title: ST173-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/56966.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 = 600, 6960; 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 = 39.17; Parameter Scan Time = 11:23:05; Parameter PMT Volts = 520; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103081; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.17; Parameter Scan Time = 11:23:05; Parameter PMT Volts = 610; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103018; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.01; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson


title: Diagnostic_acute_leukemia i16-#8, Sty2 SNP array

status: Public on Jan 04 2010

type: genomic

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: As per manufacturer (Affymetrix).

scan_protocol: As per manufacturer (Affymetrix).

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

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Diagnostic_acute_leukemia i16-#8

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: ST172-T9

type: RNA

city: Stanford

first: Lucinda

last: Thompson

state: CA

address: Fairchild Bldg., D035, 299 Campus Dr

department: Microbiology and Immunology, School of Medicine

institute: Stanford University

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/56965.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 = 600, 7040; 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 = 38.44; Parameter Scan Time = 09:50:29; Parameter PMT Volts = 510; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 102989; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.04; 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 = 38.44; Parameter Scan Time = 09:50:29; Parameter PMT Volts = 620; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 102925; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.91; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

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

molecule: total RNA

source_name: Strat. REF Human aRNA 4ug

label_protocol: not provided

extract_protocol: not provided

tag: Strat. REF Human aRNA 4ug

tag: LabeledExtract


title: Germline AE-#19, Sty2 SNP array

source_name: Germline AE-#19


title: Germline AE-#18, 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 AE-#18


title: Diagnostic_acute_leukemia AE-#2, Xba 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 AE-#2


title: ST170-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/56964.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 = 640, 6800; 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 = 39.74; Parameter Scan Time = 14:29:32; Parameter PMT Volts = 580; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103267; 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 = 39.74; Parameter Scan Time = 14:29:32; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103203; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.11; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson


title: ST173-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/56967.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, 6520; 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 = 39.57; Parameter Scan Time = 13:29:03; Parameter PMT Volts = 500; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103206; 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 = 39.57; Parameter Scan Time = 13:29:03; Parameter PMT Volts = 680; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103143; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.06; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson


title: Diagnostic_acute_leukemia AE-#20, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#20


title: Germline AE-#1, Xba SNP array

source_name: Germline AE-#1


title: Germline AE-#17, Nsp SNP array

source_name: Germline AE-#17


title: ST170-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/56963.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 = 840, 7080; 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 = 38.01; Parameter Scan Time = 09:08:44; Parameter PMT Volts = 560; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 102947; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.02; 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 = 38.01; Parameter Scan Time = 09:08:44; Parameter PMT Volts = 670; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 102884; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.89; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson


title: Diagnostic_acute_leukemia AE-#19, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#19


title: Diagnostic_acute_leukemia AE-#18, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#18


title: Diagnostic_acute_leukemia i16-#5, Nsp SNP array

source_name: Diagnostic_acute_leukemia i16-#5


title: Clone1979_LPI5_N+_8w_rep2

city: Athens

first: Chung-Jui

last: Tsai

state: GA

address: 120 Green Street

department: School of Forestry and Natural Resources

institute: University of Georgia

description: Gene expression data from a 8-week N experiment

hyb_protocol: Affymetrix

scan_protocol: 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.

label: biotin

organism: Populus fremontii x Populus angustifolia

source_name: LPI5, normal nitrogen, 8-week

label_protocol: Affymetrix

growth_protocol: Rooted cuttings, 10-15 cm in height, were transferred into aerated nutrient solution containing 5 mM nitrogen.  Distilled water was added daily as needed to maintain a constant nutrient volume.  Nutrient solution was replaced weekly, and a pH of 5.8±0.3 was maintained by daily additions of 2N KOH or 2N HCl.

extract_protocol: CTAB protocol

treatment_protocol: Plants of ~1 m height were distributed into two large ebb and flow hydroponic tubs, one receiving 5 mM nitrogen (N+) and the other with 0.125 mM nitrogen (N-).  Plants were maintained as described in Growth Protocol for 8 weeks prior to sampling

tag: clone


title: Germline AE-#18, Sty2 SNP array


title: Diagnostic_acute_leukemia i16-#1, Nsp SNP array

source_name: Diagnostic_acute_leukemia i16-#1


title: Diagnostic_acute_leukemia AE-#18, Sty2 SNP array


title: Clone1979_LPI5_N+_8w_rep1


title: Diagnostic_acute_leukemia AE-#17, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#17


title: Germline i16-#4, Sty2 SNP array

source_name: Germline i16-#4


title: ST169-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/56962.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 = 760, 7040; 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 = 38.75; Parameter Scan Time = 10:26:42; Parameter PMT Volts = 500; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103024; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.12; 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 = 38.75; Parameter Scan Time = 10:26:42; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 102961; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 0.93; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson


title: Diagnostic_acute_leukemia AE-#1, Xba SNP array

source_name: Diagnostic_acute_leukemia AE-#1


title: Germline i16-#1, Nsp SNP array

source_name: Germline i16-#1


title: Clone1979_LPI5_N-_8w_rep2

source_name: LPI5, low nitrogen, 8-week


title: Germline AE-#17, Sty2 SNP array


title: Germline AE-#19, Nsp SNP array


title: Clone1979_LPI5_N-_8w_rep1


title: Diagnostic_acute_leukemia AE-#16, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#16


title: Diagnostic_acute_leukemia AE-#15, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#15


title: Clone1979_LPI5_N-_4w_rep2

description: Gene expression data from a 4-week N experiment

source_name: LPI5, low nitrogen, 4-week

treatment_protocol: Plants of ~1 m height were distributed into two large ebb and flow hydroponic tubs, one receiving 5 mM nitrogen (N+) and the other with 0.125 mM nitrogen (N-).  Plants were maintained as described in Growth Protocol for 4 weeks prior to sampling


title: Diagnostic_acute_leukemia AE-#17, Sty2 SNP array


title: ST179-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56818.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 = 1800, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.42; Parameter Scan Time = 16:09:13; Parameter PMT Volts = 620; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102729; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.31; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.42; Parameter Scan Time = 16:09:13; Parameter PMT Volts = 700; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102666; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.16; 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

source_name: ST179-T1_4ug aRNA

tag: ST179-T1_4ug aRNA


title: ST169-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/56960.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1200, 5720; 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 = 39.70; Parameter Scan Time = 14:05:04; Parameter PMT Volts = 490; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103243; 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 = 39.70; Parameter Scan Time = 14:05:04; Parameter PMT Volts = 630; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103180; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.09; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST169-T1_4ug aRNA

tag: ST169-T1_4ug aRNA


title: ST169-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/56961.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 = 840, 6800; 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 = 39.55; Parameter Scan Time = 13:05:03; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103183; 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 = 39.55; Parameter Scan Time = 13:05:03; Parameter PMT Volts = 660; Parameter Scan Date = 2004-10-24; Parameter Pixel Size = 10; Parameter Laser on time = 103119; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.05; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson


title: Clone1979_LPI5_N+_4w_rep2

source_name: LPI5, normal nitrogen, 4-week


title: Diagnostic_acute_leukemia AE-#16, Sty2 SNP array


title: Diagnostic_acute_leukemia AE-#15, Sty2 SNP array


title: Diagnostic_acute_leukemia AE-#14, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#14


title: Diagnostic_acute_leukemia AE-#14, Sty2 SNP array


title: Diagnostic_acute_leukemia AE-#11, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#11


title: ST178-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56817.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 = 1960, 6720; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.38; Parameter Scan Time = 17:40:37; Parameter PMT Volts = 600; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102820; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.36; 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 = 17:40:37; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102756; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.20; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST178-T9_4ug aRNA

tag: ST178-T9_4ug aRNA


title: ST176-T28

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56813.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, 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 = 39.44; Parameter Scan Time = 15:57:06; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102717; 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 = 39.44; Parameter Scan Time = 15:57:06; Parameter PMT Volts = 750; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102654; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.16; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST176-T28_4ug aRNA

tag: ST176-T28_4ug aRNA


title: Clone1979_LPI5_N-_4w_rep1


title: Clone1979_LPI5_N+_4w_rep1


title: Diagnostic_acute_leukemia AE-#13, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#13


title: ST176-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56812.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 = 1560, 6840; 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 = 39.17; Parameter Scan Time = 18:05:44; Parameter PMT Volts = 550; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102846; 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 = 39.17; Parameter Scan Time = 18:05:44; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102782; 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: ST176-T3_4ug aRNA

tag: ST176-T3_4ug aRNA


title: Diagnostic_acute_leukemia AE-#12, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#12


title: ST177-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56814.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 6200; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Lucinda,,Thompson Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.54; Parameter Scan Time = 14:27:58; Parameter PMT Volts = 620; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102628; 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 = 39.54; Parameter Scan Time = 14:27:58; Parameter PMT Volts = 630; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102564; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.11; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST177-T3_4ug aRNA

tag: ST177-T3_4ug aRNA


title: ST178-T1

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56816.gif
Compound Based Treatment: Azithromycin
Disease State: Typhoid

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1480, 7040; 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 = 39.75; Parameter Scan Time = 13:04:45; Parameter PMT Volts = 540; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102545; 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 = 39.75; Parameter Scan Time = 13:04:45; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102482; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.07; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST178-T1_4ug aRNA

tag: ST178-T1_4ug aRNA


title: LNCaP H3K9me2 ChIP-chip

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

description: LNCaP H3K9me2 ChIP-chip on promoter array

hyb_protocol: As per standard Affymetrix protocol for the Human Promoter 1.0R tiling arrays

data_processing: All analysis was performed with UCSC hg18 version of the human genome. The model-based analysis of tiling array (MAT) algorithm (Johnson WE et al PNAS 2006) was used with a bandwidth of 1kb to generate the bar files.

source_name: LNCaP H3K9me2 ChIP DNA

label_protocol: Samples (7.5μg of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments

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

extract_protocol:
ChIP assays were carried out according to the manufacturer’s protocol_ch1(Upstate Biotechnology).  Briefly, ~ 1 x 106 cells, in a 10 cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37C.  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 µg/ml aprotinin and 1µg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice.  The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs.  The complexes were immunoprecipitated with antibodies specific for acetylated-histone H3 lysine 9 (H3K9ac) (Millipore #06-599), trimethylation –histone H3 lysine 4 (H3K4me3) (Abcam #ab8580), dimethyl-histone H3 lysine 9 (H3K9me2) (Abcam #ab1220) and tri-methyl-histone H3 lysine 27 (H3K27me3) (Millipore #07-449).  Ten µl of antibody was used for each immunoprecipitation.  No antibody controls were also included for each ChIP assay and no precipitation was observed by quantitative Real-Time PCR (qPCR) analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by either salmon sperm DNA/protein A agarose slurry or Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times.  The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 µl H2O.
Immunoprecipitated and Input DNA was amplified with 14 cycles of whole genome amplification (WGA2 kit, Sigma) according to manufacturers instructions.

tag: tissue type

value: :Prostate

tag: cell type

value: Cancer cell line

tag: growth medium

value: T-medium w/ 10% FCS

tag: antibody

value: H3K9me2 Ab

source_name: LNCaP Input Chromatin

extract_protocol:
ChIP assays were carried out according to the manufacturer’s protocol_ch2(Upstate Biotechnology).  Briefly, ~ 1 x 106 cells, in a 10 cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37C.  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1 µg/ml aprotinin and 1µg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice.  The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs.  The complexes were immunoprecipitated with antibodies specific for acetylated-histone H3 lysine 9 (H3K9ac) (Millipore #06-599), trimethylation –histone H3 lysine 4 (H3K4me3) (Abcam #ab8580), dimethyl-histone H3 lysine 9 (H3K9me2) (Abcam #ab1220) and tri-methyl-histone H3 lysine 27 (H3K27me3) (Millipore #07-449).  Ten µl of antibody was used for each immunoprecipitation.  No antibody controls were also included for each ChIP assay and no precipitation was observed by quantitative Real-Time PCR (qPCR) analysis. Input samples were processed in parallel. The antibody/protein complexes were collected by either salmon sperm DNA/protein A agarose slurry or Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times.  The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 µl H2O.
Immunoprecipitated and Input DNA was amplified with 14 cycles of whole genome amplification (WGA2 kit, Sigma) according to manufacturers instructions.

value: Prostate


title: Diagnostic_acute_leukemia AE-#11, Sty2 SNP array


title: Diagnostic_acute_leukemia AE-#10, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#10


title: Diagnostic_acute_leukemia AE-#12, Nsp SNP array


title: LNCaP H3K4me3 ChIP-chip

description: LNCaP H3K4me3 ChIP-chip on promoter array

scan_protocol: As per standard Affymetrix protocol for the Human Promoter 1.0R tiling arrays

source_name: LNCaP H3K4me3 ChIP DNA

value: H3K4me3 Ab


title: Diagnostic_acute_leukemia AE-#10, Nsp SNP array


title: Diagnostic_acute_leukemia AE-#9, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#9


title: LNCaP H3K9Ac ChIP-chip

description: LNCaP H3K9Ac ChIP-chip on promoter array

source_name: LNCaP H3K9Ac ChIP DNA

value: H3K9Ac Ab


title: IL-4-/- inf 1 & 2

city: Fort Worth

first: Jerry

last: Simecka

state: TX

address: 3500 Camp Bowie Blvd

department: Molecular Biology & Immunology

institute: UNT Health Science Center

description: Oligonucleotide probes are spotted on a membrane with 128 spots. Positive and negative probes are included. SuperArray GEArray cat. Num. OM-011 used.

hyb_protocol: following manufacturers' instructions (SuperArray)

data_processing: Online analysis and data processing, at SuperArray's website. Signal intensities were normalized with respect to Gapdh and Ppia genes. AP threshold was set at 1.5 and comparison between groups was a ratio between averaged normalized spot intensities of infected and uninfected mice.

organism: Mus musculus

source_name: Lungs

label_protocol: According to True-labeling AMP protocol (SuperArray)

extract_protocol: Total RNA extracted from homogenized lungs using Trizol (Invitrogen)

treatment_protocol: Mice were either infected with Mycoplasma pulmonis or inoculated with Mycoplasma broth (uninfected)

tag: genotype/variation

tag: strain

value: BALB/cJ

tag: age

value: 4-6 weeks

tag: gender

value: female

tag: infection

value: Mycoplasma pulmonis


title: Diagnostic_acute_leukemia AE-#9, Sty2 SNP array

tag: tissue


title: ST174-T9

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56811.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, 5360; 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 = 39.73; Parameter Scan Time = 13:16:15; Parameter PMT Volts = 540; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102556; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 2.29; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.73; Parameter Scan Time = 13:16:15; Parameter PMT Volts = 650; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102493; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.06; 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: ST174-T9_4ug aRNA

tag: ST174-T9_4ug aRNA


title: LNCaP H3K27me3 ChIP-chip

description: LNCaP H3K27me3 ChIP-chip on promoter array

source_name: LNCaP H3K27me3 ChIP DNA

value: H3K27me3 Ab


title: Clone1979_LPI2_N-_4w_rep2

source_name: LPI2, low nitrogen, 4-week

tag: clone


title: Germline AE-#8, Sty2 SNP array

scan_protocol: As per manufacturer (Affymetrix).

source_name: Germline AE-#8


title: ST173-T3

description:
Simple annotation: Pathogen, Salmonella
Image: http://smd.stanford.edu/MicroArray/gifs/2004-10/56810.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, 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 = 39.43; Parameter Scan Time = 11:36:16; Parameter PMT Volts = 620; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102457; 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 = 39.43; Parameter Scan Time = 11:36:16; Parameter PMT Volts = 640; Parameter Scan Date = 2004-10-22; Parameter Pixel Size = 10; Parameter Laser on time = 102393; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47902]; Parameter Laser Power = 1.05; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Lucinda,,Thompson

source_name: ST173-T3_4ug aRNA

tag: ST173-T3_4ug aRNA


title: PrEC H3K27me3 ChIP-chip

description: PrEC H3K27me3 ChIP-chip on promoter array

source_name: PrEC H3K27me3 ChIP DNA

value: Normal cells

value: PrEGM media (Cambrex)

source_name: PrEC Input Chromatin


title: Diagnostic_acute_leukemia AE-#13, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#13


title: Germline AE-#8, Nsp SNP array


title: Germline AE-#7, Nsp SNP array

source_name: Germline AE-#7


title: IL-4-/- uninf 1 & 2

scan_protocol: following manufacturers' instructions (SuperArray)

value: Mycoplasma broth


title: LNCaP MeDIP ChIP-chip

description: LNCaP MeDIP ChIP-chip on promoter array

source_name: LNCaP MeDIP DNA

extract_protocol:
The MeDIP assay was performed on 4 µg of sonicated genomic DNA (300-500 bp) in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl and 0.05% Triton X-100).  Ten µg anti-5-methylcytosine mouse monoclonal antibody (Calbiochem clone 162 33 D3 Cat No. NA81) was incubated overnight in 500 µl 1x IP buffer and the DNA/antibody complexes were collected with 80 µl Protein A/G PLUS agarose beads (Santa Cruz sc-2003).  The beads were washed 3 times with 1x IP buffer at 4C and twice with 1 ml TE buffer at room temperature. The immune complexes were eluted with freshly prepared 1% SDS, 0.1 M NaHCO3, and the DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30 µl H2O.
Immunoprecipitated and Input DNA was amplified with 14 cycles of whole genome amplification (WGA2 kit, Sigma) according to manufacturers instructions.

value: anti-5-methylcytosine mAb

source_name: LNCaP Input DNA


title: Diagnostic_acute_leukemia AE-#8, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#8

value: acute myeloid leukemia


title: Clone1979_LPI2_N+_4w_rep2

description: Gene expression data from a 4-week N experiment

source_name: LPI2, normal nitrogen, 4-week


title: IFN-g-/- uninf 1 & 2

value: IFN-g-/-


title: IFN-g-/- inf 1 & 2


title: PrEC H3K4me3 ChIP-chip

description: PrEC H3K4me3 ChIP-chip on promoter array

source_name: PrEC H3K4me3 ChIP DNA

value: :Prostate


title: Diagnostic_acute_leukemia AE-#7, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#7


title: PrEC H3K9Ac ChIP-chip

description: PrEC H3K9Ac ChIP-chip on promoter array

source_name: PrEC H3K9Ac ChIP DNA


title: Clone1979_LPI2_N-_4w_rep1


title: PrEC H3K9me2 ChIP-chip

description: PrEC H3K9me2 ChIP-chip on promoter array

source_name: PrEC H3K9me2 ChIP DNA


title: Clone1979_LPI2_N+_4w_rep1


title: PrEC MeDIP ChIP-chip

description: PrEC MeDIP ChIP-chip on promoter array

source_name: PrEC MeDIP DNA

source_name: PrEC Input DNA


title: Diagnostic_acute_leukemia AE-#8, Sty2 SNP array


title: Triple mutant, 7 weeks

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

description: Gene expression of triple mutant.

hyb_protocol: Hybridization of the high-density oligonucleotide microarrays (Arabidopsis ATH1 genome array; Affymetrix, Santa Clara, CA) was performed according to the manufacturer's GeneChip Expression Analysis Technical Manual.

scan_protocol: Scanning was performed according to the manufacturer's GeneChip Expression Analysis Technical Manual.

data_processing: RMA.

organism: Arabidopsis thaliana

source_name: leafs, triple mutant, 7 weeks

label_protocol: cRNA was prepared following the manufacturer's instructions. Labelled cRNA transcripts were purified using the Sample Cleanup Module (Affymetrix, Santa Clara, CA). Fragmentation of cRNA transcripts was performed according to the manufacturer's GeneChip Expression Analysis Technical Manual.

growth_protocol: Normal conditions. Mature rosette leaves were harvested at 5, 6 and 7 weeks after sowing.

extract_protocol: Total RNA was extracted using the Trizol reagent.

treatment_protocol: Time

value: Mature rosette leafs

tag: time

value: 7 weeks

tag: genotype

value: mlo2 mlo6 mlo12 triple mutant


title: Triple mutant, 6 weeks

description: Gene expression of triple mutant.

source_name: leafs, triple mutant, 6 weeks

value: 6 weeks


title: Triple mutant, 5 weeks

description: Gene expression of triple mutant.

source_name: leafs, triple mutant, 5 weeks

value: 5 weeks


title: WT, 7 weeks

description: Gene expression of WT.

source_name: leafs, WT, 7 weeks

value: WT


title: WT, 6 weeks

description: Gene expression of WT.

source_name: leafs, WT, 6 weeks


title: WT, 5 weeks

description: Gene expression of WT.

source_name: leafs, WT, 5 weeks


title: Germline AE-#6, Sty2 SNP array

source_name: Germline AE-#6


title: UACC62_melanoma_cell _line_rep1

status: Public on Jan 02 2010

city: Dunedin

last: Jeffs

address: PO Box 56

country: New Zealand

institute: University of Otago

hyb_protocol: Five ug of Alexa-647-labelled melanoma cell line aRNA was combined with 5 ug Alexa-555-labelled common universal human reference aRNA (Stratagene), fragmented, vacuum concentrated, re-suspended in 40 uL SlideHyb Glass Array Hybridization Buffer #1 (Ambion), then hybridised to the array under 22 mm x 50 mm LifterSlips (Erie) for 20 hours at 42°C inside a DeRisi-design hybridisation chamber (Monterey Industries). Post-hybridisation, arrays were washed with 2 x SSC/0.2% SDS (5 min.), 2 x SSC (5 min.), and 0.2 x SSC, then dried by centrifugation (200 g, 3 min.)

scan_protocol: Arrays were imaged by using an Axon 4000B scanner. Fluoresecent intensity data was extracted by using GenePix v5.0 software

data_processing: BRB ArrayTools was used to generate log2 ratios (test/reference) from background-subtracted and Lowess normalised (print tip group) fluoresecent intenisty data.

source_name: UACC62 melanoma cell  line

label_protocol: 500 ng of Total RNA (Bioanalyzer RIN of 8.8-10) was amplified by using an Amino Allyl MessageAmp II amplification kit (Ambion) according to the manufacturer's instructions. Melanoma cell line aRNA (test) and Human Universal Reference aRNA (reference) were coupled to Alexa-647 or Alexa-555 dye (Molecular Probes), respectively,  according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated by using Tri Reagent (MRC) extraction followed by column purification (Invitrogen PureLink) according to the manufacturer's instructions

value: skin

tag: cell line

tag: tumour stage

value: metastatic melanoma

source_name: Universal Human Reference RNA

value: pooled cell lines

tag: supplier

value: Stratagene, catalog #740000


title: NZM09_melanoma_cell_line_rep2

source_name: NZM09 melanoma cell line


title: Germline AE-#5, Nsp SNP array

source_name: Germline AE-#5


title: SK-MEL-28_melanoma_cell_line_rep1

source_name: SK-MEL-28 melanoma cell line


title: Germline AE-#7, Sty2 SNP array

source_name: Germline AE-#7


title: Diagnostic_acute_leukemia AE-#7, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#7


title: Diagnostic_acute_leukemia AE-#4, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#4


title: Germline AE-#4, Sty2 SNP array

source_name: Germline AE-#4


title: NZM07.4_melanoma_cell_line_rep1

source_name: NZM07.4 melanoma cell line


title: NZM09_melanoma_cell_line_rep1


title: NZM07_melanoma_cell_line_rep1

source_name: NZM07 melanoma cell line


title: Germline AE-#5, Sty2 SNP array


title: Diagnostic_acute_leukemia AE-#5, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#5


title: Diagnostic_acute_leukemia AE-#5, Sty2 SNP array


title: NZM06_melanoma_cell_line_rep1

source_name: NZM06 melanoma cell line


title: Diagnostic_acute_leukemia AE-#4, Nsp SNP array


title: Diagnostic_acute_leukemia AE-#6, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#6


title: Diagnostic_acute_leukemia AE-#6, Nsp SNP array


title: Germline AE-#2, Sty2 SNP array

source_name: Germline AE-#2


title: NZM57_melanoma_cell_line_rep1

source_name: NZM57 melanoma cell line


title: Germline AE-#3, Sty2 SNP array

source_name: Germline AE-#3


title: Germline AE-#6, Nsp SNP array

source_name: Germline AE-#6


title: Diagnostic_acute_leukemia AE-#3, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#3


title: NZM06_melanoma_cell_line_rep2

source_name: Universal Human Reference RNA


title: NZM53_melanoma_cell_line_rep1

source_name: NZM53 melanoma cell line


title: Germline AE-#3, Nsp SNP array


title: NZM58_melanoma_cell_line_rep1

source_name: NZM58 melanoma cell line


title: Germline AE-#4, Nsp SNP array


title: Germline AE-#1, Sty2 SNP array

source_name: Germline AE-#1


title: Germline AE-#2, Nsp SNP array


title: NZM45_melanoma_cell_line_rep1

source_name: NZM45 melanoma cell line


title: NZM52_melanoma_cell_line_rep1

source_name: NZM52 melanoma cell line


title: NZM05_melanoma_cell_line_rep1

source_name: NZM05 melanoma cell line


title: NZM46_melanoma_cell_line_rep1

source_name: NZM46 melanoma cell line


title: NZM07.2_melanoma_cell_line_rep1

source_name: NZM07.2 melanoma cell line


title: Diagnostic_acute_leukemia AE-#2, Sty2 SNP array

source_name: Diagnostic_acute_leukemia AE-#2


title: NZM04_melanoma_cell_line_rep3

source_name: NZM04 melanoma cell line


title: NZM42_melanoma_cell_line_rep1

source_name: NZM42 melanoma cell line


title: NZM40_melanoma_cell_line_rep2

source_name: NZM40 melanoma cell line


title: NZM04_melanoma_cell_line_rep2


title: NZM40_melanoma_cell_line_rep1


title: Diagnostic_acute_leukemia AE-#1, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#1


title: NZM04_melanoma_cell_line_rep1


title: Germline AE-#1, Nsp SNP array


title: Diagnostic_acute_leukemia AE-#1, Sty2 SNP array


title: NZM19_melanoma_cell_line_rep1

source_name: NZM19 melanoma cell line


title: NZM03_melanoma_cell_line_rep1

source_name: NZM03 melanoma cell line


title: NZM23_melanoma_cell_line_rep1

source_name: NZM23 melanoma cell line


title: NZM15_melanoma_cell_line_rep2

source_name: NZM15 melanoma cell line

source_name: Universal Human Reference RNA


title: NZM22_melanoma_cell_line_rep2

source_name: NZM22 melanoma cell line


title: NZM22_melanoma_cell_line_rep1


title: NZM20_melanoma_cell_line_rep1

source_name: NZM20 melanoma cell line


title: Diagnostic_acute_leukemia AE-#2, Nsp SNP array


title: NZM02_melanoma_cell_line_rep1

source_name: NZM02 melanoma cell line


title: AML_M2

status: Public on Dec 31 2009

city: Sinjuku-ku

first: Masami

last: Tanaka

state: Tokyo

address: Sinjuku 6-1-1

country: Japan

institute: Tokyo Medical University

hyb_protocol: labeled RNA was hybridized to Agilent miRNA array ( 8 arrays per slide) at 55°C for 20h in rotisserie in a hybridization oven. Disassembled arrays was washed in GE wash buffer 1&2 for 5 minutes each.

scan_protocol: Images was scanned with Agilent scanner at 5µm resolution

data_processing: The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene view file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed.

label: Cy3 pCp

source_name: Blood Serum

label_protocol: 100ng total RNA was dephosphorylated at the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was then ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.0

extract_protocol: Whole blood was separated into plasma and cellular fractions by centrifugation at 1600 × g for 15 min.  Total RNA in the plasma was isolated using Isogen-LS (NIPPON GENE) according to manufacture's instructions.

tag: race

value: Japanese

value: female

tag: condition

value: AML M2

tag: discription


title: AML_M1

value: male

tag: age

value: AML M1


title: Diagnostic_acute_leukemia AE-#3, Nsp SNP array

source_name: Diagnostic_acute_leukemia AE-#3

value: acute myeloid leukemia


title: NZM01_melanoma_cell_line_rep1

source_name: NZM01 melanoma cell line


title: wild-type uninf 1 & 2

status: Public on Jan 01 2010

source_name: Lungs

tag: genotype/variation

value: wild-type

tag: strain

value: BALB/cJ

value: 4-6 weeks

tag: gender

value: Mycoplasma broth


title: wild-type inf 1 & 2

tag: infection

value: Mycoplasma pulmonis


title: NZM11_melanoma_cell_line_rep1

source_name: NZM11 melanoma cell line

tag: tissue


title: NZM15_melanoma_cell_line_rep1


title: NZM12_melanoma_cell_line_rep1

source_name: NZM12 melanoma cell line


title: BS1

value: Normal


title: BS16


title: BS17


title: C01


title: C02


title: BS14


title: BS15


title: RatLTNT48h_48_4

status: Public on Dec 25 2009

city: Vicksburg

first: Xin

last: Guan

address: 3909 Halls Ferry Rd

department: EPP

institute: USACE-ERDC

description: Gene Expression after 48hexposed toTNT_48mg/kgin rat liver

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After washing, the arrays were scanned at PMT levels 350 using GenePix 4200AL scanner (Molecular Device Inc.),

data_processing: The Feature extraction software (V. 9.5.1) from Agilent was used to automatically find and place microarray grids, reject outlier pixels, accurately determine feature intensities and ratios, flag outlier pixels, and calculate statistical confidences. First normalize be median perchip, then by median per gene, which means normalization by median value across all samples, then transformed to log2 based value.

organism: Rattus norvegicus

label_protocol: Rat whole genome oligo arrays in the format of 4X44K were purchased from Agilent. Sample cRNA synthesis, labeling, hybridization and microarray processing were performed according to manufacturer’s protocol One-Color Microarray-Based Gene Expression Analysis (version 1.0). 1ug of total RNA was used. The Agilent One-Color Spike-Mix (part number 5188-5282) was diluted 5000-fold and 5 μL of the diluted spike-in mix was added to 1000 ng of each of the total RNA samples prior to labeling reactions. The labeling reactions were performed using the Agilent Low RNA Input Linear Amplification Kit in the presence of cyanine 3-CTP.

growth_protocol: Female Sprague-Dawley rats used were from the in-house breeding colony (college of pharmacy, ULM) and treated in accordance with the guide for use and care of animals. Housing consisted of a 12 h light/dark cycle with tap water and rodent chow available ad libitum. Temperature (21 C) and humidity( 50 +/-10%) were held constant. Rats were housed individually in polycarbonate cages on hardwood bedding one week prior to dose. Food was removed the night before dosing, which occurred the next morning between 8 and 11AM.

extract_protocol: Total RNA was extracted from about 30mg of liver tissue.  Tissue were homogenized in the lysis buffer with FAST Prep-24 from MP at speed 6.0/s twice, each last 30s before using RNeasy kits (Qiagen). Total RNA concentrations were measured using NanoDrop® ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity and quality of total RNA was checked on an Agilent 2100 Bioanalyzer (Palo Alto, CA). The gel-like images generated by the Bioanalyzer show that total RNAs have two bands, represent 18S and 26S RNA of mammalian RNA . Nuclease-free water (Ambion) was used to elute total RNA.

treatment_protocol: Female Sprague-Dawley rats received a single oral gavage of five doses for each 5 compound in 5% DMSO in corn oil emulsion. Animals were monitored for seizure activity after dosing and were euthanized using CO2, tissues were collected at 24 or 48 hours

tag: compounds/dose (mg/kg)

value: Liver

value: Female

value: 2 months after weaning

tag: weight


title: RatLTNT48h_192_4

description: Gene Expression after 48hexposed toTNT_192mg/kgin rat liver


title: RatLTNT48h_96_4

description: Gene Expression after 48hexposed toTNT_96mg/kgin rat liver


title: RatLTNT48h_con_5

description: Control

value: Control


title: RatLTNT48h_4.8_2

description: Gene Expression after 48hexposed toTNT_4.8mg/kgin rat liver


title: RatLTNT48h_con_4

description: Control


title: RatLTNT48h_48_1


title: RatLTNT48h_192_3


title: RatLTNT48h_4.8_3


title: RatLTNT48h_192_2


title: RatLTNT48h_96_3


title: RatLTNT48h_96_1


title: RatLTNT48h_con_3

description: Control


title: RatLTNT24h_192_4

description: Gene Expression after 24hexposed toTNT_192mg/kgin rat liver


title: RatLTNT24h_96_4

description: Gene Expression after 24hexposed toTNT_96mg/kgin rat liver


title: RatLTNT24h_96_5


title: RatLTNT48h_48_2


title: RatLTNT24h_48_4

description: Gene Expression after 24hexposed toTNT_48mg/kgin rat liver


title: RatLTNT24h_4.8_5

description: Gene Expression after 24hexposed toTNT_4.8mg/kgin rat liver


title: RatLTNT48h_96_2


title: RatLTNT48h_4.8_5


title: RatLTNT24h_192_3


title: RatLTNT48h_192_1


title: RatLTNT48h_48_3


title: RatLTNT48h_4.8_1


title: RatLTNT24h_4.8_4


title: RatLTNT24h_con_5

description: Control


title: RatLTNT48h_con_2

description: Control


title: RatLTNT24h_48_3


title: RatLTNT24h_96_1


title: RatL4ADNT48h_ 187_5

description: Gene Expression after 48hexposed to4ADNT_187mg/kgin rat liver

source_name: RatL4ADNT48h_ 187_5


title: RatLTNT24h_192_2


title: RatLTNT24h_con_4

description: Control


title: RatLTNT24h_96_3


title: RatLTNT24h_4.8_2


title: RatLTNT24h_192_1


title: RatL4ADNT48h_ 47_5

description: Gene Expression after 48hexposed to4ADNT_47mg/kgin rat liver

source_name: RatL4ADNT48h_ 47_5


title: RatLTNT24h_4.8_1


title: RatL4ADNT48h_ C_5

description: Control

source_name: RatL4ADNT48h_ C_5


title: RatLTNT24h_con_2

description: Control


title: RatLTNT24h_con_1

description: Control


title: RatL4ADNT48h_ 4.7_5

description: Gene Expression after 48hexposed to4ADNT_4.7mg/kgin rat liver

source_name: RatL4ADNT48h_ 4.7_5


title: RatL4ADNT48h_ 93_4

description: Gene Expression after 48hexposed to4ADNT_94mg/kgin rat liver

source_name: RatL4ADNT48h_ 93_4


title: RatLTNT24h_48_1


title: RatL4ADNT48h_ 93_2

source_name: RatL4ADNT48h_ 93_2


title: RatL4ADNT48h_ 47_4

source_name: RatL4ADNT48h_ 47_4


title: RatL4ADNT48h_ 187_1

source_name: RatL4ADNT48h_ 187_1


title: RatL4ADNT48h_ 4.7_2

source_name: RatL4ADNT48h_ 4.7_2


title: RatL4ADNT48h_ 187_4

source_name: RatL4ADNT48h_ 187_4


title: RatL4ADNT48h_ 4.7_4

source_name: RatL4ADNT48h_ 4.7_4


title: RatL4ADNT48h_ 47_2

source_name: RatL4ADNT48h_ 47_2


title: RatL4ADNT48h_ C_3

description: Control

source_name: RatL4ADNT48h_ C_3


title: RatL4ADNT48h_ 187_2

source_name: RatL4ADNT48h_ 187_2


title: RatL4ADNT48h_ 93_3

source_name: RatL4ADNT48h_ 93_3


title: RatL4ADNT48h_ C_4

description: Control

source_name: RatL4ADNT48h_ C_4


title: RatL4ADNT48h_ 93_1

source_name: RatL4ADNT48h_ 93_1


title: RatL4ADNT48h_ 4.7_1

source_name: RatL4ADNT48h_ 4.7_1


title: RatL4ADNT48h_ 47_1

source_name: RatL4ADNT48h_ 47_1


title: RatL4ADNT24h_C_5

description: Control


title: RatL4ADNT24h_187_5

description: Gene Expression after 24hexposed to4ADNT_187mg/kgin rat liver


title: RatL4ADNT24h_94_5

description: Gene Expression after 24hexposed to4ADNT_94mg/kgin rat liver


title: RatL4ADNT48h_ C_2

description: Control

source_name: RatL4ADNT48h_ C_2


title: RatL4ADNT24h_47_4

description: Gene Expression after 24hexposed to4ADNT_47mg/kgin rat liver


title: RatL4ADNT24h_4.7_3

description: Gene Expression after 24hexposed to4ADNT_4.7mg/kgin rat liver


title: RatL4ADNT24h_94_3


title: RatL4ADNT24h_187_3


title: RatL4ADNT24h_4.7_2


title: RatL4ADNT24h_C_3

description: Control


title: RatL4ADNT24h_47_3


title: RatL4ADNT24h_187_4


title: RatL4ADNT24h_47_2


title: RatL4ADNT24h_C_2

description: Control


title: RatL4ADNT24h_47_1


title: RatL4ADNT24h_4.7_4


title: RatL4ADNT24h_187_1


title: RatL4ADNT24h_94_2


title: RatL4ADNT24h_4.7_1


title: RL2ADNT48h_44_4

description: Gene Expression after 48hexposed to2ADNT_44mg/kgin rat liver


title: RL2ADNT48h_C_5

description: Control


title: RatL4ADNT24h_93_1


title: RatL4ADNT24h_C_1

description: Control


title: RL2ADNT48h_174_3

description: Gene Expression after 48hexposed to2ADNT_174mg/kgin rat liver


title: RL2ADNT48h_4.4_4

description: Gene Expression after 48hexposed to2ADNT_4.4mg/kgin rat liver


title: RL2ADNT48h_44_2


title: RL2ADNT48h_C_4

description: Control


title: RL2ADNT48h_87_4

description: Gene Expression after 48hexposed to2ADNT_87mg/kgin rat liver


title: RL2ADNT48h_174_4


title: RL2ADNT48h_4.4_3


title: RL2ADNT48h_44_3


title: RL2ADNT48h_87_3


title: RL2ADNT48h_87_2


title: RL2ADNT48h_174_5


title: RL2ADNT48h_174_2


title: RL2ADNT48h_87_1


title: RL2ADNT48h_C_1

description: Control


title: RL2ADNT48h_4.4_2


title: RL2ADNT48h_4.4_1


title: RatL2ADNT24h_4.4_5

description: Gene Expression after 24hexposed to2ADNT_4.4mg/kgin rat liver


title: RL2ADNT48h_C_2

description: Control


title: RatL2ADNT24h_174_5

description: Gene Expression after 24hexposed to2ADNT_174mg/kgin rat liver


title: RatL2ADNT24h_44_4

description: Gene Expression after 24hexposed to2ADNT_44mg/kgin rat liver


title: RatL2ADNT24h_87_4

description: Gene Expression after 24hexposed to2ADNT_87mg/kgin rat liver


title: RatL2ADNT24h_44_3


title: RatL2ADNT24h_C_2

description: Control


title: RatL2ADNT24h_4.4_3


title: RatL2ADNT24h_87_3


title: RatL2ADNT24h_174_2


title: RL2ADNT48h_44_1


title: RatL2ADNT24h_87_5


title: RatL2ADNT24h_174_1


title: RatL2ADNT24h_174_3


title: RatL2ADNT24h_C_3

description: Control


title: RatL2ADNT24h_44_2


title: RatL2ADNT24h_87_1


title: RatL2ADNT24h_4.4_2


title: RatL2ADNT24h_44_1


title: RatL26DNT48h_50_6

description: Gene Expression after 48hexposed to26DNT_50mg/kgin rat liver


title: RatL26DNT48h_99_7

description: Gene Expression after 48hexposed to26DNT_99mg/kgin rat liver


title: RatL26DNT48h_con_5

description: Control


title: RatL2ADNT24h_C_4

description: Control


title: RatL26DNT48h_5_2

description: Gene Expression after 48hexposed to26DNT_5mg/kgin rat liver


title: RatL26DNT48h_25_4

description: Gene Expression after 48hexposed to26DNT_25mg/kgin rat liver


title: RatL26DNT48h_25_1


title: RatL2ADNT24h_4.4_1


title: RatL26DNT48h_99_8


title: RatL26DNT48h_con_6

description: Control


title: RatL26DNT48h_5_3


title: RatL26DNT48h_5_6


title: RatL26DNT48h_25_3


title: RatL26DNT48h_99_6


title: RatL26DNT48h_50_1


title: RatL26DNT48h_50_3


title: RatL2ADNT24h_C_1

description: Control


title: RatL26DNT48h_50_2


title: RatL26DNT48h_25_5


title: RatL26DNT48h_con_2

description: Control


title: RatL26DNT48h_5_1


title: RatL26DNT24h_99_5

description: Gene Expression after 24hexposed to26DNT_99mg/kgin rat liver


title: RatL26DNT48h_99_4


title: RatL26DNT24h_25_4

description: Gene Expression after 24hexposed to26DNT_25mg/kgin rat liver


title: RatL26DNT48h_con_1

description: Control


title: RatL26DNT24h_5_5

description: Gene Expression after 24hexposed to26DNT_5mg/kgin rat liver


title: RatL26DNT24h_50_3

description: Gene Expression after 24hexposed to26DNT_50mg/kgin rat liver


title: RatL26DNT24h_25_3


title: RatL26DNT24h_99_4


title: RatL26DNT24h_C_5

description: Control


title: RatL26DNT24h_5_3


title: RatL26DNT24h_C_4

description: Control


title: RatL26DNT24h_25_2


title: RatL26DNT24h_99_3


title: RatL26DNT24h_5_2


title: RatL26DNT24h_C_3

description: Control


title: RatL26DNT24h_50_5


title: RatL26DNT24h_50_2


title: RatL26DNT24h_99_2


title: RatL26DNT24h_25_1


title: RatL26DNT24h_C_1

description: Control


title: RatL24DNT48h_199_1

description: Gene Expression after 48hexposed to24DNT_199mg/kgin rat liver


title: RatL24DNT48h_49.8_2

description: Gene Expression after 48hexposed to24DNT_49.8mg/kgin rat liver


title: RatL24DNT48h_4.98_3

description: Gene Expression after 48hexposed to24DNT_4.98mg/kgin rat liver


title: RatL24DNT48h_C_1

description: Control


title: RatL26DNT24h_50_1


title: RatL24DNT48h_49.8_3


title: RatL24DNT48h_99.5_1

description: Gene Expression after 48hexposed to24DNT_99.5mg/kgin rat liver


title: RatL24DNT48h_99.5_5


title: RatL24DNT48h_199_5


title: RatL24DNT48h_C_4

description: Control


title: RatL24DNT48h_C_3

description: Control


title: RatL24DNT48h_4.98_4


title: RatL24DNT48h_199_3


title: RatL24DNT24h_199_4

description: Gene Expression after 24hexposed to24DNT_199mg/kgin rat liver


title: RatL24DNT24h_con_4

description: Control


title: RatL24DNT24h_4.98_3

description: Gene Expression after 24hexposed to24DNT_4.98mg/kgin rat liver


title: RatL24DNT24h_199_3


title: RatL26DNT24h_5_1


title: RatL24DNT24h_99_5

description: Gene Expression after 24hexposed to24DNT_99.5mg/kgin rat liver


title: RatL24DNT48h_C_2

description: Control


title: RatL24DNT48h_49.8_5


title: RatL24DNT48h_4.98_1


title: RatL24DNT48h_99.5_3


title: RatL24DNT48h_4.98_5


title: RatL24DNT24h_con_5

description: Control


title: RatL24DNT48h_199_2


title: RatL24DNT24h_4.98_5


title: RatL24DNT24h_49.8_5

description: Gene Expression after 24hexposed to24DNT_49.8mg/kgin rat liver


title: RatL24DNT24h_49.8_4


title: RatL24DNT48h_99.5_2


title: RatL24DNT24h_199_2


title: RatL24DNT24h_99_3


title: benign nevus, 8

status: Public on Dec 20 2009

city: Kingston

first: Harriet

last: Feilotter

state: Ontario

address: 88 Stuart St

department: Pathology and molecular department

country: Canada

institute: Queen's University

hyb_protocol: Labeled RNA was hybridized to Agilent miRNA array (8 arrays per slide) at 55°C for 22h in rotisserie in a hybridization oven. Disassembled arrays were washed in GE wash buffer 1&2 for 5 minutes each.

scan_protocol: Images were scanned with Agilent scanner at 5µm resolution.

data_processing: The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene View file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed.

source_name: FFPE benign nevus

label_protocol: 100ng total RNA was dephosphorylated in the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.5.

extract_protocol: All samples contained at least 75% hyperplasia tissues without necrosis, which was confirmed by pathologist. The RecoverAll total RNA Isolation kit (Ambion, Streetsville, Canada) was used to extract total RNA (including miRNA) from FFPE samples.

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) tissues.

value: Benign nevus


title: metastatic melanoma, 8

source_name: FFPE metastatic melanoma

value: Metastatic melanoma


title: benign nevus, 7


title: RatL24DNT24h_99_2


title: RatL24DNT48h_49.8_4


title: metastatic melanoma, 9


title: benign nevus, 4


title: benign nevus, 3


title: benign nevus, 5


title: benign nevus, 2


title: RatL24DNT24h_4.98_2


title: RatL24DNT24h_49.8_3


title: benign nevus, 1


title: RatL24DNT24h_49.8_1


title: RatL24DNT24h_con_2

description: Control


title: RatL24DNT24h_199_1


title: RatL24DNT24h_con_3

description: Control


title: benign nevus, 6


title: RatL24DNT24h_4.98_1


title: RatL24DNT24h_99_1


title: metastatic melanoma, 6


title: metastatic melanoma, 7


title: metastatic melanoma, 5


title: metastatic melanoma, 3


title: metastatic melanoma, 4


title: metastatic melanoma, 2


title: lympatic endothelial cell 72 hours post KSHV infection_4

status: Public on Dec 15 2009

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building, Huntley Street

department: Cancer Institute

country: United Kingdom

institute: UCL

hyb_protocol: Cy3 labeled total RNA was hybridized to Agilent Human miRNA Microarray v1.0 as per manufacturer's instructions.

scan_protocol: The Agilent Human miRNA Microarray was scanned using the Agilent scanner as per manufacturer's instructions.

data_processing: Summary expression text files were created using Agilent Feauture Extraction Software. From the summary text files we extracted the Log2 median (gMedianSignal) and background signal (gBGUsed). The arrays were then background subtracted, the data quantile normalized, and the median of the replicates was used as the summary expression value. A floor of -1 was also set.

source_name: lymphatic endothelial cells

label_protocol: total RNA was labeled with Cy3 using the Agilent miRNA labeling and reagent kit as per manufacturer's instructions.

growth_protocol: Human lymphatic endothelial cells (LECs) were separated from microvascular endothelial cells (MVECs) using a polyclonal antibody of podoplanin, a LEC specific marker. Six batches of MVECs were isolated from 6 different donors and were cultured in Endothelial Cell Growth Medium MV (C-22020, PromoCell, Heidelberg, Germany) plus 10 ng/ml of VEGF-C on fibronectin-coated plates. All cells were mycoplasma free.

extract_protocol: RNA was extracted using the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions.The small RNA fraction was assessed using the Agilent small RNA Kit. Quality and integrity of the RNA fraction between 6 and 150 nucleotides was quantified using the Agilent 2100 bioanalyzer (Agilent).

treatment_protocol: Lymphatic endothelial cells (LECs) and KSHV infected LECs were cultured in 10cm petri dishes until confluency and then lysed in lysis buffer prior to RNA extraction as described in the extraction protocol. Lymphatic endothelial cells (LECs) were infected with a recombinant GFP-expressing KSHV derived from the BCBL-1 cell line. 3-4 days after infection, cultures comprised of at least 45-50% GFP expressing LECs were harvested as described.

tag: cell type

value: lymphatic endothelial cells

tag: time in culture

tag: treatment

value: KSHV infection

tag: technical replicate


title: lympatic endothelial cell 72 hours post KSHV infection_3


title: lympatic endothelial cell 72 hours post KSHV infection_2


title: lympatic endothelial cell 72 hours_3


title: lympatic endothelial cell 72 hours post KSHV infection_1


title: lympatic endothelial cell 72 hours_4


title: lympatic endothelial cell 6 hours_2


title: lympatic endothelial cell 6 hours post KSHV infection_4


title: lympatic endothelial cell 6 hours_1


title: lympatic endothelial cell 6 hours_4


title: lympatic endothelial cell 6 hours post KSHV infection_3


title: lympatic endothelial cell 72 hours_2


title: lympatic endothelial cell 6 hours_3


title: lympatic endothelial cell 6 hours post KSHV infection_2


title: lympatic endothelial cell 72 hours_1


title: lympatic endothelial cell 6 hours post KSHV infection_1


title: Untreated repl 16

status: Public on Nov 11 2009

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

description: Biological replicate 16 of 24.

hyb_protocol: The Hybridization was performed acording to Ambion protocol

scan_protocol: Slides were analysed by Agilent Microarray Scanner G2565AA

data_processing: Background subtraction method: Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.Whithin Normalization method: loess. Between Normalization method: quantile

source_name: purified cell of  CLL

label_protocol: Total RNA was labelled according to Ambion protocol. 825 ng of Cy3-labeled reference aRNA (according to Agilent protocol)

extract_protocol: Total RNA was extracted according to TRIZOL reagent protocol

value: wild type

value: B-CLL

tag: agent

source_name: reference

tag: reference

value: aRNA from pooled normal PB B cells of healthy donors


title: Untreated repl 14

description: Biological replicate 14 of 24.


title: Untreated repl 21

description: Biological replicate 21 of 24.

value: deleted/mutated


title: Untreated repl 19

description: Biological replicate 19 of 24.


title: Untreated repl 24

description: Biological replicate 24 of 24.


title: Untreated repl 13

description: Biological replicate 13 of 24.


title: Untreated repl 15

description: Biological replicate 15 of 24.


title: Untreated repl 17

description: Biological replicate 17 of 24.


title: Untreated repl 20

description: Biological replicate 20 of 24.


title: Untreated repl 11

description: Biological replicate 11 of 24.


title: Untreated repl 10

description: Biological replicate 10 of 24.


title: Untreated repl 18

description: Biological replicate 18 of 24.


title: Untreated repl 12

description: Biological replicate 12 of 24.


title: Untreated repl 23

description: Biological replicate 23 of 24.


title: Untreated repl 22

description: Biological replicate 22 of 24.


title: Untreated repl 6

description: Biological replicate 6 of 24.


title: Untreated repl 9

description: Biological replicate 9 of 24.


title: Untreated repl 7

description: Biological replicate 7 of 24.


title: AML_060_D_Xba

status: Public on Dec 01 2009

city: Ulm

first: Jan

last: Kroenke

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine III

institute: University Hospital of Ulm

description:
Hybridized to 50K_Xba
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: 1) CEL files and CHP files (generated by Affymetrix GTYPE) were processed by Copy Number Analyzer for GeneChip (CNAG) version 2.0 software or 2)CEL files and TXT files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model. Normalization was performed using the reference normalization algorithm developed at St Jude and described in Mullighan et al Nature 2007;446:758. Normalization was performed against bone marrow or peripheral blood samples at remission from the same patient (paired analysis).

source_name: bone marrow

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cells preparations obtained from peripheral blood using using the Qiagen ALL-Prep DNA/RNA Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: sample

value: Acute myeloid leukemia diagnosis sample

value: mononuclear cells

tag: disease state

value: Acute myeloid leukemia


title: Untreated repl 4

description: Biological replicate 4 of 24.


title: Untreated repl 1

description: Biological replicate 1 of 24.


title: Nutlin-3 Treated repl 22

description: Biological replicate 22 of 24.

source_name: Nutlin-3 treated purified cell of  CLL


title: AML_047_D_Xba


title: Untreated repl 5

description: Biological replicate 5 of 24.


title: Nutlin-3 Treated repl 24

description: Biological replicate 24 of 24.


title: Untreated repl 2

description: Biological replicate 2 of 24.


title: Untreated repl 3

description: Biological replicate 3 of 24.


title: Nutlin-3 Treated repl 23

description: Biological replicate 23 of 24.


title: Untreated repl 8

description: Biological replicate 8 of 24.


title: Nutlin-3 Treated repl 12

description: Biological replicate 12 of 24.


title: Nutlin-3 Treated repl 16

description: Biological replicate 16 of 24.


title: Nutlin-3 Treated repl 13

description: Biological replicate 13 of 24.


title: Nutlin-3 Treated repl 20

description: Biological replicate 20 of 24.


title: Nutlin-3 Treated repl 9

description: Biological replicate 9 of 24.


title: Nutlin-3 Treated repl 21

description: Biological replicate 21 of 24.


title: Nutlin-3 Treated repl 19

description: Biological replicate 19 of 24.


title: Nutlin-3 Treated repl 8

description: Biological replicate 8 of 24.


title: Nutlin-3 Treated repl 18

description: Biological replicate 18 of 24.


title: Nutlin-3 Treated repl 17

description: Biological replicate 17 of 24.


title: Nutlin-3 Treated repl 11

description: Biological replicate 11 of 24.


title: Nutlin-3 Treated repl 7

description: Biological replicate 7 of 24.


title: Nutlin-3 Treated repl 14

description: Biological replicate 14 of 24.


title: Nutlin-3 Treated repl 6

description: Biological replicate 6 of 24.


title: Nutlin-3 Treated repl 10

description: Biological replicate 10 of 24.


title: Nutlin-3 Treated repl 1

description: Biological replicate 1 of 24.


title: Nutlin-3 Treated repl 4

description: Biological replicate 4 of 24.


title: Nutlin-3 Treated repl 5

description: Biological replicate 5 of 24.


title: Nutlin-3 Treated repl 2

description: Biological replicate 2 of 24.


title: Nutlin-3 Treated repl 3

description: Biological replicate 3 of 24.


title: Nutlin-3 Treated repl 15

description: Biological replicate 15 of 24.


title: H3K4me3 CD4+ T cell rep3

status: Public on Nov 09 2009

city: Lund

first: Joanne

last: Attema

address: Tornavagen 10

department: Immunology

country: Sweden

institute: Lund University

description: miniChIP-chip CD4+ T cells H3K4me3 replicate 3

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc.,Iceland following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Iceland, following their standard operating protocol. See www.nimblegen.com.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan ChIP data extraction. Arrays were normalized using MA2C and quantile normalization as described in Weishaupt et al., 2009 (Blood).

source_name: H3K4me3 miniChIP DNA from CD4+ T cells

label_protocol: Labeling was performed by NimbleGen Systems Inc., Iceland, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: The miniChIP method is described in detail in the Supplementary Data file of Weishaupt et al., 2009 (Blood).

treatment_protocol: CD4+ T cells were FACS sorted from the spleen of 10-12 week old mice

value: 10-12 weeks old

value: spleen

value: mature CD4+ T cells

tag: antibody

source_name: Input DNA from CD4+ T cell


title: H3K9me3 CD4+ T cell rep2

description: miniChIP-chip CD4+ T cells H3K9me3 replicate 2

source_name: H3K9me3 miniChIP DNA from CD4+ T cells

tag: age


title: H3K27me3 CD4+ T cell rep3

description: miniChIP-chip CD4+ T cells H3K27me3 replicate 3

source_name: H3K27me3 miniChIP DNA from CD4+ T cells


title: H3K79me2 CD4+ T cell rep1

description: miniChIP-chip CD4+ T cells H3K79me2 replicate 1

source_name: H3K79me2 miniChIP DNA from CD4+ T cells


title: H3K9me3 CD4+ T cell rep3

description: miniChIP-chip CD4+ T cells H3K9me3 replicate 3


title: PolII CD4+ T cell rep2

description: miniChIP-chip CD4+ T cells PolII replicate 2

source_name: PolII miniChIP DNA from CD4+ T cells

value: PolII


title: H3K9me3 PreMegE rep3

description: miniChIP-chip PreMegEs H3K9me3 replicate 3

source_name: H3K9me3 miniChIP DNA from PreMegE

treatment_protocol: PreMegEs were FACS sorted from the bone marrow of 10-12 week old mice

value: bone marrow

source_name: Input DNA from PreMegE


title: H3K9me3 CD4+ T cell rep1

description: miniChIP-chip CD4+ T cells H3K9me3 replicate 1


title: PolII CD4+ T cell rep1

description: miniChIP-chip CD4+ T cells PolII replicate 1


title: PolII PreMegE rep3

description: miniChIP-chip PreMegEs PolII replicate 3

source_name: PolII miniChIP DNA from PreMegE


title: H3ac CD4+ T cell rep1

description: miniChIP-chip CD4+ T cells H3ac replicate 1

source_name: H3ac miniChIP DNA from CD4+ T cells


title: H3K4me3 CD4+ T cell rep2

description: miniChIP-chip CD4+ T cells H3K4me3 replicate 2


title: H3K79me2 PreMegE rep3

description: miniChIP-chip PreMegEs H3K79me2 replicate 3

source_name: H3K79me2 miniChIP DNA from PreMegE


title: H3K27me3 CD4+ T cell rep1

description: miniChIP-chip CD4+ T cells H3K27me3 replicate 1


title: H3K27me3 PreMegE rep2

description: miniChIP-chip PreMegEs H3K27me3 replicate 2

source_name: H3K27me3 miniChIP DNA from PreMegE


title: PolII PreMegE rep2

description: miniChIP-chip PreMegEs PolII replicate 2


title: H3K4me3 CD4+ T cell rep1

description: miniChIP-chip CD4+ T cells H3K4me3 replicate 1


title: H3ac CD4+ T cell rep3

description: miniChIP-chip CD4+ T cells H3ac replicate 3


title: H3K9me3 PreMegE rep2

description: miniChIP-chip PreMegEs H3K9me3 replicate 2


title: H3K79me2 CD4+ T cell rep2

description: miniChIP-chip CD4+ T cells H3K79me2 replicate 2


title: H3K79me2 CD4+ T cell rep3

description: miniChIP-chip CD4+ T cells H3K79me2 replicate 3


title: H3K9me3 PreMegE rep1

description: miniChIP-chip PreMegEs H3K9me3 replicate 1


title: H3K27me3 PreMegE rep3

description: miniChIP-chip PreMegEs H3K27me3 replicate 3


title: H3K27me3 PreMegE rep1

description: miniChIP-chip PreMegEs H3K27me3 replicate 1


title: PolII PreMegE rep1

description: miniChIP-chip PreMegEs PolII replicate 1


title: H3K79me2 PreMegE rep1

description: miniChIP-chip PreMegEs H3K79me2 replicate 1


title: H3K27me3 CD4+ T cell rep2

description: miniChIP-chip CD4+ T cells H3K27me3 replicate 2


title: H3ac CD4+ T cell rep2

description: miniChIP-chip CD4+ T cells H3ac replicate 2


title: Diagnostic_acute_leukemia MLL-#17, Sty2 SNP array

source_name: Diagnostic_acute_leukemia MLL-#17

value: acute myeloid leukemia


title: H3K79me2 PreMegE rep2

description: miniChIP-chip PreMegEs H3K79me2 replicate 2


title: PolII MPP rep2

description: miniChIP-chip MPPs PolII replicate 2

source_name: PolII miniChIP DNA from MPP

treatment_protocol: MPPs were FACS sorted from the bone marrow of 10-12 week old mice

value: multipotent progenitors (MPP)

source_name: Input DNA from MPP


title: H3K4me3 PreMegE rep1

description: miniChIP-chip PreMegEs H3K4me3 replicate 1

source_name: H3K4me3 miniChIP DNA from PreMegE


title: H3K4me3 PreMegE rep3

description: miniChIP-chip PreMegEs H3K4me3 replicate 3


title: H3ac PreMegE rep2

description: miniChIP-chip PreMegEs H3ac replicate 2

source_name: H3ac miniChIP DNA from PreMegE


title: H3K9me3 MPP rep1

description: miniChIP-chip MPPs H3K9me3 replicate 1

source_name: H3K9me3 miniChIP DNA from MPP


title: H3K4me3 PreMegE rep2

description: miniChIP-chip PreMegEs H3K4me3 replicate 2


title: H3K9me3 MPP rep3

description: miniChIP-chip MPPs H3K9me3 replicate 3


title: H3ac PreMegE rep1

description: miniChIP-chip PreMegEs H3ac replicate 1


title: H3ac MPP rep2

description: miniChIP-chip MPPs H3ac replicate 2

source_name: H3ac miniChIP DNA from MPP


title: H3K79me2 MPP rep1

description: miniChIP-chip MPPs H3K79me2 replicate 1

source_name: H3K79me2 miniChIP DNA from MPP


title: PolII MPP rep1

description: miniChIP-chip MPPs PolII replicate 1


title: H3ac MPP rep3

description: miniChIP-chip MPPs H3ac replicate 3


title: H3K79me2 MPP rep2

description: miniChIP-chip MPPs H3K79me2 replicate 2


title: H3K27me3 MPP rep2

description: miniChIP-chip MPPs H3K27me3 replicate 2

source_name: H3K27me3 miniChIP DNA from MPP


title: H3ac PreMegE rep3

description: miniChIP-chip PreMegEs H3ac replicate 3


title: H3K4me3 MPP rep2

description: miniChIP-chip MPPs H3K4me3 replicate 2

source_name: H3K4me3 miniChIP DNA from MPP


title: H3K27me3 MPP rep3

description: miniChIP-chip MPPs H3K27me3 replicate 3


title: H3K79me2 MPP rep3

description: miniChIP-chip MPPs H3K79me2 replicate 3


title: PolII HSC rep2

description: miniChIP-chip HSCs PolII replicate 2

source_name: PolII miniChIP DNA from HSC

treatment_protocol: HSCs were FACS sorted from the bone marrow of 10-12 week old mice

value: hematopoieitic stem cells (HSC)

source_name: Input DNA from HSC


title: H3K27me3 MPP rep1

description: miniChIP-chip MPPs H3K27me3 replicate 1


title: H3ac MPP rep1

description: miniChIP-chip MPPs H3ac replicate 1


title: H3K9me3 MPP rep2

description: miniChIP-chip MPPs H3K9me3 replicate 2


title: H3K4me3 MPP rep1

description: miniChIP-chip MPPs H3K4me3 replicate 1


title: PolII HSC rep3

description: miniChIP-chip HSCs PolII replicate 3


title: PolII MPP rep3

description: miniChIP-chip MPPs PolII replicate 3


title: PolII HSC rep1

description: miniChIP-chip HSCs PolII replicate 1


title: H3K9me3 HSC rep3

description: miniChIP-chip HSCs H3K9me3 replicate 3

source_name: H3K9me3 miniChIP DNA from HSC


title: H3K4me3 MPP rep3

description: miniChIP-chip MPPs H3K4me3 replicate 3


title: H3K27me3 HSC rep3

description: miniChIP-chip HSCs H3K27me3 replicate 3

source_name: H3K27me3 miniChIP DNA from HSC


title: recil.stationary_phase.T45.rep1

status: Public on Nov 01 2009

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

country: France

institute: Laboratoire Biométrie et Biologie Evolutive

description: Time point 45 minutes after deciliation (rep 1)

hyb_protocol: Hybridization by NimbleGen company

scan_protocol: Scanning by NimbleGen company

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM365280.tab file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.

organism: Paramecium tetraurelia

source_name: Paramecium cells in stationary phase

label_protocol: SuperScript Invitrogen (double strand labeling)

extract_protocol: Tri-reagent and Ambion column (ref AM1924)

treatment_protocol: deciliation

value: nd7 F2 1A5a

value: mutant strain unable to discharge trichocysts. Less background in deciliation experiments

tag: caryonide

value: polycaryonide

tag: medium

value: Klebsiella pneumoniae BHB

value: stationary phase


title: recil.log_phase_growth.T30 rep2

description:
Paramecium cells in log phase growth
Time point 30 minutes after deciliation (rep 2)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM315908.pair file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes. The GSM315908_T30D.norm_RMA.tab file contains the signals after background correction, but before applying across-array normalization.

source_name: Time point 30 minutes after deciliation

treatment_protocol: A pellet of living paramecia is vortexed 30 sec. in TrisHCl 10mM pH 7.2, CaCl2 1mM, ethanol 5% v/v and centrifuged 1 min. 1000g. The pellet is essentially composed of living immobile deciliated paramecia that are transferred to fresh culture medium. Aliquotes are taken and pelleted at desired time after the treatment for total RNA extraction.

tag: strain

value: log-phase growth


title: recil.stationary_phase.T45.rep2

description: Time point 45 minutes after deciliation (rep 2)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM365281.tab file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: recil.stationary_phase.T0.rep1

description: Time point before deciliation (no replicate)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM365277.tab file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: recil.stationary_phase.T130.rep2

description: Time point 130 minutes after deciliation (rep 2)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM365279.tab file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: Oli-neu cells cocultured with cortical astrocytes in insert system _rep4

status: Public on Oct 27 2009

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Mouse immortalized oligodendrocyte precursor cell line Oli-neu received from Dr. J. Trotter (University of Mainz, Mainz, Germany) co-cultured with mouse cortical astrocytes in FalconTM cell culture 6 wells insert system, with astrocytes in the insert and Oli-neu cells on the bottom of the system. The insert had pores of 0.4µm allowing the two types of cells to exchange neurotransmitters and other signaling molecules but preventing formation of gap junction channels.

hyb_protocol: The labeled cDNA was co-hybridized with a distinct Alexa Fluor®_647-aha-dUTP labeled biological replica overnight at 50°C on a Duke Operon Mouse 30K oligonucleotide array V4.0. Hybridization design ("multiple yellow" strategy) was described in Iacobas et al. Biochem Biophys Res Commun. 2006.

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005.

label: Alexa Fluor®_555

label_protocol: 20ug total RNA extracted from the culture dish were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: Oli-neu cells were seeded in culture flasks coated with 0.01% poly-L-lysine and cultured in DMEM medium + 1% B27, N2, PSG, SP and horse serum, and passed with Trypsin-EDTA. Preparation of primary astrocyte cultures: At E19 stage of pregnancy, C-sections were performed on C57Bl/6j mothers and brains from four pups were separately minced in 500μl of 0.05% trypsin-EDTA, transferred to 1 ml Eppendorf tubes containing 500μl culture medium  (Dulbecco’s Modified Eagle medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and spun down at 2000 RPM for 10 min. Pellet was then re-suspended in culture medium and the cells were plated in 100 mm culture dishes and maintained in a humidified 5% CO2 incubator at 37°C. After 1 week in culture, primary confluent astrocyte cultures were trypsinized (0.05% trypsin) and replated (Iacobas et al. Cell Commun Adhes 2008).

extract_protocol: total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)


title: recil.log_phase_growth.T120 rep2

description:
Paramecium cells in log phase growth
Time point 120 minutes after deciliation (rep 2)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM315906.pair file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes. The GSM315906_T120D.norm_RMA.tab file contains the signals after background correction, but before applying across-array normalization.


title: H3K9me3 HSC rep2

description: miniChIP-chip HSCs H3K9me3 replicate 2


title: recil.stationary_phase.T130.rep1

description: Time point 130 minutes after deciliation (rep 1)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM365278.tab file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes, but omits all of the information that is redundant with the design file. The NORM_RMA.pair file contains the probes signal after background correction, but before applying between-array normalization.


title: recil.log_phase_growth.T30 rep1

description:
Paramecium cells in log phase growth
Time point 30 minutes after deciliation (rep 1)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM315907.pair file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes. The GSM315907_T30.norm_RMA.tab file contains the signals after background correction, but before applying across-array normalization.


title: Oli-neu cells cocultured with cortical astrocytes in insert system _rep2


title: recil.log_phase_growth.T0 rep4

description:
Paramecium cells in log phase growth
Time point before deciliation (rep 2)

data_processing:
Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).
The supplementary GSM315904.pair file corresponds to the PAIR (raw) file provided by NimbleGen. It contains the raw signal intensities for the individual probes. The GSM315904_T0D.norm_RMA.tab file contains the signals after background correction, but before applying across-array normalization.

source_name: Time point before deciliation


title: H3K79me2 HSC rep3

description: miniChIP-chip HSCs H3K79me2 replicate 3

source_name: H3K79me2 miniChIP DNA from HSC


title: Oli-neu cells cocultured with cortical astrocytes in insert system _rep3

hyb_protocol: The labeled cDNA was co-hybridized with a distinct Alexa Fluor®_555-aha-dUTP labeled biological replica overnight at 50°C on a Duke Operon Mouse 30K oligonucleotide array V4.0. Hybridization design ("multiple yellow" strategy) was described in Iacobas et al. Biochem Biophys Res Commun. 2006.

label: Alexa Fluor®_647

label_protocol: 20ug total RNA extracted from the culture dish were reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).


title: Oli-neu cells, control_rep1

description: mouse immortalized oligodendrocyte precursor cell line oli-neu received from Dr. J. Trotter (university of mainz, mainz, germany) that have been obtained as described in jung et al. eur j neurosci (1995) 7: 1245–1265

source_name: Oli-neu cells, control

growth_protocol: Cells were seeded in culture flasks coated with 0.01% poly-L-lysine and cultured in DMEM medium + 1% B27, N2, PSG, SP and horse serum, and passed with Trypsin-EDTA.

value: Oli-neu cells, control


title: Oli-neu cells, control_rep4