title: Dmock_Daphid_2_T12_138702

status: Public on Oct 13 2008

type: RNA

city: Urbana

first: min

last: li

state: IL

address: Rm230 1101 W peabody Dr

country: USA

institute: University of Illinois at Urbana-Champaign

description: Replicate 2

hyb_protocol: Hegde P et al Biotechniques 2000 29:548-56

scan_protocol: scanner: Perkin-Elmer ScanArray Express Software: ScanArray Express v2.1

data_processing:
Spot raw data from GenePix4.0
log2 transformation using R/MAANOVA
linlog normalization using R/MAANOVA

molecule: total RNA

organism: Glycine max

source_name: Pooled unifoliate leaves from 3-4 plants

label_protocol: Indirect incorporation using aa-dUTP

growth_protocol:
Growth Chamber (22C)
Light 100-120 umol photons/m2/sec
14 hour daylength

extract_protocol: Trizol Phase Lock Gel RNA Extraction

treatment_protocol: mock treated

tag: Cultivar

value: Dowling

tag: Age

value: approximately 10 days

treatment_protocol: Soybean aphid (Aphis glycines) infested


title: CMV_HTx_EMB1352

status: Public on Oct 18 2008

city: Stanford

first: Cecile

last: Holweg

state: CA

address: 300 Pasteur Drive

department: Cardiovascular Medicine

institute: Stanford University

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-05/61295.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:53:56; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:53:56; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg

data_processing: VALUE is log(EMB/reference)

organism: Homo sapiens

source_name: hum ref

label_protocol: not provided

extract_protocol: not provided

tag: hum ref

source_name: endomyocardial biopsy;T25S3

label_protocol: Holweg_RNA_amp; RNA amplification using Agilent Low RNA Input Fluorescent Linear Amplification Kit   -              To a 1.5 ml microcentrifuge tube, add 250ng total RNA in a volume of 10.3 ul or less -              Add 1.2 ul of T7 promotor primer -              Use nuclease free water to bring the total volume up to 11.5 ul -              Incubate the reaction at 65?C for 10 minutes -              Place the reaction on ice for 5 minutes -              Mix the following components (per reaction) by pipetting: - 5X First Strand Buffer                               4 ul - 0.1M DTT                                                                                2 ul - 10mM dNTP mix                                                  1 ul - MMLV RT                                                                         1 ul - RNaseOUT                                                                     0.5 ul -              Add  8.5ul of the mix to each asmple -              Incubate the samples at 40?C in a circulating waterbath for 2 hours -              Heat the samples at 65?C for 15 minutes -              Incubate the samples on ice for 5 minutes -              Add 2.4 ul Cy5-CTP (10mM) to each sample (for Human Reference sample: Cy3-CTP) -              Preheat 50% PEG solution at 40?C for 1 minute -              Mix the following components (per reaction) by pipetting: - Nuclease free water                                    15.3 ul - 4X Transcription buffer                          20 ul - 0.1M DTT                                                                                6 ul - NTP mix                                                                            8 ul - 50% PEG                                                                           6.4 ul - RNAseOUT                                                                     0.5 ul - Inorganic Pyrophosphatase               0.6 ul - T7 RNA Polymerase                                       0.8 ul -              Add 57.6 ulmix to each sample -              Incubate the samples at 40?C in a waterbath, O/N Purification of amplified cRNA using the Qiagen RNeasy Minikit   -              Add 20 ul nuclease free water to each cRNA sample -              Add 350 ul RLT buffer + 35 ul 2-ME to each sample and mix -              Add 250 ul 100% ethanol to each sample and mix -              Transfer the cRNA to an RNeasy mini column and spin for 30 seconds, full speed in a microcentrifuge -              Add 500 ul RPE to each column, spin 30 seconds, full speed in a microcentrifuge -              Add another 500 ul RPE to each column, spin 1 minute, full speed in a microcentrifuge -              Dryspin the column for 2 minutes at full speed -              Elute the cRNA with 30 ul nuclease free water, spin full speed for 1 minute -              Repeat the elution step with the same 30 ul   Note: Amplify a batch of Human Reference RNA and freeze aliquots of 750 ng. Use one aliquot per sample for the hybrization.; Protocol Type = Amplification; Performer: Cecile,,Holweg

tag: Disease State

value: Acute Rejection Grade 0


title: CMV_HTx_EMB_1355

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-07/62571.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 15:11:41; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-06; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 15:11:41; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-06; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T27S2

value: Acute Rejection Grade 1B


title: CMV_HTx_EMB1353

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-05/61296.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:46:05; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:46:05; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T25S4


title: CMV_HTx_EMB7046

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-05/61293.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:33:20; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:33:20; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T25S1

value: Acute Rejection Grade 3B


title: CMV_HTx_EMB_1354

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-07/62570.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 15:03:53; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-06; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 15:03:53; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-06; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T27S1


title: CMV_HTx_EMB1351

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-05/61294.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:41:10; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:41:10; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T25S2

value: Acute Rejection Grade 3A


title: CMV_HTx_EMB_3984

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-07/62574.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:50:42; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-08; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:50:42; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-08; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T27S5


title: CMV_HTx_EMB_3982

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-07/62573.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 15:27:30; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-06; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 15:27:30; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-06; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T27S4


title: CMV_HTx_EMB_3981

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-07/62572.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 15:19:30; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-06; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 15:19:30; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.1.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-07-06; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T27S3


title: CMV_HTx_EMB7042

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-05/61290.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:01:56; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:01:56; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T24S1


title: CMV_HTx_EMB2714

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-09/55865.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:23:56; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-10; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:23:56; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-10; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T19S4

value: Acute Rejection Grade 1A


title: AR_HTx_EMB6933

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-02/59042.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:27:11; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:27:11; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T 23S5


title: CMV_HTx_EMB7045

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-05/61292.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:25:29; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:25:29; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T24S6


title: CMV_HTx_EMB2708

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-09/55868.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 09:54:51; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-09; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 09:54:51; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-09; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T12S1


title: CMV_HTx_EMB1321

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-11/57266.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:25:58; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-10-19; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:25:58; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-10-19; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T19S1


title: CMV_HTx_EMB1885

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-09/55874.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:20:06; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-02; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:20:06; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-02; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T18S3


title: CMV_HTx_EMB1318

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-09/55872.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:28:03; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-02; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 13:28:03; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-02; Performer: Cecile,,Holweg

source_name: hum ref

source_name: endomyocardial biopsy;T18S1


title: AR_HTx_EMB6932

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-02/59041.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:19:21; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:19:21; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T 23S4


title: CMV_HTx_EMB1996

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-11/57354.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:02:53; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-09; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 10:02:53; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-09; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T19S3


title: CMV_HTx_EMB2716

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-09/55871.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:52:29; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-10; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:52:29; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-10; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T22S1


title: CMV_HTx_EMB7044

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-05/61291.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:17:38; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:17:38; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-03-29; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T24S5


title: AR_HTx_EMB1817

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-02/59037.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:11:30; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:11:30; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T 23S1


title: Daphid_Waphid_2_T12_138703

description: Replicate 2

scan_protocol: scanner: Perkin-Elmer ScanArray Express Software: ScanArray Express v2.1

source_name: Pooled unifoliate leaves from 3-4 plants

value: Williams 82


title: Waphid_Wmock_2_T12_29D6

description: Replicate 2


title: Daphid_Waphid_1_T12_27B3

description: Replicate 1


title: Wmock_Dmock_2_T12_29E1

description: Replicate 2


title: CMV_HTx_EMB1320

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-11/57265.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:17:58; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-10-19; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:17:58; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-10-19; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T18S2


title: Daphid_Waphid_2_T12_29D10

description: Replicate 2


title: Waphid_Wmock_2_T12_138520

description: Replicate 2


title: Dmock_Daphid_1_T12_29B4

description: Replicate 1


title: CMV_HTx_EMB2715

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2004-09/55870.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:00:21; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-10; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 12:00:21; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-09-10; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T18S5


title: Wmock_Dmock_2_T12_138704

description: Replicate 2


title: Daphid_Waphid_2_T6_29D7

description: Replicate 2


title: Dmock_Daphid_2_T6_138517

description: Replicate 2


title: AR_HTx_EMB6935

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-02/59043.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:42:52; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:42:52; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy; T 23S6


title: AR_HTx_EMB6931

description:
Simple annotation: Tissue Rejection, Transplant
Image: http://www.stanford.edu/MicroArray/gifs/2005-02/59039.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Cecile,,Holweg Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:35:02; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 14:35:02; Parameter Scanner Model = G2505A; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2005-01-14; Performer: Cecile,,Holweg

source_name: endomyocardial biopsy;T 23S3


title: Daphid_Waphid_1_T6_27B7

description: Replicate 1


title: Dmock_Wmock_2_T6_138688

description: Replicate 2


title: Daphid_Waphid_2_T6_138687

description: Replicate 2


title: Wmock_Dmock_1_T12_29B9

description: Replicate 1


title: Wmock_Dmock_1_T12_27B4

description: Replicate 1


title: Dmock_Daphid_1_T12_27B2

description: Replicate 1


title: Waphid_Wmock_1_T12_29B5

description: Replicate 1


title: control_DW_2_T0_29E5

description: Replicate 2

treatment_protocol: control, Time 0

treatment_protocol: control, Time0


title: Daphid_Waphid_1_T12_29B8

description: Replicate 1


title: control_DW_2_T0_138519

description: Replicate 2


title: Waphid_Wmock_2_T6_29D4

description: Replicate 2


title: Waphid_Wmock_2_T6_138518

description: Replicate 2


title: control_DW_1_T0_29D5

description: Replicate 1


title: Dmock_Daphid_2_T6_29D3

description: Replicate 2


title: control_WD_1_T0_2524D10

description: Replicate 1


title: Waphid_Wmock_1_T6_27B5

description: Replicate 1


title: Wmock_Dmock_2_T6_29D8

description: Replicate 2


title: Daphid_Waphid_1_T6_29B10

description: Replicate 1


title: slide10

status: Public on Oct 09 2008

city: Ames

first: Patrick

middle: S.

last: Schnable

state: IA

address: 2035B Roy J Carver Co-Lab

institute: Iowa State University

description: Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage.  Total RNA was isolated from ten replications of B73, Mo17 maize seedling genotypes (6 individual seedlings pooled for each genotype in each replication) using Trizol reagent (Invitrogen, Carlbad, CA) with slight modifications to manufacturer’s protocol.  Approximately 500 micrograms of total RNA were used for mRNA isolation with the OligoTex mRNA midi kit (Qiagen, Valencia, CA ) as per manufacturer’s protocol with slight modification. Two micrograms of mRNA were labeled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the GP2613 platform.

hyb_protocol: Fluorescent targets were hybridized as described in the “oligo microarray protocol” file at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.

scan_protocol: Each microarray chip (10 total) was scanned a minimum of six times in ascending amounts of laser power and PMT gain settings using a ProScanArray scanner (PerkinElmer, Boston, MA). Two scans from each chip were selected based on the median value of the natural log of the signal median for all spots on the slide.

data_processing: The lowess normalization method of Dudoit, Yang, Callow, and Speed (2002) was applied to the log of background-corrected raw signal intensities to remove signal-intensity-dependent dye effects from each slide.  Normalization was carried out separately for each slide to avoid introducing dependencies among biological replications. Following lowess normalization, the normalized data for each slide/dye combination were median centered so that expression measures would be comparable across slides.  Median-centering involves subtracting the median value for a particular slide/dye combination from each individual value associated with the particular slide/dye combination. The lowess normalized data from each scan was used for a mixed linear model analysis (Wolfinger et al., 2001).

molecule: polyA RNA

organism: Zea mays

label_protocol: Fluorescent cDNA targets were synthesized and hybridized as described at http://schnablelab.plantgenomics.iastate.edu/resources/protocols/.   Labeled targets containing a minimum of 3000 picomoles of cDNA, 50 picomoles of Cy dye, and more than one dy molecule per 50 (100) bases of Cy3 (Cy5) were used for hybridizations.

extract_protocol: total RNA extraction with Trizol (Invitrogen, Carlsbad, CA) with minor modifications to manufacturer’s instructions, mRNA isolation with Oligotex Kit (Qiagen, Valencia, CA) as per manufacturer’s instructions

tag: Genotype:	B73

tag: Tissue

value: above ground seedling

tag: Dev stage

value: 14 days old

tag: Sample name

tag: Genotype:	Mo17

tag: Tissue:		above ground seedling

tag: Dev stage:	 14 days old

tag: Sample name:	1776 Mo17 Cy5


title: Dmock_Wmock_1_T6_27B8

description: Replicate 1


title: Waphid_Wmock_1_T12_27B1

description: Replicate 1


title: Dmock_Daphid_1_T6_27B6

description: Replicate 1


title: Dmock_Daphid_1_T6_29B1

description: Replicate 1


title: slide8

tag: Sample name:	1665 Mo17 Cy5


title: Wmock_Dmock_1_T6_29D1

description: Replicate 1


title: control_DW_1_T0_138708

description: Replicate 1


title: slide6

tag: Sample name:	4844 Mo17 Cy5


title: slide4

tag: Sample name:	8894 Mo17 Cy5


title: control_WD_2_T0_2524E1

description: Replicate 2


title: control_WD_2_T0_24C9

description: Replicate 2


title: control_WD_1_T0_24C10

description: Replicate 1


title: mibta52b 24h (AH_WT24hVsta52b24h_BRII_TR3_179)

status: Public on Feb 29 2008

city: Singapore

first: Govindarajan

last: Kunde Ramamoorthy

address: 60, Biopolis Street, Genome

department: Research Computing Group

country: Singapore

institute: Genome Institute of Singapore

description: RNA from mib mutant embryos and their wild type siblings at three different time points

hyb_protocol: Standard procedure (Mathavan et al., 2005)

scan_protocol: GenePix 4000B microarray scanner (Axon Instruments)

data_processing: The intensity-based log ratio median method (Yang et al./, 2003)

label: Cy-5 d-UTP

organism: Danio rerio

source_name: mib mutant embryos

label_protocol: 20ug of total RNA was reverse transcribed to produce Cy-5 d-UTP (Sample) cDNA targets

extract_protocol: Total RNA extraction using Trizol followed by Qiagen RNeasy Mini Kit extraction

tag: mib mutant embryos

label: Cy3 d-UTP

source_name: wild type embryos

label_protocol: 20ug of total RNA was reverse transcribed to produce Cy3 d-UTP (Reference) cDNA targets

tag: wild type siblings


title: mibta52b 24h (AH_WT24hVsta52b24h_BRII_TR2_190)


title: mibta52b 24h (AH_WT24hVsta52b24h_BRI_TR2_188)


title: mibta52b 48h (AH_WT48hVsta52b48h_BRII_TR1_137)


title: mibta52b 24h (AH_WT24hVsta52b24h_BRII_TR1_189)


title: slide3

tag: Sample name:	8895 B73 Cy5


title: Dmock_Daphid_2_T12_29D9

description: Replicate 2

tag: Cultivar

tag: Age


title: slide9

tag: Sample name:	1774 B73 Cy5


title: mibta52b 48h (AH_WT48hVsta52b48h_BRII_TR2_138)


title: mibta52b 72h (AH_WT72hVsta52b72h_BRII_TR3_129)


title: mibta52b 24h (AH_WT24hVsta52b24h_BRI_TR1_187)


title: mibta52b 48h (AH_WT48hVsta52b48h_BRI_TR2_136)


title: mibm132 48h (AH_WT48hVsm13248h_BRII_TR1_182)


title: Waphid_Wmock_1_T6_29A9

description: Replicate 1


title: slide7

tag: Genotype:	B73

tag: Sample name:	1686 B73 Cy5


title: mibtfi91 72h (AH_WT72hVstfi9172h_BRII_TR4_92)


title: mibta52b 72h (AH_WT72hVsta52b72h_BRI_TR2_125)


title: slide2

description: Maize seedlings were grown under controlled conditions and were harvested at the 14 day old stage.  Total RNA was isolated from ten replications of B73, Mo17 maize seedling genotypes (6 individual seedlings pooled for each genotype in each replication) using Trizol reagent (Invitrogen, Carlbad, CA) with slight modifications to manufacturer’s protocol.  Approximately 500 micrograms of total RNA were used for mRNA isolation with the OligoTex mRNA midi kit (Qiagen, Valencia, CA ) as per manufacturer’s protocol with slight modification. Two micrograms of mRNA were labeled according to Nakozono et al. (2003) with slight modifications.  Each sample was labeled with Cy dye and hybridized to the GPL4623 platform.

tag: Tissue

tag: Dev stage

tag: Sample name:	1692 Mo17 Cy5


title: mibtfi91 72h (AH_WT72hVstfi9172h_BRI_TR4_80)


title: slide1

tag: Genotype:	Mo17

tag: Sample name

tag: Tissue:		above ground seedling

tag: Sample name:	9562 B73 Cy5


title: mibta52b 72h (AH_WT72hVsta52b72h_BRI_TR1_126)


title: slide5

tag: Dev stage:	 14 days old

tag: Sample name:	8811 B73 Cy5


title: mibm132 72h (AH_WT72hVsm13272h_BRI_TR1_38)

tag: mib mutant embryos


title: mibm132 72h (AH_WT72hVsm13272h_BRII_TR3_54)

tag: wild type siblings


title: mibta52b 72h (AH_WT72hVsta52b72h_BRII_TR1_133)


title: mibm132 72h (AH_WT72hVsm13272h_BRIII_TR1_58)


title: mibta52b 48h (AH_WT48hVsta52b48h_BRI_TR1_135)


title: mibtfi91 72h (AH_WT72hVstfi9172h_BRI_TR3_79)


title: mibm132 72h (AH_WT72hVsm13272h_BRIII_TR3_62)


title: mibta52b 72h (AH_WT72hVsta52b72h_BRII_TR2_128)


title: mibm132 72h (AH_WT72hVsm13272h_BRI_TR3_40)


title: mibm132 72h (AH_WT72hVsm13272h_BRII_TR4_56)


title: mibta52b 72h (AH_WT72hVsta52b72h_BRI_TR3_134)


title: mibtfi91 48h (AH_WT48hVstfi9148h_BRII_TR3_170)


title: mibtfi91 72h (AH_WT72hVstfi9172h_BRII_TR3_91)


title: mibm132 48h (AH_WT48hVsm13248h_BRI_TR2_140)


title: mibtfi91 72h (AH_WT72hVstfi9172h_BRI_TR1_77)


title: mibm132 48h (AH_WT48hVsm13248h_BRI_TR1_139)


title: mibtfi91 48h (AH_WT48hVstfi9148h_BRI_TR1_176)


title: mibtfi91 72h (AH_WT72hVstfi9172h_BRII_TR1_81)


title: mibm132 72h (AH_WT72hVsm13272h_BRII_TR2_52)


title: mibm132 72h (AH_WT72hVsm13272h_BRI_TR2_39)


title: mibm132 72h (AH_WT72hVsm13272h_BRIII_TR2_60)


title: mibtfi91 72h (AH_WT72hVstfi9172h_BRII_TR2_82)


title: mibtfi91 48h (AH_WT48hVstfi9148h_BRII_TR2_172)


title: H2O2 treated 15 minutes rep 3

status: Public on Jan 31 2008

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: H2O2 treated 15 minutes rep 3

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: standard Affymetrix GCOS 1.4 scale 500, Excel quality filter and ttest, Genespring clustering, Partek ANOVA

label: biotin

organism: Staphylococcus aureus

label_protocol: Standard Affymetrix procedures

extract_protocol: Standard Affymetrix procedures

tag: Wild type time series 15,30,60, 120min versus three treatments


title: Hypochlorous acid treated 15 minutes rep 2


title: Untreated 60 minutes rep 3

description: Untreated 60 minutes rep 3


title: H2O2 treated 60 minutes rep 3

description: H2O2 treated 60 minutes rep 3


title: Hypochlorous acid treated 30 minutes rep 2


title: Untreated 15 minutes rep 3

description: Untreated 15 minutes rep 3


title: Untreated 30 minutes rep 3

description: Untreated 30 minutes rep 3


title: Hypochlorous acid treated 120 minutes rep 2


title: mibtfi91 48h (AH_WT48hVstfi9148h_BRII_TR1_173)


title: Untreated 30 minutes rep 2

description: Untreated 30 minutes rep 2


title: mibtfi91 48h (AH_WT48hVstfi9148h_BRI_TR2_175)


title: mibm132 48h (AH_WT48hVsm13248h_BRII_TR2_167)


title: mibm132 48h (AH_WT48hVsm13248h_BRII_TR3_168)


title: Hypochlorous acid treated 120 minutes rep 3


title: Hypochlorous acid treated 30 minutes rep 3


title: Untreated 120 minutes rep 1

description: Untreated 120 minutes rep 1


title: Hypochlorous acid treated 15 minutes rep 3


title: H2O2 treated 120 minutes rep 3

description: H2O2 treated 120 minutes rep 3


title: Untreated 30 minutes rep 1

description: Untreated 30 minutes rep 1


title: H2O2 treated 15 minutes rep 2

description: H2O2 treated 15 minutes rep 2


title: Untreated 15 minutes rep 2

description: Untreated 15 minutes rep 2


title: Untreated 60 minutes rep 1

description: Untreated 60 minutes rep 1


title: Azurophilic granule proteins treated 60 minutes rep 3


title: Hypochlorous acid treated 60 minutes rep 3


title: Hypochlorous acid treated 60 minutes rep 1


title: Untreated 60 minutes rep 2

description: Untreated 60 minutes rep 2


title: Untreated 120 minutes rep 2

description: Untreated 120 minutes rep 2


title: Azurophilic granule proteins treated 30 minutes rep 1	2


title: H2O2 treated 60 minutes rep 1

description: H2O2 treated 60 minutes rep 1


title: H2O2 treated 30 minutes rep 1

description: H2O2 treated 30 minutes rep 1


title: H2O2 treated 15 minutes rep 1

description: H2O2 treated 15 minutes rep 1


title: H2O2 treated 120 minutes rep 2

description: H2O2 treated 120 minutes rep 2


title: H2O2 treated 30 minutes rep 3

description: H2O2 treated 30 minutes rep 3


title: Azurophilic granule proteins treated 60 minutes rep 2


title: Azurophilic granule proteins treated 60 minutes rep 1


title: H2O2_60 minutes rep 2

description: H2O2_60 minutes rep 2


title: Untreated 15 minutes rep 1

description: Untreated 15 minutes rep 1


title: Untreated 120 minutes rep 3

description: Untreated 120 minutes rep 3


title: Hypochlorous acid treated 15 minutes rep 1


title: Azurophilic granule proteins treated 15 minutes rep 1


title: Azurophilic granule proteins treated 30 minutes rep 2


title: Azurophilic granule proteins treated 15 minutes rep 3


title: H2O2 treated 30 minutes rep 2

description: H2O2 treated 30 minutes rep 2


title: Azurophilic granule proteins treated 30 minutes rep 1


title: Azurophilic granule proteins treated 120 minutes rep 3


title: mibm132 72h (AH_WT72hVsm13272h_BRIII_TR4_64)


title: H2O2 treated 120 minutes rep 1

description: H2O2 treated 120 minutes rep 1


title: Hypochlorous acid treated 60 minutes rep 2


title: Azurophilic granule proteins treated 120 minutes rep 2


title: Hypochlorous acid treated 120 minutes rep 1


title: Azurophilic granule proteins treated 120 minutes rep 1


title: Hypochlorous acid treated 30 minutes rep 1


title: Azurophilic granule proteins treated 15 minutes rep 2


title: CRC POOL vs. COLO201b

status: Public on Jan 01 2008

city: Carlsbad

first: Aimee

last: Jackson

address: 1896 Rutherford Rd

institute: Regulus Therapeutics

description: Profiling of colon cancer cell lines for correlation with KIF11i responsiveness

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: colon

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

tag: CRC POOL


title: CRC Pool vs. RKO-E6

tag: CRC Pool


title: CRC Pool vs. RKO-E6b


title: 2090_z_r2

city: Gainesville

first: Brian

last: Harfe

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: gene expression from ZPA cells

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on Mu430 2.0 A Array. GeneChips were processed on GeneChip fluidics station F450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GCOS 1.3 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Mus musculus

source_name: E10.5 mouse limb bud

label_protocol: Biotinylated cRNA was prepared according to the two-cycle Affymetrix protocol from 50ng total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).

growth_protocol: Shhgfpcre heterozygotes were harvested at E10.5.

extract_protocol: Qiagen RNeasy according to manufacturer's instructions

treatment_protocol: After dissociating the limbs into single cell suspensions, GFP-positive (ZPA) and GFP-negative (rest of the limb) cells were purified by FACS.

tag: GFP-positive, ZPA


title: CRC Pool vs. COLO320DM


title: CRC Pool vs. COLO205


title: CRC Pool vs. NCI-H716


title: CRC Pool vs. CCD 841 CoTr

tag: CCD 841 CoTr


title: CRC Pool vs. COLO320DMb


title: CRC Pool vs. COLO201


title: CRC Pool vs. Caco2


title: CRC Pool vs. HCT-8


title: CRC Pool vs. LS1034


title: CRC Pool vs. LoVo

tag: LoVo


title: CRC Pool vs. SW1463


title: CRC Pool vs. SW403


title: CRC Pool vs. SW620


title: CRC Pool vs. RKO-AS45-1


title: CRC Pool vs. RKO

tag: RKO


title: CRC Pool vs. HT29


title: CRC Pool vs. SW837


title: CRC Pool vs. WiDr

tag: WiDr


title: CRC Pool vs. SNU-C2B


title: CRC Pool vs. LS123


title: CRC Pool vs. SW480N


title: CRC Pool vs. DLD1


title: CRC Pool vs. SW48


title: CRC Pool vs. HCT116


title: SM_D_pig706_rep1

status: Public on Dec 31 2007

city: saint-gilles

first: marie

last: damon

address: domaine de la prise

country: France

institute: INRA

description: Pigs with high L* values

hyb_protocol: The arrays were hybridized with T7 oligonucleotide overnight at 42°C in 5X denhardt’s, 5X SSC, 0.5 % SDS, 100 ug/ml denatured herring sperm DNA and 2.1 kBq/ml labelled oligonucleotide in a total volume of 2 ml. The arrays were washed twice at room temperature for 10 min and 42°C for 5 min in 2x SSC containing 0.1% SDS and then apposed to Fuji Imaging Plate (BAS-TR2025, Fujifilm, Raytest France S.A.R.L., Courbevoie, France) for 24 hours. For complex target, each array was hybridized at 65°C during 48 h in 2 ml total hybridization volume. After 3 washes (1 hour 65°C, 0.1X SSC, 0.1% SDS), arrays were apposed to Fuji Imaging Plate (BAS-TR2025, Fujifilm, Raytest France S.A.R.L., Courbevoie, France) for 16 hours before scanning with a phosphor imaging system at a 25 µm resolution (BAS-5000, Fujifilm, Raytest France S.A.R.L., Courbevoie, France).

scan_protocol: Scanning was performed with a phosphor imaging system at a 25 µm resolution (BAS-5000, Fujifilm, Raytest France S.A.R.L., Courbevoie, France). Image scan; BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling.

data_processing: Signal processing was performed using the vector oligonucletide data to correct each spot signal by the actual amount of DNA present in each spot. Then signal was normalized by dividing each gene expression value by the median value of the array.

organism: Sus scrofa

source_name: semimembranosus pig muscle destructured

label_protocol: Hybridizations were performed according to Bertucci et al. (1999) with minor modifications. First, cDNA arrays were hybridized with a labelled T7 oligonucleotide (5'-taatacgactcactataggga-3' which is present at the extremity of each PCR product) to check the amount of cDNA in each spot. Briefly, 500 ng of T7 oligonucleotide was labelled with 20 units of T4 polynucleotide kinase (NEB, Beverly, MA, USA) and 1 MBq of gamma-33P-ATP (GE Healthcare Life Sciences, Orsay, France). After stripping (3 hours at 80°C, 1 mM EDTA, 0.5% SDS), the arrays were submitted to a second hybridization with labelled cDNA according to (Bernard et al., 2000). Briefly, 5µg total RNA of each muscle sample was converted to cDNA (complex target) and simultaneously labelled during 2 hours at 42°C in the presence of 200 units of SuperScriptTM II RNase H- Reverse Transcriptase (Invitrogen SARL, Life Technologies, Cergy Pontoise), 2.5 uM dCTP, 0.4 mM each dATP, dTTP, dGTP and 1.5 MBq of alpha-33P-dCTP (GE Healthcare Life Sciences, Orsay, France) in 30 ul final volume.

extract_protocol:
According to Chomczynski and Sacchi (1987)
Purify with RNA clean up (Qiagen)
Dnase treatment (Ambion)

tag: F2 pig Pietrain type and Synthetic line ( Large White X Duroc X Hampshire)


title: SM_D_pig706_rep2

description: Pigs with high L* values


title: CRC Pool vs. HCT15


title: DKK1 treated vs. untreated keratinocytes 5

city: Bethesda

first: Vincent

last: Hearing

state: MD

address: Bldg 37  Rm 2132

department: National Cancer Institute

institute: National Institutes of Health

hyb_protocol: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42?r at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 ?l COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100?r 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42?st before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42? water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to NCI Microarray Manual)

scan_protocol: Two fluorescent intensities of the oligo-DNA chip were scanned using a microarray scanner (GenePix 4000A; Axon Instruments, Inc., Sunnyvale, CA). Differential gene expression was profiled with Genepix 3.0 software and was analyzed by NCI Center for Information Technology (CIT) programs and databases.

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

source_name: Total RNA from human keratinocytes with DKK1 treatment for 2 hours labeled with Cyanine-5 (red).

label_protocol: Cy3 and Cy5 Sample Labeling Protocol - generic

growth_protocol: Neonatal human foreskin keratinocytes were obtained from Cascade Biologics, Inc. (Portland, OR). Keratinoctye cultures were grown in keratinocyte growth medium (Cascade Biologics, Inc.). Keratinocytes from the third and fifth passages were used in the experiments.

extract_protocol: Used an RNeasy mini kit (Qiagen, Valencia, CA)

treatment_protocol: Treatment type: compound  Agent: recombinant human dickkopf 1 (rhDKK1)  Treatment dose: 50 ng/ml  Treatment time: 2 hours  Treatment temperature: 37 C

tag: DKK1 treated keratinocyte

source_name: Total RNA from human keratinocytes without DKK1 treatment labeled with Cyanine-3 (green).

tag: untreated keratinocyte


title: SM_D_pig158_rep2

description: Pigs with high L* values


title: DKK1 treated vs. untreated keratinocytes 1


title: SM_Normal_pig333_rep2

description: Pigs with low L* values

source_name: semimembranosus pig muscle normal


title: SM_Normal_pig333_rep1

description: Pigs with low L* values


title: DKK1 treated vs. untreated keratinocytes 6


title: SM_D_pig158_rep1

description: Pigs with high L* values


title: DKK1 treated vs. untreated keratinocytes 4


title: SM_Normal_pigM23_rep1

description: Pigs with low L* values


title: SM_Normal_pigM23_rep2

description: Pigs with low L* values


title: SM_D_pig314_rep1

description: Pigs with high L* values


title: SM_Normal_pigN77_rep1

description: Pigs with low L* values


title: SM_D_pig782_rep1

description: Pigs with high L* values


title: SM_D_pig459_rep1

description: Pigs with high L* values


title: SM_Normal_pig467_rep2

description: Pigs with low L* values


title: DKK1 treated vs. untreated keratinocytes 2


title: SM_D_pig314_rep2

description: Pigs with high L* values


title: SM_D_pig459_rep2

description: Pigs with high L* values


title: SM_D_pig782_rep2

description: Pigs with high L* values


title: DKK1 treated vs. untreated keratinocytes 3


title: SM_Normal_pig467_rep1

description: Pigs with low L* values


title: SM_Normal_pigN77_rep2

description: Pigs with low L* values


title: SM_Normal_pig782_rep2

description: Pigs with low L* values


title: SM_Normal_pig990_rep1

description: Pigs with low L* values

extract_protocol:
According to  Chomczynski and Sacchi (1987)
Purify with RNA clean up (Qiagen)
Dnase treatment (Ambion)


title: SM_Normal_pig990_rep2

description: Pigs with low L* values


title: SM_D_pig711_rep2

description: Pigs with high L* values


title: SM_Normal_pig669_rep2

description: Pigs with low L* values


title: SM_Normal_pig782_rep1

description: Pigs with low L* values


title: SM_D_pig724_rep2

description: Pigs with high L* values


title: Wild-type NOC chemostat 3

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

description:
Campylobacter jejuni NCTC11168 was grown in 2 homemade, parallel chemostats. Cells were grown in 125 ml volumes of Mueller-Hinton Broth where the growth rate was controlled by the dilution rate  (0.1 h-1). A gas mix of 80% nitrogen, 10% carbon dioxide and 10% oxygen was pumped into the head-space of the vessels at a rate of 0.25 l/min to obtain a microaerobic environment and the culture was maintained at 42 degrees C via a water jacket. Cells were grown as above until steady-state had been reached. At steady-state one of the cultures was exposed to 10 uM NOC-5 and -7 (final concentration) for a period of 10 min. Samples of both the control and stressed cultures were harvested into phenol/ethanol to stabilize the RNA and total RNA was purified using Qiagen's RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis.
Equal quantities of RNA from control and NOC-supplemented cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 4). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

data_processing: Slides were scanned on an Affymetrix 428 scanner and the images processed using Imagine software to calculate the spot and background intensities. The genesight programme was then used to calculate LOESS normalisation and Cy3/Cy5 ratios

organism: Campylobacter jejuni

source_name: Steady-state continuous cultured experiment samples in presence of 10 uM NOC for 10 minutes

tag: Steady-state continuous culture of wild-type NCTC11168 after exposure to NOC for 10 minutes

source_name: Steady-state continuous cultured control samples in absence of NOC

tag: Steady-state continuous culture of wild-type NCTC11168 without exposure to NOC


title: SM_D_pig711_rep1

description: Pigs with high L* values


title: cgb mutant NOC chemostat 2

description:
A single-domain globin (cgb) mutant strain of Campylobacter jejuni NCTC11168 was grown in 2 homemade, parallel chemostats. Cells were grown in 125 ml volumes of Mueller-Hinton Broth where the growth rate was controlled by the dilution rate  (0.1 h-1). A gas mix of 80% nitrogen, 10% carbon dioxide and 10% oxygen was pumped into the head-space of the vessels at a rate of 0.25 l/min to obtain a microaerobic environment and the culture was maintained at 42 degrees C via a water jacket. Cells were grown as above until steady-state had been reached. At steady-state one of the cultures was exposed to 10 uM NOC-5 and -7 (final concentration) for a period of 10 min. Samples of both the control and stressed cultures were harvested into phenol/ethanol to stabilize the RNA and total RNA was purified using Qiagen's RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis.
Equal quantities of RNA from control and NOC-supplemented cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 4). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values.

tag: Steady-state continuous culture of a NCTC11168 cgb (Cj1586) mutant strain without exposure to NOC

tag: Steady-state continuous culture of a NCTC11168 cgb (Cj1586) mutant strain after exposure to NOC for 10 minutes


title: Wild-type NOC chemostat 6


title: SM_D_pig724_rep1

description: Pigs with high L* values


title: cgb mutant noc chemostat 1


title: cgb mutant NOC chemostat 3


title: Wild-type NOC chemostat 1


title: Wild-type NOC chemostat 4


title: Wild-type NOC chemostat 2


title: cgb mutant NOC chemostat 4


title: SM_Normal_pig669_rep1

description: Pigs with low L* values


title: Transcriptome analysis of GSNO treated batch cultures of C. jejuni

description: Batch cultures of Wild-type C. jejuni NCTC11168 were grown in 150 ml volumes of Mueller-Hinton broth in 250 ml baffled flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % O2, 10 % CO2, 80 % N2) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 ºC. When mid-exponential phase was reached 0.25 mM GSNO was added to half of the cultures. After a 10 minute exposure samples of both treated and untreated cells were harvested into phenol/ethenol to stabilize the RNA and total RNA was purified using Qiagen’s RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis.

data_processing: Slides were scanned on an Affymetrix 428 scanner and the images processed using Imagine software to calculate the spot and background intensities. The genesight programme was then used to calculate LOWESS normalisation and Cy3/Cy5 ratios

source_name: Batch cultured control samples in absence of GSNO

tag: Batch culture of the wild-type NCTC11168 strain without exposure to GSNO

source_name: Batch cultured experiment samples in presence of 250 uM GSNO for 10 minutes

tag: Batch culture of the wild-type NCTC11168 strain after exposure to GSNO for 10 minutes


title: Wild-type NOC chemostat 5


title: Transcriptome analysis of GSNO treated batch cultures of C. jejuni 4

description: Batch cultures of Wild-type C. jejuni NCTC11168 were grown in 150 ml volumes of Mueller-Hinton broth in 250 ml baffled flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % O2, 10 % CO2, 80 % N2) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 degrees C. When mid-exponential phase was reached 0.25 mM GSNO was added to half of the cultures. After a 10 minute exposure samples of both treated and untreated cells were harvested into phenol/ethenol to stabilize the RNA and total RNA was purified using Qiagen's RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis.


title: Transcriptome analysis of GSNO treated batch cultures of C. jejuni 3


title: Transcrip and physiological responses of chemostat-grown Campylobacter jejuni to S-nitrosoglutathione 4

description: A single-domain globin (cgb) mutant strain of Campylobacter jejuni NCTC11168 was grown in 2 homemade, parallel chemostats. Cells were grown in 125 ml volumes of Mueller-Hinton Broth where the growth rate was controlled by the dilution rate  (0.1 h-1). A gas mix of 80% nitrogen, 10% carbon dioxide and 10% oxygen was pumped into the head-space of the vessels at a rate of 0.25 l/min to obtain a microaerobic environment and the culture was maintained at 42 ?C via a water jacket. Cells were grown as above until steady-state had been reached. At steady-state one of the cultures was exposed to 0.25 mM GSNO (final concentration) for a period of 10 min. Samples of both the control and stressed cultures were harvested into phenol/ethanol to stabilize the RNA and total RNA was purified using Qiagen?s RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis.

source_name: Steady-state continuous cultured experiment samples in presence of 250 uM GSNO for 10 minutes

tag: Steady-state continuous culture of a NCTC11168 cgb (Cj1586) mutant strain after exposure to GSNO for 10 minutes

source_name: Steady-state continuous cultured control samples in absence of GSNO

tag: Steady-state continuous culture of a NCTC11168 cgb (Cj1586) mutant strain without exposure to GSNO


title: Transcriptome analysis of GSNO treated batch cultures of C. jejuni 2


title: Transcrip and physiological responses of chemostat-grown Campylobacter jejuni to S-nitrosoglutathione 3


title: Transcrip and physiological responses of chemostat-grown Campylobacter jejuni to S-nitrosoglutathione 2


title: Transcrip and physiological responses of chemostat-grown Campylobacter jejuni to S-nitrosoglutathione

description: A single-domain globin (cgb) mutant strain of Campylobacter jejuni NCTC11168 was grown in 2 homemade, parallel chemostats. Cells were grown in 125 ml volumes of Mueller-Hinton Broth where the growth rate was controlled by the dilution rate  (0.1 h-1). A gas mix of 80% nitrogen, 10% carbon dioxide and 10% oxygen was pumped into the head-space of the vessels at a rate of 0.25 l/min to obtain a microaerobic environment and the culture was maintained at 42 ºC via a water jacket. Cells were grown as above until steady-state had been reached. At steady-state one of the cultures was exposed to 0.25 mM GSNO (final concentration) for a period of 10 min. Samples of both the control and stressed cultures were harvested into phenol/ethanol to stabilize the RNA and total RNA was purified using Qiagen’s RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis.

tag: Steady-state continuous culture of a NCTC11168 cgb (Cj1586) mutant strain after exposure to GSNO for 10 min


title: Transcrip and physiological responses of chemostat-grown Campylobacter jejuni to S-nitrosoglutathione 5


title: Sepsis Patient P17

status: Public on Dec 01 2007

city: Glebe

first: Benjamin

middle: Man Piu

last: Tang

state: NSW

address: 12/29 Cook Street

department: Intensive Care Medicine

country: Australia

institute: Nepean Hospital

hyb_protocol: SuperScriptÖ Plus Indirect cDNA Labeling System for DNA Microarrays (Invitrogen)

scan_protocol: GenePix 4000B laser scanner and GenePix software (Axon Instruments)

data_processing: Background subtraction followed by Lowess print-tip group Normalization, include genes which have 1. at least 80% of expression data with 2 fold change in either direction from the gene's median value, (2) at least 50% of expression data non-missing

source_name: Neutrophil

extract_protocol: RiboPure-Blood kit (AmbionTM)

tag: Sepsis Patient

tag: Infection type

value: Gram-Positive

source_name: Cell line

extract_protocol: not applicable

tag: Universal Human Reference RNA


title: Sepsis Patient P13

label_protocol: SuperScriptÖ Plus Indirect cDNA Labeling System for DNA Microarrays (Invitrogen)


title: Sepsis Patient P14


title: Sepsis Patient P15


title: Sepsis Patient P16


title: Sepsis Patient P10


title: Sepsis Patient P18


title: Sepsis Patient P12


title: Sepsis Patient P11


title: CRC Pool vs. SW948

tag: CRC Pool


title: Sepsis Patient P7


title: Sepsis Patient P8


title: Sepsis Patient P2


title: Sepsis Patient P9


title: Sepsis Patient P6


title: Sepsis Patient N20

value: Gram-Negative


title: Sepsis Patient N23


title: Sepsis Patient N25


title: Sepsis Patient N19


title: Sepsis Patient N22


title: Sepsis Patient P1


title: Sepsis Patient P5


title: Sepsis Patient P3


title: Sepsis Patient N24


title: Sepsis Patient N21


title: Sepsis Patient P4


title: Sepsis Patient N17


title: Sepsis Patient N16


title: Sepsis Patient N9


title: Sepsis Patient N7


title: Sepsis Patient N11


title: Sepsis Patient N5


title: Sepsis Patient N15


title: Sepsis Patient N8


title: Sepsis Patient N18


title: Sepsis Patient N4


title: Sepsis Patient N10


title: Sepsis Patient N12


title: Sepsis Patient M12

value: Mixed


title: Sepsis Patient N13


title: Sepsis Patient M10


title: Sepsis Patient N1


title: Sepsis Patient N6


title: Sepsis Patient M11


title: Sepsis Patient N14


title: Sepsis Patient M5


title: Sepsis Patient N2


title: Sepsis Patient N3


title: Sepsis Patient M4


title: Sepsis Patient M6


title: Sepsis Patient M8


title: Sepsis Patient M3


title: Sepsis Patient M7


title: K3_oligos_slide31_33Cy3_27Cy5

city: Jouy en Josas

first: Laurence

last: Flori

address: Domaine de Vilvert

department: Génétique Animale

description: The microarrays used in this study were provided by Dr Max Rothschild (Department of Animal Science, Iowa State University).

hyb_protocol: The slides were pre-soaked, prehybridized and hybridized with 40 pmoles of each Cy3 and Cy5 labelled cDNAs (Pronto Kit, Corning). After 16 hours hybridization at 42°C, the slides were washed according to commercial protocol (Pronto kit, Corning) and dried by centrifugation (1500 rpm, 3 min).

scan_protocol: Slides were scanned with the Microarrayreader scanner (Virtek). Signals were quantified with the Imagene version 5.1 software (Biodiscovery).

data_processing: The normalisation steps was performed using scripts written with R software. Raw data were log2 transformed, normalized by lowess (f=0.3) and the median of each block spotted on slide was substracted.

source_name: Porcine epithelial cells (PK15)

label_protocol: Five µg of each RNA were reverse-transcribed and labelled with Cy3 and Cy5 (reagents: Pronto kit, Corning and Amersham, Biosciences).

extract_protocol: RNAs were extracted using Trizol-chlorofrom method.

tag: Time (h) post-infection

tag: Replicate

tag: Status

value: Mock-Infected

value: PrV-Infected


title: K3_oligos_slide25_47Cy3_41Cy5


title: K3_oligos_slide22_39y3_40Cy5


title: K3_oligos_slide30_34Cy3_33Cy5


title: K3_oligos_slide29_28Cy3_34Cy5


title: K3_oligos_slide21_45Cy3_39Cy5


title: K3_oligos_slide20_44Cy3_45Cy5


title: K3_oligos_slide27_35Cy3_29Cy5


title: K3_oligos_slide26_41Cy3_35Cy5


title: K3_oligos_slide32_27Cy3_26Cy5


title: K3_oligos_slide19_38Cy3_44Cy5


title: K3_oligos_slide24_46Cy3_47Cy5


title: K3_oligos_slide17_26Cy3_32Cy5


title: K3_oligos_slide10_22Cy3_16Cy5


title: K3_oligos_slide18_32Cy3_38Cy5


title: K3_oligos_slide16_8Cy3_2Cy5


title: K3_oligos_slide23_40Cy3_46Cy5


title: K3_oligos_slide8_17Cy3_23Cy5


title: K3_oligos_slide28_29Cy3_28Cy5


title: K3_oligos_slide9_23Cy3_22Cy5


title: K3_oligos_slide12_15Cy3_21Cy5


title: K3_oligos_slide11_16Cy3_15Cy5


title: K3_oligos_slide14_20Cy3_14Cy5


title: K3_oligos_slide6_5Cy3_11Cy5


title: K3_oligos_slide5_4Cy3_5Cy5


title: K3_oligos_slide15_14Cy3_8Cy5


title: K3_oligos_slide4_10Cy3_4Cy5


title: K3_oligos_slide7_11Cy3_17Cy5


title: K3_oligos_slide13_21Cy3_20Cy5


title: Control Patient C10

tag: Control Patient


title: Sepsis Patient M1


title: K3_oligos_slide3_9Cy3_10Cy5


title: Sepsis Patient M2


title: Control Patient C7


title: Control Patient C17


title: Control Patient C15


title: Control Patient C16


title: Control Patient C5


title: K3_oligos_slide1_2Cy3_3Cy5


title: Control Patient C12


title: Control Patient C13


title: Control Patient C11


title: Control Patient C6


title: Control Patient C14


title: K3_oligos_slide2_3y3_9Cy5


title: Control Patient C8


title: Control Patient C2


title: Control Patient C4


title: Control Patient C9


title: Control Patient C3


title: Control Patient C1


title: Rpb3 antibody untreated 0612_Dm_S2_Rpb3_Untr#2_WG1

status: Public on Nov 11 2007

type: other

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Location analysis was conducted using the Drosophila Agilent LA arrays.  Starting with immunoprecipitated and WCE DNA, Cy3 and Cy5 labeled DNA was produced using a modified protocol of the Invitrogen CGH labeling kit and purification columns.  The labeled DNA samples were mixed as paired (IP to WCE) and hybridized for 40 hours at 65ºC to the probes on the array.  Chips were washed using SSPE solutions and scanned using an Agilent scanner.  The images were processed with the Agilent Feature Extraction Software to generate .txt files.

hyb_protocol: Two µg labeled DNA samples from paired immunoprecipitated and input samples were mixed with Human Cot-1 DNA (0.1mg/ml final concentration), Agilent Blocking Agent and Agilent Hybridization Buffer.  The mixture was heated to 95ºC for 3 minutes and then incubated at 37ºC for 30 minutes.  The samples were spun to collect the samples and 490 µl of sample was loaded onto the array with gasket slide.  Hybridization occurred for 40 hours at 65ºC at 10rpm in a rotating hybridization oven.  After hybridization, the arrays were disassembled in 6X SSPE and 0.005% N-lauroylsarcosine then transferred to another dish containing a slide rack and 6X SSPE and 0.005% N-lauroylsarcosine.  The slides were washed for 5 minutes with stirring and transferred for a few seconds to a container holding 0.06X SSPE.  The slides moved again to a fresh solution of 0.06X SSPE and washed with stirring for 5 minutes.  The slides were slowly removed from the solution to allow drying.  All hybridization and washing steps were performed in an ozone-regulated environment containing less than 1ppb O3.

scan_protocol: Chips were scanned with an Agilent G2565 Scanner (5micron with XDR).  XDR algorithm scans the array twice at two different PMT levels (100% and 10%, H and L respectively in .tif file names) and processed with Agilent Feature Extraction v9.1 (protocol CGH-v4_91).

data_processing: Normalized data was obtained by loading the .txt files obtained from Feature Extraction into the Agilent ChIP Analytics software.  This software uses several normalization procedures for the default work flow.  These include “Blanks subtraction normalization”, “Inter-array median normalization” and “Intra-array (dye-bias) median normalization”.  This program also contains an error-model which is used to identify the most likely binding events.  This error model uses both a probe-specific intensity based p-value as well as neighbor-specific intensity based p-values to determine a binding event.

molecule: other

organism: Drosophila melanogaster

source_name: Schneider's cells (S2)

label_protocol: Immunoprecipitated DNA samples were split into two reactions (~2-5µg/reaction) and each paired with an equimolar amount of WCE DNA labeling reaction performed in parallel. Using the Invitrogen CGH Labeling Kit components, random priming solution was added to a final concentration of 1X in a 75µl reaction. The reaction was mixed by vortexing and placed in a thermal cycler at 95ºC for 5 minutes. The sample was then cooled on ice before the Klenow-containing labeling mixture was added (112/56nM 10X dUTP Nucleotide Mix, 17µM Cy-dUTP, 60U Klenow final concentration). The reaction was mixed and incubated at 37ºC for 5-6 hours. Using the Invitrogen CGH columns, the samples were purified and eluted into 50µl water. The sample was analyzed using a nanoodrop for total DNA yield (6-13µg) and Cy label (4-9 pmol dye).

growth_protocol: Cells were grown in Shields and Sang medium, supplemented with bactopeptone and yeast extract, plus 10% Fetal Bovine Serum, as recommended by the Drosophila Genomics Resource Center

extract_protocol: Cells crosslinked with paraformaldehyde for 10 minutes were re-suspended to 1 ml/108 cells in sonication buffer containing 0.5% SDS and sonicated to produce DNA fragments of 200-500 bp length.  Samples were centrifuged to remove cellular debris.  After reversal of crosslinks, the DNA recovery was by proteinase-K digestion and phenol-chloroform extraction.

treatment_protocol: Untreated

tag: D. melanogaster S2 cells, male, largely tetraploid

extract_protocol: Cells crosslinked with paraformaldehyde for 10 minutes were re-suspended to 1 ml/108 cells in sonication buffer containing 0.5% SDS and sonicated to produce DNA fragments of 200-500 bp length.  Samples were centrifuged to remove cellular debris.  Material derived from 7.5 x 10^7 cells was immunoprecipitated using an antibody that recognizes the Rpb3 subunit of RNA polymerase II and Protein-A agarose.  Washes and DNA recovery were performed as described in Adelman, K. et al. (2005) Mol Cell, 17: pp.103-112.


title: Rpb3 antibody NELF-depleted 0612_Dm_S2_Rpb3_NELF-dep#2_Dm7

scan_protocol: Chips were scanned with an Agilent G2565 Scanner (10microns) and processed with Agilent Feature Extraction v8.5 using the CGH_44K_1005 protocol obtained from Agilent.

label_protocol: Immunoprecipitated DNA samples were split into two reactions (~2-5µg/reaction) and each paired with an equimolar amount of WCE DNA  labeling reaction performed in parallel.  Using the Invitrogen CGH Labeling Kit components, random priming solution was added to a final concentration of 1X in a 75µl reaction.  The reaction was mixed by vortexing and placed in a thermal cycler at 95ºC for 5 minutes.  The sample was then cooled on ice before the Klenow-containing labeling mixture was added (112/56nM 10X dUTP Nucleotide Mix, 17µM Cy-dUTP, 60U Klenow final concentration).  The reaction was mixed and incubated at 37ºC for 5-6 hours.  Using the Invitrogen CGH columns, the samples were purified and eluted into 50µl water.  The sample was analyzed using a Nanodrop for total DNA yield (6-13µg) and Cy label (4-9 pmol dye).

treatment_protocol: Cells were treated with dsRNA against NELF for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-73


title: Rpb3 antibody untreated 0612_Dm_S2_Rpb3_Untr#1_WG1


title: Serine2-Phosphorlyated Pol II antibody 0612_Dm_S2_Abcam ab5095_Untr#2_WG1

extract_protocol: Cells crosslinked with paraformaldehyde for 10 minutes were re-suspended to 1 ml/108 cells in sonication buffer containing 0.5% SDS and sonicated to produce DNA fragments of 200-500 bp length.  Samples were centrifuged to remove cellular debris.  Material derived from 7.5 x 10^7 cells was immunoprecipitated using an antibody raised against Serine2-Phosphorlyated Pol II (Abcam ab5095).  Washes and DNA recovery were performed as described in Adelman, K. et al. (2005) Mol Cell, 17: pp.103-112.


title: Serine2-Phosphorlyated Pol II antibody 0612_Dm_S2_Abcam ab5095_Untr#1_WG1


title: Mock immunoprecipitated 0612_Dm_S2_PrA_Untr#2_WG1

extract_protocol: Cells crosslinked with paraformaldehyde for 10 minutes were re-suspended to 1 ml/108 cells in sonication buffer containing 0.5% SDS and sonicated to produce DNA fragments of 200-500 bp length.  Samples were centrifuged to remove cellular debris.  Material derived from 7.5 x 10^7 cells was mock-immunoprecipitated using Protein-A agarose in the absence of an antibody.  Washes and DNA recovery were performed as described in Adelman, K. et al. (2005) Mol Cell, 17: pp.103-112.


title: Mock immunoprecipitated LacZ-treated 0612_Dm_S2_PrA_LacZ#1_Dm7

treatment_protocol: Cells were treated with dsRNA against LacZ for 96 hours, as described in Armknecht, S. et al. (2005) Methods in Enzymology, 392: pp. 55-73


title: Rpb3 antibody untreated 0612_Dm_S2_Rpb3_Untr#2_WG1 2


title: Rpb3 antibody untreated 0612_Dm_S2_Rpb3_Untr#2_Dm7


title: Rpb3 antibody untreated 0612_Dm_S2_Rpb3_Untr#1_Dm7


title: Rpb3 antibody LacZ-treated 0612_Dm_S2_Rpb3_LacZ#1_Dm7


title: Mock immunoprecipitated untreated 0612_Dm_S2_PrA_Untr#2_WG1 2


title: Rpb3 antibody LacZ-treated 0612_Dm_S2_Rpb3_LacZ#2_Dm7


title: Rpb3 antibody LacZ-treated 0612_Dm_S2_Rpb3_LacZ#2_Dm3


title: Mock immunoprecipitated untreated 0612_Dm_S2_PrA_Untr#1_Dm7


title: Rpb3 antibody LacZ-treated 0612_Dm_S2_Rpb3_LacZ#1_Dm3


title: Sepsis Patient M9


title: Rpb3 antibody NELF-depleted 0612_Dm_S2_Rpb3_NELF-dep#1_Dm7


title: Rpb3 antibody NELF-depleted 0612_Dm_S2_Rpb3_NELF-dep#1_Dm3


title: Rpb3 antibody NELF-depleted 0612_Dm_S2_Rpb3_NELF-dep#2_Dm3


title: Mock immunoprecipitated LacZ-treated 0612_Dm_S2_PrA_LacZ#1_Dm3


title: Rpb3 antibody untreated 0612_Dm_S2_Rpb3_Untr#1_WG1 2


title: INS37217-treated/detached retina, 7 days post-injection, replicate 3

status: Public on Nov 10 2007

city: Oklahoma City

first: Rafal

last: Farjo

state: OK

address: 940 Stanton L. Young Blvd.

department: Cell Biology

institute: The University of Oklahoma Health Sciences Center

description: We examined the effects of retinal detachment alone (Saline-injected) or detachment in the presence of a compound that facilitates the recovery process (INS37217-injected)

hyb_protocol: standard affymetrix procedures

scan_protocol: standard affymetrix procedures

data_processing: RMA

source_name: Retina detached by subretinal injection of saline, 7 days post-injection

label_protocol: standard affymetrix procedures

tag: Balb/cJ


title: INS37217-treated/detached retina, 7 days post-injection, replicate 2


title: INS37217-treated/detached retina, 2 hrs post-injection, replicate 1

source_name: Retina detached by subretinal injection of 10uM INS37217/saline, 2 hours post-injection


title: INS37217-treated/detached retina, 24 hrs post-injection, replicate 1

source_name: Retina detached by subretinal injection of saline, 24 hours post-injection


title: INS37217-treated/detached retina, 24 hrs post-injection, replicate 2


title: GOLD-0_Pool_n=8 vs Non-Smoker__5909

city: Seattle

first: serguei

middle: b

last: stepaniants

state: WA

address: 401 Terry  Ave. N

department: Rosetta

institute: Merck

description: Lung profiling from COPD patients

hyb_protocol: Labeled cRNAs were fragmented to an average size of approximately 50 to 100 nucleotides in the presence of 10 mM zinc chloride and adding a hybridization buffer containing 1 M sodium chloride, 0.5 percent sodium sarcosine, 50 mM morpholino-ethane sulfonic acid (pH 6.5), and formamide (final concentration, 30 percent at 40°C); After hybridization, the slides were washed

scan_protocol: slides were scanned using a confocal laser scanner (Agilent Technologies, Palo Alto, CA). Fluorescence intensities of the scanned images were quantified, normalized, and balanced

data_processing: Rosetta Resolver Ratio Experiment using a pair of Fluor-Reversed samples normalised using the Rosetta Resolver Agilent Error Model

source_name: Pooled Lung Samples

label_protocol: One round of RT-IVT to cRNA

extract_protocol: Trizol Lysis + RNeasy Column

treatment_protocol: Lung samples from COPD patients

source_name: Lung sample from non smoker


title: INS37217-treated/detached retina, 7 days post-injection, replicate 1


title: Saline-detached retina, 7 days post-injection, replicate 3


title: INS37217-treated/detached retina, 2 hrs post-injection, replicate 2

source_name: Retina detached by subretinal injection of saline, 2 hours post-injection


title: GOLD-0_Pool_n=8 vs Non-Smoker__3037

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-3__6034

description: Lung profiling from COPD patients

source_name: Lung samples from COPD patient


title: INS37217-treated/detached retina, 24 hrs post-injection, replicate 3


title: GOLD-0_Pool_n=8 vs Non-Smoker__3263

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-3__2751

description: Lung profiling from COPD patients


title: INS37217-treated/detached retina, 2 hrs post-injection, replicate 3


title: GOLD-0_Pool_n=8 vs GOLD-3__3467

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs Non-Smoker__3040

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-2__3412

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-2__3469

description: Lung profiling from COPD patients


title: Saline-detached retina, 7 days post-injection, replicate 1


title: GOLD-0_Pool_n=8 vs GOLD-2__5969

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs Non-Smoker__6019

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-2__3377

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-2__3380

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-2__3388

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-2__2427

description: Lung profiling from COPD patients


title: Saline-detached retina, 7 days post-injection, replicate 2


title: GOLD-0_Pool_n=8 vs GOLD-2__2142

description: Lung profiling from COPD patients


title: Saline-detached retina, 24 hrs post-injection, replicate 3


title: Saline-detached retina, 24 hrs post-injection, replicate 2


title: GOLD-0_Pool_n=8 vs GOLD-2__2086

description: Lung profiling from COPD patients


title: Saline-detached retina, 24 hrs post-injection, replicate 1


title: GOLD-0_Pool_n=8 vs GOLD-1__6191

description: Lung profiling from COPD patients


title: Saline-detached retina, 2 hrs post-injection, replicate 3


title: Saline-detached retina, 2 hrs post-injection, replicate 2


title: GOLD-0_Pool_n=8 vs GOLD-1__6280

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-1__3385

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-2__2076

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-1__2131

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-1__6020

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__6091

description: Lung profiling from COPD patients


title: Saline-detached retina, 2 hrs post-injection, replicate 1


title: GOLD-0_Pool_n=8 vs GOLD-1__5873

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__5851

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__6287

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__5726

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__5771

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-1__1984

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-1__2281

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__3492

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-1__2425

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__3491

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__5954

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__5907

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__5783

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__3501

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__3404

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__3410

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__2416

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__2028

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__3381

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__3373

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__2168

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__1979

description: Lung profiling from COPD patients


title: GOLD-0_Pool_n=8 vs GOLD-0__2415

description: Lung profiling from COPD patients


title: Melanoma (AF100KXBAWM3211)

status: Public on Nov 02 2007

type: genomic

city: King of Prussia

first: Joel

last: Greshock

state: PA

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

institute: GlaxoSmithKline

description: Melanoma

hyb_protocol: Hybridizations were performed according to the standard manufacturer's describe in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix.

scan_protocol: Scanning was done using an Affymetrix 3000 microarray scanner.  Specifications can be found in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix

data_processing: Image files were analyzed using the dChip software.  A panel of chips (n = 12)  assayed with germline DNA served as a reference in order to calculate a test/reference ratio.  The ratios were then subject global normalization that assumed that the median copy number is  diploid (2n; log2 Ratio = 0).

molecule: genomic DNA

source_name: WM3211 Cell Line

label_protocol: 250 ng Genomic DNA was biotinylated as described by manufacturer (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix).

growth_protocol: Cells were grown in in RPMI 1640 supplemented with 10% heat-inactivated FBS

extract_protocol: Genomic DNA was isolated from cultured cells with Mini DNeasy kit (Qiagen, Inc.)

tag: Melanoma


title: Melanoma (AF100KXBAWM35)

description: Melanoma

source_name: WM35 Cell Line


title: Melanoma (AF100KXBAWM3248)

description: Melanoma

source_name: WM3248 Cell Line


title: GOLD-0_Pool_n=8 vs GOLD-0__1986

description: Lung profiling from COPD patients


title: Melanoma (AF100KXBA1205LU)

description: Melanoma

source_name: 1205Lu Cell Line


title: Melanoma (AF100KXBAWM88)

description: Melanoma

source_name: WM88 Cell Line


title: Melanoma (AF100KXBAWM1366)

description: Melanoma

source_name: WM1366 Cell Line


title: Melanoma (AF100KXBAWM983)

description: Melanoma

source_name: WM983 Cell Line


title: Melanoma (AG185KWM3211)

description: Melanoma

hyb_protocol: Hybridization and assay treatment were carried out acccording to the manufacturer's recommendations

scan_protocol: Assay was scanned with an Agilent Microarray scanner

data_processing: Background corrected Test/Reference intensity ratios were calculated using the Agilent Inc. feature extraction software.  They were then subject global normalization that assumed that the median copy number is  diploid (2n; log2 Ratio = 0).

label_protocol: 2 ug of genomic DNA were labeled with the Enzo Genomic DNA Labeling Kit (Enzo Life Sciences)

source_name: Lymphocyte derived pooled male (Promega, Inc.)


title: Germline DNA derived from normal individual (AFFY100KXBAREF11)

data_processing: Raw Intensity values were calculated using the dChip sofware package.

source_name: Germline11 Cell Line

extract_protocol: Genomic DNA was isolated from cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.


title: Germline DNA derived from normal individual (AFFY100KXBAREF8)

source_name: Germline8 Cell Line


title: Germline DNA derived from normal individual (AFFY100KXBAREF6)

source_name: Germline6 Cell Line


title: Germline DNA derived from normal individual (AFFY100KXBAREF5)

source_name: Germline5 Cell Line


title: Germline DNA derived from normal individual (AFFY100KXBAREF7)

source_name: Germline7 Cell Line


title: Melanoma (AG185KWM983)

description: Melanoma

tag: Lymphocyte derived pooled male (Promega, Inc.)


title: Melanoma (AG185KWM1366)

description: Melanoma


title: Melanoma (AF100KHINDIIIWM35)

description: Melanoma


title: Germline DNA derived from normal individual (AFFY100KXBAREF12)

source_name: Germline12 Cell Line