

value: Microfollicular

tag: Connective tissue type

value: Trabecular

tag: Filter ID


title: Macrofollicular adenoma, sample 47

value: 51 years

value: Begining

value: Normal


title: Wild type, sample 185

value: female

value: 52 years


title: Microfollicular adenoma , sample 180

value: 31 years

value: medium


title: Atypical follicular adenoma, sample 184

value: 69 years

value: Follicular


title: Atypical oncocytic adenoma, sample 2

value: Multiple

value: Macrofollicular


title: Atypical oncocytic adenoma, sample 183

value: no


title: Wild type, sample 187

value: yes


title: Multinodular goiter, sample 181

value: male

value: 56 years


title: Microfollicular adenoma , sample 182

value: 59 years

value: Alone

value: Polymorphic


title: Autoimmune thyroiditis, sample 175

value: 48 years

value: Microfollicular


title: Microfollicular adenoma , sample 176

value: female

value: 55 years

value: Normal


title: Papillary carcinoma, sample 177

description: gene expression data from thyroid tissue diagnosed as Papillary carcinoma

source_name: Homo sapiens thyroid, Papillary carcinoma

value: 34 years

value: Papillary


title: Microfollicular adenoma , sample 170

value: 73 years

value: Follicular

value: Trabecular


title: Oncocytic adenoma, sample 174

value: 64 years

value: medium

value: Anisonucleosis


title: Macrofollicular adenoma, sample 179

value: 58 years

value: no

value: Macrofollicular


title: Multinodular goiter, sample 178

value: 43 years

value: Multiple


title: Atypical oncocytic adenoma, sample 171

value: male

value: 50 years

value: Alone

value: Polymorphic


title: Papillary carcinoma, sample 173

value: female

value: 34 years

value: Normal


title: Macrofollicular adenoma, sample 168

value: 63 years

value: yes

value: Follicular


title: Microfollicular adenoma , sample 172

value: Microfollicular


title: Graves’s disease, sample 169

value: 30 years

tag: Nodule type:


title: Wild type, sample 166

value: 39 years


title: Macrofollicular adenoma, sample 167

value: 70 years

value: no

value: Begining


title: Oncocytic adenoma, sample 162

value: 74 years

value: Multiple

value: Macrofollicular


title: Multinodular goiter, sample 163

value: 72 years


title: Papillary carcinoma, sample 158

value: 35 years

value: Papillary

value: Alone


title: Oncocytic adenoma, sample 160

value: female

value: 75 years

value: medium

value: Polymorphic

value: Normal


title: Autoimmune thyroiditis, sample 164

value: 52 years

value: yes

value: Follicular


title: Wild type, sample 161

value: Microfollicular


title: Wild type, sample 151

value: 62 years


title: Autoimmune thyroiditis, sample 156

value: 34 years


title: Macrofollicular adenoma, sample 149

value: 24 years

value: no


title: Microfollicular adenoma , sample 154

value: 76 years

value: Anisonucleosis


title: Atypical oncocytic adenoma, sample 153

value: 48 years

value: Trabecular


title: Wild type, sample 165

value: female

value: 45 years


title: Papillary carcinoma, sample 152

value: 19 years

value: Papillary

value: Alone


title: Papillary carcinoma, sample 157

value: 35 years

value: Normal


title: Wild type, sample 155

value: yes

value: Follicular


title: Oncocytic adenoma, sample 148

value: 62 years

value: Multiple

value: Macrofollicular


title: Wild type, sample 159

value: no

value: Microfollicular


title: Macrofollicular adenoma, sample 147

value: 36 years


title: Papillary carcinoma, sample 140

value: male


title: Wild type, sample 144

value: 60 years


title: Multinodular goiter, sample 145

value: female

value: Anisonucleosis


title: Papillary carcinoma, sample 146

value: 64 years


title: Papillary carcinoma, sample 141

value: 25 years

value: Papillary


title: Wild type, sample 139


title: Wild type, sample 142

value: 43 years


title: Microfollicular adenoma , sample 191

value: 54 years

value: Alone

value: Trabecular


title: Multinodular goiter, sample 137

value: 40 years

value: Follicular

value: Normal


title: Multinodular goiter, sample 138

value: no

value: Multiple

value: Macrofollicular


title: Follicular carcinoma, sample 135

value: male

value: yes


title: Oncocytic carcinoma, sample 129

value: female

value: 45 years

value: Microfollicular


title: Wild type, sample 132

value: 74 years


title: Oncocytic adenoma, sample 133

value: 80 years


title: Oncocytic adenoma, sample 126

value: 55 years

value: medium


title: Multinodular goiter, sample 131


title: Wild type, sample 136

value: 36 years


title: Wild type, sample 127


title: Oncocytic carcinoma, sample 122

value: Alone

value: Trabecular


title: Oncocytic adenoma, sample 134

value: 84 years

value: Follicular

value: Polymorphic


title: Oncocytic adenoma, sample 110

value: 42 years

value: no

value: Normal


title: Oncocytic adenoma, sample 112

value: 40 years


title: Oncocytic adenoma, sample 111

value: male

value: 68 years


title: Papillary carcinoma, sample 124

value: female

value: 51 years

value: yes

value: Papillary

value: Multiple

value: Microfollicular


title: Oncocytic adenoma, sample 125

value: 69 years


title: Oncocytic adenoma, sample 109

value: 58 years


title: Papillary carcinoma, sample 113

value: 55 years


title: Oncocytic adenoma, sample 114

value: 64 years

value: Follicular

value: Macrofollicular


title: Oncocytic adenoma, sample 120

value: 49 years

value: no


title: Oncocytic adenoma, sample 117

value: medium

value: Alone

value: Trabecular


title: Oncocytic adenoma, sample 115

value: female

value: Normal


title: Oncocytic adenoma, sample 121

value: 48 years


title: Follicular carcinoma, sample 130

value: male

value: 43 years

value: yes


title: Microfollicular adenoma , sample 128

value: 28 years

value: Microfollicular


title: Oncocytic adenoma, sample 108

value: 52 years

value: Multiple


title: Oncocytic adenoma, sample 106

value: 68 years

value: Follicular

value: Polymorphic


title: Oncocytic adenoma, sample 107

value: 64 years

value: no


title: Papillary carcinoma, sample 104

value: 37 years

value: Papillary

value: Alone


title: Oncocytic adenoma, sample 102

value: female

value: Unique

value: Normal


title: Oncocytic carcinoma, sample 101

value: male

value: 69 years

value: Trabecular


title: Oncocytic adenoma, sample 100

value: 46 years

value: Microfollicular


title: Multinodular goiter, sample 143

value: 39 years

value: Multiple

value: Macrofollicular


title: Papillary carcinoma, sample 98

value: 23 years

value: yes


title: HrcA regulon, 10403S vs delta hrcA, stationary phase

status: Public on Nov 03 2007

city: Ithaca

first: Sarita

last: Raengpradub

state: NY

address: 412 Stocking Hall

department: Food Science

institute: Cornell University

description: Expression profiles were measured from three independent RNA extractions, resulting in six replicate spots per gene (array contains duplicate spots).

hyb_protocol: Microarray slide blocking was performed prior to hybridization. Slides were incubated for 10 min in a solution containing methyl pyrrilidone, succinic anhydride and sodium borate, and then washed in fresh methyl pyrrilidone for 10 min. Successive 1-min washes in nanopure water (once), 0.1% SDS (3 times), nanopure water (5 times), and 95% EtOH (once). The slides were dried by centrifugation and immersed for 1 h in blocking solution (0.1% BSA, 5X SSC, 0.1% SDS) at 42°C. After blocking, the slides were washed for 1 min each in nanopure water (5 times) and 95% EtOH (2 times) and then dried by centrifugation. For the strains to be compared, labeled cDNAs were combined and dried, then resuspended in 50μl of hybridization buffer (5X SSC, 0.1% SDS, 0.1mM dithiothreitol (DTT), 0.5X formamide, 0.06 μg/μl salmon sperm DNA in DEPC-treated water), denatured at 95°C for 5 min then applied to the slides using mSeries LifterSlips™ (Erie Scientific). Following overnight hybridization at 42°C, the slides were washed in 2X SSC+0.1% SDS (5 min at 42˚C), with subsequent 5-min washes at room temperature in 2X SSC+0.1% SDS, 2X SSC, and 0.2X SSC, followed by final rinse in nanopure water. Slides were dried by centrifugation.

scan_protocol: Images were scanned using a GenePix 4000B scanner (Molecular Devices Corp.). Raw TIFF images were automatically gridded and analyzed using GenePix Pro 6.0 software.

data_processing: Analyses of microarray data were performed in R with Bioconductor using LIMMA software (Smyth, 2005). Background correction was performed using the “normexp” method. For normalization within arrays, the data were weighted for the genomic DNA controls and normalized using print-tip loess method (Smyth & Speed, 2003). The data were then scale normalized between arrays. The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis.

label: Alexa Fluor 635

organism: Listeria monocytogenes

source_name: Listeria monocytogenes 10403S

label_protocol: cDNA was synthesized from 10 μg purified total RNA (using random primers) and labeled with Alexa Fluor dyes using the SuperScript Plus Indirect cDNA Labeling System.

growth_protocol: For all experiments, Listeria monocytogenes 10403S was grown in BHI broth at 37°C with shaking (250 rpm), followed by inoculation into 5 ml of BHI broth (1:100 dilution) and growth at 37°C with shaking to an OD600=0.4, then diluted again (1:100) into BHI broth and incubated at 37 °C with shaking until stationary phase, defined as OD600=1.0+3 hrs, then harvested for RNA isolation.

extract_protocol: RNA was isolated from frozen bacterial pellets with the Qiagen RNeasy Midi kit according to the manufacturer’s protocol for enzymatic and mechanical disruption, except that cells treated with lysozyme followed by sonication on ice for three 30 s bursts at 18–21 W (30 s pauses between bursts). RQ1 DNase treatment of total RNA in the presence of RNasin Plus RNA inhibitor (Promega) was performed according to the manufacturer’s protocol, followed by subsequent phenol:chloroform and chloroform extractions. RNA was ethanol-precipitated overnight, centrifuged and washed with 70% ethanol before resuspenson of the final RNA pellet in DEPC-treated water. Total nucleic acid concentration and purity were estimated using absorbance readings (260/280 nm, 260/230 nm) on a NanoDrop ND-1000 spectrophotometer. RNA integrity was checked by agarose gel electrophoresis.

tag: Listeria monocytogenes 10403S grown at 37°C to stationary phase (OD600=1.0+3 hrs).

label: Alexa Fluor 532

growth_protocol: For all experiments, Listeria monocytogenes FSL B2-101 (hrcA null mutant) was grown in BHI broth at 37°C with shaking (250 rpm), followed by inoculation into 5 ml of BHI broth (1:100 dilution) and growth at 37°C with shaking to an OD600=0.4, then diluted again (1:100) into BHI broth and incubated at 37 °C with shaking until stationary phase, defined as OD600=1.0+3 hrs, then harvested for RNA isolation.

tag: Listeria monocytogenes FSL B2-101 (hrcA null mutant) grown at 37°C to stationary phase (OD600=1.0+3 hrs).


title: W3110 lsrK mutants, biological rep1

status: Public on Nov 02 2007

city: Bethesda

first: Jun

last: Li

state: MD

address: Rm 173, Building 14 A

institute: NIH

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Escherichia coli

source_name: W3110 lsrK mutants

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

growth_protocol: E. coli grow in LB rich medium to OD600=2.4

extract_protocol: RNA samples were extracted via Invitrogen RNAeasy Kit and treated with DNaseI to remove all DNA

treatment_protocol: Cells treated with bacterial protect reagent and freeze at -70 C

tag: Genotype

value: E. coli K12


title: E6.75_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51114.gif
Developmental Stage: E6.75

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.36; Parameter Scan Time = 17:06:10; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 22917; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 3.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku

tag: REF

tag: EXP


title: E7.25_rep2

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/51116.gif
Developmental Stage: E7.25

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nesanet,,Mitiku 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 = 31.88; Parameter Scan Time = 17:39:39; Parameter PMT Volts = 540; Parameter Scan Date = 2004-02-07; Parameter Pixel Size = 10; Parameter Laser on time = 22950; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [82695]; Parameter Laser Power = 2.94; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nesanet,,Mitiku Mouse Early Embryonic Timecourse- - > scanning parameters; All arrays were scanned using a single Axon 4000B scanner.  The power settings for scanning were optimized to generate a 1:1 ratio of overall Cy3 to Cy5 signal for self-self hybridization experiments using our common reference.  Once optimal PMT settings were determined (Cy5 channel = 660; Cy3 channel = 540), they were kept constant for all arrays in this dataset.; Protocol Type = Scanning parameters; Performer: Nesanet,,Mitiku


title: Papillary carcinoma, sample 97

tag: Gender

tag: Age

value: 67 years

value: no

tag: Metastasis