title: 372S3-3-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61499.gif
Individual: 372
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 35410; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-22; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 520; Parameter Laser on time = 63462; Parameter Laser Power = 3.60; Parameter Scan Time = 11:19:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.51; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-22; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 63173; Parameter Laser Power = 3.71; Parameter Scan Time = 11:19:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.51; Performer: Nina,,Salama

source_name: 500 ng 372S3-3-1, Disease State: Duodenal Ulcer


title: 510S3-3-1

status: Public on Sep 25 2009

type: genomic

city: Seattle

first: Nina

middle: Reda

last: Salama

state: WA

address: 1100 Fairview Ave. N

department: Division of Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61500.gif
Individual: 510
Disease State: Gastric Cancer
Replicate: 3

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1960, 8480; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 63587; Parameter Laser Power = 3.47; Parameter Scan Time = 10:45:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.21; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 520; Parameter Scan Power = 100; Parameter Laser on time = 63302; Parameter Laser Power = 3.69; Parameter Scan Time = 10:45:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.21; Performer: Nina,,Salama

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: genomic DNA

organism:
Helicobacter pylori 26695
Helicobacter pylori J99

source_name: 0.25 ng 26695/J99 genomic DNA mix

label_protocol: not provided

extract_protocol: not provided

tag: 0.25 ng 26695/J99 genomic DNA mix

organism: Helicobacter pylori

source_name: 500 ng 510S3-3-1, Disease State: Gastric Cancer


title: 336S3-2-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61518.gif
Individual: 336
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 390, 35860; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 64306; Parameter Laser Power = 3.48; Parameter Scan Time = 15:29:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 600; Parameter Scan Power = 100; Parameter Laser on time = 64188; Parameter Laser Power = 3.80; Parameter Scan Time = 15:29:09; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Nina,,Salama

source_name: 500 ng 336S3-2-1, Disease State: Duodenal Ulcer


title: colorectal cancer DNA hypermethylome: TSA vs mock in HT-29

status: Public on Sep 23 2009

type: RNA

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in HT-29

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufacturer's protocol (G4140-90050)

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays. with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor

molecule: total RNA

organism: Homo sapiens

source_name: Mock treated HT-29 cells

label_protocol: Agilent low RNA input linear amplification kit

growth_protocol: McCoy's 5A medium with 10% BCS and 1x P/S

extract_protocol: TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment

treatment_protocol: 1x PBS for 96 hours

tag: HT-29 human colorectal cancer cell line

source_name: TSA treated HT-29 cells

treatment_protocol: 300 nanomolar TSA for 18 hours

tag: HT-29 human colorectal cancer cell line treated with TSA


title: breast cancer DNA hypermethylome: DAC vs mock in MDA-MB-231

description: Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in MDA-MB-231

source_name: Mock treated MDA-MB-231 cells

source_name: 5-AZA treated MDA-MB-231 cells

treatment_protocol: 5 micromolar 5-AZA for 96 hours

tag: MDA-MB-231 human breast cancer cell line treated with 5-AZA


title: colorectal cancer DNA hypermethylome: TSA vs mock in Caco-2

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in Caco-2

source_name: Mock treated Caco-2 cells

source_name: TSA treated Caco-2 cells

tag: Caco-2 human colorectal cancer cell line treated with TSA


title: 386S3-3-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61516.gif
Individual: 386
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 520, 33440; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 580; Parameter Laser on time = 64289; Parameter Laser Power = 3.48; Parameter Scan Time = 15:11:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 610; Parameter Scan Power = 100; Parameter Laser on time = 64171; Parameter Laser Power = 3.79; Parameter Scan Time = 15:11:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.92; Performer: Nina,,Salama

source_name: 500 ng 386S3-3-1, Disease State: Non-atrophic Gastritis


title: colorectal cancer DNA hypermethylome: DAC vs mock in COLO320

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in COLO320

source_name: Mock treated COLO 320 cells

source_name: 5-AZA treated COLO 320 cells

tag: COLO 320 human colorectal cancer cell line treated with 5-AZA


title: 263S4-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61492.gif
Individual: 263
Disease State: Duodenal Ulcer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 400, 7960; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 65544; Parameter Laser Power = 3.50; Parameter Scan Time = 11:27:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.16; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-19; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 620; Parameter Scan Power = 100; Parameter Laser on time = 65766; Parameter Laser Power = 3.74; Parameter Scan Time = 11:27:06; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.16; Performer: Nina,,Salama

source_name: 500 ng 263S4-1-1, Disease State: Duodenal Ulcer


title: 284S3-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61523.gif
Individual: 284
Disease State: Non-atrophic Gastritis
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 430, 34340; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 64331; Parameter Laser Power = 3.48; Parameter Scan Time = 15:54:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 700; Parameter Scan Power = 100; Parameter Laser on time = 64212; Parameter Laser Power = 3.80; Parameter Scan Time = 15:54:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.98; Performer: Nina,,Salama

source_name: 500 ng 284S3-1-1, Disease State: Non-atrophic Gastritis


title: breast cancer DNA hypermethylome: TSA vs mock in MDA-MB-231

description: Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in MDA-MB-231

source_name: TSA treated MDA-MB-231 cells

treatment_protocol: 300 nanomolar TSA for 18 hour

tag: MDA-MB-231 human breast cancer cell line treated with TSA


title: breast cancer DNA hypermethylome: DAC vs mock in T-47D

description: Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in T-47D

source_name: Mock treated T-47D cells

tag: T-47D human breast cancer cell line

source_name: 5-AZA treated T-47D cells

tag: T-47D human breast cancer cell line treated with 5-AZA


title: colorectal cancer DNA hypermethylome: DAC vs mock in RKO

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in RKO

source_name: Mock treated RKO cells

tag: RKO human colorectal cancer cell line

source_name: 5-AZA treated RKO cells

tag: RKO human colorectal cancer cell line treated with 5-AZA


title: 387S3-1-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61508.gif
Individual: 387
Disease State: Duodenal Ulcer
Replicate: 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1240, 8240; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 63963; Parameter Laser Power = 3.60; Parameter Scan Time = 13:36:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.25; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-05-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 670; Parameter Scan Power = 100; Parameter Laser on time = 63813; Parameter Laser Power = 3.75; Parameter Scan Time = 13:36:17; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 32.25; Performer: Nina,,Salama

source_name: 0.25 ng 26695/J99 genomic DNA mix

source_name: 500 ng 387S3-1-1, Disease State: Duodenal Ulcer


title: colorectal cancer DNA hypermethylome: DAC vs mock in Caco-2

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in Caco-2

source_name: 5-AZA treated Caco-2 cells

tag: Caco-2 human colorectal cancer cell line treated with 5-AZA


title: breast cancer DNA hypermethylome: TSA vs mock in T-47D

description: Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in T-47D

source_name: TSA treated T-47D cells

tag: T-47D human breast cancer cell line treated with TSA


title: 510S4-4-1

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2005-05/61503.gif
Individual: 510
Disease State: Gastric Cancer
Replicate: 4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1810, 34750; Software: type: feature extraction; Performer: Nina,,Salama Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.0; Parameter Scan Power = 100; Parameter PMT Volts = 470; Parameter Laser on time = 63599; Parameter Laser Power = 3.60; Parameter Scan Time = 10:57:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.48; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-04-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.0; Parameter Pixel Size = 10; Parameter PMT Volts = 640; Parameter Scan Power = 100; Parameter Laser on time = 63315; Parameter Laser Power = 3.70; Parameter Scan Time = 10:57:01; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [92865]; Parameter Focus Position = 0; Parameter Scan Temperature = 31.48; Performer: Nina,,Salama

source_name: 500 ng 510S4-4-1, Disease State: Gastric Cancer


title: CBX7 overexpression in TERA2

description: CBX7 overexpression in TERA2

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufacturer's protocol.

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: Log ratio of red signal to green signal was calculated. Loess normalization as implemented in the Limma package from Bioconductor.

source_name: TERA2 empty vector cells

label_protocol: Agilent low RNA input linear amplification kit.

growth_protocol: Cells were maintained in McCoy's with 15% fetal bovine serum and 0.2 micrograms per ml puromycin.

extract_protocol: Trisol extraction based on manufacturer's instructions followed by RNeasy cleanup as per manufacturer's instructions.

treatment_protocol: Stable transfection with plasmid containing EF1 alpha promoter and puromycin resistance gene downstream from IRES.

tag: malignant embryonal carcinoma

tag: derived from metastatic site

value: lung

tag: adherent cells with epithelial morphology

source_name: TERA2 CBX7 overexpressing cells

treatment_protocol: Stable transfection with plasmid containing EF1 alpha promoter driving expression of CBX7 containing 3' HA tag and puromycin resistance gene downstream from IRES.


title: breast cancer DNA hypermethylome: TSA vs mock in MCF7

description: Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in MCF7

source_name: Mock treated MCF7 cells

tag: MCF7 human breast cancer cell line

source_name: TSA treated MCF7 cells

tag: MCF7 human breast cancer cell line treated with TSA


title: colorectal cancer DNA hypermethylome: TSA vs mock in COLO320

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in COLO320

source_name: Mock treated COLO 320 cells

source_name: TSA treated COLO 320 cells

tag: COLO 320 human colorectal cancer cell line treated with TSA


title: Adipose_1%_14days_ind6

status: Public on Sep 22 2009

city: Aalborg

first: Vladimir

last: Zachar

address: Fredrik Bajers Vej 3B

country: Denmark

institute: Aalborg University

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761007_F

hyb_protocol: Biotin labled cRNA (1.5μg) was hybridized to Illumina Human-6 v2.0 arrays using the IlluminaHybChamber and gasket for 16 hours at 58ºC. After a series of washes, including high temperature (55ºC) wash, room temperature washes and an EtOH wash, the arrays were blocked for 10min and developed using streptavidin-Cy3. All buffers, blocking and staining solutions were from llumina and were used according to standard protocol (Whole-Genome Gene Expression with IntelliHybTM Seal Experienced User Card, Illumina Part # 11226048, Rev B.). Before scanning the arrays were dried by centrifugation at 275RCF for 4min.

scan_protocol: Illumina Human-6 v2.0 arrays were scanned on the Illumina Bead station 500GX System

data_processing: Raw intensity values were background subtracted using Illumina's BeadStudio software version 3.0.14 and exported into the R Bioconductor statistical package where the data were transformed and normalised using the vsn2 BioConductor package (Huber et al., 2002).

label: Biotin

label_protocol: With 400 ng totalRNA as entry material, the Illumina Total Prep RNA Amplification Kit (Illumina Inc, San Diego, CA) was used according to standard protocols to produce in vitro transcribed and biotin labeled cRNA.

growth_protocol: The ASC cultures were maintained in growth medium, alpha Modified Eagle Medium (αMEM, Invitrogen, CarlsBad, Ca) supplemented with 1% Penicilin/Streptamicin (Invitrogen), 0.5% Gentamicin (Invitrogen) and 10% Fetal Calf Serum (Invitrogen) in a humidified atmosphere, containing 5% CO2 buffered with air of varying oxygen tensions (ambient, 15, 10, 5 and 1% oxygen tension) at 37°C and with medium change twice a week.

extract_protocol: Total RNA was isolated from cultured adipose tissue derived stem cells using the BioRad Aurum total RNA mini kit (Bio-Rad, Copenhagen, Denmark) according to manufacturer's instructions.

treatment_protocol: Adipose tissue was harvested using a tumescent technique with pump-assisted aspiration (Oedayrajsingh-Varma MJ et al, 2006). Adipose tissue derived stromal cells (ASCs) were isolated as previously described (Zuk PA et al, 2001) with slight modifications. In brief, prior to digestion, the tissue was washed three times in equal volumes of prewarmed D-PBS and then digested in equal volumes of collagenase buffer, 0.28Wünch U/ml crude collagenase mix (Lot. No. LTQ5230; Wako, Neuss, Germany) in D-PBS with 20mg/ml BSA (Roche Applied Science, Hvidovre, Denmark). Following digestion at 37°C with gentle agitation for 1 hour, the released cells were isolated by fractional sedimentation centrifugation at 400 x g for 10 min and the pelleted cells were filtered through a 70 μm mesh cell strainer (BD Bioscience, Broendby, Denmark). Contaminating erythrocytes were lysed using erythrocyte lysis buffer (8,3g/l NH4Cl (Merck Chemicals, Darmstadt, Germany) and 0.993g/l K2HPO4 (Bie & Berntsen, Aabyhoej, Denmark) in 0.04g/l EDTA-Na (Merck). The remaining nucleated cells were further purified through a second round of centrifugation and filtration and seeded at a cell density corresponding to 150μl adipose tissue/cm2 in growth medium. Twelve hours post seeding the medium was changed to remove nonadherent cells. The freshly isolated cells were expanded for 11 days before cryopreservation and storage at -140°C. The ASCs were thawed and cultured for one week in growth medium in a humidified atmosphere containing 5% CO2 buffered with ambient air at 37°C. At 80% confluence the cultures were passaged at 1000 cells/cm2 and left for 24 hours to adhere.

tag: Donor Id

tag: Gender

value: Female

tag: Harvest site

value: Inner thigh

tag: BMI

tag: Tissue

value: Adipose

tag: Oxygen tension

tag: Days in culture


title: Murine model of gastrointestinal stromal tumors harboring a germline Kit K641E oncogenic mutant_Biological replica 2_1

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

institute: ULB

description: Sample were hybridized to MEEBO arrays containing 38784 mouse 70mer oligonucleotide probes (Stanford Functional Genomics Facility, California, USA).

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of mouse cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and expression levels were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing:
A non-linear Lowess (locally weighted scatter plot) normalization method applied to each individual block (print-tip option) was carried out.
VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2

organism: Mus musculus

source_name: Antrum  harboring a germline Kit K641E oncogenic mutant

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30min in 50% DMSO at room temperature in a dark environment.

growth_protocol: No growth

extract_protocol: Antrum total RNA was extracted using the Mirvana kit (Ambion, Texas, USA)

treatment_protocol: Animals were housed in a temperature (21±1°C) and humidity (55±10%)-controlled room with a 12 h light: 12 h dark cycle. Food and water were available ad libitum. Animal procedures were conducted in accordance with the guidelines of the European Communities Directive 86/609/EEC regulating animal research and were approved by the Local Ethical Committee of the Faculty of medicine, Université Libre de Bruxelles, Brussels, Belgium.

tag: A mouse model of gastrointestinal stromal tumor (GIST) has been developed by a knock-in gene targeting strategy, which introduced a Kit gene K641E mutation, originally identified in sporadic human GISTs and in the germ line of familial GIST syndrome patients. All Kit K641E homozygotes die by age 3 weeks due to gastrointestinal obstruction by hyperplastic interstitial cells of Cajal or GISTs. Total RNA was extracted from antral tissue of three independent Kit K641E:Neo homozygote littermates at P14 stage. Biological replica 2, technical replica 1 (dye-swap)

source_name: Antrum Kit wt/wt

treatment_protocol: Animals were maintained and experiments performed as described above.

tag: Reference RNA  was extracted from the antrum of a Kit wt/wt of the same littermate P14 as the knock-in GIST Kit K641E mice.


title: Adipose_5%_14days_ind6

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761007_E


title: breast cancer DNA hypermethylome: TSA vs mock in MDA-MB-468

description: Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in MDA-MB-468

source_name: Mock treated MDA-MB-468 cells

source_name: TSA treated MDA-MB-468 cells

tag: MDA-MB-468 human breast cancer cell line treated with TSA


title: colorectal cancer DNA hypermethylome: TSA vs mock in RKO

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in RKO

source_name: Mock treated RKO cells

tag: RKO human colorectal cancer cell line

source_name: TSA treated RKO cells

tag: RKO human colorectal cancer cell line treated with TSA


title: Adipose_15%_14days_ind6

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761007_C


title: breast cancer DNA hypermethylome: DAC vs mock in MDA-MB-468

description: Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in MDA-MB-468

source_name: 5-AZA treated MDA-MB-468 cells

tag: MDA-MB-468 human breast cancer cell line treated with 5-AZA


title: Adipose_Ambient_14days_ind4

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1833442073_B

value: Abdomen, hip

value: Ambient


title: Adipose_Ambient_14days_ind6

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761007_B


title: colorectal cancer DNA hypermethylome: DAC vs mock in HT-29

description: Identification of the colorectal cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in HT-29

source_name: Mock treated HT-29 cells

tag: HT-29 human colorectal cancer cell line

source_name: 5-AZA treated HT-29 cells

tag: HT-29 human colorectal cancer cell line treated with 5-AZA


title: breast cancer DNA hypermethylome: DAC vs mock in MCF7

description: Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: DAC vs mock in MCF7

tag: MCF7 human breast cancer cell line

source_name: 5-AZA treated MCF7 cells

tag: MCF7 human breast cancer cell line treated with 5-AZA


title: Adipose_10%_14days_ind4

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1833442073_D

tag: Donor Id


title: Adipose_15%_14days_ind3

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1814647011_C

tag: Gender


title: Adipose_10%_14days_ind3

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1814647011_D

tag: Harvest site


title: Adipose_5%_14days_ind2

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761028_E

value: Abdomen, hip, loin, inner thigh

tag: BMI


title: Adipose_Ambient_0days_ind3

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1814647011_A

tag: Tissue


title: Adipose_5%_14days_ind4

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1833442073_E

tag: Oxygen tension


title: Adipose_10%_14days_ind6

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761007_D

tag: Days in culture


title: Adipose_Ambient_0days_ind4

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1833442073_A


title: Adipose_Ambient_0days_ind6

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761007_A


title: Adipose_15%_14days_ind4

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1833442073_C


title: Adipose_5%_14days_ind3

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1814647011_E


title: Adipose_1%_14days_ind4

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1833442073_F


title: Adipose_1%_14days_ind3

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1814647011_F


title: Adipose_15%_14days_ind1

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1718911586_C


title: Adipose_1%_14days_ind1

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1718911586_F


title: Adipose_Ambient_0days_ind2

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761028_A


title: Adipose_Ambient_14days_ind3

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1814647011_B


title: Adipose_1%_14days_ind2

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761028_F


title: Gene expression of Bacillus subtilis 168 during exponentially growing period_1

status: Public on Sep 20 2009

city: Tianjin

first: shuobo

last: shi

address: Weijin Road

country: China

institute: Tianjin University

description: Gene expression data from Bacillus subtilis 168 during exponentially growing period were taken to study the riboflavin biosynthesis process.

hyb_protocol: The microarray was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 (Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Datas were processed by the software of GCOS  (Affymetrix).

label: biotin

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis 168, LBG, exponentially growing period

label_protocol: 5 µg of total RNA was amplified and labeled using the GeneChip® one-cycle target labeling and control reagents  (Affymetrix).

extract_protocol: Total RNA were extracted by using RiboPure™-Bacteria Kit

tag: Strain

value: Bacillus subtilis 168

tag: Medium

value: LB medium with 1% glucose

tag: Time:exponentially growing period


title: Gene expression of Bacillus subtilis RH33 during exponentially growing period_1

description: Gene expression data from Bacillus subtilis during exponentially growing period were taken to study the riboflavin biosynthesis process.

organism: Bacillus subtilis

source_name: Bacillus subtilis RH33, LBG, exponentially growing period

value: Bacillus subtilis  RH33


title: Gene expression of Bacillus subtilis 168 during exponentially growing period_2


title: Gene expression of Bacillus subtilis RH33 during exponentially growing period_2

value: Bacillus subtilis RH33


title: Adipose_10%_14days_ind2

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761028_D


title: Adipose_15%_14days_ind2

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761028_C


title: IPA220_day1 dye swap

status: Public on Sep 19 2009

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: IPA220_day1 dye swap

hyb_protocol: 825ng of Cy3 and Cy5 labeled cRNA were hybridized for 16 hrs at 65 C (hybridization oven G2545A, Agilent), according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at on an Agilent DNA Microarray Scanner using the default settings for 4x44k format two-color arrays.

data_processing: Image analysis was performed using feature extraction software version 9.5 (Agilent Technologies). The Agilent GE2-v5_95 protocol was applied using default settings. All data pre-processing and analysis was performed using the R-Bioconductor package Limma20. A robust Edwards background correction was applied

source_name: Gastric cell line treated with cotrol siRNA

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol: Total RNA was extracted from each cell line using the RNeasy kit (Qiagen) including a DNase digestion step, according to the manufacturer’s instructions

source_name: Gastric cell line treated with siRNA UPF-1


title: IPa220_day3 dye swap

description: IPa220_day3 dye swap

source_name: Gastric cell line treated with control siRNA

tag: Gastric cell line treated with siRNA UPF-1


title: VirRS mutant vs WT at 2 h

status: Public on Sep 17 2009

city: Fukuoka

first: Hideki

last: Hirakawa

state: Fukuoka

address: 6-10-1, Hakozaki, Higashi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

description: VirRS mutant vs WT at 2 h

hyb_protocol: Hybridization solution (25 μl of Cy-dye-labeled cDNA solution, 10 μl of x20 SSC, 3 μl of water, and 2 μl of 10% SDS) was poured onto the slide glass and covered with a cover-glass with a gap (Matsunami Glass). The slide was inserted into the hybridization chamber, and hybridization was performed at 60 °C overnight.

scan_protocol: Scanned on an FLA-8000 scanner (Fuji Film, Japan). The density of the scanned spots was measured by ArrayVision software (Imaging Research, USA)

data_processing: Normalized by the median of the raw intensities for all spots in each control and sample. LOWESS normalization was performed. GeneSpring software was used.

organism: Clostridium perfringens str. 13

source_name: strain 13, wild type, 2 h from strart of culture

label_protocol: 15 µg of total RNA from was mixed with 2 µl of random primers (d(N)6, d(N)9, 0.5 µg/µl each, Takara, Japan) and adjusted to 22 µl with water. The solution was kept at 65°C for 5 min to denature the RNA. The annealing reaction was performed at 42°C for 5 min. The premix solution (18 µl) was mixed into RNA solution, and reverse transcription was performed at 42 °C for 60 min. The premix solution was a mixture of 8 µl of x5 power script reaction buffer, 4 µl of dNTPs (5 mM dATP, 5 mM dCTP, 5 mM dGTP, 2 mM dTTP, 3 mM amino-allyl dUTP (Sigma, USA)), 4 µl of 0.1 M DTT, 0.1 µl of RNase inhibitor (TakaRa, Japan), and 2 µl of Powerscript reverse transcriptase (BD Biosciences, USA). After incubation, 5 µl of 0.5M EDTA (pH 8.0) and 10 µl of 1 N NaOH were mixed, and the mixture was incubated at 65°C for 30 min to stop the reaction and remove the RNA templates, followed by the addition of 25 µl of 1 M Tris-Cl (pH 7.5) for neutralization. The mixture was transferred to a Microcon-30 filter (Millipore, USA) and centrifuged. The filter was washed with 100 µl of water 4 times, and the sample was eluted in 25 µl of water.  The solution was completely dried, re-suspended in 10 µl of 50 mM NaCO3, and incubated at room temperature (RT) for 3 min.  Ten microliters of Cy3 or Cy5 (GE Healthcare, USA) was mixed and incubated at RT for 60 min in a dark place. Ten microliters of Na2OH (Sigma) was added to remove un-reacted Cy-dye. Finally, the labeled product was purified by a QIAquick column (Qiagen, Germany).

growth_protocol: strains  were cultured in GAM (Gifu Anaerobic Medium)

extract_protocol: Total RNA extracted using hot-phenol method

tag: Wild type

tag: 2 h from strart of culture

source_name: TS133, virR/virS mutant, 2 h from strart of culture

tag: virR/virS mutant


title: VR-RNA mutant vs WT at 1.5 h

description: VR-RNA mutant vs WT at 1.5 h

source_name: strain 13, wild type, 1.5 h from strart of culture

tag: 1.5 h from strart of culture

source_name: TS140, VR-RNA mutant, 1.5 h from strart of culture

tag: VR-RNA mutant


title: Adipose_Ambient_14days_ind2

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1842761028_B


title: Adipose_5%_14days_ind1

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1718911586_E


title: GP202_day1 dye swap

description: GP202_day1 dye swap

tag: Gastric cell line treated with control siRNA


title: Adipose_10%_14days_ind1

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1718911586_D

tag: Donor Id


title: IPA220_aCGH

description:
IPA220_aCGH
protocols according to manufacturer (Enzo Life Sciences, www.agilent.com)

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: For both Cy3 and Cy5 channels, local background was subtracted from the median intensities. The log2 tumour to normal ratio was calculated for each spot and normalized against the median of the ratios of all autosomes

source_name: Gastric cancer cell line

label_protocol: DNA labeling protocol according to Enzo Life Sciences

extract_protocol: Genomic DNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol with some modifications  (http://www.english.vumc.nl/afdelingen/microarrays/).

tag: Gastric cancer cell line

source_name: Pooled DNA from the blood of 18 normal individuals

extract_protocol: DNAzol (Invitrogen) according to manufacturer's protocol


title: GP202_day1

data_processing:
Image analysis was performed using feature extraction software version 9.5 (Agilent Technologies). The Agilent GE2-v5_95 protocol was applied using default settings.
All data pre-processing and analysis was performed using the R-Bioconductor package Limma20. A robust Edwards background correction was applied

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).


title: Adipose_Ambient_14days_ind1

description:
One outlier sample was excluded from the normalisation step (Ambient 0days Sample A).
1718911586_B

tag: Gender

tag: Harvest site


title: VR-RNA mutant vs WT at 2.5 h

description: VR-RNA mutant vs WT at 2.5 h

source_name: strain 13, wild type, 2.5 h from strart of culture

tag: 2.5 h from strart of culture

source_name: TS140, VR-RNA mutant, 2.5 h from strart of culture


title: VR-RNA mutant vs WT at 2 h

description: VR-RNA mutant vs WT at 2 h

source_name: TS140, VR-RNA mutant, 2 h from strart of culture


title: IPA220_day1


title: IPA220_day3


title: GP202_day3 dye swap

description: GP202_day3 dye swap


title: IPA220_day2 dye swap

description: IPA220_day2 dye swap


title: IPA220_day2


title: GP202_day2 dye swap

description: GP202_day2 dye swap


title: GP202_day3


title: VirRS mutant vs WT at 1.5 h

description: VirRS mutant vs WT at 1.5 h

source_name: TS133, virR/virS mutant, 1.5 h from strart of culture


title: GP202_aCGH

description:
GP202_aCGH
protocols according to manufacturer (Enzo Life Sciences www.agilent.com)

tag: Pooled DNA from the blood of 18 normal individuals


title: GP202_day2


title: VirRS mutant vs WT at 2.5 h

description: VirRS mutant vs WT at 2.5 h

source_name: TS133, virR/virS mutant, 2.5 h from strart of culture


title: dol_1_liver_KnockOut1

status: Public on Sep 10 2009

city: Los Angeles

first: Nicole

middle: Kim

last: MacLennan

state: CA

address: 10833 LeConte Ave

department: Pediatrics

institute: University of California, Los Angeles

description: Further details are available at www.affymetrix.com.

hyb_protocol: Ten micrograms of cRNA was hybridized at 45 degrees C with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640) to an Affymetrix Mouse Genome 430 2.0 GeneChip as per the manufacturer’s instructions (Affymetrix, Inc.). The GeneChip arrays were washed and then stained with streptavidin–phycoerythrin on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on a GeneChipScanner 3000.  Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).

data_processing: Results were quantified and analyzed with GeneChip Operating Software (GCOS) 1.2 software (Affymetrix, Inc.) using default values (scaling, target signal intensity 500; normalization, all probe sets; parameters, all set at default values).  We used Affymetrix GeneChip Mouse Expression set 430 2.0 Array which uses mouse maintenance genes for normalization.  Details are available on the Affymetrix website (www.affymetrix.com/support/technical/mask_files.affx).

label_protocol: cDNA was synthesized from the poly(A) mRNA present in the isolated total RNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Life Technologies) and poly(T)-nucleotide primers. Biotin-tagged cRNA was generated using the BioArray High-Yield RNA Transcript Labeling Kit (T7) (Enzo Diagnostics, Inc., Farmingdale, NY, USA) and fragmented to an average strand length of 100 bases (range 35–200 bases) following prescribed protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

extract_protocol: Total RNA from one KnockOut liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).

treatment_protocol: glycerol kinase knockout mice

value: male

tag: Age

value: day of life 1

tag: Tissue

value: liver


title: dol_1_liver_KnockOut4

tag: Strain


title: dol_1_liver_KnockOut3


title: dol_1_liver_wildtype3

extract_protocol: Total RNA from one wildtype liver was isolated individually using TRIzol Reagent (Invitrogen Life Technologies) and purified using RNeasy MiniElute Cleanup Kit (Qiagen Inc., Chatsworth, CA, USA).

treatment_protocol: Age-matched wiltype littermates of glycerol kinase knockout mice


title: dol_1_liver_wildtype2


title: dol_1_liver_KnockOut2


title: dol_1_liver_wildtype1


title: T_N_rep1

status: Public on Sep 05 2009

city: Beijing

first: mei

last: li

address: Haidian district

institute: China Agricultural University

description: Gene expression data from the embryonic heart of Tibetan Chicken in normoxia.

hyb_protocol: Fragmented cRNA was hybridized to Affymetrix GeneChip® Chicken Genome Array for 16 h at 45°C. The hybridized probe array was automatically washed and then stained with streptavidin-phycoerythrin (SAPE) in a GeneChip® Fluidics Station 450.

scan_protocol: The arrays were scanned on a Affymetrix GeneChip® Scanner 3000.

data_processing: The data were analyzed by GeneChip® Operating Software (GCOS) with Affymetrix default analysis settings.

organism: Gallus gallus

source_name: embryonic heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual,P/N900223 or 90365, Affymetrix).

extract_protocol: The extraction of total RNA with TRIzol reagent was performed according to the manufacturer's instructions.


title: T_H_rep2

description: Gene expression data from the embryonic heart of Tibetan Chicken in hypoxia.


title: T_N_rep2

tag: the embryonic heart of Tibetan Chicken in normoxia


title: T_H_rep1

tag: the embryonic heart of Tibetan Chicken in hypoxia


title: DRW_N_rep1

description: Gene expression data from the embryonic heart of Dwarf Recessive White Chicken in normoxia.


title: S_N_rep1

description: Gene expression data from the embryonic heart of Shouguang Chicken in normoxia.


title: DRW_H_rep1

description: Gene expression data from the embryonic heart of Dwarf Recessive White Chicken in hypoxia.


title: S_H_rep2

description: Gene expression data from the embryonic heart of Shouguang Chicken in hypoxia.


title: DRW_N_rep2

tag: the embryonic heart of Dwarf Recessive White Chicken in normoxia


title: S_N_rep2

tag: the embryonic heart of Shouguang Chicken in normoxia


title: DRW_H_rep2

tag: the embryonic heart of Dwarf Recessive White Chicken in hypoxia


title: P114-slide7_low

status: Public on Sep 04 2009

city: Puddle Alley

first: Alan

middle: Francis

last: McCulloch

state: Mosgiel

address: Invermay

country: New Zealand

institute: AgResearch NZ

description: For this experiment, 18 slides were used in a loop design which requires three aliquots of each test sample labeled alternately with the Cy5 and Cy3 dyes and co-hybridized on arrays with two other test samples. Data from a third treatment group will be published elsewhere. Definition of "normal" and "low" as used in the slide names : "Normal" scan detects the majority of the differentially expressed spots excluding those with very low signal (undetectable) and with very high signal (saturated) ; "low" scan used a lower PMT setting to capture the very high signal (saturated) spots. This was necessary to maximize the capture of all the relevant data (not possible with just one setting).

hyb_protocol: Micro array slides were prehybridized in a preheated (42oC) 0.22 µm filtered solution of 5 x SSC, 0.1% SDS and 0.25% BSA (A-788; Sigma Chemical company, St. Louis, MO, USA) for 20 min at 42oC. Slides were rinsed in deionised water then isopropanol and air dried before hybridization. cDNA labeled samples were heat-denatured (95oC for 10 min) and mixed with 60 µL of pre-warmed (68oC) SlideHyb No1 (Ambion, Austin, TX, USA) added. The final cDNA labeled solution was loaded onto the slides with lifter coverslips (Erie Scientific, Portsmouth, NH, USA). Hybridizations were conducted for 20 h in sealed humidified chambers (CMT Hybridization Chambers, Corning, NY, USA). Following hybridization, slides were washed for 5 min each in (1) 2 x SSC, 0.1% SDS, (2) 1 x SSC and (3) 0.1 x SSC then centrifuged at 1000 g for 5 min

scan_protocol: The slides were stored in the dark to minimize photo bleaching, and scanned for both dye channels at 532 and 635 nm within two days using an GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA) with a 10-μm resolution. The photomultiplier tube voltage was adjusted to obtain an equal global intensity in both channels.

data_processing:
The method used was as in
Normalization of microarray data using a spatial mixed model analysis which includes splines
Bioinformatics
Volume 20 , Issue 17 (November 2004)
Pages: 3196 - 3205
Authors David Baird AgResearch, Lincoln, New Zealand,
Peter Johnstone AgResearch, Invermay Research Centre, Mosgiel, New Zealand,
Theresa Wilson AgResearch Molecular Biology Unit, Department of Biochemistry, University of Otago, Dunedin, New Zealand

organism: Bos taurus

source_name: Mammary gland tissue

label_protocol: Fluorescent-labeling reactions used the SuperScript Indirect cDNA Labeling System (Invitrogen, Auckland, NZ). cDNA was labeled in the presence of either mono-functional N-hydroxysuccinimide (NHS)-ester Cy5 or Cy3 dyes (Amersham Biosciences, Piscataway, NJ, USA), and concentrated to a final volume of 20 microL using Microcon columns (Millipore, North Ryde, NSW, AUS). Labeled cDNAs were purified to remove unincorporated dyes using the QIA-Quick PCR purification kit (Quiagen, San Diego, CA, USA), concentrated to 10 µL and combined.

extract_protocol: Total RNA was extracted using Trizol® Reagent (Invitrogen Auckland, NZ), a modification of the acid guanidinium thiocyanate-phenol-chloroform extraction method according to the manufacturers’ protocol and incorporated the optional step (for tissues with high content of protein, fat, polysaccharides) during sample homogenization.

treatment_protocol: Growth Hormone Cow 698

tag: Mammary gland tissue from non-pregnant second lactation spring-calved Jersey cows between 178 to 200 days postpartum

treatment_protocol: Control Cow 706


title: P114-slide2_low

treatment_protocol: Atropine Cow 701

treatment_protocol: Growth Hormone Cow 696


title: 32D, trasducted with wt FLT3, biological rep2

status: Public on Sep 12 2009

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Gene expression data from myeloblast-like cell line 32D transduced with wt FLT3

hyb_protocol: Fragmented and Labeled DNA Target was hybridized for 17 hr at 45C on GeneChip Mouse Exon 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Expression Console 1.1 and Bioconductor 2.1 and R statistics (version 2.6). Data were preprocessed using the RMA-Sketch normalization, probeset and metaprobeset summarization based on the default annotation from Affymetrix.

source_name: An immortalized myeloblast-like cell line 32D transduced with wt FLT3

label_protocol: 1ug of total RNA were used to prepare biotinylated cDNA according to the standard GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual,  including rRNA reduction step (Version 4, 701880 Rev. 4, Affymetrix).

growth_protocol: Large-scale cultivation of 32D cell lines for high-throughput transcriptome and proteome profiling  Nine stable 32D cell lines carrying individual FLT3/ITD mutants, as well as parental 32D cell line, 32D cell line harboring wild type human FLT3 and 32D cell line carrying the pLXRN cloning vector were seeded into cultivation flasks at the cell density of 50,000/mL in RPMI 1640 cultivation media (Sigma, Germany) supplemented with 10% heat-inactivated fetal calf serum (Gibco BRL, UK). The cultivation medium for the control 32D cell lines (parental, human wild type FLT3 and 32D harboring the cloning vector) were further supplemented with 1 ng/mL murine IL-3 (mIL-3, Sigma, Germany); FLT3/ITD-positive cell lines grew exponentially without mIL-3.  32D control cell line harboring wild type human FLT3 were split and cultivated in the presence or absence of FL (20 ng/ml, Sigma, Germany). Cells cultures were subjected to repeated passages at a constant cell density to achieve optimal growth rate. All cell lines were grown in the same lot of cultivation medium, serum, mIL-3, FL; in identical lot of cultivation flasks to make the cultivation conditions as uniform as possible. When the cultures reached sufficient density for both RNA and protein analyses (50 million for RNA analyses + 100 million for proteomics studies), individual 32D cell lines were repeatedly washed in 1xPBS (Sigma, Germany) to remove cultivation media and any traces of serum.

extract_protocol: 50 million cells each were harvested into Trizol (Sigma, Germany). Trizol–isolated RNAs were DNA-ase I treated (NEB, UK) and re-purified using RNeasy MinElute Cleanup Kit (Quiagen, Germany).  100 million cells each from identical cultivation lots as those used for the RNA analyses were harvested and subjected to 5 gentle washes in 1x PBS to remove traces of sera from the cultivation media, the cells were lysed with the Pulverisette® 23 from FRITSCH GmbH (Idar-Oberstein, Germany). Subsequently, the cell debris was removed by centrifugation. The supernatant was acetone precipitated and solubilized in sample solution for 2-DE (9 M urea, 4% (w/v) CHAPS, 5 mM TBP, 1% Biolyte, 5% (v/v) protease inhibitor cocktail) at room temperature under gentle shaking for at least 1 h.

treatment_protocol: To create stable 32D cell lines expressing wild type human FLT3 and the nine FLT3/ITD variants, ecotropic retroviral transduction system was used (Clontech, Mountain View, CA, USA). The packaging cell line EcoPack 293 was transiently transfected with the retroviral pLXRN constructs using standard lipofectamine method (Lipofectamine 2000, Invitrogen, UK). 48 hours post transfection, the supernatants containing infectious retroviral particles were harvested and applied on the recipient 32D cells seeded at the cell density of 50,000/mL in RPMI 1640 with 10% FCS and supplemented with 1 ng/mL of mouse IL-3 (mIL-3; Sigma, Germany). Two days after retroviral transduction, 32D cell lines harboring ITDs were transferred into cultivation RPMI 1640 media supplemented with 10% FCS, without any mIL-3 added. 32D cell lines transduced with the pLXRN vector backbone and wt hFLT3 were cultivated in the presence of mIL-3, under G418 (Sigma, Germany) antibiotics selection. Polyclonal 32D populations – to exclude the effect of the retroviral integration site on the expression levels of transgenes – were subjected to further analyses.

tag: Genotype

value: trasducted with wt FLT3


title: S_H_rep1

tag: the embryonic heart of Shouguang Chicken in hypoxia


title: P114-slide1_low

treatment_protocol: Control Cow 699


title: P114-slide19_low

treatment_protocol: Control Cow 705

treatment_protocol: Atropine Cow 703


title: 32D, trasducted with mt FLT3 number A419

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number A419

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number A419

value: trasducted with mt FLT3 number A419


title: 32D, trasducted with mt FLT3 number A034

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number A034

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number A034

value: trasducted with mt FLT3 number A034


title: 32D, biological rep1

description: Gene expression data from myeloblast-like cell line 32D

source_name: An immortalized myeloblast-like cell line 32D

value: not-transduced


title: P114-slide12_low

treatment_protocol: Growth Hormone Cow 700


title: 32D, trasducted with empty pLXRN vector, biological rep2

description: Gene expression data from myeloblast-like cell line 32D transduced with empty pLXRN vector

source_name: An immortalized myeloblast-like cell line 32D transduced with empty pLXRN vector

value: trasducted with empty pLXRN vector


title: P114-slide17_low


title: P114-slide9_low

treatment_protocol: Control Cow 707


title: P114-slide8_low


title: 32D, trasducted with mt FLT3 number B056

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number B056

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number B056

value: trasducted with mt FLT3 number B056


title: 32D, trasducted with mt FLT3 number A405

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number A405

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number A405

value: trasducted with mt FLT3 number A405


title: 32D, trasducted with wt FLT3, biological rep1


title: P114-slide15_low

treatment_protocol: Atropine Cow 702


title: 32D, trasducted with mt FLT3 number A725

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number A725

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number A725

value: trasducted with mt FLT3 number A725


title: P114-slide11_low

treatment_protocol: Atropine Cow 704


title: P114-slide16_low


title: P114-slide5_low

treatment_protocol: Growth Hormone Cow 697


title: P114-slide10_low

data_processing:
The method used as as in
Normalization of microarray data using a spatial mixed model analysis which includes splines
Bioinformatics
Volume 20 , Issue 17 (November 2004)
Pages: 3196 - 3205
Authors David Baird AgResearch, Lincoln, New Zealand,
Peter Johnstone AgResearch, Invermay Research Centre, Mosgiel, New Zealand,
Theresa Wilson AgResearch Molecular Biology Unit, Department of Biochemistry, University of Otago, Dunedin, New Zealand


title: 32D, trasducted with mt FLT3 number A046

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number A046

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number A046

value: trasducted with mt FLT3 number A046


title: 32D, trasducted with mt FLT3 number A492

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number A492

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number A492

value: trasducted with mt FLT3 number A492


title: 32D, trasducted with mt FLT3 number A264

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number A264

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number A264

value: trasducted with mt FLT3 number A264


title: 32D, trasducted with mt FLT3 number A425

description: Gene expression data from myeloblast-like cell line 32D transduced with mt FLT3 number A425

source_name: An immortalized myeloblast-like cell line 32D transduced with mt FLT3 number A425

value: trasducted with mt FLT3 number A425


title: 32D, trasducted with wt FLT3 Ligand, biological rep2

description: Gene expression data from myeloblast-like cell line 32D transduced with wt FLT3 Ligand

source_name: An immortalized myeloblast-like cell line 32D transduced with wt FLT3 Ligand

value: trasducted with wt FLT3 Ligand


title: 32D, biological rep2


title: P114-slide3_low


title: P114-slide4_low


title: P114-slide14_low


title: P114-slide8_normal


title: P114-slide9_normal


title: P114-slide7_normal


title: P114-slide6_normal


title: 32D, trasducted with wt FLT3 Ligand, biological rep1


title: P114-slide4_normal


title: P114-slide10_normal


title: P114-slide5_normal


title: 32D, trasducted with empty pLXRN vector, biological rep1


title: P114-slide3_normal


title: P114-slide13_low


title: P114-slide19_normal


title: P114-slide14_normal


title: P114-slide13_normal


title: P114-slide1_normal


title: P114-slide2_normal


title: P114-slide17_normal


title: P114-slide16_normal


title: P114-slide15_normal


title: P114-slide12_normal


title: P114-slide11_normal

description: For this experiment, 18 slides were used in a loop design which requires three aliquots of each test sample labeled alternately with the Cy5 and Cy3 dyes and co-hybridized on arrays with two other test samples. Data from a third treatment group will be published elsewhere. Definition of "normal" and "low" as used in the slide names : "Normal"  scan detects the majority of the differentially expressed spots excluding those with very low signal (undetectable) and with very high signal (saturated) ; "low" scan used a lower PMT setting to capture the very high signal (saturated) spots.  This was necessary to maximize the capture of all the relevant data (not possible with just one setting).

data_processing:
The method used as as in
Normalization of microarray data using a spatial mixed model analysis which includes splines
Bioinformatics
Volume 20 ,  Issue 17  (November 2004)
Pages: 3196 - 3205
Authors  David Baird   AgResearch, Lincoln, New Zealand,
Peter Johnstone   AgResearch, Invermay Research Centre, Mosgiel, New Zealand,
Theresa Wilson   AgResearch Molecular Biology Unit, Department of Biochemistry, University of Otago, Dunedin, New Zealand

extract_protocol: Total RNA was extracted using Trizol® Reagent (Invitrogen  Auckland, NZ), a modification of the acid guanidinium thiocyanate-phenol-chloroform extraction method according to the manufacturers’ protocol and incorporated the optional step (for tissues with high content of protein, fat, polysaccharides) during sample homogenization.


title: Patient 11006-4

status: Public on Sep 03 2009

city: Tokyo

first: TERAO

last: KIMIO

address: 2-1-1,Nihombashimuromachi, Chuo-ku

department: Clinicalpharmacology

institute: Chugai Pharmaceutical co.,ltd.

description: Gene expression in peripheral blood cells from RA patient

hyb_protocol: Ten microgram of the aminoallyl-labeled cRNA sample was vacuum-dried and the pellet was resuspended in 0.1 M sodium carbonate (pH 9.0) (Sigma). Then, the sample was coupled with Cy3 or Cy5 N-hydroxysuccinimide (Amersham Biosciences) prepared in DMSO (Wako) on the Vortexer for 1 h at room temperature in the dark. The sample was purified by RNeasy Mini kit (QIAGEN) to remove uncoupled dyes. The sample was mixed with RLT buffer. The sample was further mixed with ethanol (Wako) and applied to the column (RNeasy mini spin column). Then, the column was centrifuged at 9,100g  for 15 sec and washed by RW1 buffer by centrifugation at 9,100g  for 1 min. Furthermore, the column was washed by RPE buffer twice by centrifugation at 9,100g   for 15 sec and 2 min, respectively. The sample was eluted with of RNase-free water (QIAGEN) twice by centrifugation at 9,100g for 1 min. Cy3 or Cy5 labeled cRNA was denatured at 70°C for 5 min and mixed with 308 micro l of 1.25× hybridization buffer (pH 6.5), containing 4.25×SSC (Wako), 50% formamide (Kanto chemical), 0.94% SDS (GIBCO). Then, the hybridization solution was applied to Hitachi human oligo chip (Hitachi) and incubated at 45 °C for 19 h in the hybridization incubator (Taitec). The hybridized slide was washed for 10 min in the hybridization wash buffer #1 (Hitachi) by using the slide washer (BIOLABO), and further for 2 min in the hybridization wash buffer #3 (Hitachi) three times. The chip was centrifuged at 1,188g for 2 min to dry in 50 ml falcon tube and furthermore vacuum-dried. The three times of repeated hybridization experiment were performed separately for each blood sample.

scan_protocol: The hybridized slides were scanned by using Scan Array 5000 (GSI Lumonics) and two images with high- and low-photomultiplier gain setting per each slide were obtained. The raw signal intensity extraction was performed by using QuantArray software (Perkin Elmer).

data_processing: The signal intensity of the negative control was used for the background correction and that was extracted from the signal intensity of each spot. The signal intensity of every spot on the slide was normalized using the global normalization method.

source_name: RA Patient 11006

label_protocol: The pellet was suspended with DEPC water. In vitro transcription and aminoallyl labeling was performed using MEGAscript in vitro transcription kit (Ambion). The aminoallyl-labeled cRNA sample was mixed with RLT buffer, further mixed with ethanol (Wako) and applied to the column. Then, the column（RNeasy mini spin column）was centrifuged at 9,100g  for 15 sec and washed by RW1 buffer by centrifugation at 9,100g for 1 min. Furthermore, the column was washed by RPE buffer twice by centrifugation at 9,100g  for 15 sec and 2 min, respectively. The aminoallyl-labeled cRNA sample was eluted with RNase-free water (QIAGEN) twice by centrifugation at 9,100g  for 1 min.

extract_protocol: Peripheral blood was collected directly into PAXgene tubes (Qiagen). Total RNA was extracted using PAXgene Blood RNA kit with the optimal on-column DNase digestion accordinh to the manufactures’s instruction.

value: Female

tag: Disease

value: RA

source_name: Human peripheral blood leukocyte total RNA

extract_protocol: Supplied by BD Bioscience Clontech, USA

tag: Human leukocyte


title: Patient 11008-1

source_name: RA Patient 11008

tag: Gender


title: Patient 11008-2


title: Patient 11007-2

source_name: RA Patient 11007

value: Male


title: Patient 11008-3


title: Patient 11007-3


title: Patient 11008-4


title: Patient 11007-4


title: Patient 11005-4

source_name: RA Patient 11005


title: Patient 11006-2


title: Patient 11006-3


title: Patient 11006-1


title: Patient 11005-2


title: Patient 11005-1


title: P114-slide6_low

source_name: Mammary gland tissue


title: Patient 11007-1


title: Patient 11005-3


title: Patient 11003-4

source_name: RA Patient 11003


title: Patient 11004-4

source_name: RA Patient 11004


title: Patient 11004-3


title: Patient 11003-2


title: Patient 11004-2


title: Patient 11004-1


title: Patient 11003-3


title: Patient 11002-3

source_name: RA Patient 11002


title: Patient 11018-3

source_name: RA Patient 11018


title: Patient 11001-3

source_name: RA Patient 11001


title: Patient 11001-2


title: Patient 11015-2

hyb_protocol: Ten microgram of the aminoallyl-labeled cRNA sample was vacuum-dried and the pellet was resuspended in 0.1 M sodium carbonate (pH 9.0) (Sigma). Then, the sample was coupled with Cy3 or Cy5 N-hydroxysuccinimide (Amersham Biosciences) prepared in DMSO (Wako) on the Vortexer for 1 h at room temperature in the dark. The sample was purified by RNeasy Mini kit (QIAGEN) to remove uncoupled dyes. The sample was mixed with RLT buffer. The sample was further mixed with ethanol (Wako) and applied to the column (RNeasy mini spin column). Then, the column was centrifuged at 9,100g  for 15 sec and washed by RW1 buffer by centrifugation at 9,100g  for 1 min. Furthermore, the column was washed by RPE buffer twice by centrifugation at 9,100g   for 15 sec and 2 min, respectively. The sample was eluted with of RNase-free water (QIAGEN) twice by centrifugation at 9,100g for 1 min. Cy3 or Cy5 labeled cRNA was denatured at 70°C for 5 min and mixed with 308 l of 1.25× hybridization buffer (pH 6.5), containing 4.25×SSC (Wako), 50% formamide (Kanto chemical), 0.94% SDS (GIBCO). Then, the hybridization solution was applied to Hitachi human oligo chip (Hitachi) and incubated at 45 °C for 19 h in the hybridization incubator (Taitec). The hybridized slide was washed for 10 min in the hybridization wash buffer #1 (Hitachi) by using the slide washer (BIOLABO), and further for 2 min in the hybridization wash buffer #3 (Hitachi) three times. The chip was centrifuged at 1,188g for 2 min to dry in 50 ml falcon tube and furthermore vacuum-dried.

source_name: RA Patient 11015

extract_protocol: Supplyed by BD Bioscience Clontech, USA


title: Patient 11017-2

source_name: RA Patient 11017


title: Patient 11016-4

source_name: RA Patient 11016


title: Patient 11017-4


title: Patient 11016-2


title: Patient 11017-3


title: Patient 11002-4


title: Patient 11003-1


title: Patient 11018-4


title: Patient 11002-2


title: Patient 11018-1


title: Patient 11002-1


title: Patient 11018-2


title: Patient 11001-1

hyb_protocol: Ten microgram of the aminoallyl-labeled cRNA sample was vacuum-dried and the pellet was resuspended in 0.1 M sodium carbonate (pH 9.0) (Sigma). Then, the sample was coupled with Cy3 or Cy5 N-hydroxysuccinimide (Amersham Biosciences) prepared in DMSO (Wako) on the Vortexer for 1 h at room temperature in the dark. The sample was purified by RNeasy Mini kit (QIAGEN) to remove uncoupled dyes. The sample was mixed with RLT buffer. The sample was further mixed with ethanol (Wako) and applied to the column (RNeasy mini spin column). Then, the column was centrifuged at 9,100g  for 15 sec and washed by RW1 buffer by centrifugation at 9,100g  for 1 min. Furthermore, the column was washed by RPE buffer twice by centrifugation at 9,100g   for 15 sec and 2 min, respectively. The sample was eluted with of RNase-free water (QIAGEN) twice by centrifugation at 9,100g for 1 min. Cy3 or Cy5 labeled cRNA was denatured at 70°C for 5 min and mixed with 308 l of 1.25× hybridization buffer (pH 6.5), containing 4.25×SSC (Wako), 50% formamide (Kanto chemical), 0.94% SDS (GIBCO). Then, the hybridization solution was applied to Hitachi human oligo chip (Hitachi) and incubated at 45 °C for 19 h in the hybridization incubator (Taitec). The hybridized slide was washed for 10 min in the hybridization wash buffer #1 (Hitachi) by using the slide washer (BIOLABO), and further for 2 min in the hybridization wash buffer #3 (Hitachi) three times. The chip was centrifuged at 1,188g for 2 min to dry in 50 ml falcon tube and furthermore vacuum-dried. The three times of repeated hybridization experiment were performed separately for each blood sample.


title: Patient 11017-1


title: Patient 11016-1


title: Patient 11001-4


title: Patient 11015-4


title: Patient 11015-3


title: Patient 11016-3


title: Patient 11014-4

source_name: RA Patient 11014


title: Patient 11015-1


title: Patient 11014-3


title: Patient 11014-2


title: Patient 11010-4

source_name: RA Patient 11010


title: Patient 11011-2

source_name: RA Patient 11011


title: Patient 11013-4

source_name: RA Patient 11013


title: Patient 11010-3

source_name: Human peripheral blood leukocyte total RNA


title: Patient 11013-2


title: Patient 11014-1


title: Patient 11012-1

source_name: RA Patient 11012


title: Patient 11011-1


title: Patient 11011-4


title: Etsrp_RNA_injected_embryos_rep3

status: Public on Sep 01 2009

city: Tampa

first: Saulius

last: Sumanas

state: FL

address: 560 Channelside Dr

department: Department of Pathology and Cell Biology

institute: University of South Florida

description: No additional description.

hyb_protocol: RNA was hybridized to the microarrays for 16 hours at 42°C according to Nimblegen protocol.

scan_protocol: The arrays were washed, dried, and scanned at 5μm resolution using a GenePix 4000B microarray scanner (Molecular Devices, Sunnyvale, CA) by Nimblegen.

data_processing: Data were extracted from scanned images using NimbleScan software (Roche NimbleGen). Quantile normalization was performed across replicate arrays, and RMA (Robust Multichip Average) analysis was performed to generate gene expression values by Nimblegen. The data table contains gene-level data. The probe-level data linked as a supplementary file on a Series record.

organism: Danio rerio

source_name: Etsrp RNA-injected embryos, tailbud stage

label_protocol: RNA was converted into cDNA using the SuperScript II cDNA Conversion Kit (Invitrogen, Carlsbad, CA) by Nimblegen. Double-stranded cDNA was random-prime labeled with Cy3-nonamer by Nimblegen.

extract_protocol: Embryos were frozen on dry ice at the tailbud stage. Embryos were homogenized by passing 10 times through a 23 gauge needle. Total RNA was purified using the RNAquous-4PCR kit (Ambion) according to manufacturer's instructions.

tag: Strain 'Ekkwill';

tag: Stage

value: tailbud;

value: 150 Whole embryos


title: Control_embryos_rep3

description: No additional description.

source_name: Uninjected control embryos, tailbud stage


title: Patient 11013-3


title: Control_embryos_rep2

description: No additional description.


title: Patient 11012-3


title: Patient 11012-4


title: Etsrp_RNA_injected_embryos_rep2

description: No additional description.


title: Patient 11013-1


title: Patient 11010-1


title: Patient 11011-3


title: Patient 11009-2

source_name: RA Patient 11009


title: Patient 11010-2


title: Patient 11009-4


title: Control_embryos_rep1

description: No additional description.


title: Etsrp_RNA_injected_embryos_rep1

description: No additional description.


title: Patient 11009-3


title: Patient 11012-2


title: Patient 11009-1


title: RSV-infected Rice_15DAI_rep1

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

description:
RSV-infected rice at 15 DAI
Biological replicate 1 of 1

hyb_protocol: Kit: in situ Hybridization Plus Manufacturer: Agilent Technologies Manual: Agilent Technologies

scan_protocol: Scanner: Agilent DNA microarray scanner Manufacturer: Agilent Technologies Software: Scanner Control software Manual: Agilent Technologies

data_processing:
Software: Feature Extraction ver 9.5
Manufacturer: Agilent Technologies
Manual: Agilent Technologies
Normalization algorithm: Lowess

organism: Oryza sativa Japonica Group

source_name: Rice, infected with rice stripe virus, 15 days after inoculation

label_protocol:
Kit: Low RNA Input Linear Amplification Kit
Manufacturer: Agilent Technologies
Manual: Low RNA Input Linear Amplification Kit standard protocol

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media: commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 15 DAI

extract_protocol:
Separation: trimming
Extraction source: frozen
Extraction source: shoots pooled from 5 individual plants
Kit: Qiagen Rneasy Maxi Kit
Manual: Qiagen

treatment_protocol:
Growth environment: growth chamber study (W: 34cm, D: 26cm, H: 34cm)
Growth stage: two leaves visible
Light condition: continuous light
Temperature: 25±3℃
Virus inoculation: Rice Stripe Virus
Virus inoculation: five viruliferous small brown planthoppers (Laodelphax striatellus) per 1 seedling
Virus inoculation: 24 hours

tag: Cultivar

value: Nipponbare

value: shoot

source_name: Rice, mock-infected, 15 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 15 DAI

treatment_protocol:
Growth environment: growth chamber study (W: 34cm, D: 26cm, H: 34cm)
Light condition: continuous light
Temperature: 25±3℃
Virus inoculation: mock inoculation
Virus inoculation: five virus-free small brown planthoppers (Laodelphax striatellus) per 1 seedling
Virus inoculation: 24 hours


title: Stress

status: Public on Aug 09 2009

city: Suwon

first: Sangdun

last: Choi

address: Woncheon-dong, Yeongtong-gu

department: Department of Molecular Science and Technology

country: South Korea

institute: Ajou University

description: red ginseng effects on immobilization stressed mice brain

hyb_protocol: Add HYB solution to each cRNA sample. Preheat the assay sample at 65°C for 5 minutes. Dispense assay sample onto the large sample port of each array. Seal lid onto the Hyb Chamber carefully to avoid dislodging the Hyb Chamber insert(s). Incubate for 16-20 hours at 58°C with rocker speed at 5.

scan_protocol: Hardware : Beadstation 500GX, Software : Beadstudio Analysis software

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method, which were then used for fitting of a non-linear normalization curve.

source_name: primary brain from stressed mice

label_protocol: After hybridization, washing and blocking with E1 buffer, Pipette 2 ml Block E1 buffer + streptavidin-Cy3 into fresh wash tray. Transfer the BeadChip, face up, into wash tray(s) on rocker. Place cover on tray and rock at medium speed for 10 minutes

growth_protocol: Housed in a temperature-controlled environment for 12 - h under dark: 12 - h light cycle under the condition where food and water were freely available.

extract_protocol: Total RNA of mouse brain was isolated by using TRIzol reagent (Invitrogen, U.S.A.) and purified using RNeasy mini kit (Qiagen, U.S.A.) according to the manufacturer’s instructions.

treatment_protocol: Mice were divided into three groups (3 mice / group): control, stress + no treat, and stress + Korean Red Ginseng (KRG, 100 mg). Stress + KRG group were given KRG  100 mg orally for 7 days and then exposed to immobilization stress for 45 min. stress + no treat group were administrated with phosphate buffer saline (d-PBS, pH 7.4) together with IMO stress for 45 min. For stress experiments, mice were immobilized for 45 min in tightly fitted, 50 ml conical tube. After immobilization stress, the animals were immediately decapitated, and the brain was rapidly extracted and frozen.

tag: Male ICR mice (20 - 25 g, Orient Co., Korea)


title: RSV-infected Rice_12DAI_rep1

description:
RSV-infected rice at 12 DAI
Biological replicate 1 of 3

source_name: Rice, infected with rice stripe virus, 12 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media: commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 12 DAI

tag: Tissue

source_name: Rice, mock-infected, 12 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 12 DAI


title: RSV-infected Rice_6DAI_rep1

description:
RSV-infected rice at 6 DAI
Biological replicate 1 of 3

source_name: Rice, infected with rice stripe virus, 6 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media: commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 6 DAI

source_name: Rice, mock-infected, 6 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 6 DAI


title: RSV-infected Rice_6DAI_rep2

description:
RSV-infected rice at 6 DAI
Biological replicate 2 of 3


title: Control 1

source_name: primary brain from control mice


title: RSV-infected Rice_12DAI_rep3

description:
RSV-infected rice at 12 DAI
Biological replicate 3 of 3


title: Control 2


title: Chip_day_14

status: Public on Aug 01 2009

city: Dresden

first: Philipp

middle: Friedrich

last: Seib

address: Hohe Strasse 6

department: Max Bergmann Centre for Biomaterials Dresden

country: Germany

institute: Leibniz Institute for Polymer Research

hyb_protocol: Corresponding Cy3- and Cy5-labeled samples were combined and hybridised overnight on a PIQOR Stem Cell Microarray (Miltenyi Biotec) employing a-Hyb hybridisation station.

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

data_processing: Mean signal and local background intensities were determined for each spot on the array using ImaGen software (Biodiscovery, El Segundo USA). Spots were analysed using PIQOR analyser software that included background substration to obtain the net signal intensity, data normalisation and subsequent calculations of the Cy5/Cy3 ratios.

source_name: MSC cultured on plasma-treated polystyrene for 14 days

label_protocol: For cDNA samples, 250 ng of sample was labeled with Cy3 according to the Miltenyi Biotec protocol (proprietary protocol).

growth_protocol: MSC were cultured on plasma-treated polystyrene for 14 days

extract_protocol: RNA was isolated using NucleoSpin RNA II columns (Macherey-Nagel, Düren Germany) according to the manufacturer’s protocol. The quality of the RNA was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara USA) yielding RNA integrity numbers of 7.3–9.9. Due to the low yields of RNA, samples were amplified using SuperAmp Service at Miltenyi Biotec, employing a global polymerase chain reaction (PCR) protocol (proprietary protocol). The integrity of the cDNA was verified using the Agilent 2100 Bioanalyzer and the total amount of cDNA ranged from 2.9–3.7 μg and the average length of the highly amplified cDNA products was 200–1,000 bp.

tag: Bone marrow-derived human multipotent mesenchymal stromal cells

source_name: MSC cultured on human cancellous bone for 14 days

label_protocol: For cDNA samples, 250 ng of sample was labeled with Cy5 according to the Miltenyi Biotec protocol (proprietary protocol).

growth_protocol: MSC were cultured on human cancellous bone for 14 days


title: RSV-infected Rice_9DAI_rep1

description:
RSV-infected rice at 9 DAI
Biological replicate 1 of 3

source_name: Rice, infected with rice stripe virus, 9 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media: commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 9 DAI

source_name: Rice, mock-infected, 9 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 9 DAI


title: RSV-infected Rice_3DAI_rep3

description:
RSV-infected rice at 3 DAI
Biological replicate 3 of 3

source_name: Rice, infected with rice stripe virus, 3 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media: commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 3 DAI

source_name: Rice, mock-infected, 3 days after inoculation

growth_protocol:
Growth environment: greenhouse study
Growth: pot culture (D: 85mm x H: 75mm)
Growth media commercial soil (Bonsol: Sumitomo Chemical, Osaka, Japan)
No of seedlings per pot: 14
Light condition: natural conditions
Temperature: 25±3℃
Growth length: 3 DAI


title: RSV-infected Rice_6DAI_rep3

description:
RSV-infected rice at 6 DAI
Biological replicate 3 of 3


title: RSV-infected Rice_9DAI_rep2

description:
RSV-infected rice at 9 DAI
Biological replicate 2 of 3


title: RSV-infected Rice_9DAI_rep3

description:
RSV-infected rice at 9 DAI
Biological replicate 3 of 3


title: Chip_day_3

description: Mean signal and local background intensities were determined for each spot on the array using ImaGen software (Biodiscovery, El Segundo USA).

source_name: MSC cultured on plasma-treated polystyrene for 3 days

growth_protocol: MSC were cultured on plasma-treated polystyrene for 3 days

source_name: MSC cultured on human cancellous bone for 3 days

growth_protocol: MSC were cultured on human cancellous bone for 3 days


title: Collagen_Hyaluronic_acid_day6

source_name: MSC cultured on plasma-treated polystyrene for 6 days

growth_protocol: MSC were cultured on plasma-treated polystyrene for 6 days

source_name: MSC cultured on engineered collagen-Hyaluronic acid surfaces for 6 days

growth_protocol: MSC were cultured on engineered collagen-Hyaluronic acid surfaces for 6 days


title: RSV-infected Rice_3DAI_rep1

description:
RSV-infected rice at 3 DAI
Biological replicate 1 of 3


title: RSV-infected Rice_12DAI_rep2

description:
RSV-infected rice at 12 DAI
Biological replicate 2 of 3


title: RSV-infected Rice_3DAI_rep2

description:
RSV-infected rice at 3 DAI
Biological replicate 2 of 3


title: Collagen_Hyaluronic_acid_day3

source_name: MSC cultured on engineered collagen-Hyaluronic acid surfaces for 3 days

growth_protocol: MSC were cultured on engineered collagen-Hyaluronic acid surfaces for 3 days


title: Collagen_day3

source_name: MSC cultured on engineered collagen surfaces for 3 days

growth_protocol: MSC were cultured on engineered collagen surfaces for 3 days


title: Collagen_Hep_day14

source_name: MSC cultured on engineered collagen-heparin surfaces for 14 days

growth_protocol: MSC were cultured on engineered collagen-heparin surfaces for 14 days


title: MSC_Collagen_day14

source_name: MSC cultured on engineered collagen surfaces for 6 days

growth_protocol: MSC were cultured on engineered collagen surfaces for 6 days


title: Tropo_day14

source_name: MSC cultured on engineered tropocollagen surfaces for 14 days

growth_protocol: MSC were cultured on engineered tropocollagen surfaces for 14 days


title: Collagen_Hep_day6

source_name: MSC cultured on engineered collagen-heparin surfaces for 6 days

growth_protocol: MSC were cultured on engineered collagen-heparin surfaces for 6 days


title: Collagen_Hep_day3

source_name: MSC cultured on engineered collagen-heparin surfaces for 3 days

growth_protocol: MSC were cultured on engineered collagen-heparin surfaces for 3 days


title: Chip_day_6

source_name: MSC cultured on human cancellous bone for 6 days

growth_protocol: MSC were cultured on human cancellous bone for 6 days


title: Tropocollagen_day6

source_name: MSC cultured on engineered tropocollagen surfaces for 6 days

growth_protocol: MSC were cultured on engineered tropocollagen surfaces for 6 days


title: Collagen_Hyaluronic_acid_day14

source_name: MSC cultured on plasma-treated polystyrene for 14 days

growth_protocol: MSC were cultured on plasma-treated polystyrene for 14 days

source_name: MSC cultured on engineered collagen-Hyaluronic acid surfaces for 14 days

growth_protocol: MSC were cultured on engineered collagen-Hyaluronic acid surfaces for 14 days


title: Tropocollagen_day3

source_name: MSC cultured on plasma-treated polystyrene

growth_protocol: MSC were cultured on plasma-treated polystyrene

source_name: MSC cultured on engineered tropocollagen surfaces

growth_protocol: MSC were cultured on engineered tropocollagen surfaces


title: Collagen_day6


title: Stress + KRG

source_name: primary brain from stressed mice with KRG treatment

growth_protocol: Housed in a temperature-controlled environment for 12 - h under dark: 12 - h light cycle under the condition where food and water were freely available.


title: Calf 151 gd T cells PBS

status: Public on Feb 10 2009

city: Bozeman

first: Jodi

middle: Fern

last: Hedges

state: MT

address: 960 Technology Blvd.

department: Veterinary Molecular Biology

institute: Montana State University

description: gd T cells derived from peripheral blood of calf 151 stimulated 4 hours with PBS

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix GeneChip Operating Software V.1.2

label_protocol: RNA was amplified using Affymetrix One-cycle protocol with approximately 1.7 micrograms of total RNA as described in the GeneChip® Expression Analysis Technical Manual (June 2004).

extract_protocol: PBLs were stained with GD3.8, and anti-Mouse IgG magnetic beads and sorted with MACS magnetic bead system (Miltenyi Biotec) as previously described to a purity of >98%.  Sorted cells were rested overnight then stimulated for 4 hours, lysed in Buffer RLT and genomic DNA sheared using Qiashredder columns then frozen at -80oC.  RNA was extracted following the manufacturer’s protocol for RNeasy (Qiagen) column purification.

tag: purified gd T cells derived from peripheral blood stimulated with PBS for 4 hours


title: 345365

status: Public on Jun 01 2009

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
LynDN-1 vs WT-1
Date:2008/06/26

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

label_protocol: Ambion

extract_protocol: Qiagen

value: skin


title: Calf 151 gd T cells MDP

description: gd T cells derived from peripheral blood of calf 151 stimulated 4 hours with MDP

tag: purified gd T cells derived from peripheral blood stimulated with MDP for 4 hours


title: 345362

description:
WT-1 vs LynDN-1
Date:2008/06/26


title: 345364

description:
WT-2 vs LynDN-3
Date:2008/06/26


title: 345363

description:
WT-3 vs LynDN-2
Date:2008/06/25


title: 0 hour N2B27 treatment-library1-replicate2

status: Public on Dec 31 2008

city: shanghai

first: huang

last: bing

state: shanghai

address: yueyang road 320

department: chemistry

institute: Chinese Academy of Sciences

description: analysis of mouse microRNAs expression under neural differentiation

hyb_protocol: Microscope glass slides were activated as described.The antisense sequences of microRNAs were used for probes. The melting temperatures of all probes were adjusted to 55 ± 3 °C as described.In addition, each probe contains a 5′ C6-amino modified 10 deoxyadenosines spacer at the 5′ end of the probe.The probes were dissolved in printing buffer (2× SSC/1 M betaine hydrochloride/5% formamide/0.01% SDS, pH 8.5) at the concentration of 20 μM, and then printed onto the epoxy coated slides with PixSys 5500 spotting robot in quadruplicate under 60% humidity. The printed microarrays were further chemically covalently coupled under 60% humidity overnight. Before hybridization, printed microarrays were quenched by quenching buffer (0.1 M Tris–HCl/50 mM ethanolamine, pH 8.0). Small RNA cDNA libraries of samples were amplified and labeled by PCR using the 5′primer (5′-Cy5-CTGGAATTCTGACGATCTGC) and the 3′primer (5′-ACCGAATTCACAGTCAGACC) as described [11]. The PCR product was precipitated, washed, resuspended in 10 μl ddH2O, and cleaned up by a Sephadex G-50 column. Heat the PCR product at 95 °C for 3 min to denature and chill on ice immediately. Combine the PCR product with equal volume of 2× hybridization buffer (8× SSC/0.2% SDS, pH 7.0) that has been heated to 48 °C and mix thoroughly. Immediately, inject the mixture into the hybridization chamber. Hybridization was carried out at 45 °C for 16 h. After hybridization, slides were washed (2× SSC/0.03% SDS, 2 min; 0.2× SSC, 2 min; 0.1× SSC, 1 min) at 25 °C.

scan_protocol: scaned by ScanArray5000

data_processing: Signal intensities for each spot were calculated by subtracting local background from total intensities. No further process was performed.

source_name: P19C6, N2B27 treated, 0 hour

label_protocol: labeled by PCR using a Cy5 labeled primer

extract_protocol: The total RNAs were extracted with the RNarose reagent (Watson and Sangon).

treatment_protocol: For N2B27 induction,nearly confluent P19 cells were dissociated into single cells by Trypsin-EDTA ,and allowed to aggregate in the bacteriological petri dishes at a seeding density of 1 × 105/ml in N2B27 medium (1:1 mix of DMEM/F12 supplemented with 25 μg/ml insulin, 100 μg/ml apo-transferrin, 6 ng/ml progesterone, 16 μg/ml putrescine, 30 nM sodium selenite, 50 μg/ml bovine serum albumin fraction V, and neurobasal medium supplemented with B27 without Vitamin A). After 4 days of culture in suspension, the cell aggregates were collected, rinsed once with phosphate-buffered saline (PBS), fixed in 4% paraformaldehyde for 30 min, incubated in 20% sucrose overnight, embedded in cryomedium OCT,cryo-sectioned at a thickness of 15 μm, and stored at −20°C for further use. The factors and inhibitors, such as bone morphogenetic protein 4 (BMP4) (10 ng/ml), Noggin (100 ng/ml), SU5402 (5 μM), U0126 (5 μM), Wortmannin (100 nM), or U73122 (100 nM), were added at the beginning of the suspension culture, and were present throughout the experiments. To caudalize the N2B27-induced neural stem cells, the RA (2 μM) was added to the N2B27 medium for another 2–4 days, and the cell aggregates cultured in N2B27 medium for 6–8 days served as the control.

tag: P19C6, a subclone of the mouse EC P19 cell line

tag: 0 hour treatment


title: 0 hour N2B27 treatment-library1-replicate3


title: Calf 150 gd T cells PBS

description: gd T cells derived from peripheral blood of calf 150 stimulated 4 hours with PBS