title: Lin-CD34-

source_name: Lineage-CD34- cells purified from peripheral blood (PB) of normal donors

tag: To obtain PB Hematopoietic Stem Cells (HSC), 12 healthy donors received glycosylated recombinant human (rh) G-CSF (Lenograstim, Rhone-Poulenc Rorer, Milan, Italy) administered subcutaneously at 10 g/kg/d for 5-6 days. Leukaphereses were performed on days 5 and 6 as previously described (Lemoli et al, 1997; Lemoli et al, 2000). HSCs purification and subsequent studies were always performed using day-5 collections at the peak time of PB CD34+ cells. The protocol was approved by the ethical committee of the University Hospital and each donor gave written informed consent.

tag: Mononuclear light density (<1·077 g/ml) cells (MNC) were enriched using Ficoll-Paque (Pharmacia, Uppsala, Sweden) and resuspended in 1% bovine serum albumin (BSA; Sigma Chemical Co, St Louis, MO, USA).

tag: MNC were stained for 30 min at 4°C with a mixture of lineage-specific antibodies (CD2, CD3, CD14, CD16, CD19, CD24, CD56, CD38, CD66b, CD41 and Glycophorin A) provided by the manufacturer (Stem Cell Technologies, Vancouver, Canada), followed by addition of secondary antibody conjugated to magnetic dextran-iron particles for a further 30 min at 4°C. Cells were then eluted through a magnetized column (StemSep; Stem Cell Technologies) to remove Lin+ cells. Lin- cells were then collected according to the manufacturers instructions, incubated with anti-human CD34-fluorescein isothiocyanate (FITC) monoclonal antibody (MoAb) (HPCA-2; Becton Dickinson, San Jose, CA, USA) and sorted on a FACStar Plus equipment (Becton Dickinson). The sorting gates were set on isotype control antibody-stained samples. Sort windows were adjusted to minimize the chance of weakly positive cells contaminating the CD34 cell population. Aliquots of sorted Lin-CD34-, Lin-CD34+ and Lin+CD34+ were reanalyzed by FacScan (Becton Dickinson, Franklin Lakes, NJ) to assess their purities which were 98.9±1%, 99.2± 0.8% and 98±1%, respectively. Contamination of CD34+ cells in the CD34- cell population was ruled out by reverse transcription-polymerase chain reaction (RT-PCR) for CD34 mRNA .


title: Germline N-#21, Hind SNP array

status: Public on Jan 04 2010

type: genomic

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: As per manufacturer (Affymetrix).

scan_protocol: As per manufacturer (Affymetrix).

data_processing: CEL files and CHP files (generated by Dynamic Model 3.0) were processed by dChip and model-based expression performed using the PM-only model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. The data matrix contains the normalized expression values produced by that algorithm.

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Germline N-#21

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Cryopreserved peripheral blood or bone marrow samples obtained at diagnosis or remission.

extract_protocol: Qiagen DNA blood mini or phenol chloroform.

tag: tissue

value: acute myeloid leukemia


title: Germline N-#20, Hind SNP array

source_name: Germline N-#20


title: ST182-T9M

type: RNA

city: Stanford

first: Lucinda

last: Thompson

state: CA

address: Fairchild Bldg., D035, 299 Campus Dr

department: Microbiology and Immunology, School of Medicine

institute: Stanford University

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65058.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.74; Parameter Scan Time = 07:32:09; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45535; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.74; Parameter Scan Time = 07:32:09; Parameter PMT Volts = 620; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118670; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.04; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

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

molecule: total RNA

source_name: Strat. aRNA 4ug

label_protocol: not provided

extract_protocol: not provided

tag: Strat. aRNA 4ug

tag: LabeledExtract

source_name: ST182-T9M_4ug aRNA

tag: ST182-T9M_4ug aRNA


title: Diagnostic_acute_leukemia N-#21, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#21


title: ST178-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65054.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6040; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.45; Parameter Scan Time = 06:55:10; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45497; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.13; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.45; Parameter Scan Time = 06:55:10; Parameter PMT Volts = 630; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118632; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.97; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST178-T9M 4ug aRNA

tag: ST178-T9M 4ug aRNA


title: ST173-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64974.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.01; Parameter Scan Time = 09:03:35; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43232; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.35; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.01; Parameter Scan Time = 09:03:35; Parameter PMT Volts = 580; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116367; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST173-T9M_ 4ug aRNA

tag: ST173-T9M_ 4ug aRNA


title: ST180-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65056.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.58; Parameter Scan Time = 07:20:02; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45523; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.58; Parameter Scan Time = 07:20:02; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118658; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.06; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST180-T9M 4ug aRNA

tag: ST180-T9M 4ug aRNA


title: ST181-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64978.gif
Compound Based Treatment: Azithromycin
Disease State: Paratyphoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.03; Parameter Scan Time = 09:28:31; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43258; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.33; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.03; Parameter Scan Time = 09:28:31; Parameter PMT Volts = 650; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116393; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.19; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST181-T9M_4ug aRNA

tag: ST181-T9M_4ug aRNA


title: ST167-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65053.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 6440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.34; Parameter Scan Time = 09:00:30; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45623; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.34; Parameter Scan Time = 09:00:30; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118758; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST167-T9M_4ug aRNA

tag: ST167-T9M_4ug aRNA


title: HC4-2nd repeat

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65052.gif
Compound Based Treatment: N/A
Disease State: Healthy Control

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6080; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.57; Parameter Scan Time = 13:44:16; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45905; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.28; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.57; Parameter Scan Time = 13:44:16; Parameter PMT Volts = 680; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 119040; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.41; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: HC4-2nd repeat 4ug aRNA

tag: HC4-2nd repeat 4ug aRNA


title: ST177-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64976.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.19; Parameter Scan Time = 09:40:23; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43269; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.17; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.19; Parameter Scan Time = 09:40:23; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116404; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.19; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST177-T9M_4ug aRNA

tag: ST177-T9M_4ug aRNA


title: KK47 cell line relative to normal diploid cell

status: Public on Jan 05 2010

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

hyb_protocol: The samples were hybridized for 40 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions. Agilent Feature Extractor software was used to extract the data.

data_processing: Data were extracted using Agilent's Feature Extraction software, version 9.1 (P/N G2565BA), Cy3 corresponding to the gProcessed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file. Normalized log10 ratio (Cy5/Cy3) was calculated using CGH-v4_95_Feb07 protocol of FE software.

source_name: Normal human diploid genomic DNA

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating CyDye labeled dUTP.

extract_protocol: Chromosomal DNA was isolated from BC cell lines using FlexiGene(QIAGEN) according manufacturer's protocol.

tag: sample type

value: normal human genomic DNA purchased from Promega

source_name: KK47 genomic DNA

tag: cell line

value: human bladder cancer KK47


title: ST175-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64975.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.71; Parameter Scan Time = 09:16:13; Parameter PMT Volts = 530; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43246; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.16; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.71; Parameter Scan Time = 09:16:13; Parameter PMT Volts = 710; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116381; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.20; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST175-T9M 4ug aRNA

tag: ST175-T9M 4ug aRNA


title: HC2

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65051.gif
Compound Based Treatment: N/A
Disease State: Healthy Control

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.83; Parameter Scan Time = 13:32:27; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45893; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.28; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.83; Parameter Scan Time = 13:32:27; Parameter PMT Volts = 690; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 119028; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.40; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: HC2 4ug aRNA

tag: HC2 4ug aRNA


title: HCT116_Input_2

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

institute: The University of Tokyo

description: Input sample for Methylated DNA immunoprecipitation-on-chip analysis of HCT116

hyb_protocol: The mixture containing 2 ug of the labeled DNA was directly used for hybridization.

scan_protocol: Scanning was performed in an Affymetrix GeneChip scanner 3000 7G.

data_processing: raw data

label: biotin

source_name: Colon cancer cell line

label_protocol: The digested cDNA was labeled using 50 U of terminal transferase (Roche, Penzberg, Germany) and 71.4 uM of Biotin-11-ddATP (PerkinElmer, Boston, MA, USA) at 37degrees Celsius for 2 h

extract_protocol: DNA was extracted using QIAamp DNA Micro Kit (QIAGEN, Hilden, Germany). Genomic DNA was fragmented by sonication, ranging in size from 200 to 700 bp and denatured at 95degrees Celsius for 5 min. 30 ng of input DNA (whole genome) were amplified by in vitro transcription (IVT) randomly. After IVT, amplified cRNA was purified using an RNeasy Mini Kit (QIAGEN). Six hundred nanogram of cRNA were converted into double-strand cDNA with random primers using SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). After single-stranded cDNA synthesis, 0.4 uM of T7-A18B primer was added and incubated at 70degrees Celsius for 6 min. Double-stranded cDNA was purified using a QIAquick PCR purification kit (QIAGEN). After 2 cycles of IVT and cDNA synthesis reactions were performed for target amplification, the labeling step was performed. Ten microgram of amplified cDNA was digested into 25-100 bp with 0.008 U of DNase I (Invitrogen), 1 x  One-Phor-All Buffer PLUS (Amersham), and 1.4 mM of CoCl2 by incubation at 37degrees Celsius for 8 min.


title: Germline N-#19, Hind SNP array

source_name: Germline N-#19


title: ST60-T3-repeat

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65050.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.75; Parameter Scan Time = 13:20:45; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45882; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.75; Parameter Scan Time = 13:20:45; Parameter PMT Volts = 650; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 119017; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.39; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST60-T3-repeat_4ug aRNA

tag: ST60-T3-repeat_4ug aRNA


title: Diagnostic_acute_leukemia N-#20, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#20


title: ST168-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64972.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.17; Parameter Scan Time = 11:29:25; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43379; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.17; Parameter Scan Time = 11:29:25; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116514; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.50; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: Strat. aRNA 4ug

source_name: ST168-T9M_ 4ug aRNA

tag: ST168-T9M_ 4ug aRNA


title: Diagnostic_acute_leukemia N-#19, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#19

tag: tissue


title: WT_90minW_biorep2

city: La Jolla

first: Justin

last: Walley

address: 9500 Gilman Ave

department: Biological Sciences

institute: UCSD

hyb_protocol: Labeled cy3 and cy5 cRNA was mixed and hybridized according to Agilent protocol.

scan_protocol: Arrays were scanned on an Agilent G2505B DNA microarray scanner. The raw TIFF images were analyzed and normalized using the Agilent Feature Extraction software using the recommended default settings.

organism: Arabidopsis thaliana

source_name: Pooled reference

label_protocol: Labeled cRNA was produced using the Agilent low RNA input linear amp kit according to the manufactures protocol.  Total RNA was used as a template for cDNA synthesis primed with oligo(dT) followed by production of cRNA labeled with cy5.

extract_protocol: RNA was isolated using TRIzol reagent and further purified using Qiagen RNeasy kit with on column DNase treatment

tag: ecotype

value: 3 week old rosette leaves

source_name: WT 90minW

label_protocol: Labeled cRNA was produced using the Agilent low RNA input linear amp kit according to the manufactures protocol.  Total RNA was used as a template for cDNA synthesis primed with oligo(dT) followed by production of cRNA labeled with cy3.

treatment_protocol: 90 min wound


title: ST166-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64971.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.66; Parameter Scan Time = 11:40:52; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43390; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.50; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.66; Parameter Scan Time = 11:40:52; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116525; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.53; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

tag: Strat. aRNA 4ug

tag: LabeledExtract

source_name: ST166-T9M 4ug aRNA

tag: ST166-T9M 4ug aRNA


title: Diagnostic_acute_leukemia N-#18, Hind SNP array

scan_protocol: As per manufacturer (Affymetrix).

source_name: Diagnostic_acute_leukemia N-#18


title: ST184-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64979.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.03; Parameter Scan Time = 08:39:27; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43209; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.03; Parameter Scan Time = 08:39:27; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116344; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.26; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST184-T9M_4ug aRNA

tag: ST184-T9M_4ug aRNA


title: Diagnostic_acute_leukemia N-#13, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#13


title: Diagnostic_acute_leukemia N-#17, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#17


title: Diagnostic_acute_leukemia N-#16, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#16


title: Diagnostic_acute_leukemia N-#15, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#15


title: Diagnostic_acute_leukemia N-#11, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#11


title: Diagnostic_acute_leukemia N-#14, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#14


title: HC1-repeat

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64970.gif
Compound Based Treatment: N/A
Disease State: Healthy Control

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.45; Parameter Scan Time = 11:05:17; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43354; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.45; Parameter Scan Time = 11:05:17; Parameter PMT Volts = 640; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116489; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.44; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: HC1-repeat 4ug aRNA

tag: HC1-repeat 4ug aRNA


title: Diagnostic_acute_leukemia N-#9, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#9


title: BOY cell line relative to normal diploid cell

source_name: Normal human diploid genomic DNA

source_name: BOY genomic DNA

value: human bladder cancer BOY


title: Diagnostic_acute_leukemia N-#12, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#12


title: ST170-T1-repeat

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65049.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.46; Parameter Scan Time = 13:08:39; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.30; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.46; Parameter Scan Time = 13:08:39; Parameter PMT Volts = 630; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 119005; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.38; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: Strat. aRNA 4ug

source_name: ST170-T1-repeat 4ug aRNA

tag: ST170-T1-repeat 4ug aRNA


title: Diagnostic_acute_leukemia N-#10, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#10


title: Germline N-#8, Hind SNP array

source_name: Germline N-#8


title: Diagnostic_acute_leukemia N-#7, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#7


title: ST66-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65081.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.29; Parameter Scan Time = 08:49:08; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45611; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.29; Parameter Scan Time = 08:49:08; Parameter PMT Volts = 580; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118746; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST66-T1 4ug aRNA

tag: ST66-T1 4ug aRNA


title: ST169-T1-repeat

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64969.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 5920; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.40; Parameter Scan Time = 11:17:17; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43366; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.42; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.40; Parameter Scan Time = 11:17:17; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116501; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.47; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST169-T1-repeat_ 4ug aRNA

tag: ST169-T1-repeat_ 4ug aRNA


title: ST67-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65012.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.43; Parameter Scan Time = 06:59:39; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43110; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.22; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.43; Parameter Scan Time = 06:59:39; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116245; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.03; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST67-T9 4ug aRNA

tag: ST67-T9 4ug aRNA


title: ST66-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65082.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5680; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.21; Parameter Scan Time = 08:37:04; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45600; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.21; Parameter Scan Time = 08:37:04; Parameter PMT Volts = 610; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118735; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST66-T9 4ug aRNA

tag: ST66-T9 4ug aRNA


title: Germline N-#7, Hind SNP array

source_name: Germline N-#7


title: ST67-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65083.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1240, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.07; Parameter Scan Time = 08:08:19; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45571; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.07; Parameter Scan Time = 08:08:19; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118706; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.16; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST67-T3 4ug aRNA

tag: ST67-T3 4ug aRNA


title: Diagnostic_acute_leukemia N-#6, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#6


title: ST67-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65011.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.62; Parameter Scan Time = 07:24:00; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43133; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.62; Parameter Scan Time = 07:24:00; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116268; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST67-T1 4ug aRNA

tag: ST67-T1 4ug aRNA


title: ST66-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65010.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.55; Parameter Scan Time = 07:11:49; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43122; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.16; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.55; Parameter Scan Time = 07:11:49; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116257; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.08; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST66-T3 4ug aRNA

tag: ST66-T3 4ug aRNA


title: ST64-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65009.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.70; Parameter Scan Time = 07:36:07; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43145; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.28; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.70; Parameter Scan Time = 07:36:07; Parameter PMT Volts = 580; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116280; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.17; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST64-T9 4ug aRNA

tag: ST64-T9 4ug aRNA


title: Diagnostic_acute_leukemia N-#5, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#5


title: Germline N-#5, Hind SNP array

source_name: Germline N-#5


title: ST64-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65080.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.16; Parameter Scan Time = 08:21:26; Parameter PMT Volts = 510; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45584; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.28; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.16; Parameter Scan Time = 08:21:26; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118719; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.14; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: Strat. aRNA 4ug

source_name: ST64-T3 4ug aRNA

tag: ST64-T3 4ug aRNA


title: ST64-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65008.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.78; Parameter Scan Time = 07:48:12; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43158; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.78; Parameter Scan Time = 07:48:12; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116293; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.19; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST64-T1 4ug aRNA

tag: ST64-T1 4ug aRNA


title: ST182-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65002.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.54; Parameter Scan Time = 10:53:06; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43342; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.54; Parameter Scan Time = 10:53:06; Parameter PMT Volts = 690; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116477; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.41; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST182-T1_4ug aRNA

tag: ST182-T1_4ug aRNA


title: ST171-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64973.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.42; Parameter Scan Time = 11:52:16; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43401; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.39; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.42; Parameter Scan Time = 11:52:16; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116536; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.56; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

tag: Strat. aRNA 4ug

source_name: ST171-T9M_4ug aRNA

tag: ST171-T9M_4ug aRNA


title: ST63-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65007.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.46; Parameter Scan Time = 10:03:50; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43293; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.20; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.46; Parameter Scan Time = 10:03:50; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116428; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

tag: LabeledExtract

source_name: ST63-T3 4ug aRNA

tag: ST63-T3 4ug aRNA


title: Diagnostic_acute_leukemia N-#8, Hind SNP array

scan_protocol: As per manufacturer (Affymetrix).

source_name: Diagnostic_acute_leukemia N-#8

tag: tissue


title: Diagnostic_acute_leukemia N-#3, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#3


title: ST182-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65004.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.56; Parameter Scan Time = 10:41:09; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43331; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.56; Parameter Scan Time = 10:41:09; Parameter PMT Volts = 670; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116466; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.38; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST182-T28_4ug aRNA

tag: ST182-T28_4ug aRNA


title: Diagnostic_acute_leukemia N-#4, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#4


title: ST185-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65077.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.91; Parameter Scan Time = 10:41:03; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45723; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.91; Parameter Scan Time = 10:41:03; Parameter PMT Volts = 580; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118858; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.13; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST185-T3 4ug aRNA

tag: ST185-T3 4ug aRNA


title: Germline N-#3, Hind SNP array

source_name: Germline N-#3


title: Germline N-#2, Hind SNP array

source_name: Germline N-#2


title: ST63-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65079.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.97; Parameter Scan Time = 07:56:27; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45558; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.25; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.97; Parameter Scan Time = 07:56:27; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118693; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.14; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST63-T9 4ug aRNA

tag: ST63-T9 4ug aRNA


title: Diagnostic_acute_leukemia N-#1, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#1


title: ST63-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65078.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.93; Parameter Scan Time = 10:53:07; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45735; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.10; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.93; Parameter Scan Time = 10:53:07; Parameter PMT Volts = 560; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118870; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.16; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST63-T1 4ug aRNA

tag: ST63-T1 4ug aRNA


title: ST185-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65005.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 5760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.51; Parameter Scan Time = 10:27:28; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43316; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.51; Parameter Scan Time = 10:27:28; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116451; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.22; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST185-T1_4ug aRNA

tag: ST185-T1_4ug aRNA


title: Diagnostic_acute_leukemia misc-#23, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#23


title: Germline N-#6, Hind SNP array

source_name: Germline N-#6


title: ST175-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64999.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.64; Parameter Scan Time = 12:40:10; Parameter PMT Volts = 510; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43449; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.64; Parameter Scan Time = 12:40:10; Parameter PMT Volts = 730; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116584; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.51; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: Strat. aRNA 4ug

source_name: ST175-T28 4ug aRNA

tag: ST175-T28 4ug aRNA


title: Germline misc-#22, Hind SNP array

source_name: Germline misc-#22


title: ST179-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65074.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 6440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.70; Parameter Scan Time = 10:01:18; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45683; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.70; Parameter Scan Time = 10:01:18; Parameter PMT Volts = 660; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118818; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST179-T28_4ug aRNA

tag: ST179-T28_4ug aRNA


title: Germline N-#1, Hind SNP array

source_name: Germline N-#1


title: ST185-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65006.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.51; Parameter Scan Time = 10:15:49; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43305; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.51; Parameter Scan Time = 10:15:49; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116440; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.21; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST185-T9 4ug aRNA

tag: ST185-T9 4ug aRNA


title: ST183-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65076.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.85; Parameter Scan Time = 10:28:40; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45710; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.85; Parameter Scan Time = 10:28:40; Parameter PMT Volts = 570; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118845; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.11; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST183-T1_4ug aRNA

tag: ST183-T1_4ug aRNA


title: ST519-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65072.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.88; Parameter Scan Time = 11:18:56; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45761; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.88; Parameter Scan Time = 11:18:56; Parameter PMT Volts = 620; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118895; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.24; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST519-T1 4ug aRNA

tag: ST519-T1 4ug aRNA


title: ST175-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65073.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.87; Parameter Scan Time = 11:55:21; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45797; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.87; Parameter Scan Time = 11:55:21; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118932; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.30; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST175-T3 4ug aRNA

tag: ST175-T3 4ug aRNA


title: ST166-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64996.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.64; Parameter Scan Time = 12:28:03; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43437; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.35; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.64; Parameter Scan Time = 12:28:03; Parameter PMT Volts = 680; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116572; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST166-T9_4ug aRNA

tag: ST166-T9_4ug aRNA


title: Germline misc-#23, Hind SNP array

source_name: Germline misc-#23


title: ST515-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65071.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1320, 6440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.88; Parameter Scan Time = 11:43:40; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45785; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.29; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.88; Parameter Scan Time = 11:43:40; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118920; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.27; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

tag: Strat. aRNA 4ug

source_name: ST515-T1 4ug aRNA

tag: ST515-T1 4ug aRNA


title: ST513-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65070.gif
Compound Based Treatment: Azithromycin
Disease State: Paratyphoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.97; Parameter Scan Time = 11:06:32; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45748; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.97; Parameter Scan Time = 11:06:32; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118883; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.17; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

tag: LabeledExtract

source_name: ST513-T1 4ug aRNA

tag: ST513-T1 4ug aRNA


title: Diagnostic_acute_leukemia misc-#22, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#22

tag: tissue


title: Diagnostic_acute_leukemia N-#2, Hind SNP array

source_name: Diagnostic_acute_leukemia N-#2


title: ST182-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65075.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.77; Parameter Scan Time = 10:13:23; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45696; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.77; Parameter Scan Time = 10:13:23; Parameter PMT Volts = 610; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118831; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST182-T9_4ug aRNA

tag: ST182-T9_4ug aRNA


title: Diagnostic_acute_leukemia misc-#21, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#21


title: Germline misc-#20, Hind SNP array

source_name: Germline misc-#20


title: Diagnostic_acute_leukemia misc-#19, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#19


title: Diagnostic_acute_leukemia misc-#20, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#20


title: Diagnostic_acute_leukemia misc-#16, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#16


title: Diagnostic_acute_leukemia misc-#18, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#18


title: Diagnostic_acute_leukemia misc-#17, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#17


title: Germline misc-#18, Hind SNP array

source_name: Germline misc-#18


title: ST64-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65065.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.91; Parameter Scan Time = 12:07:24; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45810; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.91; Parameter Scan Time = 12:07:24; Parameter PMT Volts = 610; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118945; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.33; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: Strat. aRNA 4ug

source_name: ST64-T28 4ug aRNA

tag: ST64-T28 4ug aRNA


title: Diagnostic_acute_leukemia misc-#12, Hind SNP array

scan_protocol: As per manufacturer (Affymetrix).

source_name: Diagnostic_acute_leukemia misc-#12


title: Diagnostic_acute_leukemia misc-#15, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#15


title: ST509-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65068.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 6280; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.72; Parameter Scan Time = 12:56:26; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45858; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.29; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.72; Parameter Scan Time = 12:56:26; Parameter PMT Volts = 660; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118993; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.37; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST509-T1 4ug aRNA

tag: ST509-T1 4ug aRNA


title: Germline misc-#15, Hind SNP array

source_name: Germline misc-#15


title: Germline misc-#13, Hind SNP array

source_name: Germline misc-#13


title: ST67-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65066.gif
Compound Based Treatment: Gatifloxicin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 6440; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.61; Parameter Scan Time = 12:43:47; Parameter PMT Volts = 510; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45845; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.27; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 36.61; Parameter Scan Time = 12:43:47; Parameter PMT Volts = 620; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118980; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.36; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST67-T28 4ug aRNA

tag: ST67-T28 4ug aRNA


title: Diagnostic_acute_leukemia misc-#13, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#13


title: Diagnostic_acute_leukemia misc-#14, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#14


title: Diagnostic_acute_leukemia misc-#11, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#11