title: 673 Barrett's(L)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54589.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 5640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 39.22; Parameter Scan Time = 13:53:02; Parameter PMT Volts = 570; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 173593; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 39.22; Parameter Scan Time = 13:53:02; Parameter PMT Volts = 680; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 538397; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.96; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 673 Duodenum

status: Public on Oct 18 2006

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54512.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 39.16; Parameter Scan Time = 13:35:46; Parameter PMT Volts = 560; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 173576; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 39.16; Parameter Scan Time = 13:35:46; Parameter PMT Volts = 830; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 538380; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao

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: ref

label_protocol: not provided

extract_protocol: not provided

tag: ref


title: MCF7_DamID_SUV39H1V5EcoDam(Cy3)-EcoDam(Cy5)_HO44-51_SeriesE

status: Public on Oct 17 2006

type: genomic

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: Please see www.nki.nl/nkidep/vansteensel for detailed protocols.

scan_protocol: Arrays were scanned using a Agilent Technologies Scanner, Model: G2505B and ChipScan software. Image analyses were done using Imagene 6.0 software (BioDiscvovery)

data_processing: Data was normalized using R-packages limma 2.0.8 and vsn 1.6.3. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized between different arrays (method=vsn). Column VALUE contains the normalized log2 ratios (Dam/Dam) for each individual array.

molecule: genomic DNA

label_protocol: For detailed protocols go to www.nki.nl/nkidep/vansteensel.

growth_protocol: MCF7 cells were maintained in DMEM medium supplemented with 10% FCS and antibiotics.

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this experiment, MCF7 cells were transfected with Dam or Dam-fusion protein expressing constructs.  Cells were selected with G418 for stable integration of the constructs. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays.
For detailed protocols please go to www.nki.nl/nkidep/vansteensel.

tag: MCF7 human breast carcinoma cells expressing EcoDam protein.

tag: MCF7 human breast carcinoma cells expressing SUV39H1-V5-EcoDam fusion protein.


title: MCF7_DamID_EcoDam(Cy3)-EcoDam(Cy5)_suv_HO44-37_SeriesB

description: this is a control experiment where we hybridized amplified methylated DNA from cells expressing Dam protein.

extract_protocol: For detailed protocols go to www.nki.nl/nkidep/vansteensel.

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this control experiment, MCF7 cells were transfected with Dam protein expressing constructs.  Cells were selected with G418 for stable integration of the constructs. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays.
For detailed protocols please go to www.nki.nl/nkidep/vansteensel.


title: 675 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54480.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1680, 6520; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 34.87; Parameter Scan Time = 12:45:42; Parameter PMT Volts = 600; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 179669; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 34.87; Parameter Scan Time = 12:45:42; Parameter PMT Volts = 600; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 544473; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.57; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: MCF7_DamID_EcoDam(Cy3)-EcoDam(Cy5)_cbx_HO44-37_SeriesB

description: this is a control experiment where we hybridized amplified methylated DNA from cells expressing Dam alone.

data_processing: Data was normalized using R-packages limma 2.0.8 and vsn 1.6.3. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized between different arrays (method=vsn).


title: 681Barrett's (S)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54503.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 39.24; Parameter Scan Time = 12:17:34; Parameter PMT Volts = 550; Parameter Scan Date = 2004-07-23; Parameter Pixel Size = 10; Parameter Laser on time = 177702; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 39.24; Parameter Scan Time = 12:17:34; Parameter PMT Volts = 640; Parameter Scan Date = 2004-07-23; Parameter Pixel Size = 10; Parameter Laser on time = 542506; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: MCF7_DamID_SUV39H1V5EcoDam(Cy5)-EcoDam(Cy3)_HO44-39_SeriesB


title: 680 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54478.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 7000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.04; Parameter Scan Time = 14:38:13; Parameter PMT Volts = 570; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 179782; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.04; Parameter Scan Time = 14:38:13; Parameter PMT Volts = 600; Parameter Scan Date = 2004-08-03; Parameter Pixel Size = 10; Parameter Laser on time = 544586; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.66; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: MCF7_DamID_SUV39H1V5EcoDam(Cy5)-EcoDam(Cy3)_HO44-47_SeriesD


title: MCF7_DamID_EcoDam(Cy3)-EcoDam(Cy5)_suv_HO44-43_SeriesD


title: 668 Normal

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54492.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 39.66; Parameter Scan Time = 14:04:09; Parameter PMT Volts = 600; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 178886; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 39.66; Parameter Scan Time = 14:04:09; Parameter PMT Volts = 630; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 543690; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.02; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: MCF7_DamID_EcoDam(Cy3)-EcoDam(Cy5)_suv_HO44-36_SeriesC


title: MCF7_DamID_SUV39H1V5EcoDam(Cy3)-EcoDam(Cy5)_HO44-33_SeriesC


title: MCF7_DamID_EcoDam(Cy3)-EcoDam(Cy5)_cbx_HO44-54_SeriesE


title: MCF7_DamID_EcoDam(Cy3)-EcoDam(Cy5)_suv_HO44-54_SeriesE


title: 680 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54479.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5640; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 39.42; Parameter Scan Time = 14:17:34; Parameter PMT Volts = 510; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 173615; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 39.42; Parameter Scan Time = 14:17:34; Parameter PMT Volts = 910; Parameter Scan Date = 2004-07-07; Parameter Pixel Size = 10; Parameter Laser on time = 538419; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 680 AdenoCa

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54477.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 39.13; Parameter Scan Time = 10:22:19; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-02; Parameter Pixel Size = 10; Parameter Laser on time = 172818; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 39.13; Parameter Scan Time = 10:22:19; Parameter PMT Volts = 800; Parameter Scan Date = 2004-07-02; Parameter Pixel Size = 10; Parameter Laser on time = 537622; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: MCF7_DamID_CBX1V5EcoDam(Cy5)-EcoDam(Cy3)_HO44-44_SeriesD

data_processing: Data was normalized using R-packages limma 2.0.8 and vsn 1.6.3. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized between different arrays (method=�vsn�).

tag: MCF7 human breast carcinoma cells expressing CBX1-V5-EcoDam fusion protein.


title: MCF7_DamID_CBX1V5EcoDam(Cy3)-EcoDam(Cy5)_HO44-42_SeriesC

tag: MCF7 human breast carcinoma cells expressing CBX1-V5-EcoDam fusion protein


title: MCF7_DamID_CBX5V5T4Dam(Cy3)-T4Dam(Cy5)_H265-26

data_processing: Data was normalized using R-package limma 2.0.8. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized within arrays (method=loess). Column VALUE contains the normalized log2 ratios (CBX-Dam/Dam).

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this experiment, MCF7 cells were transiently transfected with T4Dam or T4Dam-fusion protein expressing constructs. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays. For detailed protocols, please go to www.nki.nl/nkidep/vansteensel.

tag: MCF7 human breast carcinoma cells expressing T4Dam protein.

tag: MCF7 human breast carcinoma cells expressing CBX5-V5-T4Dam fusion protein.


title: MCF7_DamID_CBX1V5EcoDam(Cy3)-EcoDam(Cy5)_HO44-50_SeriesE


title: MCF7_DamID_CBX5V5T4Dam(Cy5)-T4Dam(Cy3)_H265-24


title: MCF7_DamID_EcoDam(Cy3)-EcoDam(Cy5)_cbx_HO44-36_SeriesC


title: MCF7_DamID_EcoDamCBX1(Cy5)-EcoDam(Cy3)_H208-33

data_processing: Data was normalized using R-package limma 2.0.8. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized within arrays (method=loess). Column VALUE contains the averaged normalized log2 ratios (CBX-Dam/Dam).

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this experiment, MCF7 cells were transiently transfected with EcoDam or EcoDam-fusion protein expressing constructs. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays. For detailed protocols, please go to www.nki.nl/nkidep/vansteensel.

tag: MCF7 human breast carcinoma cells expressing EcoDamCBX1 fusion protein.


title: MCF7_DamID_EcoDamCBX1 (Cy3)-EcoDam(Cy5)_H208-34


title: NIH3T3 cells heavy fraction serum stressed_4

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

organism: Mus musculus

source_name: NIH3T3 polyA


title: 668 Duodenum

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54493.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 39.74; Parameter Scan Time = 14:29:07; Parameter PMT Volts = 610; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 178911; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.12; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 39.74; Parameter Scan Time = 14:29:07; Parameter PMT Volts = 530; Parameter Scan Date = 2004-07-29; Parameter Pixel Size = 10; Parameter Laser on time = 543715; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 4E cells heavy fraction basal_3

description: 4E cells heavy fraction basal

source_name: 4E cells heavy fraction basal


title: 669 Barrett's(S)

description:
Simple annotation: Diseased tissue, Amplification and Labeling
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54497.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Ying,,Hao 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 = 39.12; Parameter Scan Time = 11:24:20; Parameter PMT Volts = 620; Parameter Scan Date = 2004-07-27; Parameter Pixel Size = 10; Parameter Laser on time = 178221; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao 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 = 39.12; Parameter Scan Time = 11:24:20; Parameter PMT Volts = 610; Parameter Scan Date = 2004-07-27; Parameter Pixel Size = 10; Parameter Laser on time = 543024; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.95; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Ying,,Hao


title: 4E cells heavy fraction basal_2

description: 4E cells heavy fraction basal


title: MCF7_DamID_CBX3V5T4Dam(Cy5)-T4Dam(Cy3)_H265-25

tag: MCF7 human breast carcinoma cells expressing CBX3-V5-T4Dam fusion protein.


title: 4E cells light fraction basal_3

description: 4E cells light fraction basal

source_name: 4E cells light fraction basal


title: NIH3T3 cells light fraction basal_4

description: NIH3T3 cells light fraction basal

source_name: NIH3T3 cells light fraction basal


title: 4E cells light fraction basal_4

description: 4E cells light fraction basal


title: 4E cells heavy fraction basal_4

description: 4E cells heavy fraction basal


title: NIH3T3 cells light fraction basal_3

description: NIH3T3 cells light fraction basal


title: MEF_DamID_EcoDamV5CBX1(Cy3)-EcoDam(Cy5)_MO55-102

data_processing: Data was normalized using R-packages limma 2.0.8 and vsn 1.6.3. DamID data were normalized between different arrays (method=vsn). Column VALUE contains the normalized log2 ratios (EcoDamV5CBX1/EcoDam).

source_name: MEFs

treatment_protocol:
In short, DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA.
In this experiment, MEFs cells were infected with lentiviral construct expressing Dam or Dam-fusion protein. Subsequently, the methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to microarrays.
For detailed protocols please go to www.nki.nl/nkidep/vansteensel.

tag: MEFs mouse INK4a-/- embryonal fibroblasts expressing EcoDam protein.

tag: MEFs mouse INK4a-/- embryonal fibroblasts expressing EcoDam-V5-CBX1 fusion protein.


title: 4E cells heavy fraction basal_1

description: 4E cells heavy fraction basal


title: NIH3T3 cells light fraction serum stressed_4


title: NIH3T3 cells heavy fraction serum stressed_3


title: NIH3T3 cells light fraction serum stressed_1


title: MEF_DamID_EcoDamV5CBX1(Cy5)-EcoDam(Cy3)_MO55-104


title: MEF_DamID_EcoDamV5CBX1(Cy3)-EcoDam(Cy5)_MO55-101


title: 4E cells light fraction serum stressed_4

description: 4E cells light fraction serum stressed

source_name: 4E cells light fraction serum stressed


title: 4E cells light fraction basal_1

description: 4E cells light fraction basal


title: 4E cells light fraction serum stressed_3

description: 4E cells light fraction serum stressed


title: NIH3T3 cells light fraction serum stressed_2


title: 4E cells light fraction basal_2

description: 4E cells light fraction basal


title: NIH3T3 cells light fraction serum stressed_3


title: NIH3T3 cells heavy fraction serum stressed_2


title: NIH3T3 cells heavy fraction basal_3

description: NIH3T3 cells heavy fraction basal

source_name: NIH3T3 cells heavy fraction basal


title: NIH3T3 cells heavy fraction basal_4

description: NIH3T3 cells heavy fraction basal


title: NIH3T3 cells heavy fraction serum stressed_1


title: NIH3T3 cells heavy fraction basal_2

description: NIH3T3 cells heavy fraction basal


title: 4E cells heavy fraction serum stressed_1

description: 4E cells heavy fraction stressed

source_name: 4E cells heavy fraction serum stressed


title: NIH3T3 cells light fraction basal_2

description: NIH3T3 cells light fraction basal


title: NIH3T3 cells light fraction basal_1

description: NIH3T3 cells light fraction basal


title: 4E cells light fraction serum stressed_2

description: 4E cells light fraction stressed


title: 4E cells heavy fraction serum stressed_3

description: 4E cells heavy fraction stressed


title: NIH3T3 cells heavy fraction basal_1

description: NIH3T3 cells heavy fraction basal


title: 4E cells heavy fraction serum stressed_2

description: 4E cells heavy fraction stressed


title: siFBP1_Set B - 2nd array - mAdbID:74111

city: Bethesda

first: David

last: Levens

state: MD

address: 10 Center Drive

department: NCI/CCR

institute: NIH

description: mAdb experiment ID: 74111

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

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

source_name: Set B_control siRNA

label_protocol: Cy3 Sample Labeling Protocol - generic

extract_protocol:
Sample Extraction Protocol
Extraction method: Trizol

treatment_protocol:
Treatment type: compound
Agent: Stealth negative control siRNA
Treatment dose: 50 nM
Treatment time: 2 days

tag: Cell type

value: primary skin fibroblast (Hs68)

source_name: Set B_siFBP1

label_protocol: Cy5 Sample Labeling Protocol - generic

treatment_protocol:
Treatment type: compound
Agent: Stealth siRNA targeting FBP1
Treatment dose: 50 nM
Treatment time: 2 days


title: MCF7_DamID_CBX1V5T4Dam(Cy5)-T4Dam(Cy3)_H208-29

data_processing: Data was normalized using R-package limma 2.0.8. Raw data files were loaded in R and the weight of control spots and poor quality spot was set to zero, to exclude them from the results. We did not apply a background correction to the data. DamID data were normalized within arrays (method=�loess�). Column �VALUE� contains the normalized log2 ratios (CBX1-Dam/Dam).

tag: MCF7 human breast carcinoma cells expressing CBX1-V5-T4Dam fusion protein.


title: 4E cells heavy fraction serum stressed_4

description: 4E cells heavy fraction stressed


title: siFBP3_Set B - 2nd array - mAdbID:74113

description: mAdb experiment ID: 74113

source_name: Set B_siFBP3

treatment_protocol:
Treatment type: compound
Agent: Stealth siRNA targeting FBP3
Treatment dose: 50 nM
Treatment time: 2 days


title: siFBP2_Set B - 2nd array - mAdbID:74112

description: mAdb experiment ID: 74112

source_name: Set B_siFBP2

treatment_protocol:
Treatment type: compound
Agent: Stealth siRNA targeting FBP2
Treatment dose: 50 nM
Treatment time: 2 days


title: siFBP3_Set A - 1st array - mAdbID:73262

description: mAdb experiment ID: 73262

source_name: Set A_control siRNA

source_name: Set A_siFBP3


title: 4E cells light fraction serum stressed_1

description: 4E cells light fraction stressed


title: NK1.1 minus TGFbeta RII KO T cells T_KO

city: Seattle

first: Jeffrey

last: Rasmussen

state: WA

department: Immunology

institute: University of Washington

description: RNA isolation and gene array analysis was performed with mouse 430 2.0 Affymetrix DNA microarrays as described elsewhere (Fontenot et al., 2005).

data_processing: GCRMA v 1.1.3, default settings

label: Biotin

source_name: NK1.1 minus TGFbeta RII KO T cells

tag: NK1.1 minus TGFbeta RII KO CD8+ T cells from Tgfbr2fl/fl x CD4-Cre (KO) mice


title: NK1.1 minus control T cells T_WT

source_name: NK1.1 minus control T cells

tag: NK1.1 minus control CD8+ T cells from littermate control Tgfbr2fl/WT x CD4-Cre mice


title: siFBP1_Set A - 1st array - mAdbID:73261

description: mAdb experiment ID: 73261

source_name: Set A_siFBP1


title: NK1.1 plus TGFbeta RII KO T cells KO_NKT

source_name: Source name

tag: NK1.1 plus TGFbeta RII KO CD8+ T cells from Tgfbr2fl/fl x CD4-Cre (KO) mice


title: MCF7_Self-Self_ExpressionProfile_HO87-H6

description: Self-Self Expression profile. Both channels contain amplified RNA isolated from MCF7 cells.

hyb_protocol: Detailed protocols for RNA isolation, amplification, labeling, and hybridization can be found at http://microarrays.nki.nl/download/protocols.html.

data_processing: Data was background corrected and normalized using a LOWESS fit per subarray, Column VALUE contains the normalized log2 expression ratios for each individual array.

tag: MCF7 human breast carcinoma cells


title: siFBP2_Set A - 1st array - mAdbID:73427

description: mAdb experiment ID: 73427

source_name: Set A_siFBP2


title: MCF7_Self-Self_ExpressionProfile_HO87-H7

label_protocol: Detailed protocols for RNA isolation, amplification, labeling, and hybridization can be found at http://microarrays.nki.nl/download/protocols.html.


title: MCF7_Self-Self_ExpressionProfile_HO87-H8

extract_protocol: Detailed protocols for RNA isolation, amplification, labeling, and hybridization can be found at http://microarrays.nki.nl/download/protocols.html.


title: mixed_adult_vs_brood_rep2

status: Public on Oct 14 2006

city: Lausanne

first: John

last: Wang

address: Batiment Biophore

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description: Grids and features were first aligned using the GenePix spot finder. Then we visually inspected the array to flag bad spots.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing: printTipLoess normalization (marray, Bioconductor)

organism: Solenopsis invicta

source_name: adult

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA was labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

tag: Mixed adult (males, queens and workers) from both monogynous and polygynous colony social forms.

source_name: brood

tag: Mixed brood (males, queens and workers) from both monogynous and polygynous colony social forms.


title: Anther tetrads rep1

city: Adelaide

first: Jason

middle: Alan

last: Able

state: SA

address: Waite Main Building

department: School of Agriculture, Food & Wine

country: Australia

institute: The University of Adelaide

description:
Our understanding of the mechanisms that govern the cellular process of
meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChip® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350
transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation,recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to
known sequences in NCBI and TIGR databases. This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat.

hyb_protocol: Crismani W, Baumann U, Sutton T, Shirley N, Webster T, Spangenberg G, Langridge P, Able JA (2006) 'Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat', BMC Genomics (in press)

data_processing: RMA normalized (not log scaled)

organism: Triticum aestivum

source_name: whole wheat anther, tetrads

growth_protocol: Wild-type wheat was grown in a temperature-controlled glass house at 23 degrees Celsius (day) and 15 degrees Celsius (night) with a 14 hour photoperiod.

tag: Cultivar

value: Chinese Spring

tag: Tissue

value: Anther

tag: Stage

value: Tetrads


title: mixed_brood_vs_adult_rep1


title: Anther maturea nthers rep1

scan_protocol: Crismani W, Baumann U, Sutton T, Shirley N, Webster T, Spangenberg G, Langridge P, Able JA (2006) 'Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat', BMC Genomics (in press)

source_name: whole wheat anther, mature anthers

value: Mature anthers


title: mixed_brood_vs_adult_rep3


title: Anther tetrads rep3

label_protocol: Crismani W, Baumann U, Sutton T, Shirley N, Webster T, Spangenberg G, Langridge P, Able JA (2006) 'Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat', BMC Genomics (in press)


title: Anther immature pollen rep2

source_name: whole wheat anther, immature pollen

extract_protocol: Crismani W, Baumann U, Sutton T, Shirley N, Webster T, Spangenberg G, Langridge P, Able JA (2006) 'Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat', BMC Genomics (in press)

value: Immature pollen


title: Anther immature pollen rep3


title: Anther mature anthers rep3


title: Anther mature anthers rep2


title: Anther diplotene-anaphaseI rep1

source_name: whole wheat anther, diplotene-anaphaseI

value: Diplotene-AnaphaseI


title: Anther tetrads rep2


title: Anther telophaseI-telophaseII rep3

source_name: whole wheat anther, telophaseI-telophaseII

value: TelophaseI-TelophaseII


title: Anther immature pollen rep1


title: Anther diplotene-anaphaseI rep3


title: Anther telophaseI-telophaseII rep1


title: Anther leptotene-pachytene rep3

source_name: whole wheat anther, leptotene-pachytene

value: Leptotene-Pachytene


title: Anther telophaseI-telophaseII rep2


title: MCF7_Self-Self_ExpressionProfile_HO087-H5


title: Anther diplotene-anaphaseI rep2


title: Anther leptotene-pachytene rep2


title: Anther pre-meiosis rep3

source_name: whole wheat anther, pre-meiosis

value: Pre-meiosis


title: healthy control C4

status: Public on Oct 13 2006

city: Gothenburg

first: Mikael

last: Benson

address: Smorslottsgatan

department: Paediatrics

institute: Queen Silvia Children's Hospital

description: Gene expression data from skin biopsy from healthy control.

hyb_protocol: According to the instructions from Affymetrix.

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.

source_name: Skinbiopsy from healthy controls

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: RNA extracted from frozen biopsy

tag: Atopic eczema


title: A549DCA: DCA treated lung carcinoma cells

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
Characteristics: Organ: Lung
		   disease : Carcinoma
		   Morphology: epithelial
		   Age: 58 years old
		   Sex: Male
		    Ethnicity : Caucasian

source_name: DCA treated Cultured Lung carcinoma cells

growth_protocol: The A549 cells were maintained on F12K medium, Media was supplemented with 10% FBS and 5% PSF (Gibco) as antibiotic. Cultures were incubated for up to 48h prior to harvesting.

extract_protocol: Total RNA from A549 cells was extracted using Quiagen RNeasy kit (Ontario, Canada).

treatment_protocol: 48 h with dichloroacetate 0.5 mM (Sigma, St Louis)

tag: 'Organ

value: Lung',

tag: 'disease

value: Carcinoma',

tag: 'Morphology

value: epithelial',

tag: 'Age

value: 58 years old',

tag: 'Sex

value: Male',

tag: 'Ethnicity

value: Caucasian'


title: mixed_adult_vs_brood_rep4


title: Anther leptotene-pachytene rep1


title: healthy control C10


title: healthy control C7


title: healthy control C8


title: healthy control C6


title: Anther pre-meiosis rep2


title: healthy control C9


title: healthy control C3


title: healthy control C2


title: Anther pre-meiosis rep1

value: Pre-Meiosis


title: M059K: control glioblastoma cells

description:
Characteristics: Organ: Brain
		   disease : malignant glioblastoma; glioma
		   Morphology: fibroblast
		   Age: 33 years old
		   Sex: Male

source_name: malignant brain glioblastoma; glioma

growth_protocol: The M059K cells glioblastoma were maintained on DMEM/F12, (Gibco/Invitrogen, Ontario), Media was supplemented with 10% FBS and 5% PSF (Gibco) as antibiotic. Cultures were incubated for up to 48h prior to harvesting.

extract_protocol: Total RNA from M059K cells was extracted using Quiagen RNeasy kit (Ontario, Canada).

treatment_protocol: no treatment

value: Brain',

value: malignant glioblastoma; glioma',

value: fibroblast'.

value: 33 years old',

value: Male'


title: atopic eczema P6

source_name: Skinbiopsy from patient with atopic eczema

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


title: atopic eczema P8


title: atopic eczema P7


title: healthy control C1


title: atopic eczema P10


title: healthy control C5


title: atopic eczema P9


title: atopic eczema P3


title: atopic eczema P1

label: /biotin

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


title: atopic eczema P4


title: atopic eczema P2

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


title: D11-canine 3 weeks Pacing induced heart failure

city: Valhalla

first: Caroline

last: Ojaimi

state: NY

institute: New York Medical College

description: hearts are removed after 3 weeks of pacing induced heart failure in dogs.

data_processing: MAS 5.0

organism: Canis lupus familiaris

source_name: Cardiac Tissues

tag: Male dogs weighing 23-27 kg; tissue

value: total cardiac cells;


title: atopic eczema P5


title: D10-canine 3 weeks Pacing induced heart failure


title: D12-canine 3 weeks Pacing induced heart failure


title: D9-canine 3 weeks Pacing induced heart failure

source_name: Cardia Tissues


title: D4-canine 4 weeks Pacing induced heart failure

description: heart samples are removed after 4 weeks of pacing induced heart failure in dogs

source_name: Cardiac tissue


title: Testicular biopsy with Johnsen Score 5 #10

city: 20246 Hamburg

first: Andrej-Nikolai

last: Spiess

address: Martinistr. 52

department: Andrology

country: Germany

institute: University Hospital Hamburg-Eppendorf

description: Testicular sandwich biopsy from a patient with pre/meiotic arrest, categorized by Johnsen scoring

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 37C according to Codelink protocol 080075-00 Rev. AA

scan_protocol: Arrays were scanned on an Affymetrix 428 Array Scanner at PMT gain 70

data_processing: The data were analyzed with the Codelink expression software v4.1

label_protocol: Biotinylated cRNA were prepared according to Codelink protocol 080074-00 Rev. AA

extract_protocol: RNAPure (Biozym) extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was post-purified with RNeasy columns (Qiagen).

treatment_protocol: post-surgically immersed in RNALater (Ambion)

tag: Testicular biopsy with Johnsen Score 5 (pre/meiotic arrest)


title: Testicular biopsy with Johnsen Score 5 #9


title: D2-canine 4 weeks Pacing induced heart failure

source_name: cardiac tisuue


title: Testicular biopsy with Johnsen Score 5 #6


title: Testicular biopsy with Johnsen Score 8 #7

description: Testicular sandwich biopsy from a patient with severe hypospermatogenesis, categorized by Johnsen scoring

tag: Testicular biopsy with Johnsen Score 8 (severe hypospermatogenesis)


title: Testicular biopsy with Johnsen Score 5 #11


title: Testicular biopsy with Johnsen Score 5 #7


title: D1-canine 4 weeks Pacing induced heart failure


title: S. cerevisiae dbr1delta, biological rep1

status: Public on Oct 16 2006

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

description: Gene expression data from log phase BY4743 yeast cells

data_processing: Data was processed using Affymetrix Tiling Array Software.  Data was quantile normalized, and log2 signals from each probe were reported.

label: Double-stranded cDNA was created using the Affymetrix WT Double-Stranded cDNA Synthesis Kit, and cDNA probes were labeled using the Affymetrix WT Double-Stranded DNA Terminal Labeling Kit.

organism: Saccharomyces cerevisiae

source_name: Log phase yeast culture

label_protocol: Samples were labeled according to the manufacturer's instructions.

growth_protocol: Yeast were grown in a shaking flask to log phase in YPD at 30 C

extract_protocol: Total RNA was harvested using phenol extraction, treated with DNase and purified using a Qiagne RNeasy kit.

treatment_protocol: Log phase yeast cultures harvested by centrifugation

tag: Diploid yeast strain; Genotype MATa/MATalpha his3?delta1/his3delta1 leu2delta0/leu2?delta0 lys2delta0/+ met15delta0/+ ura3delta0/ura3delta0 dbr1


title: Testicular biopsy with Johnsen Score 6 #2

description: Testicular sandwich biopsy from a patient with meiotic arrest, categorized by Johnsen scoring

tag: Testicular biopsy with Johnsen Score 6 (meiotic arrest)


title: Testicular biopsy with Johnsen Score 10 #13

description: Testicular sandwich biopsy from a patient with full spermatogenesis, categorized by Johnsen scoring

tag: Testicular biopsy with Johnsen Score 10 (full spermatogenesis)


title: Testicular biopsy with Johnsen Score 5 #8


title: Testicular biopsy with Johnsen Score 7 #3

tag: Testicular biopsy with Johnsen Score 7 (severe hypospermatogenesis)


title: Testicular biopsy with Johnsen Score 2 #8

description: Testicular sandwich biopsy from a patient with SCOS, categorized by Johnsen scoring

tag: Testicular biopsy with Johnsen Score 2 (Sertoli-Cell-Only syndrome)


title: D3-canine 4 weeks Pacing induced heart failure


title: Testicular biopsy with Johnsen Score 2 #10


title: Testicular biopsy with Johnsen Score 2 #7


title: Testicular biopsy with Johnsen Score 2 #11


title: Testicular biopsy with Johnsen Score 9 #5

description: Testicular sandwich biopsy from a patient with weak hypospermatogenesis, categorized by Johnsen scoring

tag: Testicular biopsy with Johnsen Score 9 (weak hypospermatogenesis)


title: S. cerevisiae dbr1delta, biological rep2


title: S. cerevisiae BY4743, biological rep2

tag: Diploid yeast strain BY4743; Genotype MATa/MATalpha his3?delta1/his3delta1 leu2delta0/leu2?delta0 lys2delta0/+ met15delta0/+ ura3delta0/ura3delta0


title: Testicular biopsy with Johnsen Score 2 #9


title: S. cerevisiae BY4743, biological rep3


title: S. cerevisiae BY4743, biological rep1


title: N-AKPZF-II, NORM, M, PRF

status: Public on Oct 12 2006

city: Kiel

first: Paul-Martin

last: Holterhus

address: Campus Kiel, Schwanenweg 20

department: Pädiatrische Endokrinologie und Diabetologie

institute: Universitätsklinikum Schleswig-Holstein

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18335.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: prostate fibroblast
Culture Synchrony: Go-arrest due to confluency

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

source_name: mixed reference (FR + CRG)

tag: mixed reference (FR + CRG)

source_name: AKPZF, peripheral prostate fibroblasts, 14 days DMEM F12, 12.9% FCS, G0


title: N-56, NORM, M, GSF, 1 x 100nM DHT, 24h

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16662.gif; format: GIF
Compound Based Treatment: 1 x 100nM DHT
Cell Line: foreskin fibroblast
Culture Synchrony: proliferation

source_name: nGSF56, proliferating, 24h 100nM DHT

tag: nGSF56, proliferating, 24h 100nM DHT


title: N-40, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17595.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF40, 14 days DMEM F12, 12.9% FCS, G0

tag: nGSF40, 14 days DMEM F12, 12.9% FCS, G0


title: N-33, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18090.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF33, 14 days DMEM F12, 12.9% FCS, G0

tag: nGSF33, 14 days DMEM F12, 12.9% FCS, G0


title: N-56, NORM, M, GSF, 6 x 100nM DHT, 14d

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15582.gif; format: GIF
Compound Based Treatment: 6 x 100nM DHT
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: mixed reference

tag: mixed reference

source_name: nGSF56, 14 days DMEM F12 12.9% D/S  FCS + 6 x 100nM DHT


title: N-33, NORM, M, GSF, 6 x 100nM DHT, 14d

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15719.gif; format: GIF
Compound Based Treatment: 6 x 100nM DHT
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: mixed reference (CRG + FR)

tag: mixed reference (CRG + FR)

source_name: nGSF33, G0, 6 x 100nM DHT, 14 days

tag: nGSF33, G0, 6 x 100nM DHT, 14 days


title: S. cerevisiae dbr1delta, biological rep3


title: LNCaP, 24h 1000nM DHT/MR

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17023.gif; format: GIF
Compound Based Treatment: 1000nM DHT
Cell Line: LNCaP
Culture Synchrony: proliferation

source_name: LNCaP, 24h 1000nM DHT

tag: LNCaP, 24h 1000nM DHT


title: N-56, NORM, M, GSF, 1 x ETOH, 24h

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16657.gif; format: GIF
Compound Based Treatment: 1 x ethanol
Cell Line: foreskin fibroblast
Culture Synchrony: proliferation

source_name: nGSF56, proliferating, 24h ETOH

tag: nGSF56, proliferating, 24h ETOH


title: LNCaP, 24h ETOH/MR-b

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18362.gif; format: GIF
Compound Based Treatment: ethaonl
Cell Line: LNCaP
Culture Synchrony: proliferation

source_name: LNCaP, 24h ETOH, against mixed reference


title: N-AKPZF-I, NORM, M, PRF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-07/18022.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: prostate fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: AKPZF (prostate fibroblasts) 14 days DMEM F12, 12.9% FCS, Go


title: N-56, NORM, M, GSF, 1 x 1000nM DHT, 24h

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16686.gif; format: GIF
Compound Based Treatment: 1 x 1000nM DHT
Cell Line: foreskin fibroblast
Culture Synchrony: proliferation

source_name: nGSF56, proliferating cells, 24h 1000nM DHT


title: N-58, NORM, M, GSF, 1 x ETOH, 24h

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16890.gif; format: GIF
Compound Based Treatment: 1 x ethanol
Cell Line: foreskin fibroblast
Culture Synchrony: proliferation

source_name: nGSF58, proliferating cells, 24h ETOH

tag: nGSF58, proliferating cells, 24h ETOH


title: N-58, NORM, M, GSF, 6 x ETOH, 14d

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17292.gif; format: GIF
Compound Based Treatment: 6 x ETOH
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF58, G0, 6 x ETOH, 14 days

tag: nGSF58, G0, 6 x ETOH, 14 days


title: N-52, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16278.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF52, 14 days DMEM F12, 12.9% FCS, Go, against mixed reference (CRG + FR)


title: N-58, NORM, M, GSF, 6 x 100nM DHT, 14d

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17307.gif; format: GIF
Compound Based Treatment: 6 x 100nM DHT
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: mixed reference (FR + CRG)

source_name: nGSF58, G0, 6 x 100nM DHT, 14 days

tag: nGSF58, G0, 6 x 100nM DHT, 14 days


title: N-56, NORM, M, GSF, 6 x ETOH, 14d

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15581.gif; format: GIF
Compound Based Treatment: 6 x ethanol
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF56, 14 days DMEM F12 12.9% D/S FCS + 6 x ETOH


title: N-58, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16247.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF58, 14 days DMEM F12, 12.9% FCS, G0, against mixed reference


title: N-60, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17604.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF60, 14 days DMEM F12, 12.9% FCS, G0

tag: nGSF60, 14 days DMEM F12, 12.9% FCS, G0


title: N-56, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/16271.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF56, 14 days DMEM F12, 12.9% FCS, Go, against mixed reference


title: M059KDCA: DCA treated glioblastoma cells.

description:
Characteristics: Organ: Brain
		   disease : malignant glioblastoma; glioma
		   Morphology: fibroblast
		   Age: 33 years old
		   Sex: Male

source_name: malignant brain glioblastoma; glioma

treatment_protocol: 48 h with Dichloroacetate (0.5 mM, Sigma, St Louis)

tag: 'Organ

tag: 'disease

tag: 'Morphology

value: fibroblast',

tag: 'Age

tag: 'Sex


title: LNCaP, 24h ETOH/MR

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16903.gif; format: GIF
Compound Based Treatment: ethanol
Cell Line: LNCaP
Culture Synchrony: proliferation

source_name: mixed reference (CRG + FR)

source_name: LNCaP, 24h ETOH

tag: LNCaP, 24h ETOH


title: Spn_D39LillyvsD39NCTC_BHI_rep3

status: Public on Oct 10 2006

city: Bloomington

first: Krystyna

middle: M

last: Kazmierczak

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate, dye swap

hyb_protocol: Performed as per microarray manufacturer's recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf).  Fluorescently-labeled cDNAs were resuspended in the manufacturer's salt-based hybridization buffer.  Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide.  Slides were hybridized at 42C overnight (~18 hrs).  Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635 nm.  Slides were scanned at gain settings which balanced the signal acquired in both channels (pixel ratio ~ 1.0).  Images were analyzed using GenePix Pro 5.0 software (Molecular Devices).

data_processing: Data were normalized with GeneTraffic 3.2 software (Iobion Informatics) using the Lowess (subgrid) method without background subtraction.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae bacterial strain D39 (Lilly)

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer's recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf)

growth_protocol: Bacterial strains were grown statically in brain heart infusion media (Bacto BHI, Becton Dickinson) at 37C and an atmosphere of 5% CO2 overnight.  Overnight cultures which displayed no lysis were adjusted to an OD620 of ~0.1, diluted a further 50-fold into BHI and grown at 37C and an atmosphere of 5% CO2.  Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

extract_protocol: Total RNA was extracted from exponentially growing cultures (OD620~0.1) using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification using the RNAeasy mini kit (Qiagen) as described in Robertson et al, J. Bact (2002) 184:3508-3520.

tag: S. pneumoniae D39 (Lilly) (strain IU1680), virulent, type 2 capsule

source_name: S. pneumoniae bacterial strain D39 (NCTC)

tag: S. pneumoniae D39 (NCTC) (strain IU1690), virulent, type 2 capsule


title: Spn_R6vsD39NCTC_BHI_rep1

description: Independent biological replicate

hyb_protocol: Performed as per microarray manufacturer’s recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf).  Fluorescently-labeled cDNAs were resuspended in the manufacturer’s salt-based hybridization buffer.  Samples were heated for 3 min at 95C, then chilled on ice for 3 min before application to the microarray slide.  Slides were hybridized at 42C overnight (~18 hrs).  Slides were washed sequentially for 5 min in the following buffers pre-warmed to 30C: Buffer 1, 2X SSC, 0.1% SDS; Buffer 2, 1X SSC; Buffer 3, 0.1X SSC.

source_name: S. pneumoniae bacterial strain R6

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer’s recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf)

growth_protocol: Bacteria strains were grown statically in brain heart infusion media (Bacto BHI, Becton Dickinson) at 37C and an atmosphere of 5% CO2 overnight.  Overnight cultures which displayed no lysis were adjusted to an OD620 of ~0.1, diluted a further 50-fold into BHI and grown at 37C and an atmosphere of 5% CO2.  Growth was monitored by change in OD620 (13mm cuvette) as measured in a Spectronic 20 spectrophotometer.

tag: S. pneumoniae R6 (strain EL59), avirulent unencapsulated derivative of S. pneumoniae D39


title: Spn_D39LillyvsD39NCTC_BHI_rep2

description: Independent biological replicate


title: Spn_R6vsD39NCTC_BHI_rep2


title: A549: control lung carcinoma

description:
Characteristics: Organ: Lung
		   disease : Carcinoma
		   Morphology: epithelial
		   Age: 58 years old
		   Sex: Male
		    Ethnicity : Caucasian

source_name: cultured epithelial lung carcinoma cells

treatment_protocol: No treatment

tag: Male, Caucasian, 58 years old


title: Spn_R6vsD39NCTC_BHI_rep3

description: Independent biological replicate


title: N-58, NORM, M, GSF, 1 x 100nM DHT, 24h

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16891.gif; format: GIF
Compound Based Treatment: 1 x 100nM DHT
Cell Line: foreskin fibroblast
Culture Synchrony: proliferation

tag: mixed reference (FR + CRG)

source_name: nGSF58, 24h 100nM DHT

tag: nGSF58, 24h 100nM DHT


title: LN24r1,0.1

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15176.gif; format: GIF

source_name: ethanol control

tag: ethanol control


title: GM15510 chromosome 22-wide analysis by high-resolution comparative genome hybridization

city: New Haven

first: Jan

middle: Oliver

last: Korbel

state: CT

address: 266 Whitney Avenue

institute: Yale University

data_processing: Qspline algorithm

source_name: Human lymphoblasts

tag: Human lymphoblasts

source_name: PROMEGA pool (Homo sapiens)

tag: PROMEGA pool of genomic DNA


title: LNCaP, 24h 100nM DHT/MR

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16990.gif; format: GIF
Compound Based Treatment: 100nM DHT
Cell Line: LNCaP
Culture Synchrony: proliferation

source_name: mixed reference (CRG+ FR)

tag: mixed reference (CRG+ FR)

source_name: LNCaP, 24h 100nM DHT

tag: LNCaP, 24h 100nM DHT


title: 93-171F chromosome 22-wide analysis by high-resolution comparative genome hybridization


title: N-33, NORM, M, GSF, 6 x ETOH, 14d

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15601.gif; format: GIF
Compound Based Treatment: 6 x ethanol
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

tag: mixed reference (CRG + FR)

source_name: nGSF33, G0, 6 x ETOH, 14 days

tag: nGSF33, G0, 6 x ETOH, 14 days


title: N-58, NORM, M, GSF, 1 x 1000nM DHT, 24h

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16893.gif; format: GIF
Compound Based Treatment: 1 x 1000nM DHT
Cell Line: foreskin fibroblast
Culture Synchrony: proliferation

source_name: mixed reference (FR + CRG)

source_name: nGSF58, 24h 1000nM DHT

tag: nGSF58, 24h 1000nM DHT


title: LN24r1,0.001

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14563.gif; format: GIF
Compound Based Treatment: 0.001nM R1881, 24h

source_name: ethanol  control

tag: ethanol  control


title: LN24DHT100

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14520.gif; format: GIF

source_name: 100 nM DHT 24 hrs

tag: 100 nM DHT 24 hrs


title: N-59, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17501.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: mixed reference (CRG + FR)

source_name: nGSF59, 14 days DMEM F12, 12.9% FCS, G0

tag: nGSF59, 14 days DMEM F12, 12.9% FCS, G0


title: N-62, NORM, M, GSF

description:
Simple annotation: Development, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-06/17506.gif; format: GIF
Compound Based Treatment: no treatment
Cell Line: foreskin fibroblast
Culture Synchrony: Go-arrest due to confluency

source_name: nGSF62, DMEM F12, 12.9% FCS, 14 days, G0


title: LN24r1,0.01

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14625.gif; format: GIF
Compound Based Treatment: 0.01nM R1881, 24h


title: LNCaP, 1000nM DHT, 24h

description:
Simple annotation: Development, development
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14622.gif; format: GIF

source_name: LNCaP, 24h ETOH

tag: LNCaP, 24h ETOH

source_name: LNCaP, 24h 1000nM DHT

tag: LNCaP, 24h 1000nM DHT


title: Spn_D39LillyvsD39NCTC_BHI_rep1

description: Independent biological replicate

source_name: S. pneumoniae bacterial strain D39 (Lilly)

tag: S. pneumoniae D39 (Lilly) (strain IU1680), virulent, type 2 capsule

source_name: S. pneumoniae bacterial strain D39 (NCTC)

tag: S. pneumoniae D39 (NCTC) (strain IU1690), virulent, type 2 capsule


title: Digestive gland gene expression profiling from Site 2 native mussels of the Venice lagoon area (A)

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description:
Frozen digestive gland (DG) tissues, from Site 2 native mussels in the Venice lagoon area (close to the industrial district of Marghera) and control mussels (located offshore), were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = digestive gland
Keywords = Venice lagoon
Keywords = chemical pollution
Keywords = native mussels
Keywords = transcriptional profiling

organism: Mytilus galloprovincialis

source_name: digestive gland from control mussels (offshore) – Reference

source_name: digestive gland from Site 2 native mussels in the Venice lagoon


title: Digestive gland gene expression profiling from Site 3 native mussels of the Venice lagoon area (B)

description:
Frozen digestive gland (DG) tissues, from Site 3 native mussels in the Venice lagoon area (close to the Lido lagoon outlet) and control mussels (located offshore), were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = digestive gland
Keywords = Venice lagoon
Keywords = chemical pollution
Keywords = native mussels
Keywords = transcriptional profiling

source_name: digestive gland from Site 3 native mussels in the Venice lagoon


title: Digestive gland gene expression profiling from mussels treated with organic compounds (B)

description:
Frozen digestive gland (DG) tissues, from mussels treated with organic compaunds (benzo[a]pyrene, 1-nitro/amino-pyrene, fluoranthene, TCDD) and control mussels, were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = digestive gland
Keywords = organic compaunds
Keywords = transcriptional profiling

source_name: digestive gland from control mussels (non treated) – Reference

source_name: digestive gland from mussels treated with organic compounds


title: Digestive gland gene expression profiling from mussels treated with heavy metals (B)

description:
Frozen digestive gland (DG) tissues, from mussels treated with heavy metals (cadmium, cupper, mercury) and control mussels, were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = digestive gland
Keywords = heavy metals
Keywords = transcriptional profiling

source_name: digestive gland from mussels treated with heavy metals


title: LN24r1,1

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15186.gif; format: GIF

source_name: ethanol treated

tag: ethanol treated


title: Digestive gland gene expression profiling from mussels treated with heavy metals (A)

description:
Frozen digestive gland (DG) tissues, from mussels treated with haeavy metals (cadmium, cupper, mercury) and control mussels, were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = digestive gland
Keywords = heavy metals
Keywords = transcriptional profiling

source_name: Digestive gland from control mussels (non treated) – Reference

source_name: Digestive gland gills from mussels treated with heavy metals


title: Digestive gland gene expression profiling from Site 2 native mussels of the Venice lagoon area (B)


title: Digestive gland gene expression profiling from Site 3 native mussels of the Venice lagoon area (A)


title: Digestive gland gene expression profiling from mussels treated with organic compounds (A)


title: Digestive gland gene expression profiling from Site 1 native mussels in the Venice lagoon area (A)

description:
Frozen digestive gland (DG) tissues, from Site 1 native mussels in the Venice lagoon area (close to the industrial district of Marghera) and control mussels (located offshore), were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = digestive gland
Keywords = Venice lagoon
Keywords = chemical pollution
Keywords = native mussels
Keywords = transcriptional profiling

source_name: digestive gland from Site 1 native mussels in the Venice lagoon


title: Foot/adductor muscles/ligaments gene expression profiling from mussels in normal conditions (B)

description:
Frozen gills (G), digestive gland (DG), foot/adductor muscles/ligaments (FML) and gonads/mantle (GM) tissues were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = foot/adductor muscles/ligaments
Keywords = normal conditions
Keywords = transcriptional profiling

source_name: pool of 4 different mussel tissues (G, DG, FML and GM) in equal quantity - Reference

source_name: foot/adductor muscles/ligaments from mussels


title: LN24r1,10nM

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15235.gif; format: GIF

source_name: ethanol

tag: ethanol


title: Gonads/mantle gene expression profiling from mussels in normal conditions (B)

description:
Frozen gills (G), digestive gland (DG), foot/adductor muscles/ligaments (FML) and gonads/mantle (GM) tissues were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = gonads/mantle
Keywords = normal conditions
Keywords = transcriptional profiling

source_name: Gonads/mantle from mussels


title: Gonads/mantle gene expression profiling from mussels in normal conditions (A)

source_name: gonads/mantle from mussels


title: Left temple fibroblasts (S63.1 i), serum starved

description:
Simple annotation: tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48248.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1000, 5720; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 03:01:48; Parameter PMT Volts = 570; Parameter Scan Date = 2003-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 138301; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 03:01:48; Parameter PMT Volts = 760; Parameter Scan Date = 2003-12-11; Parameter Pixel Size = 10; Parameter Laser on time = 357271; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.88; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: Stratagene UR

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

tag: Stratagene UR

source_name: S63.1 i (left temple fibroblasts) mRNA, serum starved

label_protocol: Brown Lab : human mRNA labeling del; Preparation of Fluorescent DNA Probe from HUMAN mRNA or Total RNA using Direct Incorporation  (Max Diehn/Ash Alizadeh  protocol; 3/15/01)  http://cmgm.stanford.edu/pbrown/protocols/4_human_RNA.html  Includes  I. Preparing fluoresenctly labeled cDNA (probe) II. Washing Arrays  for deletion; Protocol Type = Labeling; Performer: Julie,,Sneddon

growth_protocol: Fibroblast_serum_starvation; Fibroblasts were cultured in DMEM, 10% FBS, glutamine, penicillin-streptomycin at 5% C02 and 37 C.  48 hours before mRNA harvest, cells were subjected to serum starvation by changing medium to DMEM, 0.1% FBS, glutamine, penicillin-streptomycin.; Protocol Type = Growth Conditions; Performer: Julie,,Sneddon

extract_protocol:
fibroblast_from_tissue; Fibroblast cells were isolated from discarded human tissue.  Fat was removed using sterile scalpel and forceps; tissue was minced into ca. 1 mm cubes.  Incubation in a 6-well dish without medium at 37 0C for 10 minutes allowed for adhesion of the tissue to the plate.  Fresh media containing DMEM, 10% FBS, and penicillin-streptomycin was added, and samples were maintained at 37 0C and 5% CO2.  Media was replaced every 2 days.  Outgrowth of spindle-shaped cells was typically apparent after 5-15 days in culture.  When the cells were near confluence, they were subcultured with 0.25% trypsin-EDTA.  Cultures were expanded until sufficient for RNA isolations (typically 4 passages).; Protocol Type = Biological Sample; Performer: Julie,,Sneddon
FastTrack; mRNA was isolated using the FastTrack kit from Invitrogen, according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Julie,,Sneddon


title: Foot/adductor muscles/ligaments gene expression profiling from mussels in normal conditions (A)


title: BCC-2 fibroblasts, serum starved

description:
Simple annotation: tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52928.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 5760; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon 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 = 39.37; Parameter Scan Time = 15:03:38; Parameter PMT Volts = 550; Parameter Scan Date = 2004-05-18; Parameter Pixel Size = 10; Parameter Laser on time = 166201; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon 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 = 39.37; Parameter Scan Time = 15:03:38; Parameter PMT Volts = 590; Parameter Scan Date = 2004-05-18; Parameter Pixel Size = 10; Parameter Laser on time = 531104; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.20; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: BCC-2 mRNA, serum starved

tag: BCC-2 mRNA, serum starved


title: Right scalp fibroblasts (A14.1), serum starved

description:
Simple annotation: tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47261.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.15; Parameter Scan Time = 13:32:55; Parameter PMT Volts = 660; Parameter Scan Date = 2003-12-02; Parameter Pixel Size = 10; Parameter Laser on time = 139720; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.15; Parameter Scan Time = 13:32:55; Parameter PMT Volts = 710; Parameter Scan Date = 2003-12-02; Parameter Pixel Size = 10; Parameter Laser on time = 504785; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: A14.1 (right scalp fibroblasts) mRNA, serum starved


title: LN24DHT1000

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14516.gif; format: GIF

source_name: ethanol control

tag: ethanol control

source_name: 1000 nM DHT

tag: 1000 nM DHT


title: Right preauric skin fibroblasts (S55.1), serum starved

description:
Simple annotation: tumor, Fibroblasts
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47262.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 520, 5480; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Julie,,Sneddon Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 13:51:09; Parameter PMT Volts = 670; Parameter Scan Date = 2003-12-02; Parameter Pixel Size = 10; Parameter Laser on time = 139739; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.36; Parameter Scan Time = 13:51:09; Parameter PMT Volts = 690; Parameter Scan Date = 2003-12-02; Parameter Pixel Size = 10; Parameter Laser on time = 504804; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Julie,,Sneddon

source_name: S55.1 (right preauric skin) mRNA, serum starved


title: Digestive gland gene expression profiling from mussels in normal conditions (B)

description:
Frozen gills (G), digestive gland (DG), foot/adductor muscles/ligaments (FML) and gonads/mantle (GM) tissues were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = Digestive gland
Keywords = normal conditions
Keywords = transcriptional profiling

source_name: digestive gland from mussels


title: Digestive gland gene expression profiling from Site 1 native mussels of the Venice lagoon area (B)

source_name: digestive gland from control mussels (offshore) – Reference


title: Digestive gland gene expression profiling from mussels in normal conditions (A)

description:
Frozen gills (G), digestive gland (DG), foot/adductor muscles/ligaments (FML) and gonads/mantle (GM) tissues were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = digestive gland
Keywords = normal conditions
Keywords = transcriptional profiling


title: Gills gene expression profiling from mussels in normal conditions (B)

description:
Frozen gills (G), digestive gland (DG), foot/adductor muscles/ligaments (FML) and gonads/mantle (GM) tissues were dispersed separately into TRizol solution (Invitrogen, Carlsbad, CA, USA), and homogenized with an Diax 900 blender (Heidolph, Kelheim, Germany). Total RNA (15 µg), extracted following the manufacturer instructions, was reverse transcribed with SuperScript II (Invitrogen) and oligo-dT(18) as the primer, in the presence of either Cy3-dCTP or Cy5-dCTP (Amersham Biosciences, Uppsala, Sweden). Competitive hybridizations were carried out in a dual slide chamber (HybChamber, GeneMachines, San Carlos, CA, USA). Pellets of purified, labeled cDNAs were dissolved in hybridization buffer (Northern max, Ambion), applied on the MytArray 1.0, and covered with a 22×22 mm glass coverslip. After an overnight hybridization at 42°C, slides were washed sequentially for 4 min in buffer A (1X SSC/0.2% SDS) at 42°C, for 4 min buffer B (0.1X SSC/0.2% SDS) at room temperature and finally in 0.1X SSC for 2 min at room temperature. Digital images were generated in a GSI Lumonics LITE dual confocal laser scanner (ScanArray Microarray Analysis Software) and processed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada). Normalized data were determined using the publicly available software MIDAS (TIGR Microarray Data Analysis System: http://www.tigr.org/softlab/). Normalized values (lowess normalization) were calculated for each spot, and converted in logarithmic scale. Final values correspond to log(2) ratio of the normalized intensities.
Keywords = gills
Keywords = normal conditions
Keywords = transcriptional profiling

source_name: of 4 different mussel tissues (G, DG, FML and GM) in equal quantity - Reference

source_name: gills from mussels


title: Human Trachea Tissue

status: Public on Oct 07 2006

city: Berkeley

first: Jonathan

middle: L

last: Bingham

address: 733 Allston Way

institute: Jivan Biologics, Inc

description: Human Trachea Tissue

hyb_protocol: Following fragmentation, 5 microg of cRNA were hybridized for 16 hr at 42C

data_processing: Raw data from Mergen

source_name: Human trachea tissue

label_protocol: Cy3-labeled cRNA were prepared from total RNA using Mergen protocol

tag: Adult male, single-patient, purchased from Ambion


title: Human Thyroid Tissue

description: Human Thyroid Tissue

source_name: Human thyroid tissue


title: Human Control Pool Tissue

description: Human Control Pool Tissue

source_name: Human pooled tissue from multiple tissues

tag: Adult male, multiple patients, purchased from Ambion


title: Human Thymus Tissue

description: Human Thymus Tissue

source_name: Human thymus tissue


title: Human Stomach Tissue

description: Human Stomach Tissue

source_name: Human stomach tissue


title: Human Spleen Tissue

description: Human Spleen Tissue

source_name: Human spleen tissue


title: Human Vena Cava Tissue

description: Human Vena Cava Tissue

source_name: Human vena cava tissue


title: Human Testicle Tissue

description: Human Testicle Tissue

source_name: Human testicle tissue


title: Human Small Intestine Tissue

description: Human Small Intestine Tissue

source_name: Human small intestine tissue