title: Tumor_179

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71342.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.98; Parameter Scan Time = 11:43:56; Parameter PMT Volts = 470; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15734; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.98; Parameter Scan Time = 11:43:56; Parameter PMT Volts = 510; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258483; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.45; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: 00PB697

status: Public on Aug 09 2007

type: RNA

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47447.gif

hyb_protocol: not provided

scan_protocol: na Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5040; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Lars,,Bullinger Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 23:20:30; Parameter PMT Volts = 600; Parameter Scan Date = 2003-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 127594; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.76; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.81; Parameter Scan Time = 23:20:30; Parameter PMT Volts = 740; Parameter Scan Date = 2003-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 346565; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.91; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger

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

molecule: total RNA

organism: Homo sapiens

source_name: CRH

label_protocol: not provided

extract_protocol: not provided

tag: CRH

source_name: 00PB697; Sample source=PB; CBF group=inv(16)


title: OVX-34 vs 26695/J99 mix

type: genomic

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68907.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1840, 9130; Parameter Datafile type = GenePix Results 3; 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 Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.55; Parameter Scan Time = 11:45:51; Parameter PMT Volts = 630; Parameter Scan Date = 2006-06-09; Parameter Pixel Size = 10; Parameter Laser on time = 86935; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.47; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.55; Parameter Scan Time = 11:45:51; Parameter PMT Volts = 760; Parameter Scan Date = 2006-06-09; Parameter Pixel Size = 10; Parameter Laser on time = 87362; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.65; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama

molecule: genomic DNA

organism: Helicobacter pylori

source_name: 0.5 ug genomic DNA OVX-34

tag: 0.5 ug genomic DNA OVX-34


title: GVA 104 90d B vs OVX-34

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/69057.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2120, 8880; Parameter Datafile type = GenePix Results 3; 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 Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.04; Parameter Scan Time = 13:29:35; Parameter PMT Volts = 590; Parameter Scan Date = 2006-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 87197; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 33.04; Parameter Scan Time = 13:29:35; Parameter PMT Volts = 830; Parameter Scan Date = 2006-06-29; Parameter Pixel Size = 10; Parameter Laser on time = 87623; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.68; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama

source_name: 0.5 ug genomic DNA GVA 104 90d B

tag: 0.5 ug genomic DNA GVA 104 90d B


title: OVX-34 vs 26695/J99 mix-2

description:
Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68912.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2040, 8560; Parameter Datafile type = GenePix Results 3; 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 Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 09:21:15; Parameter PMT Volts = 630; Parameter Scan Date = 2006-06-14; Parameter Pixel Size = 10; Parameter Laser on time = 87026; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.73; Parameter Scan Time = 09:21:15; Parameter PMT Volts = 890; Parameter Scan Date = 2006-06-14; Parameter Pixel Size = 10; Parameter Laser on time = 87452; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama


title: WT_vs_DNMT3b

status: Public on Aug 08 2007

city: Baltimore

first: Wayne

last: Yu

state: MD

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufecturer's recommended 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 after background subtraction and loess normalization as implemented in the Limma package from Bioconductor

source_name: Wild type HCT116

label_protocol: Agilent Low RNA Input Linear Amplification Kit using manufacturer's recommended protocol

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

extract_protocol: TriZol extraction followed by RNeasy clean-up with on-column DNase treatment

tag: HCT116 human colorectal cancer cell line

source_name: DNMT3b deficient HCT116


title: WT_vs_DKO

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

source_name: DNMT1 and DNMT3b deficient HCT116


title: WT_vs_DNMT1

source_name: DNMT1 deficient HCT116


title: AR-knockdown

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54496.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1720, 4840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 11:54:27; Parameter PMT Volts = 580; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 185449; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.75; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.70; Parameter Scan Time = 11:54:27; Parameter PMT Volts = 580; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 404417; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.65; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: Stratagene Universal Human Reference RNA

source_name: AR-knockdown Total RNA

tag: AR-knockdown Total RNA


title: DNMT3b_vs_WT


title: Tumor_175

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71341.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.26; Parameter Scan Time = 12:00:21; Parameter PMT Volts = 470; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15751; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 29.26; Parameter Scan Time = 12:00:21; Parameter PMT Volts = 520; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258500; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.46; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler

source_name: Universal Human Reference

label_protocol: Human Cy3 - Chen et al; Incorporation of Cy3-labeled deoxynucleotides was as described (Chen et al., Mol Biol Cell,2002).; Protocol Type = Labeling; Performer: Adam,,Adler

extract_protocol:
StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Adam,,Adler
MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Adam,,Adler

tag: Universal Human Reference

label_protocol: Human Cy5 - Chen et al; Incorporation of Cy5-labeled deoxynucleotides was as described (Chen et al., Mol Biol Cell, 2002).; Protocol Type = Labeling; Performer: Adam,,Adler

extract_protocol:
Primary Tumor; RNA was obtained from primary tumor sample.; Protocol Type = Biological Sample; Performer: Adam,,Adler
MessageAmpII; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Adam,,Adler


title: Differential methylation profile of monocyte vs testis, array1, repl.1

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description: Comparative hybridization of MCIp-depleted hypomethylated DNA-fragements from human testis versus male monocytes

hyb_protocol: Hybridisation was performed using the Agilent oligo aCGH Hybridization Kit (Agilent Technologies, Boeblingen, Germany).

scan_protocol: Images were scanned using a DNA Microarray Scanner (Agilent).

data_processing: Microarray images were processed using Feature Extraction Software 8.5 (Agilent Technologies, Boeblingen, Germany) using the standard CGH protocol and a rank consistent list of normalization genes. The latter contained all probes with a CpG index above 78 (more than 78 CpG residues in a region of 350 bp upstream and downstream of a probe). Processed data was imported into Microsoft Office Excel 2003 for further analysis.

label: Alexa Fluor 555

source_name: Human peripheral blood monocyte

label_protocol: DNA fragments were labelled using the BioPrime Plus Array CGH Genomic Labeling System (Invitrogen, Carlsbad, CA).

growth_protocol: Peripheral blood mononuclear cells were separated by leukapheresis of healthy male donors, followed by density gradient centrifugation over Ficoll/Hypaque. Monocytes were isolated from mononuclear cells by countercurrent centrifugal elutriation in a J6M-E centrifuge (Beckman, Muenchen, Germany)

extract_protocol: Genomic DNA (gDNA) from monocytes was prepared using the Blood and Cell Culture DNA Midi Kit from Qiagen (Hilden, Germany) and fragmented to a mean size of 400-500 bp by ultrasonication. Hypomethylated DNA-fragments were obtained using Methyl-CpG-Immunoprecipitation (MCIp)

tag: healthy donor, gender male

label: Alexa Fluor 647

source_name: Human testis

extract_protocol: Genomic testis DNA (gDNA) was fragmented to a mean size of 400-500 bp by ultrasonication. Hypomethylated DNA-fragments were obtained using Methyl-CpG-Immunoprecipitation (MCIp)

tag: gender male


title: 00PB711

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47448.gif

scan_protocol: na Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Lars,,Bullinger Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 23:33:18; Parameter PMT Volts = 600; Parameter Scan Date = 2003-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 127608; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.90; Parameter Scan Time = 23:33:18; Parameter PMT Volts = 720; Parameter Scan Date = 2003-10-12; Parameter Pixel Size = 10; Parameter Laser on time = 346578; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.91; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger

source_name: 00PB711; Sample source=PB; CBF group=t(8;21)


title: Differential methylation profile of brain vs testis, array1, repl.2

description: Comparative hybridization of MCIp-depleted hypomethylated DNA-fragements from human testis versus male brain

source_name: Human brain

extract_protocol: Genomic DNA (gDNA) was fragmented to a mean size of 400-500 bp by ultrasonication. Hypomethylated DNA-fragments were obtained using Methyl-CpG-Immunoprecipitation (MCIp)


title: Differential methylation profile of brain vs testis, array1, repl.1


title: Differential methylation profile of monocyte vs testis, array1, repl.2


title: 02PB2036

description:
Simple annotation: Myeloid Leukemias, Acute Myeloid Leukemia
Image: http://smd.stanford.edu/MicroArray/gifs/2003-12/47494.gif

scan_protocol: na Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Lars,,Bullinger Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 02:32:18; Parameter PMT Volts = 620; Parameter Scan Date = 2003-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 123453; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.00; Parameter Scan Time = 02:32:18; Parameter PMT Volts = 690; Parameter Scan Date = 2003-10-02; Parameter Pixel Size = 10; Parameter Laser on time = 342423; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.97; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lars,,Bullinger

source_name: 02PB2036; Sample source=PB; CBF group=inv(16)


title: DNMT1_vs_WT

source_name: wild type HCT116


title: Tumor_127

description:
Simple annotation: Liver, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71339.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 4360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Adam,,Adler Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 11:08:15; Parameter PMT Volts = 490; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 15699; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 28.25; Parameter Scan Time = 11:08:15; Parameter PMT Volts = 520; Parameter Scan Date = 2006-12-06; Parameter Pixel Size = 10; Parameter Laser on time = 258448; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [84947]; Parameter Laser Power = 3.44; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Adam,,Adler


title: 5Aza_vs_mock

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

source_name: 5Aza-treated HCT116

label_protocol: Agilent low RNA input linear amplification kit

growth_protocol: McCoys 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: 5 micromolar 5Aza for 96 hours

source_name: mock-treated HCT116

treatment_protocol: 1x PBS for 96 hours


title: TSA_vs_mock

source_name: TSA treated HCT116

label_protocol: Agilent Low RNA Input Linear Amplification Kit using manufecturer's recommendated protocol

treatment_protocol: 300 nanomolar TSA for 18 hour


title: C4-2B

status: Public on Aug 07 2007

city: Ann Arbor

first: Scott

last: Tomlins

state: MI

address: 1400 E. Medical Center Dr., 5410 CCGC

department: Pathology

institute: University of Michigan

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization. Only features passing standard Agilent Feature Extraction filtering on all four arrays were used to identify differentially expressed features between LNCaP and C4-2B

source_name: Clontech prostate pool (CPP)

label_protocol: One ug 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).

growth_protocol: LNCaP was grown in RPMI with 10% fetal bovine serum. C4-2B was grown in T-medium (Invitrogen) with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.

treatment_protocol: Cells were not treated prior to RNA extraction.

tag: Commercially available pooled benign prostate tissue total RNA

tag: prostate cancer cell line, androgen insensitive derivative of LNCaP


title: Differential methylation profile of brain vs testis, array2, repl.1


title: Differential methylation profile of monocyte vs testis, array2, repl.2


title: LNCaP

source_name: LNCaP

tag: prostate cancer cell line, androgen sensitive


title: RWPE-ETV1_dye_rep2

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization. To identify differentially expressed features, we filtered the data to only include features showing significant differential expression in (PValueLogRatio < 0.01) in all four hybridizations with at least 2 fold average over- or under-expression (LogRatio) after dye flip correction.

growth_protocol: RWPE-GUS or RWPE-ETV1 cells were maintained in Keratinocyte-SFM supplemented with bovine pituitary extract (25 mg/ 500 ml) human recomninant EGF (2.5 ug/500 ml medium) and 3ug/ml blasticidin

tag: benign prostate cell line RWPE stably expressing ETV1

source_name: RWPE-GUS

tag: benign prostate cell line RWPE stably expressing the GUS control gene


title: Primary human neuroblastoma cS204

status: Public on Aug 06 2007

city: Chiba

first: Akira

last: Nakagawara

address: 666-2 Nitona, Chuoh-ku

country: Japan

institute: Chiba Cancer Center Research Institute

description: The 500-ng aliquots of tumors and reference DNAs were labeled by random priming with each Cy3-dCTP and Cy5-dCTP (Amersham Pharmacia, Piscataway, NJ). Hybridization was performed as previously reported [Pinkel D. et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998;20:207-11.].

data_processing: UCSF Spot and UCSF Sproc programs to analyze values for spotted clones [Jain A.N. et al. Fully automatic quantification of microarray image data. Genome Res 2002;12:325-32.] were used.

tag: Primary human neuroblastoma

source_name: normal human reference genomic DNA

tag: normal human reference genomic DNA


title: Primary human neuroblastoma cS197


title: Primary human neuroblastoma cS175


title: RWPE-ETV1_rep2


title: DKO_vs_WT

source_name: DNMT1 and DNMT3b deficient HCT116

source_name: Wild type HCT116


title: C4-2B_dye


title: Primary human neuroblastoma cS166


title: CS

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54486.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1560, 5040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 11:19:41; Parameter PMT Volts = 570; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 185414; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.33; Parameter Scan Time = 11:19:41; Parameter PMT Volts = 620; Parameter Scan Date = 2004-08-06; Parameter Pixel Size = 10; Parameter Laser on time = 404382; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.64; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

source_name: Stratagene Universal Human Reference RNA

source_name: CS Total RNA

tag: CS Total RNA


title: Differential methylation profile of brain vs testis, array2, repl.2


title: RWPE-ETV1_rep1


title: Primary human neuroblastoma cS203


title: RWPE-ETV1_dye_rep1


title: LNCaP_dye


title: Primary human neuroblastoma cS165


title: Primary human neuroblastoma cS151


title: Primary human neuroblastoma cS152


title: DHT

description:
Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54491.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 5440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Hongjuan,,Zhao Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.00; Parameter Scan Time = 12:14:21; Parameter PMT Volts = 580; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 180158; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.41; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.00; Parameter Scan Time = 12:14:21; Parameter PMT Volts = 590; Parameter Scan Date = 2004-08-05; Parameter Pixel Size = 10; Parameter Laser on time = 544962; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Hongjuan,,Zhao

tag: Stratagene Universal Human Reference RNA

source_name: DHT Total RNA

tag: DHT Total RNA


title: Primary human neuroblastoma cS153


title: Primary human neuroblastoma cS095


title: Primary human neuroblastoma cS048


title: Primary human neuroblastoma cS059


title: Primary human neuroblastoma cS062


title: Primary human neuroblastoma cS058


title: Primary human neuroblastoma cS039


title: Primary human neuroblastoma cS066


title: Primary human neuroblastoma cS268


title: Primary human neuroblastoma cS265


title: Primary human neuroblastoma cS083


title: Primary human neuroblastoma cS269


title: Primary human neuroblastoma cS263


title: Primary human neuroblastoma cS266


title: Primary human neuroblastoma cS092


title: Primary human neuroblastoma cS034


title: Primary human neuroblastoma cS264


title: Primary human neuroblastoma cS267


title: Primary human neuroblastoma cS262


title: Primary human neuroblastoma cS065


title: Primary human neuroblastoma cS030


title: Primary human neuroblastoma cS010


title: Primary human neuroblastoma cS259


title: Primary human neuroblastoma cS261


title: Primary human neuroblastoma cS260


title: Primary human neuroblastoma cS256


title: Primary human neuroblastoma cS257


title: Primary human neuroblastoma cS258


title: Primary human neuroblastoma cS254


title: Primary human neuroblastoma cS255


title: Primary human neuroblastoma cS253


title: Primary human neuroblastoma cS242


title: Primary human neuroblastoma cS246


title: Primary human neuroblastoma cS245


title: Primary human neuroblastoma cS249


title: Primary human neuroblastoma cS247


title: Primary human neuroblastoma cS244


title: Primary human neuroblastoma cS250


title: Primary human neuroblastoma cS248


title: Primary human neuroblastoma cS237


title: Primary human neuroblastoma cS241


title: Primary human neuroblastoma cS238


title: Primary human neuroblastoma cS239


title: Primary human neuroblastoma cS252


title: Primary human neuroblastoma cS243


title: Primary human neuroblastoma cS235


title: Primary human neuroblastoma cS233


title: Primary human neuroblastoma cS228


title: Primary human neuroblastoma cS232


title: Primary human neuroblastoma cS230


title: Primary human neuroblastoma cS227


title: Primary human neuroblastoma cS240


title: Primary human neuroblastoma cS234


title: Primary human neuroblastoma cS251


title: Primary human neuroblastoma cS236


title: Primary human neuroblastoma cS229


title: Primary human neuroblastoma cS223


title: Primary human neuroblastoma cS225


title: Primary human neuroblastoma cS212


title: Primary human neuroblastoma cS222


title: Primary human neuroblastoma cS215


title: Primary human neuroblastoma cS216


title: Primary human neuroblastoma cS213


title: Primary human neuroblastoma cS217


title: Primary human neuroblastoma cS218

source_name: Primary human neuroblastoma


title: Primary human neuroblastoma cS194


title: Primary human neuroblastoma cS193


title: Primary human neuroblastoma cS220


title: Primary human neuroblastoma cS196


title: Primary human neuroblastoma cS226


title: Primary human neuroblastoma cS221


title: Differential methylation profile of monocyte vs testis, array2, repl.1

source_name: Human peripheral blood monocyte

source_name: Human testis


title: Primary human neuroblastoma cS192


title: Primary human neuroblastoma cS191


title: Primary human neuroblastoma cS202


title: Primary human neuroblastoma cS210


title: Primary human neuroblastoma cS211


title: Primary human neuroblastoma cS208


title: Primary human neuroblastoma cS206


title: Primary human neuroblastoma cS207


title: Primary human neuroblastoma cS224


title: Primary human neuroblastoma cS190


title: Primary human neuroblastoma cS188


title: Primary human neuroblastoma cS189


title: Primary human neuroblastoma cS214


title: Primary human neuroblastoma cS187


title: Primary human neuroblastoma cS186


title: Primary human neuroblastoma cS183


title: Primary human neuroblastoma cS185


title: Primary human neuroblastoma cS180


title: Primary human neuroblastoma cS179


title: Primary human neuroblastoma cS181


title: Primary human neuroblastoma cS173


title: Primary human neuroblastoma cS161


title: Primary human neuroblastoma cS177


title: Primary human neuroblastoma cS182


title: Primary human neuroblastoma cS160


title: Primary human neuroblastoma cS164


title: Primary human neuroblastoma cS172


title: Primary human neuroblastoma cS163


title: Primary human neuroblastoma cS159


title: Primary human neuroblastoma cS169


title: Primary human neuroblastoma cS168


title: Primary human neuroblastoma cS167


title: Primary human neuroblastoma cS219


title: Primary human neuroblastoma cS170


title: Primary human neuroblastoma cS157


title: Primary human neuroblastoma cS158


title: Primary human neuroblastoma cS184


title: Primary human neuroblastoma cS156


title: Primary human neuroblastoma cS174


title: UO-31 hgu95d

city: Bethesda

first: Uma

middle: T

last: Shankavaram

address: 9000 Rockville Pike

department: NCI

institute: NIH

hyb_protocol: Affymetrix Hybridization Protocol; The exact protocol is not available.          But Standard Operating Proceadure can be found at          http://www.affymetrix.com/support/technical/manual/expression_manual.affx          or          http://www.affymetrix.com/Auth/support/downloads/manuals/expression_ever_manual.zip          Manual number: 701025 Revision 6, page 2.2.3; Protocol Type = hybridization; Parameter Chamber type = Affymetrix- GeneChip Hyb Oven 640; Parameter Quantity of label target used = 100; Parameter Time = 100; Parameter Volume = 100; Parameter Temperature = 100;

scan_protocol: Affymetrix U95 Scanning Protocol; 100; Protocol Type = image_acquisition; Software: Default scanner software, type: image_acquisition_software; Hardware: Scanning hardware, make: Affymetrix- GeneChip Scanner 3000, type: array_scanner;

label: biotin

source_name: Renal cell carcinoma

label_protocol: Affymetrix Labeling Protocol; The exact protocol is not available. But Standard Operating Proceadure can be found at          http://www.affymetrix.com/support/technical/manual/expression_manual.affx         or         http://www.affymetrix.com/Auth/support/downloads/manuals/expression_ever_manual.zip         Manual number: 701025 Revision 6, page 2.1.3; Protocol Type = labeling; Parameter Amount of nucleic acid labeled = 100; Parameter Used Label = biotin; Parameter Amplification = none;

growth_protocol: NCI60Adherent; RNA harvesting protocol for adherent cells           Media used:         RPMI 1640 500 ml          FBS 25 ml -use the DTP serum if possible, from Bio Whittaker, not heat         inactivated          200 mM Glutamine 5 ml           1 flask = ~15 x 106 cells yields ~ 100 ugr RNA. Grow 10 flasks.                    Cells: start from growing cells from Frederick (not frozen). Started before at         passage #8-12. Do not use past passage 20.                    Growth schedule prior to harvest: Grow cells to         ~80 confluencey. Trypsinize cells with 5 ml try-EDTA per T162, 15 min., 370C. Pipet up and         down several times w 10 ml pipet to get good dispersment of cells. Count cells. Pass cells         to as many flasks as there are cells for. When passing cells, combine flasks into a single         pool. Pass 1x106 cells into each T162 w 30 ml media.  Repeat growth cycle until 10 flasks         are available.   Refeed Refeed cells the day prior to harvest without harvesting).  Draw off         media (wo cells). Add back media, 30 ml per T162. Add back to T-162âs. 37 deg C, ON  Harvest         Target confluency 80%  # of flasks = 10   Draw off media from 1st flask. Lyse cells in 15         ml lysis buffer (w 10 ul fresh BME per ml). Scrape cells. Draw off media from 2nd flask.         Pipet lysis buffer from flask 1 into flask 2. Repeat lysis with up to 4 T162âs. Pipet into         50 ml tube.  Repeat w next set of 4 flasks.  When done, vortex 10 sec.. Draw lysate thru a         20 guage needle 12xâs. Freeze at ö800C.  Purify using Quiagen Midi Kit.  Use a maximun of         100 x 106 cells per column. More will not bind to the column.                           Company Info         ------------           Quiagen Midi Kit Cat # 75144  RLT Buffer (lysis buffer) Cat. # 79216 $60-list, $51- discounted 1-800-362-7737                    Fetal Bovine Serum 500 ml, list $261- Cat #14-502F Lot # 9S083F Cambrex (old Bio Whittaker) 1-800-638-8174                   1x PBS pH 7.3-7.5 Bio Whittaker cat #17-516F $5.30 per 500 ml bottle (1-11)                    250 ml conical tubes Corning cat #25350-250                    RPMI-1640 wo L-glutamine cat # 12-167F  $13.25 per 500 ml bottle (for 1-11 bottles) Cambrex (old Bio Whittaker) Walkersville, Md. 21793 301-898-7025 1-800-638-8174                 Trypsin (0.05%)-EDTA (0.1%) In phosphate buffered saline without calcium and magnesium. cat # 118-087-061 $4.20 per 100 ml bottle Quality Biological, Inc. 301-840-9331                    L-glutamine 200 mM, 100x Gibco-BRL cat # 25030-149 20 ml 1-800-828-6686                    162 cm2 flask cat # 3150                    Costar Tissue Culture Cell Scrapper, 25 cm Sarstedt Cat. # 83.1830                    Cells are received from Nick Scudiero,  E-mail: SCUDIERO@dtpax2.ncifcrf.gov          Also trypsin, FBS and glutamine have been coming from there as well.; Protocol Type = grow; Parameter start Time = 0; Parameter min temperature = 37; Parameter media = RPMI 1640,5% FBS, 1% L-Glutamine;

extract_protocol: NCI60 Extraction Protocol; Harvest Target confluency  80%    # of flasks = 10   Draw off media from 1st flask. Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml). Scrape cells. Draw off media from 2nd flask. Pipet lysis buffer from flask 1 into flask 2. Repeat lysis with up to 4 T162’s. Pipet into 50 ml tube.  Repeat w next set of 4 flasks.  When done, vortex 10 sec.. Draw lysate thru a 20 guage needle 12x’s. Freeze at –800C.  Purify using Quiagen Midi Kit.  Use a maximun of 100 x 106 cells per column. More will not bind to the column. ; Protocol Type = nucleic_acid_extraction; Parameter Extracted product = total RNA; Parameter Amplification = none;

tag: MDR Function

tag: Prior Treatment

tag: p53 Status

value: wild             type

tag: BioSourceType

value: other[unknown]

tag: CellLine

tag: DiseaseState

value: Renal cell carcinoma-very poorly             differentiated

tag: Individual:

tag: InitialTimePoint

value: birth

tag: OrganismPart

value: kidney

tag: Sex

value: male

tag: TargetedCellType

value: Renal cell carcinoma


title: TK-10 hgu95d

source_name: Renal Spindle cell carcinoma

value: mutant

tag: Age

value: Renal Spindle cell carcinoma

tag: TimeUnit

value: years


title: Primary human neuroblastoma cS162

tag: Primary human neuroblastoma

tag: normal human reference genomic DNA


title: SN12C hgu95d

value: Renal cell carcinoma-poorly differentiated


title: Primary human neuroblastoma cS154


title: Primary human neuroblastoma cS155


title: Primary human neuroblastoma cS149


title: Primary human neuroblastoma cS150


title: Primary human neuroblastoma cS148


title: Primary human neuroblastoma cS142


title: Primary human neuroblastoma cS209


title: Primary human neuroblastoma cS143


title: Primary human neuroblastoma cS147


title: Primary human neuroblastoma cS145


title: RXF 393 hgu95d

source_name: hypernephroma

value: RXF 393

value: hypernephroma-poorly differentiated

value: hypernephroma


title: NCI/ADR-RES hgu95d

source_name: Adenocarcinoma

tag: Disputed

value: yes

value: unknown

value: NCI/ADR-RES

value: Adenocarcinoma

value: ovary

value: female


title: CAKI-1 hgu95d

source_name: Clear cell carcinoma

value: wild             type

value: other[metastasis]

value: carcinoma

value: birth

value: Clear cell carcinoma


title: Primary human neuroblastoma cS144


title: ACHN hgu95d

value: other[unknown]

value: ACHN

value: Renal cell carcinoma-poor or moderately             differentiated

value: kidney

value: male

value: Renal cell carcinoma


title: OVCAR-8 hgu95d

source_name: Carcinoma

value: Ctx/Adr/Cisplatin/CyPh

value: mutant

value: Carcinoma-undifferntiated

value: Carcinoma

value: years


title: OVCAR-5 hgu95d

value: Adenocarcinoma-wd

value: ovary

value: female

value: Adenocarcinoma


title: PC-3 hgu95d

source_name: Prostate Adenocarcinoma

value: unknown

tag: ClinicalInformation

value: metastatic site:bone

value: Prostate Adenocarcinoma

value: birth

value: prostate


title: 786-0 hgu95d

tag: MDR Function

value: other[unknown]

value: kidney


title: A498 hgu95d

tag: MD

tag: Prior Treatment

value: wild             type

value: male


title: SK-OV-3 hgu95d

value: Thiotepa

tag: p53 Status

tag: BioSourceType

value: other[ascites]


title: DU-145 hgu95d

source_name: carcinoma

value: Androgen independent and unresposive to hormone th

value: other[metastasis]

tag: CellLine

value: prostate; metastatic site:brain;             carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of             lymphocytic leukemia.)

tag: DiseaseState

value: carcinoma


title: OVCAR-4 hgu95d

tag: Individual:

tag: InitialTimePoint

value: ovary

value: female

value: years


title: Primary human neuroblastoma cS141

source_name: normal human reference genomic DNA


title: Primary human neuroblastoma cS140


title: Primary human neuroblastoma cS137


title: Primary human neuroblastoma cS136


title: Primary human neuroblastoma cS135


title: Primary human neuroblastoma cS134


title: Primary human neuroblastoma cS139


title: Primary human neuroblastoma cS138


title: OVCAR-3 hgu95d

value: mutant

tag: OrganismPart

tag: Sex

value: Adenocarcinoma


title: NCI-H460 hgu95d

source_name: Large Cell Carcinoma-undifferntiated

value: unknown

value: other[pleural effusion]

value: Carcinoma

value: birth

value: lung

tag: TargetedCellType

value: Large Cell Carcinoma-undifferntiated


title: IGR-OV1 hgu95d

source_name: Cystoadenocarcinoma

value: radiation

tag: Age

value: other[unknown]

value: Cystoadenocarcinoma

tag: TimeUnit


title: NCI-H522 hgu95d

value: male


title: Primary human neuroblastoma cS132

tag: Primary human neuroblastoma

tag: normal human reference genomic DNA


title: Primary human neuroblastoma cS131


title: Primary human neuroblastoma cS130


title: NCI-H322 hgu95d

source_name: Small cell Bronchioalveolar Carcinoma

value: Small cell Bronchioalveolar Carcinoma


title: Primary human neuroblastoma cS128


title: Primary human neuroblastoma cS129


title: A549/ATCC hgu95d

value: wild             type

tag: ClinicalInformation

value: Adenocarcinoma-poor or moderately             differentiated


title: Primary human neuroblastoma cS127


title: NCI-H23 hgu95d

source_name: Adenocarcinoma-undifferntiated

tag: MDR Function

value: Adenocarcinoma-undifferntiated


title: Primary human neuroblastoma cS133


title: MDA-N hgu95d

source_name: Melanoma

tag: Disputed

value: yes

value: MDA-N

value: MDA-N was derived from MDA-MB435 by             transfection with a plasmid designed to express erbB2. MDA-N and MDA-MB435 are very             similar under non selective conditions.

value: not available

value: skin

value: female

value: Melanoma

value: years


title: NCI-H226 hgu95d

source_name: Squamous cell carcinoma

tag: Prior Treatment

value: mutant

value: Squamous cell carcinoma-very poorly             differentiated

value: carcinoma

value: birth

value: lung

value: Squamous cell carcinoma


title: HOP-92 hgu95d

source_name: Large cell-undifferntiated

tag: p53 Status

value: other[unknown]

value: nonsmoker

value: Large cell-undifferntiated

value: male


title: Primary human neuroblastoma cS146


title: MDA-MB-435 hgu95d

source_name: Ductal Breast Carcinoma

value: yes

value: un

tag: BioSourceType

value: other[pleural effusion]

value: metastatic site:pleural effusion; In             a recent study using cDNA microarrays, the parent line (MD A-MB-435) of MDA-MB-435S             clustered with cell lines of melanoma origin. Ross DT et al. Nature Genetics 24:            227-235, 2000 )

value: Ductal Breast Carcinoma


title: UACC-62 hgu95d

value: unknown

value: wild             type

tag: CellLine

value: Melanoma

value: skin


title: HOP-62 hgu95d

value: mutant

value: Adenocarcinoma-undifferntiated

tag: DiseaseState

value: Adenocarcinoma

value: female

value: years


title: EKVX hgu95d

value: other[unknown]

value: EKVX

value: Adenocarcinoma-moderately             differentiated

tag: Individual:

value: birth

value: lung


title: Primary human neuroblastoma cS126


title: UO-31 hgu95e

source_name: Renal cell carcinoma

value: Renal cell carcinoma-very poorly             differentiated

tag: InitialTimePoint

value: kidney

value: male

value: Renal cell carcinoma


title: TK-10 hgu95e

source_name: Renal Spindle cell carcinoma

value: Renal Spindle cell carcinoma

tag: OrganismPart


title: SN12C hgu95e

value: Renal cell carcinoma-poorly differentiated

tag: Sex


title: Primary human neuroblastoma cS124


title: UACC-257 hgu95d

source_name: Melanoma-melanotic

value: unknown

value: wild             type

value: Melanoma-melanotic

value: skin

tag: TargetedCellType


title: RXF 393 hgu95e

source_name: hypernephroma

value: mutant

tag: Age

value: RXF 393

value: hypernephroma-poorly differentiated

value: hypernephroma


title: CAKI-1 hgu95e

source_name: Clear cell carcinoma

value: other[metastasis]

value: carcinoma

value: Clear cell carcinoma

tag: TimeUnit

value: years


title: Primary human neuroblastoma cS123

tag: Primary human neuroblastoma


title: ACHN hgu95e

value: other[unknown]

value: ACHN

value: Renal cell carcinoma-poor or moderately             differentiated

value: birth

value: kidney


title: SK-MEL-5 hgu95d

value: Melanoma-premelanotic

value: female

value: Melanoma


title: SK-MEL-2 hgu95d

value: wild             type

value: skin

value: male


title: 786-0 hgu95e

source_name: Adenocarcinoma

value: mutant

value: Adenocarcinoma


title: M14 hgu95d

value: unknown

value: Melanoma-melanotic


title: PC-3 hgu95e

source_name: Prostate Adenocarcinoma

value: metastatic site:bone

value: Prostate Adenocarcinoma

value: prostate


title: OVCAR-8 hgu95e

source_name: Carcinoma

value: Ctx/Adr/Cisplatin/CyPh

value: other[unknown]

value: Carcinoma-undifferntiated

value: ovary

value: Carcinoma

value: years


title: DU-145 hgu95e

source_name: carcinoma

value: Androgen independent and unresposive to hormone th

value: other[metastasis]

value: prostate; metastatic site:brain;             carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of             lymphocytic leukemia.)

value: carcinoma

value: birth


title: SK-OV-3 hgu95e

value: Thiotepa

value: other[ascites]

value: female

value: Adenocarcinoma


title: Primary human neuroblastoma cS121

source_name: normal human reference genomic DNA

tag: normal human reference genomic DNA


title: OVCAR-5 hgu95e

value: mutant

value: Adenocarcinoma-wd


title: A498 hgu95e

tag: MD

value: unknown

value: wild             type

value: kidney

value: male


title: Primary human neuroblastoma cS119


title: Primary human neuroblastoma cS122


title: Primary human neuroblastoma cS120


title: MALME-3M hgu95d

source_name: Malignant melanoma

tag: MDR Function

value: Malignant melanoma

value: skin


title: LOX IMVI hgu95d

source_name: amelanotic melanoma

value: other[unknown]

value: LOX IMVI

value: Malignant amelanotic melanoma

value: amelanotic melanoma

value: years


title: SR hgu95d

source_name: Lymphoma

growth_protocol: NCI60Suspended; RNA harvesting protocol for suspended cells:           Media used:          RPMI 1640 500 ml          FBS 25 ml          200 mM Glutamine 5 ml                    Cells:          start from growing cells from Frederick (not frozen). Started before at passage #8-12. Do not use past passage 20. Grow 10         flasks. 1 flask = ~15 x 106 cells yields ~ 100 ugr RNA.  Growth schedule prior to harvest         Count cells as necessary to follow growth. Grow cells to ~0.52 x 106 cells /ml  Pass 1x106         cells into each T162 w 30 ml media. Pass cells to as many flasks as there are cells for.         When passing cells, combine into a single pool.  Repeat growth cycle until 10 flasks are         available.  Refeed Refeed cells the day prior to harvest (without passsing). To do so: Spin         down cells 1.7k rpm, 10 min., in a 50 ml tube. Draw off media. Resuspend in 30 ml media.         Return to flask.  Harvest Harvest at 0.52 x 106cells per ml when 10 flasks are available.         Spin  4 flasks of cells at  1.7k rpm (~ 500 x g), 10 min (speed setting at 3.5), in a 250 ml         centrifuge tube.   Draw off media, leaving ~0.5 ml behind. Flick centirifuge tube to break         up cells. Lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml) per 4 T162âs.  Vortex         10 sec. Draw thru a 20 guage needle 12xâs. Freeze at ö800C.   Purify using Quigen Midi         Kit.Use a maximum of 100 x 106 cells per column. More will not bind to the column.                  Company Info:           Fetal bovine serum Do not heat inactivate. Bio Whittaker Cat# 14-501F Lot #9S083F 301-898-7025                    Quiagen Midi Kit Cat # 75144                    DTT Fluka or Gallard  1x PBS pH 7.3-7.5                  Bio Whittaker cat #17-516F $5.30 per 500 ml bottle (1-11)                    250 ml conical centrifuge tubes Corning cat # 25350-250                    RPMI-1640 wo L-glutamine cat # 12-167F  $13.25 per 500 ml bottle         (for 1-11 bottles) Cambrex (old Bio Whittaker) Walkersville, Md. 21793 301-898-7025         1-800-638-8174                    Trypsin (0.05%)-EDTA (0.1%) In phosphate buffered saline without calcium and         magnesium. cat # 118-087-061 Quality Biological, Inc. 301-840-9331                    L-glutamine 200 mM, 100x Gibco-BRL cat # 25030-081  162 cm2 flask cat # 3150                   Costar Tissue Culture Cell Scrapper, 25cm Sarstedt Cat. # 83.1830                    Cells are recieved from Nick Scudiero,  E-mail:SCUDIERO@dtpax2.ncifcrf.gov          Also trypsin, FBS and glutamine have been coming from there as well.; Protocol Type = grow; Parameter start Time = 0; Parameter min temperature = 37; Parameter media = RPMI 1640,5% FBS, 1% L-Glutamine;

value: yes

value: SR

value: Lymphoma

value: birth

value: blood


title: NCI/ADR-RES hgu95e

tag: Disputed

value: mutant

value: NCI/ADR-RES

value: Adenocarcinoma

value: ovary

value: female


title: OVCAR-4 hgu95e

tag: Prior Treatment

value: wild             type


title: IGR-OV1 hgu95e

source_name: Cystoadenocarcinoma

value: radiation

tag: p53 Status

value: Cystoadenocarcinoma


title: SK-MEL-28 hgu95d

source_name: Melanoma

tag: BioSourceType

value: other[unknown]

value: Malignant melanoma

value: skin

value: male

value: Melanoma


title: Primary human neuroblastoma cS117


title: Primary human neuroblastoma cS118


title: NCI-H322 hgu95e

source_name: Small cell Bronchioalveolar Carcinoma

tag: CellLine

value: Carcinoma

value: lung

value: Small cell Bronchioalveolar Carcinoma

value: years


title: NCI-H23 hgu95e

source_name: Adenocarcinoma-undifferntiated

value: mutant

tag: DiseaseState

value: birth

value: Adenocarcinoma-undifferntiated


title: NCI-H460 hgu95e

source_name: Large Cell Carcinoma-undifferntiated

value: unknown

value: other[pleural effusion]

tag: Individual:

value: Large Cell Carcinoma-undifferntiated


title: RPMI-8226 hgu95d

source_name: Myeloma

value: wild             type

value: other[Peripheral Blood]

tag: ClinicalInformation

value: cells were taken when patient was in             relapse

value: Myeloma

tag: InitialTimePoint

value: blood


title: MOLT-4 hgu95d

source_name: Lymphoblastic Leukemia

value: Acute Lymphoblastic Leukemia

tag: OrganismPart

tag: Sex

value: male

value: Lymphoblastic Leukemia


title: NCI-H226 hgu95e

source_name: Squamous cell carcinoma

value: other[unknown]

value: Squamous cell carcinoma-very poorly             differentiated

value: carcinoma

value: lung

tag: TargetedCellType

value: Squamous cell carcinoma


title: K-562 hgu95d

source_name: Myelogenous Leukemia

value: Bisulfan/PiBr

value: mutant

tag: Age

value: Chronic Myelogenous Leukemia

value: birth

value: female

value: Myelogenous Leukemia

tag: TimeUnit

value: years


title: Primary human neuroblastoma cS116

tag: Primary human neuroblastoma

tag: normal human reference genomic DNA


title: HL-60(TB) hgu95d

source_name: promyelocytic leukemia

tag: MDR Function

value: acute promyelocytic leukemia

value: promyelocytic leukemia


title: NCI-H522 hgu95e

source_name: Adenocarcinoma

value: Adenocarcinoma


title: Primary human neuroblastoma cS113


title: Primary human neuroblastoma cS114


title: MDA-MB-435 hgu95e

source_name: Ductal Breast Carcinoma

tag: Disputed

value: yes

value: un

value: other[pleural effusion]

value: metastatic site:pleural effusion; In             a recent study using cDNA microarrays, the parent line (MD A-MB-435) of MDA-MB-435S             clustered with cell lines of melanoma origin. Ross DT et al. Nature Genetics 24:            227-235, 2000 )

value: Ductal Breast Carcinoma

value: skin


title: UACC-62 hgu95e

tag: Prior Treatment

value: unknown

value: wild             type

value: other[unknown]

value: Melanoma


title: Primary human neuroblastoma cS115


title: Primary human neuroblastoma cS112


title: SK-MEL-5 hgu95e

tag: p53 Status

value: other[metastasis]

value: Melanoma-premelanotic

value: birth


title: Primary human neuroblastoma cS125


title: HT29 hgu95d

value: mutant

tag: BioSourceType

value: other[primary]

value: Adenocarcinoma-moderately             differentiated

value: colon

value: female

value: years


title: UACC-257 hgu95e

source_name: Melanoma-melanotic

tag: CellLine

value: Melanoma-melanotic


title: A549/ATCC hgu95e

value: Adenocarcinoma-poor or moderately             differentiated

tag: DiseaseState

value: Adenocarcinoma

value: lung

value: male


title: MDA-N hgu95e

value: yes

value: unknown

value: other[pleural effusion]

value: MDA-N

value: MDA-N was derived from MDA-MB435 by             transfection with a plasmid designed to express erbB2. MDA-N and MDA-MB435 are very             similar under non selective conditions.

value: not available

tag: Individual:

value: skin


title: HOP-62 hgu95e

value: mutant

value: other[unknown]

tag: ClinicalInformation

value: Adenocarcinoma-undifferntiated

value: birth


title: CCRF-CEM hgu95d

value: radiation

value: CCRF-CEM

value: Acute Lymphoblastic Leukemia

tag: InitialTimePoint

value: blood

value: female

value: Lymphoblastic Leukemia

value: years


title: SW-620 hgu95d

source_name: Carcinoma

value: unknown

value: Carcinoma-undifferntiated

value: Carcinoma

tag: OrganismPart

value: colon

value: male


title: KM12 hgu95d

value: Adenocarcinoma-poorly differentiated

value: Adenocarcinoma

tag: Sex


title: OVCAR-3 hgu95e

value: mutant

value: other[ascites]

value: ovary

tag: TargetedCellType


title: SK-MEL-28 hgu95e

tag: Age

value: other[unknown]

value: Malignant melanoma

value: birth

value: skin

value: Melanoma


title: EKVX hgu95e

value: EKVX

value: Adenocarcinoma-moderately             differentiated

value: lung


title: HCT-15 hgu95d

value: unknown

value: Adenocarcinoma poor or moderately             differentiated


title: Primary human neuroblastoma cS111

source_name: Primary human neuroblastoma


title: Primary human neuroblastoma cS110

source_name: normal human reference genomic DNA


title: Primary human neuroblastoma cS109


title: M14 hgu95e

value: Melanoma-melanotic


title: MALME-3M hgu95e

source_name: Malignant melanoma

value: wild             type

value: other[metastasis]

value: male

tag: TimeUnit

value: years


title: SK-MEL-2 hgu95e


title: Primary human neuroblastoma cS108

tag: Primary human neuroblastoma


title: LOX IMVI hgu95e

source_name: amelanotic melanoma

value: LOX IMVI

value: Malignant amelanotic melanoma

value: amelanotic melanoma


title: SR hgu95e

source_name: Lymphoma

value: yes

value: other[unknown]

value: SR

value: Lymphoma

value: blood


title: RPMI-8226 hgu95e

value: other[Peripheral Blood]

value: cells were taken when patient was in             relapse

value: Myeloma

value: birth


title: HCT-116 hgu95d

value: unknown

value: Carcinoma very poorly differentiated

value: Carcinoma

value: colon


title: MOLT-4 hgu95e

value: wild             type

value: Acute Lymphoblastic Leukemia

value: male

value: Lymphoblastic Leukemia

value: years


title: K-562 hgu95e

value: Bisulfan/PiBr

value: mutant

value: other[pleural effusion]

value: Chronic Myelogenous Leukemia

value: female

value: Myelogenous Leukemia


title: Primary human neuroblastoma cS107

tag: normal human reference genomic DNA


title: COLO 205 hgu95d

source_name: adenocarcinoma

tag: MDR Function

value: other[ascites]

value: COLO 205

value: adenocarcinoma


title: HCC-2998 hgu95d

value: unknown

value: birth


title: Primary human neuroblastoma cS106


title: Primary human neuroblastoma cS104


title: Primary human neuroblastoma cS103


title: HL-60(TB) hgu95e

value: blood

value: acute promyelocytic leukemia

value: promyelocytic leukemia


title: CCRF-CEM hgu95e

value: radiation

value: other[unknown]

value: CCRF-CEM

value: Acute Lymphoblastic Leukemia


title: Primary human neuroblastoma cS105


title: SW-620 hgu95e

value: mutant

value: Carcinoma-undifferntiated

value: Carcinoma

value: colon

value: male

value: years


title: Primary human neuroblastoma cS102


title: KM12 hgu95e

value: Adenocarcinoma-poorly differentiated

value: Adenocarcinoma


title: U251 hgu95d

source_name: Glioblastoma undifferntiated

value: unknown

value: Glioblastoma undifferntiated

value: central nervous system


title: HCC-2998 hgu95e

value: other[pleural effusion]

value: birth


title: SNB-75 hgu95d

source_name: Astrocytoma

value: Astrocytoma

value: female


title: SNB-19 hgu95d

value: other[unknown]


title: SF-539 hgu95d

source_name: Glial Neoplasm

value: radiation

value: wild             type

value: Glial Neoplasm


title: HT29 hgu95e

value: mutant

value: other[primary]

value: Adenocarcinoma-moderately             differentiated


title: COLO 205 hgu95e

value: other[ascites]

value: COLO 205

value: adenocarcinoma

value: colon

value: male

value: years


title: Primary human neuroblastoma cS080


title: SNB-19 hgu95e

value: Glioblastoma undifferntiated

value: central nervous system


title: Primary human neuroblastoma cS101


title: SF-539 hgu95e

value: birth


title: HCT-15 hgu95e

value: unknown

value: Adenocarcinoma poor or moderately             differentiated

value: Adenocarcinoma


title: Primary human neuroblastoma cS081


title: SNB-75 hgu95e

value: other[unknown]

value: Astrocytoma

value: female


title: SF-295 hgu95d

value: radiation

value: mutant


title: HCT-116 hgu95e

value: Carcinoma very poorly differentiated

value: Carcinoma


title: SF-268 hgu95d


title: Primary human neuroblastoma cS079


title: U251 hgu95e


title: T-47D hgu95d

source_name: breast epithelial carcinoma

value: Infiltrating Ductal Carcinoma

value: breast

value: breast epithelial carcinoma


title: SF-295 hgu95e

value: years


title: BT-549 hgu95d

source_name: Papillary infiltrating ductal carcinoma

value: other[metastasis]

value: Invasive Papillary Breast Carcinoma

value: Papillary infiltrating ductal carcinoma


title: SF-268 hgu95e

value: Glioblastoma undifferntiated

value: birth

value: central nervous system


title: T-47D hgu95e

value: unknown

value: other[unknown]


title: BT-549 hgu95e

value: female


title: HS 578T hgu95d

source_name: breast epithelial carcinosarcoma

value: other[primary]

value: HS 578T

value: carcinosarcoma

value: breast epithelial carcinosarcoma


title: MDA-MB-231/ATCC hgu95d

source_name: breast epithelial adenocarcinoma

value: mutant

value: other[pleural effusion]

value: adenocarcinoma

value: breast epithelial adenocarcinoma


title: MDA-MB-231/ATCC hgu95e

value: breast

value: years


title: Primary human neuroblastoma cS075


title: Primary human neuroblastoma cS074


title: Primary human neuroblastoma cS073


title: MCF7 hgu95e

value: wild             type


title: HS 578T hgu95e


title: UO-31 hgu95a

source_name: Renal cell carcinoma

value: Renal cell carcinoma-very poorly             differentiated

value: kidney

value: male

value: Renal cell carcinoma


title: UO-31 hgu95c

value: other[unknown]

value: birth


title: SN12C hgu95a

value: Renal cell carcinoma-poorly differentiated


title: UO-31 hgu95b


title: TK-10 hgu95a

source_name: Renal Spindle cell carcinoma

value: Renal Spindle cell carcinoma


title: Primary human neuroblastoma cS072


title: Primary human neuroblastoma cS071


title: TK-10 hgu95c


title: TK-10 hgu95b


title: SN12C hgu95c


title: CAKI-1 hgu95a

source_name: Clear cell carcinoma

value: other[metastasis]

value: carcinoma

value: Clear cell carcinoma


title: RXF 393 hgu95a

source_name: hypernephroma

value: mutant

value: RXF 393

value: hypernephroma-poorly differentiated

value: hypernephroma


title: Primary human neuroblastoma cS070


title: SN12C hgu95b

value: years


title: RXF 393 hgu95c


title: MCF7 hgu95d

value: unknown

value: wild             type

value: other[pleural effusion]

value: adenocarcinoma

value: breast

value: female

value: breast epithelial adenocarcinoma


title: RXF 393 hgu95b

value: other[unknown]

value: birth

value: kidney

value: male


title: Primary human neuroblastoma cS069


title: Primary human neuroblastoma cS068


title: A498 hgu95a

source_name: Adenocarcinoma

tag: MD

value: Adenocarcinoma


title: ACHN hgu95b

tag: Prior Treatment

value: ACHN

value: Renal cell carcinoma-poor or moderately             differentiated

value: Renal cell carcinoma


title: A498 hgu95b

tag: p53 Status


title: DU-145 hgu95a

source_name: carcinoma

value: Androgen independent and unresposive to hormone th

tag: BioSourceType

value: other[metastasis]

value: prostate; metastatic site:brain;             carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of             lymphocytic leukemia.)

value: carcinoma

value: prostate


title: CAKI-1 hgu95b

value: wild             type

tag: CellLine

value: Clear cell carcinoma

value: years


title: ACHN hgu95a

tag: DiseaseState


title: Primary human neuroblastoma cS100

source_name: normal human reference genomic DNA


title: HOP-92 hgu95e

source_name: Large cell-undifferntiated

value: mutant

value: nonsmoker

value: Large cell-undifferntiated

tag: Individual:

value: lung


title: Primary human neuroblastoma cS067


title: 786-0 hgu95b

value: other[unknown]

value: birth

value: kidney

value: male


title: PC-3 hgu95a

source_name: Prostate Adenocarcinoma

value: unknown

tag: ClinicalInformation

value: metastatic site:bone

value: Prostate Adenocarcinoma


title: SK-OV-3 hgu95a

value: Thiotepa

value: other[ascites]

tag: InitialTimePoint

value: ovary

value: female

value: Adenocarcinoma


title: 786-0 hgu95a

tag: OrganismPart

value: years


title: PC-3 hgu95b

value: mutant

value: prostate

tag: Sex


title: DU-145 hgu95b

value: Androgen independent and unresposive to hormone th

value: other[metastasis]

value: prostate; metastatic site:brain;             carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of             lymphocytic leukemia.)

value: carcinoma

tag: TargetedCellType


title: Primary human neuroblastoma cS097


title: Primary human neuroblastoma cS094


title: OVCAR-8 hgu95a

source_name: Carcinoma

value: Ctx/Adr/Cisplatin/CyPh

tag: Age

value: other[unknown]

value: Carcinoma-undifferntiated

value: birth

value: Carcinoma


title: Primary human neuroblastoma cS098


title: NCI/ADR-RES hgu95a

tag: Disputed

value: yes

value: unknown

value: NCI/ADR-RES


title: ACHN hgu95c

value: wild             type

value: ACHN

value: Renal cell carcinoma-poor or moderately             differentiated

value: kidney

value: male

value: Renal cell carcinoma

tag: TimeUnit


title: NCI/ADR-RES hgu95c

value: mutant

value: Adenocarcinoma

value: ovary

value: female


title: SK-OV-3 hgu95c

value: Thiotepa

value: other[ascites]

value: years


title: Primary human neuroblastoma cS055

tag: Primary human neuroblastoma

tag: normal human reference genomic DNA


title: A498 hgu95c

tag: MD

value: other[unknown]

value: birth


title: CAKI-1 hgu95c

tag: MDR Function

tag: Prior Treatment

value: other[metastasis]

value: carcinoma

value: Clear cell carcinoma


title: 786-0 hgu95c

tag: p53 Status

tag: BioSourceType


title: Primary human neuroblastoma cS054


title: OVCAR-5 hgu95a

tag: CellLine

tag: DiseaseState

value: Adenocarcinoma-wd


title: Primary human neuroblastoma cS053


title: PC-3 hgu95c

value: unknown

tag: ClinicalInformation

value: metastatic site:bone

value: Prostate Adenocarcinoma

tag: Individual:

value: prostate


title: NCI/ADR-RES hgu95b

value: yes

value: mutant

value: NCI/ADR-RES

tag: InitialTimePoint

tag: OrganismPart


title: Primary human neuroblastoma cS052


title: OVCAR-8 hgu95c

value: Ctx/Adr/Cisplatin/CyPh

value: Carcinoma-undifferntiated

value: ovary

tag: Sex

value: female

tag: TargetedCellType

value: Carcinoma


title: OVCAR-3 hgu95c

tag: Age

value: other[ascites]

value: birth

value: Adenocarcinoma

value: years


title: OVCAR-4 hgu95a

value: wild             type

value: other[unknown]

tag: TimeUnit


title: Primary human neuroblastoma cS093

tag: Primary human neuroblastoma


title: DU-145 hgu95c

value: Androgen independent and unresposive to hormone th

value: unknown

value: other[metastasis]

value: prostate; metastatic site:brain;             carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of             lymphocytic leukemia.)

value: carcinoma

value: male


title: OVCAR-3 hgu95a

value: mutant


title: SK-OV-3 hgu95b

value: Thiotepa


title: Primary human neuroblastoma cS099

tag: normal human reference genomic DNA


title: Primary human neuroblastoma cS051


title: OVCAR-4 hgu95c

value: ovary


title: IGR-OV1 hgu95a

source_name: Cystoadenocarcinoma

value: radiation

value: female

value: Cystoadenocarcinoma


title: NCI-H522 hgu95a

value: birth

value: lung


title: OVCAR-5 hgu95c

value: Adenocarcinoma-wd

value: Adenocarcinoma

value: years


title: IGR-OV1 hgu95b

value: other[unknown]


title: OVCAR-3 hgu95b

value: other[ascites]


title: NCI-H460 hgu95c

source_name: Large Cell Carcinoma-undifferntiated

value: unknown

value: wild             type

value: other[pleural effusion]

value: Carcinoma

value: Large Cell Carcinoma-undifferntiated


title: OVCAR-8 hgu95b

value: Ctx/Adr/Cisplatin/CyPh

value: mutant

value: Carcinoma-undifferntiated


title: NCI-H522 hgu95b

value: male


title: OVCAR-4 hgu95b

value: ovary

value: female


title: OVCAR-5 hgu95b

value: birth


title: Primary human neuroblastoma cS091


title: IGR-OV1 hgu95c

value: radiation

value: Cystoadenocarcinoma


title: NCI-H522 hgu95c

value: lung

value: Adenocarcinoma


title: NCI-H460 hgu95b


title: NCI-H460 hgu95a


title: NCI-H322 hgu95a

source_name: Small cell Bronchioalveolar Carcinoma

value: other[unknown]

value: Small cell Bronchioalveolar Carcinoma

value: years


title: Primary human neuroblastoma cS090


title: NCI-H23 hgu95a

source_name: Adenocarcinoma-undifferntiated

value: Adenocarcinoma-undifferntiated


title: NCI-H322 hgu95c

value: Carcinoma


title: NCI-H322 hgu95b


title: Primary human neuroblastoma cS046


title: Primary human neuroblastoma cS044


title: Primary human neuroblastoma cS045


title: NCI-H23 hgu95c


title: NCI-H226 hgu95c

source_name: Squamous cell carcinoma

value: Squamous cell carcinoma-very poorly             differentiated

value: carcinoma

value: Squamous cell carcinoma


title: HOP-62 hgu95a

value: mutant


title: HOP-62 hgu95c


title: HOP-92 hgu95c

value: nonsmoker

value: Large cell-undifferntiated

value: male


title: NCI-H23 hgu95b

value: birth


title: NCI-H226 hgu95b


title: NCI-H226 hgu95a


title: HOP-92 hgu95b


title: HOP-62 hgu95b

value: female


title: EKVX hgu95a

value: unknown

value: EKVX

value: Adenocarcinoma-moderately             differentiated


title: EKVX hgu95b

value: other[unknown]

value: Adenocarcinoma

value: lung


title: A549/ATCC hgu95c

value: wild             type

value: Adenocarcinoma-poor or moderately             differentiated

value: years


title: EKVX hgu95c


title: HOP-92 hgu95a


title: MDA-MB-435 hgu95b

source_name: Ductal Breast Carcinoma

tag: Disputed

value: yes

value: un

value: other[pleural effusion]

value: metastatic site:pleural effusion; In             a recent study using cDNA microarrays, the parent line (MD A-MB-435) of MDA-MB-435S             clustered with cell lines of melanoma origin. Ross DT et al. Nature Genetics 24:            227-235, 2000 )

value: Ductal Breast Carcinoma

value: skin


title: A549/ATCC hgu95a

tag: MDR Function

value: birth

value: male


title: MDA-N hgu95c

source_name: Melanoma

tag: Prior Treatment

value: unknown

value: mutant

value: MDA-N

value: MDA-N was derived from MDA-MB435 by             transfection with a plasmid designed to express erbB2. MDA-N and MDA-MB435 are very             similar under non selective conditions.

value: not available

value: female

value: Melanoma


title: Primary human neuroblastoma cS040


title: UACC-62 hgu95a

tag: p53 Status

value: wild             type

value: other[unknown]


title: Primary human neuroblastoma cS088


title: Primary human neuroblastoma cS037


title: Primary human neuroblastoma cS036


title: Primary human neuroblastoma cS041


title: A549/ATCC hgu95b

tag: BioSourceType

value: Adenocarcinoma-poor or moderately             differentiated

value: Adenocarcinoma

value: lung

value: years


title: MDA-MB-435 hgu95c

value: yes

value: un

value: other[pleural effusion]

tag: CellLine

value: metastatic site:pleural effusion; In             a recent study using cDNA microarrays, the parent line (MD A-MB-435) of MDA-MB-435S             clustered with cell lines of melanoma origin. Ross DT et al. Nature Genetics 24:            227-235, 2000 )

value: Ductal Breast Carcinoma


title: UACC-257 hgu95a

source_name: Melanoma-melanotic

value: unknown

tag: DiseaseState

value: Melanoma-melanotic

value: birth

value: skin


title: MDA-N hgu95b

value: mutant

value: MDA-N

tag: ClinicalInformation

value: MDA-N was derived from MDA-MB435 by             transfection with a plasmid designed to express erbB2. MDA-N and MDA-MB435 are very             similar under non selective conditions.

value: not available

value: female


title: MDA-MB-435 hgu95a

tag: Individual:


title: UACC-62 hgu95c

value: wild             type

value: other[unknown]

value: Melanoma

tag: InitialTimePoint


title: UACC-257 hgu95c

tag: OrganismPart


title: Primary human neuroblastoma cS035


title: UACC-257 hgu95b

tag: Sex


title: SK-MEL-5 hgu95a

value: other[metastasis]

value: Melanoma-premelanotic

tag: TargetedCellType

value: years


title: Primary human neuroblastoma cS031


title: UACC-62 hgu95b


title: MDA-N hgu95a

value: yes

tag: Age

value: other[pleural effusion]


title: SK-MEL-28 hgu95a

value: Malignant melanoma

value: male

tag: TimeUnit


title: Primary human neuroblastoma cS033

tag: Primary human neuroblastoma


title: SK-MEL-5 hgu95b

value: birth


title: SK-MEL-5 hgu95c

value: skin


title: M14 hgu95a

value: unknown

value: mutant

value: Melanoma-melanotic


title: SK-MEL-28 hgu95b


title: SK-MEL-2 hgu95b


title: M14 hgu95b


title: MALME-3M hgu95a

source_name: Malignant melanoma


title: SK-MEL-28 hgu95c


title: SK-MEL-2 hgu95c


title: Primary human neuroblastoma cS096

tag: normal human reference genomic DNA


title: M14 hgu95c


title: Primary human neuroblastoma cS028


title: Primary human neuroblastoma cS029


title: SK-MEL-2 hgu95a


title: Primary human neuroblastoma cS025


title: Primary human neuroblastoma cS087


title: MALME-3M hgu95c


title: SR hgu95a

source_name: Lymphoma

value: SR

value: Lymphoma

value: blood


title: Primary human neuroblastoma cS024


title: RPMI-8226 hgu95a

source_name: Myeloma

value: wild             type

value: other[Peripheral Blood]

value: cells were taken when patient was in             relapse

value: Myeloma


title: MALME-3M hgu95b

value: other[metastasis]

value: years


title: LOX IMVI hgu95b

source_name: amelanotic melanoma

value: other[unknown]

value: LOX IMVI

value: Malignant amelanotic melanoma

value: amelanotic melanoma


title: LOX IMVI hgu95c

value: birth

value: skin

value: male


title: SR hgu95c

value: yes

value: unknown


title: LOX IMVI hgu95a


title: RPMI-8226 hgu95c


title: RPMI-8226 hgu95b


title: MOLT-4 hgu95c

source_name: Lymphoblastic Leukemia

value: Acute Lymphoblastic Leukemia

value: Lymphoblastic Leukemia


title: MOLT-4 hgu95a

value: wild             type

value: blood


title: HL-60(TB) hgu95a

source_name: promyelocytic leukemia

value: mutant

value: acute promyelocytic leukemia

value: promyelocytic leukemia


title: K-562 hgu95a

source_name: Myelogenous Leukemia

value: Bisulfan/PiBr

value: other[pleural effusion]

value: Chronic Myelogenous Leukemia

value: female

value: Myelogenous Leukemia

value: years


title: HL-60(TB) hgu95c

value: birth


title: K-562 hgu95c


title: Primary human neuroblastoma cS022

source_name: normal human reference genomic DNA


title: Primary human neuroblastoma cS023


title: Primary human neuroblastoma cS021


title: SR hgu95b

value: other[unknown]

value: SR

value: Lymphoma

value: male


title: CCRF-CEM hgu95a

value: radiation

value: CCRF-CEM

value: Acute Lymphoblastic Leukemia

value: Lymphoblastic Leukemia


title: KM12 hgu95a

source_name: Adenocarcinoma

value: mutant

value: Adenocarcinoma-poorly differentiated

value: Adenocarcinoma

value: colon


title: K-562 hgu95b

value: Bisulfan/PiBr

value: other[pleural effusion]

value: Chronic Myelogenous Leukemia

value: blood


title: MOLT-4 hgu95b

value: wild             type

value: other[Peripheral Blood]

value: birth

value: years


title: SW-620 hgu95b

source_name: Carcinoma

value: unknown

value: other[unknown]

value: Carcinoma-undifferntiated

value: Carcinoma

value: male


title: HL-60(TB) hgu95b

value: mutant

value: acute promyelocytic leukemia

value: promyelocytic leukemia


title: CCRF-CEM hgu95c

value: radiation

value: CCRF-CEM

value: Acute Lymphoblastic Leukemia

value: female

value: Lymphoblastic Leukemia


title: Primary human neuroblastoma cS020


title: SW-620 hgu95a

value: colon


title: CCRF-CEM hgu95b

value: blood


title: Primary human neuroblastoma cS019


title: SW-620 hgu95c

value: birth


title: KM12 hgu95c

value: Adenocarcinoma-poorly differentiated

value: Adenocarcinoma


title: Primary human neuroblastoma cS013


title: HT29 hgu95c

value: other[primary]

value: Adenocarcinoma-moderately             differentiated

value: years


title: KM12 hgu95b

value: other[unknown]


title: Primary human neuroblastoma cS018


title: HCT-116 hgu95a

value: unknown

value: Carcinoma very poorly differentiated

value: Carcinoma

value: male


title: Primary human neuroblastoma cS017


title: HT29 hgu95a

value: mutant


title: HT29 hgu95b


title: HCT-15 hgu95b

value: Adenocarcinoma poor or moderately             differentiated


title: HCT-15 hgu95a


title: HCC-2998 hgu95a

value: other[pleural effusion]


title: HCT-15 hgu95c


title: HCT-116 hgu95c


title: HCC-2998 hgu95b


title: HCT-116 hgu95b


title: Primary human neuroblastoma cS086


title: HCC-2998 hgu95c


title: Primary human neuroblastoma cS085


title: Primary human neuroblastoma cS012


title: U251 hgu95a

source_name: Glioblastoma undifferntiated

value: Glioblastoma undifferntiated

value: central nervous system


title: COLO 205 hgu95c

source_name: adenocarcinoma

value: other[ascites]

value: COLO 205

value: adenocarcinoma

value: colon


title: SNB-75 hgu95a

source_name: Astrocytoma

value: Astrocytoma

value: birth

value: female


title: U251 hgu95c

value: other[unknown]

value: years


title: Primary human neuroblastoma cS009


title: Primary human neuroblastoma cS011


title: U251 hgu95b

value: unknown


title: SNB-19 hgu95a


title: COLO 205 hgu95b


title: SNB-75 hgu95b


title: SNB-75 hgu95c


title: SF-295 hgu95a

value: radiation


title: Primary human neuroblastoma cS004


title: SNB-19 hgu95b

value: male


title: SNB-19 hgu95c

value: mutant


title: Primary human neuroblastoma cS005


title: Primary human neuroblastoma cS008


title: Primary human neuroblastoma cS006


title: SF-268 hgu95a


title: SF-268 hgu95b


title: BT-549 hgu95a

source_name: Papillary infiltrating ductal carcinoma

value: other[metastasis]

value: Invasive Papillary Breast Carcinoma

value: breast

value: Papillary infiltrating ductal carcinoma


title: T-47D hgu95a

source_name: breast epithelial carcinoma

value: Infiltrating Ductal Carcinoma

value: breast epithelial carcinoma


title: T-47D hgu95b


title: SF-539 hgu95b

source_name: Glial Neoplasm

value: wild             type

value: Glial Neoplasm

value: central nervous system


title: SF-295 hgu95b

value: Glioblastoma undifferntiated

value: birth


title: SF-539 hgu95c

value: other[unknown]

value: female


title: SF-539 hgu95a

value: years


title: COLO 205 hgu95a

value: unknown

value: other[ascites]

value: COLO 205

value: adenocarcinoma

value: colon


title: T-47D hgu95c

value: mutant

value: breast


title: SF-268 hgu95c

value: radiation


title: BT-549 hgu95c

value: other[metastasis]

value: Invasive Papillary Breast Carcinoma

value: Papillary infiltrating ductal carcinoma


title: HS 578T hgu95c

source_name: breast epithelial carcinosarcoma

value: other[primary]

value: HS 578T

value: carcinosarcoma

value: breast epithelial carcinosarcoma


title: Primary human neuroblastoma cS002


title: HS 578T hgu95a

value: birth

value: female


title: Primary human neuroblastoma cS001


title: MDA-MB-231/ATCC hgu95a

source_name: breast epithelial adenocarcinoma

value: unknown

value: other[pleural effusion]

value: breast epithelial adenocarcinoma

value: years


title: HS 578T hgu95b


title: MDA-MB-231/ATCC hgu95c

value: adenocarcinoma


title: MCF7 hgu95c

value: wild             type


title: MCF7 hgu95b

value: breast


title: MCF7 hgu95a


title: Primary human neuroblastoma cS003


title: Stage T2N1 NSCLC 3108890

status: Public on Aug 01 2007

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

country: Netherlands

institute: Vrije Universiteit Medical Center

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).

hyb_protocol: Hybridization protocol available via the microarrays website of VU medisch centrum

scan_protocol: Microarray Scanner G2505B (Agilent Technologies), default settings

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratios of spots that were not excluded after quality flagging and mapping were normalized to their mode value. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004)  Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.).

label_protocol: DNA labeling protocol available via the microarrays website of VU medisch centrum

extract_protocol: DNA isolation protocol available via the microarrays website of VU medisch centrum

tag: Gender

value: Male

tag: Tissue

value: NSCLC

tag: Histology

value: SSC

tag: Stage

source_name: Female reference DNA

tag: Pooled DNA from the blood of 10 normal female individuals


title: 3rd MPSS library produced from activated CD4+ T cell clone 29

status: Public on Aug 02 2007

type: MPSS

city: Oxford

first: Edward

middle: J

last: Evans

state: Oxfordshire

address: HIU, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Nuffield Dept. Clinical Medicine

country: United Kingdom

institute: University of Oxford

description: 3rd MPSS library produced from a single sample of RNA from an activated CD4+ T-cell clone.

data_processing: Data file includes simply the tags identified and their counts in the library

source_name: human CD4+ T cell clone 29

growth_protocol: The clone was established in culture with IL-7 and the HIV-1 gag peptides KRWIILGLNKVIRMY and GEIYKRWIILGLNKI (but later shown to be specific for the former)

extract_protocol:
Total RNA was extracted from T cells using Trizol according to standard
methods and sent to Lynx therpeutics for the generation and sequencing of an MPSS library.

treatment_protocol:
T cells were activated with beads coated in monoclonal antibodies
specific for CD3 and CD28.

tag: CD4+ T cell clone 29 derived from PBMC from subject

tag: Immunogen

value: MVA virus containing HIV-1 gag gene

tag: Peptide Specificity

value: KRWIILGLNKVIRMY

tag: TCR usage


title: Stage T2N0 NSCLC 2193761

value: ADC


title: MDA-MB-231/ATCC hgu95b

tag: MDR Function

tag: Prior Treatment

tag: p53 Status

value: mutant

tag: BioSourceType

tag: CellLine

tag: DiseaseState

tag: Individual:

tag: InitialTimePoint


title: BT-549 hgu95b

tag: Age

value: other[metastasis]

value: Invasive Papillary Breast Carcinoma

tag: OrganismPart

tag: Sex

tag: TargetedCellType

value: Papillary infiltrating ductal carcinoma

tag: TimeUnit


title: Stage T2N0 NSCLC 5321534

tag: Gender

tag: Tissue

tag: Histology

tag: Stage

tag: Pooled DNA from the blood of 10 normal female individuals


title: Stage T2N1 NSCLC 5968419

value: SCC


title: Stage T1N0 NSCLC 0879381

value: Female

source_name: Male reference DNA

tag: Pooled DNA from the blood of 10 normal male individuals


title: Stage T2N0 NSCLC 6899012

value: LCC


title: Stage T1N0 NSCLC 5139023

value: other


title: Stage T2N1 NSCLC 3139379


title: Stage T2N0 NSCLC 7967970


title: Stage T2N1 NSCLC 5364014


title: Stage T1N0 NSCLC 1152999

value: ADSC


title: Stage T2N1 NSCLC 4705981


title: 2nd MPSS library produced from activated CD4+ T cell clone 29

description: 2nd MPSS library produced from a single sample of RNA from an activated CD4+ T-cell clone.

tag: CD4+ T cell clone 29 derived from PBMC from subject

tag: Immunogen

tag: Peptide Specificity

tag: TCR usage


title: Stage T1N0 NSCLC 0951411


title: Stage T1N0 NSCLC 6868842


title: Stage T1N1 NSCLC 4870462


title: Stage T1N0 NSCLC 0113862


title: Stage T1N1 NSCLC 8885065


title: Stage T2N1 NSCLC 7998902


title: Stage T1N0 NSCLC 5148421


title: Stage T2N1 NSCLC 6123993


title: Stage T1N0 NSCLC 4645929

value: SCCC


title: Stage T1N0 NSCLC 7919568


title: Stage T2N0 NSCLC 7686512


title: Stage T2N0 NSCLC 3677075


title: Stage T2N0 NSCLC 4909209


title: 99-032-09_DS7189_WGA_4ug F

status: Public on Jun 23 2007

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: DnaseI enriched

hyb_protocol: Labeled samples were hybridized for 16 hr at 45C on Affymetrix whole Genome Tiling Arrays.  Arrays were washed and post stained using the Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetrix's GCOS software and Analyzed using the Affymetrix TAS analysis software.

source_name: GM06990c; DnaseI enriched

label_protocol: Fragments were cleaned using Qiagen PCR columns.  Samples were amplified using the Sigma WGA amplification kit.  Cleaned and fragmented to an avg size of 75 bp using DNaseI and labeled with Biotin 16-ddUTP and Terminal Transferase.  (See Affymetrix Chip Chip protocol)

growth_protocol: (follow vendor recommendations for medium) with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum

extract_protocol: Samples were extracted with an equal volume of Phenol and Chloroform and small fragments separated out by running the sample through a 10% sucrose cushion for 24 hrs at 25000 rpm on a Beckman Ultracentrfuge using a SW41 rotor.

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40 and treated for 3 minutes with varying concentrations of DNaseI


title: 99-032-05_DS7185_WGA_4ug F

description: DnaseI enriched


title: Stage T1N0 NSCLC 2916372


title: Stage T2N0 NSCLC 4900647


title: 79-177-02_GM050513-4u-042 F

description: DnaseI enriched

growth_protocol: RPMI 1640 medium with 2 mM L-glutamine adjusted to contain 1.5 g-L sodium bicarbonate. 4.5 g-L glucose. 10 mM HEPES and 1.0 mM sodium pyruvate and supplemented with 0.5 mg-ml G418 and 10percent  fetal bovine serum


title: Stage T1N0 NSCLC 3059619

description: For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies)

data_processing: Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratios of spots that were not excluded after quality flagging and mapping were normalized to their mode value. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004)  Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.)


title: Stage T2N0 NSCLC 3977909

tag: Pooled DNA from the blood of 10 normal Male individuals


title: 91-021-02_GM050127_0u_cont F

description: Control genomic dna (untreated)

source_name: GM06990c; Control genomic dna (untreated)

extract_protocol: Samples were extracted/cleaned using Qiagen Midi Preps according to manufacturer

treatment_protocol: Cells were lysed and Intact nuclei were isolated using NP40.  Nuclei were lysed using SDS and treated overnight with Proteinase K


title: 79-177-01_GM060224_0cont F

description: Control genomic dna (untreated)


title: 91-021-01_GM050127_0u_cont F

description: Control genomic dna (untreated)


title: 91-022-01_DS6697_A_42 C

description: DnaseI enriched


title: Stage T1N0 NSCLC 0464832


title: 99-032-05_DS7185_WGA_4ug D

description: DnaseI enriched


title: Stage T1N0 NSCLC 3460541

tag: Pooled DNA from the blood of 10 normal Female individuals


title: Primary human neuroblastoma cS007

tag: Primary human neuroblastoma

tag: normal human reference genomic DNA


title: Stage T1N0 NSCLC 1989395

tag: Age


title: 91-029-03_DS6855_5u_D F

description: DnaseI enriched


title: 91-029-01_DS6853_5u_D F

description: DnaseI enriched


title: 251368310013: fiber initials versus ovules

status: Public on Jun 26 2007

city: Raleigh

first: Earl

middle: William

last: Taliercio

state: NC

address: 3127 Ligon St

institute: USDA/ARS

description: Images were quantified using Agilent Feature Extraction Software

hyb_protocol: protocol of MoGene (St Louis, MO)

scan_protocol: Scanned on an Agilent G2565AA scanner

data_processing: value_experiment and statistics calculated from three reps including dye swap

organism: Gossypium hirsutum

source_name: total RNA from 1 dpa cotton ovules

label_protocol: MicroMax kit from Perkin Elmer

growth_protocol: field grown

extract_protocol: polyribosomal RNA isolation

tag: cultivar DES119

source_name: total RNA from 1dpa fiber

tag: cultivar DES11


title: 251368310014: fiber initials versus 10 dpa fiber

source_name: total RNA from 1 dpa cotton fiber

source_name: total RNA from 10 dpa fiber


title: SF-295 hgu95c

source_name: Glioblastoma undifferntiated

tag: MDR Function

tag: Prior Treatment

value: radiation

tag: p53 Status

tag: BioSourceType

value: other[unknown]

tag: CellLine

tag: DiseaseState

value: Glioblastoma undifferntiated

tag: Individual:

tag: InitialTimePoint

value: birth

tag: OrganismPart

value: central nervous system

tag: Sex

value: female

tag: TargetedCellType

tag: TimeUnit

value: years


title: 99-032-09_DS7189_WGA_4ug D

description: DnaseI enriched


title: 251368310012: fiber initials versus 10 dpa fiber

source_name: total RNA from 10 dpa cotton fiber

source_name: total RNA from 1 dpa fiber


title: 251368310002: fiber initials versus 10 dpa fiber

source_name: total RNA from 1dpa cotton fiber


title: 91-029-03_DS6855_5u_D D

description: DnaseI enriched


title: 79-177-01_GM060224_0cont D

description: Control genomic dna (untreated)


title: 251368310001: fiber initials versus ovules

data_processing: for LSR values and statistics calculated from three reps including dye swap

source_name: total RNA from 1dpa ovules

growth_protocol:
field grown
field grown


title: 99-032-09_DS7189_WGA_4ug B

description: DnaseI enriched


title: 91-021-02_GM050127_0u_cont D

description: Control genomic dna (untreated)


title: 91-021-01_GM050127_0u_cont D

description: Control genomic dna (untreated)


title: 251368310011: fiber initials versus ovules

data_processing: values and statistics calculated from three reps including dye swap

label_protocol: MicroMax Kit from Perkin Elmer


title: 79-177-02_GM050513-4u-042 D

description: DnaseI enriched


title: 91-022-01_DS6697_A_42 G

description: DnaseI enriched


title: 79-177-01_GM060224_0cont B

description: Control genomic dna (untreated)


title: 91-021-02_GM050127_0u_cont B

description: Control genomic dna (untreated)


title: 91-029-01_DS6853_5u_D D

description: DnaseI enriched


title: 99-032-05_DS7185_WGA_4ug B

description: DnaseI enriched


title: 79-177-01_GM060224_0cont C

description: Control genomic dna (untreated)


title: 91-021-01_GM050127_0u_cont B

description: Control genomic dna (untreated)


title: 91-022-01_DS6697_A_42 E

description: DnaseI enriched


title: 99-032-09_DS7189_WGA_4ug C

description: DnaseI enriched


title: 91-029-01_DS6853_5u_D B

description: DnaseI enriched


title: 99-032-05_DS7185_WGA_4ug C

description: DnaseI enriched


title: 79-177-02_GM050513-4u-042 B

description: DnaseI enriched


title: 91-022-01_DS6697_A_42 F

description: DnaseI enriched


title: 91-029-03_DS6855_5u_D C

description: DnaseI enriched


title: 91-021-01_GM050127_0u_cont C

description: Control genomic dna (untreated)


title: 99-032-05_DS7185_WGA_4ug A

description: DnaseI enriched


title: 99-032-09_DS7189_WGA_4ug A

description: DnaseI enriched


title: 79-177-02_GM050513-4u-042 C

description: DnaseI enriched


title: 99-032-09_DS7189_WGA_4ug G

description: DnaseI enriched


title: 91-021-02_GM050127_0u_cont C

description: Control genomic dna (untreated)


title: 79-177-01_GM060224_0cont G

description: Control genomic dna (untreated)


title: 91-029-03_DS6855_5u_D G

description: DnaseI enriched


title: 91-014-03_GM050127_0u_8ug_D G

description: Control genomic dna (untreated)


title: 79-177-02_GM050513-4u-042 A

description: DnaseI enriched


title: 91-022-01_DS6697_A_42 D

description: DnaseI enriched