title: ST514-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64989.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, 5240; 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 = 38.49; Parameter Scan Time = 12:04:07; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43413; 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 = 38.49; Parameter Scan Time = 12:04:07; Parameter PMT Volts = 610; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116548; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.57; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST514-T1 4ug aRNA

tag: ST514-T1 4ug aRNA


title: ST66-T4M

status: Public on Jan 04 2010

type: RNA

city: Stanford

first: Lucinda

last: Thompson

state: CA

address: Fairchild Bldg., D035, 299 Campus Dr

department: Microbiology and Immunology, School of Medicine

country: USA

institute: Stanford University

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65064.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 = 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 = 37.19; Parameter Scan Time = 12:32:33; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45834; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.26; 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 = 12:32:33; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118969; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.34; 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

organism: Homo sapiens

source_name: Strat. aRNA 4ug

label_protocol: not provided

extract_protocol: not provided

tag: Strat. aRNA 4ug

tag: LabeledExtract

source_name: ST66-T4M 4ug aRNA

tag: ST66-T4M 4ug aRNA


title: ST64-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65067.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, 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 = 37.60; Parameter Scan Time = 12:20:22; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45822; 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 = 37.60; Parameter Scan Time = 12:20:22; Parameter PMT Volts = 600; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118957; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.34; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST64-T9M_4ug aRNA

tag: ST64-T9M_4ug aRNA


title: ST63-T3M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65063.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 = 36.51; Parameter Scan Time = 07:07:58; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45510; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.06; 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 = 36.51; Parameter Scan Time = 07:07:58; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118645; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.99; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST63-T3M 4ug aRNA

tag: ST63-T3M 4ug aRNA


title: ST511-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65069.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 = 1480, 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 = 37.86; Parameter Scan Time = 11:31:08; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45773; 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 = 37.86; Parameter Scan Time = 11:31:08; Parameter PMT Volts = 660; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118908; 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: ST511-T1 4ug aRNA

tag: ST511-T1 4ug aRNA


title: ST60-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65061.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 = 1240, 5960; 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 = 36.85; Parameter Scan Time = 07:44:27; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45547; 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 = 36.85; Parameter Scan Time = 07:44:27; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118682; 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: ST60-T9M 4ug aRNA

tag: ST60-T9M 4ug aRNA


title: ST516-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64990.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 = 1240, 5240; 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 = 38.59; Parameter Scan Time = 12:15:55; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43424; 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 = 38.59; Parameter Scan Time = 12:15:55; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116559; 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: ST516-T1 4ug aRNA

tag: ST516-T1 4ug aRNA


title: Diagnostic_acute_leukemia misc-#9, Hind SNP array

type: genomic

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

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

source_name: Diagnostic_acute_leukemia misc-#9

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: ST176-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65062.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, 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 = 37.61; Parameter Scan Time = 09:48:11; Parameter PMT Volts = 500; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45670; 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 = 37.61; Parameter Scan Time = 09:48:11; Parameter PMT Volts = 620; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118805; 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: ST176-T9M 4ug aRNA

tag: ST176-T9M 4ug aRNA


title: Diagnostic_acute_leukemia misc-#10, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#10


title: Germline misc-#9, Hind SNP array

source_name: Germline misc-#9


title: ST67-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64986.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 = 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 = 38.71; Parameter Scan Time = 13:16:22; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43485; 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 = 38.71; Parameter Scan Time = 13:16:22; Parameter PMT Volts = 620; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116620; 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: ST67-T9M 4ug aRNA

tag: ST67-T9M 4ug aRNA


title: ST66-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64985.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 = 38.72; Parameter Scan Time = 13:40:15; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43509; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.51; 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 = 38.72; Parameter Scan Time = 13:40:15; Parameter PMT Volts = 640; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116644; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.57; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST66-T9M 4ug aRNA

tag: ST66-T9M 4ug aRNA


title: ST512-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64988.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, 5640; 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 = 38.73; Parameter Scan Time = 13:28:35; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43497; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.48; 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 = 38.73; Parameter Scan Time = 13:28:35; Parameter PMT Volts = 650; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116632; 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

source_name: ST512-T1 4ug aRNA

tag: ST512-T1 4ug aRNA


title: ST510-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64987.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, 5400; 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 = 38.71; Parameter Scan Time = 13:04:23; Parameter PMT Volts = 490; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43474; 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 = 38.71; Parameter Scan Time = 13:04:23; Parameter PMT Volts = 650; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116609; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.45; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST510-T1 4ug aRNA

tag: ST510-T1 4ug aRNA


title: ST174-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65060.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, 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 = 37.54; Parameter Scan Time = 09:36:41; Parameter PMT Volts = 510; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 45659; 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 = 37.54; Parameter Scan Time = 09:36:41; Parameter PMT Volts = 620; Parameter Scan Date = 2005-10-31; Parameter Pixel Size = 10; Parameter Laser on time = 118794; 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: ST174-T9M 4ug aRNA

tag: ST174-T9M 4ug aRNA


title: Germline misc-#7, Hind SNP array

source_name: Germline misc-#7


title: Diagnostic_acute_leukemia misc-#8, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#8


title: Germline misc-#8, Hind SNP array

source_name: Germline misc-#8


title: ST518-T1 (Second phase of study)

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64993.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, 6120; 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 = 38.67; Parameter Scan Time = 12:52:17; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43461; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.48; 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 = 38.67; Parameter Scan Time = 12:52:17; Parameter PMT Volts = 660; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116596; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.48; 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: ST518-T1 4ug aRNA

tag: ST518-T1 4ug aRNA


title: Diagnostic_acute_leukemia misc-#, Hind SNP array7

source_name: Diagnostic_acute_leukemia misc-#7


title: Diagnostic_acute_leukemia misc-#6, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#6


title: Diagnostic_acute_leukemia misc-#5, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#5


title: Germline misc-#5, Hind SNP array

source_name: Germline misc-#5


title: Germline misc-#4, Hind SNP array

source_name: Germline misc-#4


title: ST63-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64981.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 = 37.08; Parameter Scan Time = 08:51:45; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43221; 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 = 37.08; Parameter Scan Time = 08:51:45; Parameter PMT Volts = 640; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116356; 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: ST63-T28 4ug aRNA

tag: ST63-T28 4ug aRNA


title: Germline misc-#1, Hind SNP array

source_name: Germline misc-#1


title: Diagnostic_acute_leukemia misc-#3, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#3


title: Diagnostic_acute_leukemia M7-#9, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#9


title: Diagnostic_acute_leukemia misc-#2, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#2


title: Diagnostic_acute_leukemia M7-#8, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#8


title: ST57-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64980.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, 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 = 36.99; Parameter Scan Time = 08:25:02; Parameter PMT Volts = 480; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43194; 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 = 36.99; Parameter Scan Time = 08:25:02; Parameter PMT Volts = 580; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116329; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.23; 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: ST57-T9M_4ug aRNA

tag: ST57-T9M_4ug aRNA


title: Diagnostic_acute_leukemia M7-#5, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#5


title: Diagnostic_acute_leukemia M7-#6, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#6


title: Diagnostic_acute_leukemia M7-#7, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#7


title: Diagnostic_acute_leukemia (N-#21)

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: As per manufacturer (Affymetrix)

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

extract_protocol: Trizol total RNA extraction

tag: Tissue


title: Diagnostic_acute_leukemia M7-#4, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#4


title: Diagnostic_acute_leukemia misc-#1, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#1


title: Germline M7-#2, Hind SNP array

source_name: Germline M7-#2


title: Germline M7-#7, Hind SNP array

source_name: Germline M7-#7


title: Diagnostic_acute_leukemia (N-#19)


title: Diagnostic_acute_leukemia (N-#20)


title: Germline M7-#5, Hind SNP array

source_name: Germline M7-#5


title: Germline M7-#1, Hind SNP array

source_name: Germline M7-#1


title: Diagnostic_acute_leukemia (N-#18)


title: Diagnostic_acute_leukemia M7-#3, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#3


title: Diagnostic_acute_leukemia M7-#1, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#1


title: Germline M7-#3, Hind SNP array

source_name: Germline M7-#3


title: Diagnostic_acute_leukemia M7-#2, Hind SNP array

source_name: Diagnostic_acute_leukemia M7-#2


title: Germline M7-#4, Hind SNP array

source_name: Germline M7-#4


title: Diagnostic_acute_leukemia (N-#17)


title: Germline MLL-#17, Hind SNP array

source_name: Germline MLL-#17


title: Diagnostic_acute_leukemia (N-#15)


title: ST64-T3M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64983.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 = 1460, 6300; 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 = 36.92; Parameter Scan Time = 08:13:39; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43183; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.34; 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 = 36.92; Parameter Scan Time = 08:13:39; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116318; 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: Strat. aRNA 4ug

tag: LabeledExtract

source_name: ST64-T3M 4ug aRNA

tag: ST64-T3M 4ug aRNA


title: Diagnostic_acute_leukemia (N-#16)


title: Diagnostic_acute_leukemia MLL-#17, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#17


title: Diagnostic_acute_leukemia (N-#8)


title: Diagnostic_acute_leukemia (N-#10)


title: Diagnostic_acute_leukemia (N-#9)


title: Diagnostic_acute_leukemia (N-#13)


title: Diagnostic_acute_leukemia (N-#11)


title: Germline misc-#2, Hind SNP array

source_name: Germline misc-#2


title: Diagnostic_acute_leukemia MLL-#16, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#16


title: Diagnostic_acute_leukemia misc-#4, Hind SNP array

source_name: Diagnostic_acute_leukemia misc-#4


title: Diagnostic_acute_leukemia MLL-#13, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#13


title: Diagnostic_acute_leukemia (N-#14)


title: Diagnostic_acute_leukemia (N-#12)


title: Diagnostic_acute_leukemia MLL-#14, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#14


title: Diagnostic_acute_leukemia (N-#7)


title: Germline MLL-#11, Hind SNP array

source_name: Germline MLL-#11


title: Diagnostic_acute_leukemia MLL-#15, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#15


title: Diagnostic_acute_leukemia MLL-#10, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#10


title: Diagnostic_acute_leukemia MLL-#11, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#11


title: Diagnostic_acute_leukemia MLL-#8, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#8


title: Diagnostic_acute_leukemia MLL-#12, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#12


title: Diagnostic_acute_leukemia (misc-#23)


title: Diagnostic_acute_leukemia MLL-#7, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#7


title: ST63-T9M

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64982.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, 5480; 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 = 36.81; Parameter Scan Time = 08:00:37; Parameter PMT Volts = 470; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 43170; 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 = 36.81; Parameter Scan Time = 08:00:37; Parameter PMT Volts = 590; Parameter Scan Date = 2005-10-17; Parameter Pixel Size = 10; Parameter Laser on time = 116305; 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: ST63-T9M 4ug aRNA

tag: ST63-T9M 4ug aRNA


title: Diagnostic_acute_leukemia (N-#1)


title: Germline MLL-#8, Hind SNP array

source_name: Germline MLL-#8


title: Diagnostic_acute_leukemia (misc-#22)


title: Diagnostic_acute_leukemia (N-#2)


title: Germline MLL-#5, Hind SNP array

source_name: Germline MLL-#5


title: Diagnostic_acute_leukemia (N-#6)


title: Diagnostic_acute_leukemia (N-#4)


title: Diagnostic_acute_leukemia (N-#5)


title: Diagnostic_acute_leukemia (N-#3)


title: Diagnostic_acute_leukemia (misc-#21)


title: Germline MLL-#3, Hind SNP array

source_name: Germline MLL-#3


title: Diagnostic_acute_leukemia MLL-#5, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#5


title: Germline MLL-#1, Hind SNP array

source_name: Germline MLL-#1


title: Diagnostic_acute_leukemia MLL-#9, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#9


title: Diagnostic_acute_leukemia MLL-#1, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#1


title: Germline PML-#7, Hind SNP array

source_name: Germline PML-#7


title: Diagnostic_acute_leukemia (misc-#20)


title: Diagnostic_acute_leukemia (misc-#13)


title: Diagnostic_acute_leukemia MLL-#2, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#2


title: Diagnostic_acute_leukemia (misc-#14)


title: Diagnostic_acute_leukemia (misc-#15)


title: Diagnostic_acute_leukemia (misc-#16)


title: Diagnostic_acute_leukemia (misc-#11)


title: Diagnostic_acute_leukemia (misc-#19)


title: Diagnostic_acute_leukemia (misc-#12)


title: Diagnostic_acute_leukemia (misc-#18)


title: Germline PML-#3, Hind SNP array

source_name: Germline PML-#3


title: Germline PML-#6, Hind SNP array

source_name: Germline PML-#6


title: Diagnostic_acute_leukemia (misc-#9)


title: Diagnostic_acute_leukemia (misc-#10)


title: Diagnostic_acute_leukemia PML-#4, Hind SNP array

source_name: Diagnostic_acute_leukemia PML-#4


title: Diagnostic_acute_leukemia PML-#6, Hind SNP array

source_name: Diagnostic_acute_leukemia PML-#6


title: Diagnostic_acute_leukemia (misc-#8)


title: Germline PML-#2, Hind SNP array

source_name: Germline PML-#2


title: Diagnostic_acute_leukemia PML-#3, Hind SNP array

source_name: Diagnostic_acute_leukemia PML-#3


title: Diagnostic_acute_leukemia MLL-#3, Hind SNP array

source_name: Diagnostic_acute_leukemia MLL-#3


title: Diagnostic_acute_leukemia PML-#1, Hind SNP array

source_name: Diagnostic_acute_leukemia PML-#1


title: Diagnostic_acute_leukemia PML-#7, Hind SNP array

source_name: Diagnostic_acute_leukemia PML-#7


title: Diagnostic_acute_leukemia PML-#2, Hind SNP array

source_name: Diagnostic_acute_leukemia PML-#2


title: Diagnostic_acute_leukemia (misc-#5)


title: Diagnostic_acute_leukemia (misc-#7)


title: Diagnostic_acute_leukemia PML-#5, Hind SNP array

source_name: Diagnostic_acute_leukemia PML-#5


title: Diagnostic_acute_leukemia i16-#16, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#16


title: Germline PML-#1, Hind SNP array

source_name: Germline PML-#1


title: Diagnostic_acute_leukemia (misc-#1)


title: Germline i16-#16, Hind SNP array

source_name: Germline i16-#16


title: Diagnostic_acute_leukemia (misc-#2)


title: Diagnostic_acute_leukemia (M7-#8)


title: Diagnostic_acute_leukemia (M7-#9)


title: Diagnostic_acute_leukemia (misc-#6)


title: Diagnostic_acute_leukemia (M7-#7)


title: Diagnostic_acute_leukemia (misc-#3)


title: Diagnostic_acute_leukemia i16-#14, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#14


title: Diagnostic_acute_leukemia i16-#10, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#10


title: Diagnostic_acute_leukemia i16-#15, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#15


title: Diagnostic_acute_leukemia i16-#9, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#9


title: Germline i16-#14, Hind SNP array

source_name: Germline i16-#14


title: Diagnostic_acute_leukemia i16-#11, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#11


title: Germline i16-#11, Hind SNP array

source_name: Germline i16-#11


title: Diagnostic_acute_leukemia (M7-#6)


title: Diagnostic_acute_leukemia i16-#13, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#13


title: Diagnostic_acute_leukemia i16-#8, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#8


title: Diagnostic_acute_leukemia (M7-#1)


title: Germline i16-#8, Hind SNP array

source_name: Germline i16-#8


title: Diagnostic_acute_leukemia i16-#12, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#12


title: Diagnostic_acute_leukemia (MLL-#14)


title: Diagnostic_acute_leukemia (M7-#2)


title: Diagnostic_acute_leukemia (MLL-#13)


title: Diagnostic_acute_leukemia (MLL-#15)


title: Diagnostic_acute_leukemia (M7-#4)


title: Diagnostic_acute_leukemia (MLL-#11)


title: Germline i16-#4, Hind SNP array

source_name: Germline i16-#4


title: Diagnostic_acute_leukemia (MLL-#9)


title: Diagnostic_acute_leukemia (MLL-#12)


title: Germline i16-#7, Hind SNP array

source_name: Germline i16-#7


title: Diagnostic_acute_leukemia (MLL-#8)


title: Diagnostic_acute_leukemia i16-#4, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#4


title: Germline i16-#6, Hind SNP array

source_name: Germline i16-#6


title: Diagnostic_acute_leukemia i16-#5, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#5


title: Diagnostic_acute_leukemia (MLL-#6)


title: Diagnostic_acute_leukemia i16-#7, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#7


title: Germline i16-#3, Hind SNP array

source_name: Germline i16-#3


title: Germline i16-#1, Hind SNP array

source_name: Germline i16-#1


title: Diagnostic_acute_leukemia (MLL-#1)


title: Diagnostic_acute_leukemia (MLL-#4)


title: Diagnostic_acute_leukemia i16-#2, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#2


title: Diagnostic_acute_leukemia (MLL-#7)


title: Diagnostic_acute_leukemia (MLL-#5)


title: Diagnostic_acute_leukemia i16-#6, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#6


title: Germline i16-#5, Hind SNP array

source_name: Germline i16-#5


title: Germline i16-#2, Hind SNP array

source_name: Germline i16-#2


title: Diagnostic_acute_leukemia i16-#1, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#1


title: Germline AE-#20, Hind SNP array

source_name: Germline AE-#20


title: Diagnostic_acute_leukemia (MLL-#2)


title: Diagnostic_acute_leukemia AE-#19, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#19


title: Diagnostic_acute_leukemia i16-#3, Hind SNP array

source_name: Diagnostic_acute_leukemia i16-#3


title: Diagnostic_acute_leukemia (PML-#6)


title: Germline AE-#19, Hind SNP array

source_name: Germline AE-#19


title: Diagnostic_acute_leukemia AE-#20, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#20


title: Diagnostic_acute_leukemia (PML-#7)


title: Germline AE-#18, Hind SNP array

source_name: Germline AE-#18


title: Diagnostic_acute_leukemia (i16-#16)


title: Diagnostic_acute_leukemia AE-#18, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#18


title: Diagnostic_acute_leukemia (MLL-#3)


title: Germline AE-#17, Hind SNP array

source_name: Germline AE-#17


title: Diagnostic_acute_leukemia (PML-#4)


title: Diagnostic_acute_leukemia AE-#17, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#17


title: Diagnostic_acute_leukemia (i16-#15)


title: Diagnostic_acute_leukemia AE-#16, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#16


title: Diagnostic_acute_leukemia (i16-#14)


title: Diagnostic_acute_leukemia (i16-#13)


title: Diagnostic_acute_leukemia (i16-#12)


title: Diagnostic_acute_leukemia AE-#13, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#13


title: Diagnostic_acute_leukemia AE-#14, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#14


title: Diagnostic_acute_leukemia AE-#15, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#15


title: Diagnostic_acute_leukemia (i16-#10)


title: Diagnostic_acute_leukemia (i16-#9)


title: Diagnostic_acute_leukemia (i16-#6)


title: Diagnostic_acute_leukemia (i16-#7)


title: Germline AE-#7, Hind SNP array

source_name: Germline AE-#7


title: Diagnostic_acute_leukemia AE-#9, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#9


title: Diagnostic_acute_leukemia AE-#12, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#12


title: Diagnostic_acute_leukemia (i16-#8)


title: Diagnostic_acute_leukemia (i16-#11)


title: Diagnostic_acute_leukemia AE-#8, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#8


title: Diagnostic_acute_leukemia AE-#10, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#10


title: Vector + compound 6 vs Vector at time = 4 hours (#1)

city: Cambridge

first: Linhui

middle: Julie

last: Su

state: MA

address: 9 Cambridge Center

institute: Whitehead Institite for Biomedical Research

description: Yeast cells were induced to a starting O.D. of 0.3 in galactose media and harvested at 0, 2, 4, and 6 hours post-induction (50 ml aliquot per timepoint).  For each comparison, 3 pairs of biological replicates were hybridized to 3 different arrays.  Labeling, hybridization and scanning performed by the Whitehead Institute Center for Microarray Technology.

hyb_protocol: Gene Expression Hybridization Kit (Agilent)

scan_protocol: GenePix 4000B

data_processing: Data were analyzed using the limma package from Bioconductor. Spots were background corrected using a normal and exponential convolutional model and an offset of 50 was added.  After loess normalization by print tip, log2 ratios were calculated.  Differential expression was assayed at each timepoint using a moderated t-test, corrected for false discovery rate.

organism: Saccharomyces cerevisiae

source_name: Yeast vector control + compound 6 ((4R)-6-bromo-4-(4-ethylphenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours

label_protocol: MICROMAX ASAP RNA Labeling Kit (Perkin Elmer)

extract_protocol: hot phenol-chloroform extraction (Schmitt et al., 1990)

tag: w303 pump mutants (MATa can1-100, his3-11,15, leu2-3,112, trp1-1, ura3-1, ade2-1, pdr1::kanMX, pdr3::kanMX), containing two copies of empty vector (pRS304Gal, pRS306GAL)

source_name: Yeast vector control at time = 4 hours


title: Diagnostic_acute_leukemia (PML-#5)


title: Germline AE-#8, Hind SNP array

source_name: Germline AE-#8


title: Diagnostic_acute_leukemia AE-#11, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#11


title: Diagnostic_acute_leukemia AE-#7, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#7


title: Germline AE-#6, Hind SNP array

source_name: Germline AE-#6


title: Vector + compound 4 vs Vector at time = 4 hours (#1)

source_name: Yeast vector control + compound 4 (4-(3-bromo-4-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: Diagnostic_acute_leukemia (i16-#5)


title: Diagnostic_acute_leukemia AE-#5, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#5


title: Diagnostic_acute_leukemia (i16-#4)


title: Vector + compound 1 vs Vector at time = 4 hours (#2)

source_name: Yeast vector control + compound 1 (4-(3-iodophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: Vector + compound 3 vs Vector at time = 4 hours (#1)

source_name: Yeast vector control + compound 3 (4-(5-bromo-2-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: 2-copy alpha-synuclein + compound 3 vs Vector + compound 3 at time = 4 hours (#1)

source_name: Yeast 2-copy alpha-synuclein + compound 3 (4-(5-bromo-2-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours

tag: w303 pump mutants (MATa can1-100, his3-11,15, leu2-3,112, trp1-1, ura3-1, ade2-1, pdr1::kanMX, pdr3::kanMX), containing two copies (pRS304GAL- a-syn -GFP, pRS306GAL- a-syn -GFP) of alpha synuclein fused to Green Fluorescent Protein.


title: Diagnostic_acute_leukemia (i16-#3)


title: Germline AE-#4, Hind SNP array

source_name: Germline AE-#4

tag: tissue


title: 2-copy alpha-synuclein + compound 5 vs 2-copy alpha-synuclein at time = 4 hours (#2)

source_name: Yeast 2-copy alpha-synuclein + compound 5 (4-(4-ethyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours

source_name: Yeast 2-copy alpha-synuclein at time = 4 hours


title: Diagnostic_acute_leukemia AE-#6, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#6


title: 2-copy alpha-synuclein vs Vector at time = 4 hours (#4)


title: Diagnostic_acute_leukemia (AE-#20)


title: Diagnostic_acute_leukemia (i16-#1)


title: 2-copy alpha-synuclein vs Vector at time = 4 hours (#6)


title: 2-copy alpha-synuclein + compound 5 vs 2-copy alpha-synuclein at time = 4 hours (#3)


title: 2-copy alpha-synuclein + compound 2 vs Vector + compound 2 at time = 4 hours (#3)

source_name: Yeast 2-copy alpha-synuclein + compound 2 (4-(3-bromophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours

source_name: Yeast vector control + compound 2 (4-(3-bromophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: 2-copy alpha-synuclein + compound 1 vs Vector + compound 1 at time = 4 hours (#2)

source_name: Yeast 2-copy alpha-synuclein + compound 1 (4-(3-iodophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: 2-copy alpha-synuclein + compound 1 vs Vector + compound 1 at time = 4 hours (#3)


title: Vector + compound 6 vs Vector at time = 4 hours (#3)

source_name: Yeast vector control + compound 6 ((4R)-6-bromo-4-(4-ethylphenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours

source_name: Yeast vector control at time = 4 hours


title: Germline AE-#5, Hind SNP array

source_name: Germline AE-#5


title: Diagnostic_acute_leukemia AE-#4, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#4


title: Vector + compound 5 vs Vector at time = 4 hours (#3)

source_name: Yeast vector control + compound 5 (4-(4-ethyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: 2-copy alpha-synuclein + compound 4 vs 2-copy alpha-synuclein at time = 4 hours (#3)

source_name: Yeast 2-copy alpha-synuclein + compound 4 (4-(3-bromo-4-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: 2-copy alpha-synuclein + compound 6 vs 2-copy alpha-synuclein at time = 4 hours (#3)

source_name: Yeast 2-copy alpha-synuclein + compound 6 ((4R)-6-bromo-4-(4-ethylphenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: Germline AE-#3, Hind SNP array

source_name: Germline AE-#3


title: Diagnostic_acute_leukemia (AE-#17)


title: 2-copy alpha-synuclein + compound 3 vs 2-copy alpha-synuclein at time = 4 hours (#3)


title: 2-copy alpha-synuclein vs Vector at time = 4 hours (#5)


title: Diagnostic_acute_leukemia AE-#3, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#3


title: Germline AE-#2, Hind SNP array

source_name: Germline AE-#2


title: Diagnostic_acute_leukemia AE-#2, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#2


title: 2-copy alpha-synuclein + compound 6 vs Vector + compound 6 at time = 4 hours (#3)


title: 2-copy alpha-synuclein + compound 3 vs Vector + compound 3 at time = 4 hours (#3)

source_name: Yeast 2-copy alpha-synuclein + compound 3 (4-(5-bromo-2-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours

source_name: Yeast vector control + compound 3 (4-(5-bromo-2-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: 2-copy alpha-synuclein + compound 4 vs Vector + compound 4 at time = 4 hours (#3)

source_name: Yeast vector control + compound 4 (4-(3-bromo-4-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: 2-copy alpha-synuclein + compound 1 vs 2-copy alpha-synuclein at time = 4 hours (#3)

source_name: Yeast 2-copy alpha-synuclein at time = 4 hours


title: Germline AE-#1, Hind SNP array

source_name: Germline AE-#1


title: 2-copy alpha-synuclein + compound 4 vs Vector + compound 4 at time = 4 hours (#2)


title: 2-copy alpha-synuclein + compound 6 vs Vector + compound 6 at time = 4 hours (#2)


title: 2-copy alpha-synuclein + compound 3 vs 2-copy alpha-synuclein at time = 4 hours (#2)


title: 2-copy alpha-synuclein + compound 2 vs Vector + compound 2 at time = 4 hours (#2)

source_name: Yeast 2-copy alpha-synuclein + compound 2 (4-(3-bromophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours

source_name: Yeast vector control + compound 2 (4-(3-bromophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: Diagnostic_acute_leukemia (AE-#15)


title: 2-copy alpha-synuclein + compound 1 vs 2-copy alpha-synuclein at time = 4 hours (#2)

source_name: Yeast 2-copy alpha-synuclein + compound 1 (4-(3-iodophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: Germline N-#21, Xba SNP array

source_name: Germline N-#21


title: Diagnostic_acute_leukemia (AE-#14)


title: 2-copy alpha-synuclein + compound 5 vs 2-copy alpha-synuclein at time = 4 hours (#1)

source_name: Yeast 2-copy alpha-synuclein + compound 5 (4-(4-ethyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: Diagnostic_acute_leukemia AE-#1, Hind SNP array

source_name: Diagnostic_acute_leukemia AE-#1


title: Diagnostic_acute_leukemia (AE-#12)


title: 2-copy alpha-synuclein + compound 2 vs 2-copy alpha-synuclein at time = 4 hours (#2)

value: :kanMX, pdr3::kanMX), containing two copies (pRS304GAL- a-syn -GFP, pRS306GAL- a-syn -GFP) of alpha synuclein fused to Green Fluorescent Protein.


title: 2-copy alpha-synuclein + compound 1 vs 2-copy alpha-synuclein at time = 4 hours (#1)


title: Germline N-#20, Xba SNP array

source_name: Germline N-#20


title: Diagnostic_acute_leukemia N-#21, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#21


title: 2-copy alpha-synuclein + compound 2 vs 2-copy alpha-synuclein at time = 4 hours (#1)


title: Vector + compound 2 vs Vector at time = 4 hours (#2)

source_name: Yeast vector control at time = 4 hours


title: 2-copy alpha-synuclein + compound 5 vs Vector + compound 5 at time = 4 hours (#2)

source_name: Yeast vector control + compound 5 (4-(4-ethyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: Vector + compound 2 vs Vector at time = 4 hours (#3)


title: Diagnostic_acute_leukemia (AE-#13)


title: Diagnostic_acute_leukemia (AE-#9)


title: Germline N-#19, Xba SNP array

source_name: Germline N-#19


title: 2-copy alpha-synuclein + compound 5 vs Vector + compound 5 at time = 4 hours (#3)


title: Diagnostic_acute_leukemia N-#19, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#19


title: Diagnostic_acute_leukemia (AE-#11)


title: 2-copy alpha-synuclein + compound 2 vs 2-copy alpha-synuclein at time = 4 hours (#3)


title: Diagnostic_acute_leukemia (AE-#10)


title: 2-copy alpha-synuclein + compound 5 vs Vector + compound 5 at time = 4 hours (#1)


title: Diagnostic_acute_leukemia N-#18, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#18


title: Vector + compound 4 vs Vector at time = 4 hours (#3)


title: Vector + compound 6 vs Vector at time = 4 hours (#2)

source_name: Yeast vector control + compound 6 ((4R)-6-bromo-4-(4-ethylphenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: Diagnostic_acute_leukemia N-#17, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#17


title: Diagnostic_acute_leukemia (AE-#7)


title: 2-copy alpha-synuclein + compound 6 vs 2-copy alpha-synuclein at time = 4 hours (#2)

source_name: Yeast 2-copy alpha-synuclein + compound 6 ((4R)-6-bromo-4-(4-ethylphenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours

source_name: Yeast 2-copy alpha-synuclein at time = 4 hours


title: Diagnostic_acute_leukemia N-#20, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#20


title: Diagnostic_acute_leukemia (AE-#8)


title: Diagnostic_acute_leukemia (AE-#6)


title: Diagnostic_acute_leukemia N-#16, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#16


title: Vector + compound 3 vs Vector at time = 4 hours (#3)

source_name: Yeast vector control + compound 3 (4-(5-bromo-2-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: Vector + compound 5 vs Vector at time = 4 hours (#1)


title: Vector + compound 2 vs Vector at time = 4 hours (#1)

source_name: Yeast vector control + compound 2 (4-(3-bromophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: 2-copy alpha-synuclein + compound 2 vs Vector + compound 2 at time = 4 hours (#1)

source_name: Yeast 2-copy alpha-synuclein + compound 2 (4-(3-bromophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: Diagnostic_acute_leukemia N-#15, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#15


title: 2-copy alpha-synuclein + compound 4 vs 2-copy alpha-synuclein at time = 4 hours (#2)

source_name: Yeast 2-copy alpha-synuclein + compound 4 (4-(3-bromo-4-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: Vector + compound 5 vs Vector at time = 4 hours (#2)


title: 2-copy alpha-synuclein + compound 4 vs 2-copy alpha-synuclein at time = 4 hours (#1)


title: Diagnostic_acute_leukemia N-#14, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#14


title: 2-copy alpha-synuclein + compound 6 vs 2-copy alpha-synuclein at time = 4 hours (#1)


title: Diagnostic_acute_leukemia (AE-#3)


title: Diagnostic_acute_leukemia (AE-#5)


title: 2-copy alpha-synuclein + compound 3 vs 2-copy alpha-synuclein at time = 4 hours (#1)

source_name: Yeast 2-copy alpha-synuclein + compound 3 (4-(5-bromo-2-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours


title: Vector + compound 4 vs Vector at time = 4 hours (#2)

source_name: Yeast vector control + compound 4 (4-(3-bromo-4-fluorophenyl)-6,7-dimethyl-3,4-dihydro-2(1H)-quinolinone) at time = 4 hours

source_name: Yeast vector control at time = 4 hours


title: Diagnostic_acute_leukemia N-#13, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#13


title: 2-copy alpha-synuclein + compound 3 vs Vector + compound 3 at time = 4 hours (#2)


title: Vector + compound 3 vs Vector at time = 4 hours (#2)


title: 2-copy alpha-synuclein + compound 6 vs Vector + compound 6 at time = 4 hours (#1)


title: Diagnostic_acute_leukemia (AE-#4)


title: Diagnostic_acute_leukemia (AE-#1)


title: LNCaP, rep 2

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

description: Gene expression data from LNCaP cells

hyb_protocol: As per standard Affymetrix protocol for the Human 1.0ST arrays

data_processing: Background correction, quantile normalisation and Robust Multichip Average were performed using the aroma.affymetrix package in R.

label: biotin

source_name: LNCaP cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for the Human 1.0ST arrays

growth_protocol: Cells were grown at 37ºC with 5% CO2

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

value: Prostate

tag: cell line

value: LNCaP, Cancer cell line

value: T-medium w/ 10% FCS


title: Diagnostic_acute_leukemia N-#12, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#12


title: 2-copy alpha-synuclein + compound 4 vs Vector + compound 4 at time = 4 hours (#1)


title: LNCaP, rep 1

description: Gene expression data from LNCaP cells

scan_protocol: As per standard Affymetrix protocol for the Human 1.0ST arrays


title: Diagnostic_acute_leukemia N-#9, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#9


title: Diagnostic_acute_leukemia N-#10, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#10


title: Diagnostic_acute_leukemia N-#8, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#8


title: Diagnostic_acute_leukemia N-#11, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#11


title: 2-copy alpha-synuclein + compound 1 vs Vector + compound 1 at time = 4 hours (#1)

source_name: Yeast 2-copy alpha-synuclein + compound 1 (4-(3-iodophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours

source_name: Yeast vector control + compound 1 (4-(3-iodophenyl)-3,4-dihydrobenzo[h]quinolin-2(1H)-one) at time = 4 hours


title: Vector + compound 1 vs Vector at time = 4 hours (#3)


title: 2-copy alpha-synuclein vs Vector at time = 4 hours (#3)

source_name: Yeast 2-copy alpha-synuclein at time = 4 hours


title: Germline N-#8, Xba SNP array

source_name: Germline N-#8


title: Germline N-#7, Xba SNP array

source_name: Germline N-#7


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 4 hours (#3)

source_name: Yeast 1-copy alpha-synuclein at time = 4 hours

tag: w303 pump mutants (MATa can1-100, his3-11,15, leu2-3,112, trp1-1, ura3-1, ade2-1, pdr1::kanMX, pdr3::kanMX), containing one copy (pRS304Gal- a-syn -GFP, pRS306GAL) of alpha synuclein fused to Green Fluorescent Protein.


title: PrEC, rep 2

description: Gene expression data from PrEC cells

source_name: PrEC cells

tag: cell type

value: PrEC, Normal cells

value: PrEGM media (Cambrex)


title: Diagnostic_acute_leukemia N-#7, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#7


title: PrEC, rep 1

description: Gene expression data from PrEC cells


title: 1-copy alpha-synuclein vs Vector at time = 6 hours (#3)

source_name: Yeast 1-copy alpha-synuclein at time = 6 hours

source_name: Yeast vector control at time = 6 hours


title: 2-copy alpha-synuclein vs Vector at time = 6 hours (#3)

source_name: Yeast 2-copy alpha-synuclein at time = 6 hours


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 6 hours (#3)


title: 1-copy alpha-synuclein vs Vector at time = 4 hours (#3)

source_name: Yeast vector control at time = 4 hours


title: Germline N-#6, Xba SNP array

source_name: Germline N-#6


title: 2-copy alpha-synuclein vs Vector at time = 2 hours (#3)

source_name: Yeast 2-copy alpha-synuclein at time = 2 hours

source_name: Yeast vector control at time = 2 hours


title: 1-copy alpha-synuclein vs Vector at time = 2 hours (#3)

source_name: Yeast 1-copy alpha-synuclein at time = 2 hours


title: Vector + compound 1 vs Vector at time = 4 hours (#1)


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 2 hours (#3)


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 0 (#3)

source_name: Yeast 1-copy alpha-synuclein at time = 0

source_name: Yeast 2-copy alpha-synuclein at time = 0


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 6 hours (#2)


title: 1-copy alpha-synuclein vs Vector at time = 0 (#3)

source_name: Yeast vector control at time = 0


title: 2-copy alpha-synuclein vs Vector at time = 0 (#3)


title: 1-copy alpha-synuclein vs Vector at time = 6 hours (#2)


title: Diagnostic_acute_leukemia N-#5, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#5


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 4 hours (#2)

source_name: Yeast 2-copy alpha-synuclein at time = 4 hours


title: Diagnostic_acute_leukemia N-#6, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#6


title: Diagnostic_acute_leukemia N-#4, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#4


title: 2-copy alpha-synuclein vs Vector at time = 4 hours (#2)


title: 1-copy alpha-synuclein vs Vector at time = 4 hours (#2)

source_name: Yeast 1-copy alpha-synuclein at time = 4 hours


title: 2-copy alpha-synuclein vs Vector at time = 2 hours (#2)


title: 2-copy alpha-synuclein vs Vector at time = 6 hours (#2)


title: Germline N-#5, Xba SNP array

source_name: Germline N-#5


title: 1-copy alpha-synuclein vs Vector at time = 2 hours (#2)


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 2 hours (#2)


title: Germline N-#3, Xba SNP array

source_name: Germline N-#3


title: Germline N-#2, Xba SNP array

source_name: Germline N-#2


title: Diagnostic_acute_leukemia N-#2, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#2


title: 2-copy alpha-synuclein vs Vector at time = 0 (#2)


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 0 (#2)


title: Diagnostic_acute_leukemia N-#3, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#3


title: Germline N-#1, Xba SNP array

source_name: Germline N-#1


title: 1-copy alpha-synuclein vs Vector at time = 0 (#2)


title: 2-copy alpha-synuclein vs Vector at time = 6 hours (#1)

source_name: Yeast 2-copy alpha-synuclein at time = 6 hours

source_name: Yeast vector control at time = 6 hours


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 6 hours (#1)

source_name: Yeast 1-copy alpha-synuclein at time = 6 hours


title: Diagnostic_acute_leukemia N-#1, Xba SNP array

source_name: Diagnostic_acute_leukemia N-#1


title: 1-copy alpha-synuclein vs Vector at time = 6 hours (#1)


title: Germline misc-#23, Xba SNP array

source_name: Germline misc-#23


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 4 hours (#1)


title: 2-copy alpha-synuclein vs Vector at time = 4 hours (#1)

source_name: Yeast vector control at time = 4 hours


title: 2-copy alpha-synuclein vs Vector at time = 2 hours (#1)

source_name: Yeast 2-copy alpha-synuclein at time = 2 hours

source_name: Yeast vector control at time = 2 hours


title: Germline misc-#22, Xba SNP array

source_name: Germline misc-#22


title: Diagnostic_acute_leukemia misc-#23, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#23


title: 1-copy alpha-synuclein vs Vector at time = 4 hours (#1)

source_name: Yeast 1-copy alpha-synuclein at time = 4 hours


title: 1-copy alpha-synuclein vs Vector at time = 2 hours (#1)

source_name: Yeast 1-copy alpha-synuclein at time = 2 hours


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 2 hours (#1)


title: Diagnostic_acute_leukemia misc-#22, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#22


title: Diagnostic_acute_leukemia N-#21, Sty2 SNP array

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.

source_name: Diagnostic_acute_leukemia N-#21


title: Diagnostic_acute_leukemia N-#19, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#19


title: 2-copy alpha-synuclein vs Vector at time = 0 (#1)

source_name: Yeast 2-copy alpha-synuclein at time = 0

growth_protocol: A starter culture of each sample (~ 5 ml) was grown from a single colony taken from a freshly streaked plate.  To ensure synchronous induction, an aliquot of the starter culture was inoculated into fresh media and grown overnight to early stationary phase (OD 1.0).

source_name: Yeast vector control at time = 0


title: Diagnostic_acute_leukemia N-#20, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#20


title: Diagnostic_acute_leukemia N-#17, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#17


title: Germline N-#21, Sty2 SNP array

source_name: Germline N-#21


title: 1-copy alpha-synuclein vs 2-copy alpha-synuclein at time = 0 (#1)

source_name: Yeast 1-copy alpha-synuclein at time = 0


title: 1-copy alpha-synuclein vs Vector at time = 0 (#1)


title: Germline misc-#20, Xba SNP array

source_name: Germline misc-#20


title: Germline N-#20, Sty2 SNP array

source_name: Germline N-#20


title: activated satellite cell_cultured 3days_rep2

city: paris

first: didier

last: montarras

address: 25, rue du dr. Roux

department: developmental biology

country: France

institute: institut pasteur

description: Gene expression data of cultured satellite cells (Ad.cult2)

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45C on GeneChip 3' Eukaryotic Arrays Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS_450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner G3000 7G.

data_processing: RMA normalization algorithm

organism: Mus musculus

source_name: purified satellite cells form adult Pax3GFP/+ muscles (diaphragm,pectoralis,abdominal) after three days in culture

label_protocol: Biotinylated cRNA were prepared according to the GeneChip Expression Two-Cycle 3′ amplification system Affymetrix protocol from 100 ng total RNA

growth_protocol: mice were kept in the animal house of the Institut Pasteur under an ad libitum food and water regimen, cells culture was perfomed in serum rich medium on gelatine-coated plates

extract_protocol: micro RNAeasy kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: satellite cells were obtained by a pool of Pax3GFP positive muscles (diaphragm,pectoralis,abdominal) by enymatic digestion followed by flow cytometry purification using GFP positivity and size and granularity windows.

tag: genotype

value: diaphragm,pectoralis,abdominal muscles

tag: age

value: cultured (3days)

tag: origin

value: cultured


title: activated satellite cell_cultured 3days_rep1

description: Gene expression data of cultured satellite cells (Ad.cult1)


title: Diagnostic_acute_leukemia N-#16, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#16


title: activated satellite cell_1wk old growing muscle_rep2

description: Gene expression data of freshly isolated satellite cells from young muscle (1wk.2)

source_name: purified satellite cells form 1wk old Pax3GFP/+ muscles (diaphragm,pectoralis,abdominal)

value: young (1week)

value: freshly isolated


title: Diagnostic_acute_leukemia N-#15, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#15


title: Diagnostic_acute_leukemia misc-#21, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#21


title: Diagnostic_acute_leukemia misc-#20, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#20


title: Diagnostic_acute_leukemia N-#18, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#18


title: Germline N-#19, Sty2 SNP array

source_name: Germline N-#19


title: Diagnostic_acute_leukemia misc-#19, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#19


title: activated satellite cell_1wk old growing muscle_rep1

description: Gene expression data of freshly isolated satellite cells from young muscle (1wk.1)


title: activated satellite cell_1wk old growing muscle_rep3

description: Gene expression data of freshly isolated satellite cells from young muscle (1wk.3)


title: Diagnostic_acute_leukemia N-#14, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#14


title: Germline misc-#18, Xba SNP array

source_name: Germline misc-#18


title: Diagnostic_acute_leukemia misc-#17, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#17


title: activated satellite cell_cultured 3days_rep3

description: Gene expression data of cultured satellite cells (Ad.cult3)


title: Diagnostic_acute_leukemia misc-#18, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#18


title: activated satellite cell_adult regenerating mdx muscle_rep1

description: Gene expression data of freshly isolated satellite cells from adult mdx muscle (Ad.mdx1)

source_name: purified satellite cells form adult Pax3GFP/+:mdx/mdx muscles (diaphragm,pectoralis,abdominal)

value: adult (6weeks)


title: activated satellite cell_adult regenerating mdx muscle_rep2

description: Gene expression data of freshly isolated satellite cells from adult mdx muscle (Ad.mdx2)


title: quiescent satellite cell_adult muscle_rep3

description: Gene expression data of freshly isolated satellite cells from adult muscle (Ad.3)

source_name: purified satellite cells form adult Pax3GFP/+ muscles (diaphragm,pectoralis,abdominal)


title: Diagnostic_acute_leukemia N-#10, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#10


title: activated satellite cell_adult regenerating mdx muscle_rep3

description: Gene expression data of freshly isolated satellite cells from adult mdx muscle (Ad.mdx3)


title: quiescent satellite cell_adult muscle_rep2

description: Gene expression data of freshly isolated satellite cells from adult muscle (Ad.2)


title: Diagnostic_acute_leukemia N-#12, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#12


title: Germline misc-#15, Xba SNP array

source_name: Germline misc-#15


title: Diagnostic_acute_leukemia misc-#16, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#16


title: quiescent satellite cell_adult muscle_rep1

description: Gene expression data of freshly isolated satellite cells from adult muscle (Ad.1)


title: Diagnostic_acute_leukemia misc-#15, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#15


title: Diagnostic_acute_leukemia N-#11, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#11


title: Diagnostic_acute_leukemia N-#13, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#13


title: Diagnostic_acute_leukemia N-#9, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#9


title: Germline N-#7, Sty2 SNP array

source_name: Germline N-#7


title: Germline N-#8, Sty2 SNP array

source_name: Germline N-#8


title: Diagnostic_acute_leukemia misc-#14, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#14


title: Diagnostic_acute_leukemia N-#8, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#8


title: Diagnostic_acute_leukemia N-#7, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#7


title: Diagnostic_acute_leukemia misc-#13, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#13


title: Germline misc-#13, Xba SNP array

source_name: Germline misc-#13


title: Germline N-#5, Sty2 SNP array

source_name: Germline N-#5


title: Diagnostic_acute_leukemia misc-#12, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#12


title: Diagnostic_acute_leukemia misc-#11, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#11


title: Diagnostic_acute_leukemia N-#5, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#5


title: Germline N-#6, Sty2 SNP array

source_name: Germline N-#6


title: Diagnostic_acute_leukemia N-#6, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#6


title: Diagnostic_acute_leukemia misc-#10, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#10


title: Germline N-#20, Nsp SNP array

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.

source_name: Germline N-#20


title: Germline N-#21, Nsp SNP array

source_name: Germline N-#21


title: Diagnostic_acute_leukemia N-#4, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#4


title: Germline N-#3, Sty2 SNP array

source_name: Germline N-#3


title: Germline N-#19, Nsp SNP array

source_name: Germline N-#19


title: Diagnostic_acute_leukemia N-#21, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#21


title: Diagnostic_acute_leukemia N-#16, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#16


title: Diagnostic_acute_leukemia N-#19, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#19


title: Germline misc-#9, Xba SNP array

source_name: Germline misc-#9


title: Diagnostic_acute_leukemia N-#20, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#20


title: Diagnostic_acute_leukemia N-#13, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#13


title: Diagnostic_acute_leukemia N-#18, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#18


title: Germline N-#2, Sty2 SNP array

source_name: Germline N-#2


title: Diagnostic_acute_leukemia N-#3, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#3


title: Diagnostic_acute_leukemia N-#14, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#14


title: Germline N-#1, Sty2 SNP array

source_name: Germline N-#1


title: Diagnostic_acute_leukemia N-#2, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#2


title: Diagnostic_acute_leukemia N-#12, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#12


title: Diagnostic_acute_leukemia N-#17, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#17


title: Diagnostic_acute_leukemia misc-#9, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#9


title: Diagnostic_acute_leukemia misc-#8, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#8


title: Diagnostic_acute_leukemia N-#11, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#11


title: Diagnostic_acute_leukemia N-#1, Sty2 SNP array

source_name: Diagnostic_acute_leukemia N-#1


title: Germline misc-#8, Xba SNP array

source_name: Germline misc-#8


title: Germline misc-#7, Xba SNP array

source_name: Germline misc-#7


title: Diagnostic_acute_leukemia N-#15, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#15


title: Diagnostic_acute_leukemia misc-#7, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#7


title: Germline misc-#6, Xba SNP array

source_name: Germline misc-#6


title: Diagnostic_acute_leukemia N-#9, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#9


title: Germline N-#8, Nsp SNP array

source_name: Germline N-#8


title: Diagnostic_acute_leukemia N-#10, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#10


title: Germline misc-#23, Sty2 SNP array

source_name: Germline misc-#23


title: Diagnostic_acute_leukemia misc-#6, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#6


title: Diagnostic_acute_leukemia N-#7, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#7


title: Diagnostic_acute_leukemia misc-#23, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#23


title: Germline misc-#22, Sty2 SNP array

source_name: Germline misc-#22


title: Germline N-#7, Nsp SNP array

source_name: Germline N-#7


title: Germline N-#6, Nsp SNP array

source_name: Germline N-#6


title: Diagnostic_acute_leukemia N-#8, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#8


title: Diagnostic_acute_leukemia misc-#21, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#21


title: Germline N-#3, Nsp SNP array

source_name: Germline N-#3


title: Diagnostic_acute_leukemia misc-#5, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#5


title: Diagnostic_acute_leukemia misc-#22, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#22


title: Germline misc-#5, Xba SNP array

source_name: Germline misc-#5


title: Germline N-#5, Nsp SNP array

source_name: Germline N-#5


title: Diagnostic_acute_leukemia N-#4, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#4


title: Diagnostic_acute_leukemia N-#6, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#6


title: Diagnostic_acute_leukemia N-#5, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#5


title: Germline misc-#4, Xba SNP array

source_name: Germline misc-#4


title: Diagnostic_acute_leukemia N-#3, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#3


title: Germline misc-#20, Sty2 SNP array

source_name: Germline misc-#20


title: Diagnostic_acute_leukemia N-#2, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#2


title: Diagnostic_acute_leukemia misc-#3, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#3


title: Diagnostic_acute_leukemia misc-#4, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#4


title: Diagnostic_acute_leukemia misc-#20, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#20


title: Germline N-#2, Nsp SNP array

source_name: Germline N-#2


title: Germline N-#1, Nsp SNP array

source_name: Germline N-#1


title: Diagnostic_acute_leukemia N-#1, Nsp SNP array

source_name: Diagnostic_acute_leukemia N-#1


title: Germline misc-#2, Xba SNP array

source_name: Germline misc-#2


title: Germline misc-#23, Nsp SNP array

source_name: Germline misc-#23


title: Diagnostic_acute_leukemia misc-#2, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#2


title: Diagnostic_acute_leukemia misc-#23, Nsp SNP array

source_name: Diagnostic_acute_leukemia misc-#23


title: Diagnostic_acute_leukemia misc-#19, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#19


title: Germline misc-#22, Nsp SNP array

source_name: Germline misc-#22


title: Diagnostic_acute_leukemia misc-#21, Nsp SNP array

source_name: Diagnostic_acute_leukemia misc-#21


title: Germline misc-#18, Nsp SNP array

source_name: Germline misc-#18


title: Germline misc-#18, Sty2 SNP array


title: Diagnostic_acute_leukemia misc-#17, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#17


title: Diagnostic_acute_leukemia misc-#18, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#18


title: Diagnostic_acute_leukemia misc-#20, Nsp SNP array


title: Diagnostic_acute_leukemia misc-#1, Xba SNP array

source_name: Diagnostic_acute_leukemia misc-#1


title: Diagnostic_acute_leukemia M7-#9, Xba SNP array

source_name: Diagnostic_acute_leukemia M7-#9


title: Germline misc-#20, Nsp SNP array

source_name: Germline misc-#20


title: Diagnostic_acute_leukemia misc-#22, Nsp SNP array

source_name: Diagnostic_acute_leukemia misc-#22


title: Diagnostic_acute_leukemia M7-#8, Xba SNP array

source_name: Diagnostic_acute_leukemia M7-#8


title: Diagnostic_acute_leukemia misc-#16, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#16


title: Diagnostic_acute_leukemia misc-#19, Nsp SNP array


title: Diagnostic_acute_leukemia misc-#18, Nsp SNP array


title: Diagnostic_acute_leukemia misc-#17, Nsp SNP array


title: 2545

status: Public on Jan 12 2010

city: Miami

first: Maria

middle: Eugenia

last: Figueroa

state: FL

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

department: Human Genetics

institute: University of Miiami

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII and MspI signals are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After intra-array normalization each channel was centered by subtracting background noise (2.5 median absolute deviations from the median of the random probes’ log2 signal for that channel) from its log2-transformed signal intensities. The HpaII/MspI (unmethylated/reference) ratio was then determined for each probe set on array.

source_name: AML blast cells

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: digestion

tag: gender

value: male

tag: fab

value: NN

value: Intermediate

value: Neg

tag: tri 8

tag: complex

tag: other

tag: normal karyotype

value: Pos

tag: nras

tag: kras

tag: cebpa

value: HpaII


title: Germline misc-#15, Nsp SNP array

scan_protocol: As per manufacturer (Affymetrix).

source_name: Germline misc-#15

tag: tissue

value: acute myeloid leukemia


title: Diagnostic_acute_leukemia misc-#14, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#14


title: Diagnostic_acute_leukemia misc-#15, Nsp SNP array

source_name: Diagnostic_acute_leukemia misc-#15


title: Germline M7-#7, Xba SNP array

source_name: Germline M7-#7


title: Diagnostic_acute_leukemia misc-#14, Nsp SNP array


title: Germline misc-#13, Nsp SNP array

source_name: Germline misc-#13


title: Germline misc-#9, Nsp SNP array

source_name: Germline misc-#9


title: Diagnostic_acute_leukemia misc-#12, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#12


title: Germline misc-#1, Xba SNP array

source_name: Germline misc-#1


title: Diagnostic_acute_leukemia misc-#13, Sty2 SNP array

source_name: Diagnostic_acute_leukemia misc-#13


title: Diagnostic_acute_leukemia misc-#10, Nsp SNP array

source_name: Diagnostic_acute_leukemia misc-#10


title: Diagnostic_acute_leukemia misc-#13, Nsp SNP array


title: Diagnostic_acute_leukemia misc-#16, Nsp SNP array


title: Germline misc-#15, Sty2 SNP array


title: Diagnostic_acute_leukemia misc-#15, Sty2 SNP array


title: Diagnostic_acute_leukemia M7-#7, Xba SNP array

source_name: Diagnostic_acute_leukemia M7-#7


title: Germline M7-#5, Xba SNP array

source_name: Germline M7-#5


title: Diagnostic_acute_leukemia misc-#11, Nsp SNP array

source_name: Diagnostic_acute_leukemia misc-#11


title: Germline misc-#13, Sty2 SNP array


title: Diagnostic_acute_leukemia M7-#5, Xba SNP array

source_name: Diagnostic_acute_leukemia M7-#5


title: Diagnostic_acute_leukemia M7-#6, Xba SNP array

source_name: Diagnostic_acute_leukemia M7-#6


title: ST172-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56809.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 = 1760, 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 = 39.42; Parameter Scan Time = 16:23:42; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102744; 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 = 39.42; Parameter Scan Time = 16:23:42; Parameter PMT Volts = 760; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102680; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.17; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: Strat. REF Human aRNA 4ug

tag: Strat. REF Human aRNA 4ug

tag: LabeledExtract

source_name: ST172-T1_4ug aRNA

tag: ST172-T1_4ug aRNA


title: Germline M7-#4, Xba SNP array

source_name: Germline M7-#4


title: Diagnostic_acute_leukemia M7-#4, Xba SNP array

source_name: Diagnostic_acute_leukemia M7-#4


title: PF405-T7

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56868.gif
Compound Based Treatment: Artekin
Disease State: Malaria (P. falciparum)

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 6880; 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 = 35.20; Parameter Scan Time = 09:20:28; Parameter PMT Volts = 530; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 101691; 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 = 35.20; Parameter Scan Time = 09:20:28; Parameter PMT Volts = 680; Parameter Scan Date = 2004-10-20; Parameter Pixel Size = 10; Parameter Laser on time = 101627; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.94; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: PF405-T7_4ug aRNA

tag: PF405-T7_4ug aRNA


title: ST167-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56801.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 = 1120, 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 = 38.93; Parameter Scan Time = 18:31:35; Parameter PMT Volts = 640; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102871; 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 = 38.93; Parameter Scan Time = 18:31:35; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102808; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.19; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST167-T1_4ug aRNA

tag: ST167-T1_4ug aRNA


title: ST170-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56807.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 = 1680, 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 = 38.21; Parameter Scan Time = 09:32:10; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102333; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.06; 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 = 38.21; Parameter Scan Time = 09:32:10; Parameter PMT Volts = 680; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102269; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.94; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST170-T28_4ug aRNA

tag: ST170-T28_4ug aRNA


title: ST171-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56808.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 = 1800, 5880; 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 = 39.38; Parameter Scan Time = 17:28:29; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102809; 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 = 39.38; Parameter Scan Time = 17:28:29; Parameter PMT Volts = 630; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102745; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.18; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST171-T3_4ug aRNA

tag: ST171-T3_4ug aRNA


title: Diagnostic_acute_leukemia misc-#11, Sty2 SNP array