title: TSAI_B140P_A2_430A

status: Public on Sep 01 2005

city: Minneapolis

first: Michaela

middle: Long

last: Tsai

state: MN

address: 6-160 Jackson Hall, 321 Church St. SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

description: Data have been retracted (PMID: 20703210).

hyb_protocol: 15 micrograms labeled cRNA under standard conditions (Affymetrix, Santa Clara, CA)

scan_protocol: Standard (Affymetrix, Santa Clara, CA)

data_processing: Data generated by MAS5.0 transformation, median center scaled to 1

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: B140P murine leukemia cell line derived from BXH-2 mice

label_protocol: Standard (Affymetrix, Santa Clara, CA)

extract_protocol: RNeasy Midi, (QIAGEN, Valencia, CA), RNase-free DNase I treated

tag: Ara-C sensitive cell line derived from BXH-2 mice, (a C57BL/6J and C3H/HeJ recombinant inbred strain)


title: TSAI_B140P_B1_430A

type: RNA

country: USA


title: TSAI_B140P_A1_430A


title: TSAI_2B117H_430A

source_name: B117P murine leukemia cell line derived from BXH-2 mice


title: TSAI_2B140P_430A


title: B117P_B_430A


title: B140H_A2_430A


title: B117P_A1_430A


title: B117P_A2_430A


title: induction with 0.6 mM Cd(II)

status: Public on Mar 16 2007

city: MOL

first: Natalie

last: Leys

state: Please select one below:

address: 200, boeretang

department: Institute for Environment, Health & Safety

country: Belgium

description: Cupriavidus metallidurans CH34 induction with 0.5mM of Cd(II)

hyb_protocol: Labeled cDNA derived from the different bacterial cultures was resuspended in the Universal Hybridization buffer (Pronto kit, Corning-Promega, USA), mixed and added to the spotted slide for overnight hybridization at 42°C.

scan_protocol: GeneChips were scanned (at 532 and 635 nm) using the Genepix4100A from Axon Instruments.

data_processing: The data were analyzed with S-PLUS software, printTipLoess normalization was applied.

organism: Cupriavidus metallidurans CH34

source_name: Cupriavidus metallidurans CH34 induction 0.6mM of Cd(II)

label_protocol: Ten µg total RNA of high quality was reverse-transcribed by random priming according to the instructions provided with the Pronto kit (Corning-Promega, USA) and labeled by incorporation of Cy3-dCTP or Cy5-dCTP nucleotides (Amersham Bioscience, UK).

growth_protocol: Bacteria culture was grown on minimal medium until OD reached 0.6 at 30°C. Heavy metal was added to the culture and incubated for 30 minutes.

extract_protocol: total RNA extraction performed using the Qiagen RNeasy Midi Kit was performed according to the manufacturer's instructions.  The quality control of total RNA was monitored using the BioAnalyser 2100 (Agilent).

treatment_protocol: 10 ml of bacterial culture was grown on minimal medium until OD reached 0.6. Then, 0.5mM of Cd(II) was added to the culture and incubated for 30 min.

tag: strain

source_name: Cupriavidus metallidurans CH34 uninduced mid-exponential phase culture

treatment_protocol: no treatment


title: B117H_C_430A


title: induction with 0.6 mM Ni(II)

description: Cupriavidus metallidurans CH34 induction with 0.6mM of Ni(II)

source_name: Cupriavidus metallidurans CH34 induction 0.6mM of Ni(II)

treatment_protocol: 10 ml of bacterial culture was grown on minimal medium until OD reached 0.6. Then, 0.6 mM of Ni(II) was added to the culture and incubated for 30 min.

growth_protocol: Bacteria culture was grown on minimal medium until OD reached 0.6 at 30°C.


title: B117H_B_430A


title: induction with 5 uM Hg(II)

description: Cupriavidus metallidurans CH34 induction with 5uM of Hg(II)

source_name: Cupriavidus metallidurans CH34 induction 5uM of Hg(II)

treatment_protocol: 10 ml of bacterial culture was grown on minimal medium until OD reached 0.6. Then, 5µM of Hg(II) was added to the culture and incubated for 30 min.


title: induction with 0.1 mM Cu(II)

description: Cupriavidus metallidurans CH34 induction with 0.1mM of Cu(II)

source_name: Cupriavidus metallidurans CH34 induction 0.1mM of Cu(II)

treatment_protocol: 10 ml of bacterial culture was grown on minimal medium until OD reached 0.6. Then, 0.1 mM of Cu(II) was added to the culture and incubated for 30 min.


title: B140H_B_430A


title: B140H_A1_430A


title: induction with 0.5 mM Co(II)

description: Cupriavidus metallidurans CH34 induction with 0.5mM of Co(II)

source_name: Cupriavidus metallidurans CH34 induction 0.5mM of Co(II)

treatment_protocol: 10 ml of bacterial culture was grown on minimal medium until OD reached 0.6. Then, 0.5mM of Co(II) was added to the culture and incubated for 30 min.


title: induction with 0.8 mM Zn(II)

description: Cupriavidus metallidurans CH34 induction with 0.8mM of Zn(II)

source_name: Cupriavidus metallidurans CH34 induction 0.8mM of Zn(II)

treatment_protocol: 10 ml of bacterial culture was grown on minimal medium until OD reached 0.6. Then, 0.8mM of Zn(II) was added to the culture and incubated for 30 min.


title: induction with 0.4 mM Pb(II)

description: Cupriavidus metallidurans CH34 induction with 0.4mM of Pb(II)

source_name: Cupriavidus metallidurans CH34 induction 0.4mM of Pb(II)

treatment_protocol: 10 ml of bacterial culture was grown on minimal medium until OD reached 0.6. Then, 0.4 mM of Pb(II) was added to the culture and incubated for 30 min.


title: B117H_A_430A

tag: Ara-C sensitive cell line derived from BXH-2 mice


title: vcc1112 rabit exp 16

status: Public on Nov 03 2006

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41442.gif

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 480, 26080; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Nadia,,Dolganov 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 = 41.27; Parameter Scan Time = 10:12:12; Parameter PMT Volts = 540; Parameter Scan Date = 2003-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 152052; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.25; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov 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 = 41.27; Parameter Scan Time = 10:12:12; Parameter PMT Volts = 640; Parameter Scan Date = 2003-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 151081; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.28; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov

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)

organism: Vibrio cholerae

source_name: wt mid log reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: wt mid log reference RNA

source_name: wt RNA (from vibrio in ileal loop fluid) 12h rabbit

tag: experiment


title: vcc1451 rabbit experiment 24

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44705.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1530, 26890; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Nadia,,Dolganov 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 = 43.00; Parameter Scan Time = 13:32:25; Parameter PMT Volts = 500; Parameter Scan Date = 2003-09-05; Parameter Pixel Size = 10; Parameter Laser on time = 163078; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov 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 = 43.00; Parameter Scan Time = 13:32:25; Parameter PMT Volts = 690; Parameter Scan Date = 2003-09-05; Parameter Pixel Size = 10; Parameter Laser on time = 161786; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.30; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov

source_name: wt mid log in LB RNA (2 ug)

value: wt mid log in LB RNA (2 ug)

value: wt RNA (from vibrio in ileal loop fluid) 12h rabbit


title: vcc1135 rabit exp 16

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41443.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 260, 26970; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Nadia,,Dolganov 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 = 40.82; Parameter Scan Time = 11:57:57; Parameter PMT Volts = 510; Parameter Scan Date = 2003-05-26; Parameter Pixel Size = 10; Parameter Laser on time = 152537; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.21; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov 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 = 40.82; Parameter Scan Time = 11:57:57; Parameter PMT Volts = 660; Parameter Scan Date = 2003-05-26; Parameter Pixel Size = 10; Parameter Laser on time = 151502; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.26; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: vcc1136 rabit exp 16

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41447.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 300, 26600; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Nadia,,Dolganov 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 = 41.08; Parameter Scan Time = 12:23:08; Parameter PMT Volts = 490; Parameter Scan Date = 2003-05-26; Parameter Pixel Size = 10; Parameter Laser on time = 152562; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.20; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov 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 = 41.08; Parameter Scan Time = 12:23:08; Parameter PMT Volts = 660; Parameter Scan Date = 2003-05-26; Parameter Pixel Size = 10; Parameter Laser on time = 151527; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.28; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: vcc1452 rabbit experiment 24

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44703.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1520, 27460; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Nadia,,Dolganov 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 = 42.91; Parameter Scan Time = 13:03:50; Parameter PMT Volts = 500; Parameter Scan Date = 2003-09-05; Parameter Pixel Size = 10; Parameter Laser on time = 163048; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.09; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov 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 = 42.91; Parameter Scan Time = 13:03:50; Parameter PMT Volts = 670; Parameter Scan Date = 2003-09-05; Parameter Pixel Size = 10; Parameter Laser on time = 161756; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.29; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: vcc722 rabbit experiment 24

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44704.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1860, 27790; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Nadia,,Dolganov 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 = 42.67; Parameter Scan Time = 12:38:12; Parameter PMT Volts = 500; Parameter Scan Date = 2003-09-05; Parameter Pixel Size = 10; Parameter Laser on time = 163023; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov 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 = 42.67; Parameter Scan Time = 12:38:12; Parameter PMT Volts = 690; Parameter Scan Date = 2003-09-05; Parameter Pixel Size = 10; Parameter Laser on time = 161731; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.29; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: vcc702 rabit exp 16

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41446.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1810, 26920; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Nadia,,Dolganov 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 = 40.99; Parameter Scan Time = 12:11:04; Parameter PMT Volts = 500; Parameter Scan Date = 2003-05-26; Parameter Pixel Size = 10; Parameter Laser on time = 152550; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov 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 = 40.99; Parameter Scan Time = 12:11:04; Parameter PMT Volts = 660; Parameter Scan Date = 2003-05-26; Parameter Pixel Size = 10; Parameter Laser on time = 151514; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.28; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: vcc721 rabbit experiment 24

description:
Simple annotation: Enteric environment, Infection
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/44702.gif

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1810, 26990; Parameter Datafile type = GenePix Results 2; Software: type: feature extraction; Performer: Nadia,,Dolganov 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 = 42.66; Parameter Scan Time = 12:32:16; Parameter PMT Volts = 500; Parameter Scan Date = 2003-09-05; Parameter Pixel Size = 10; Parameter Laser on time = 163017; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov 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 = 42.66; Parameter Scan Time = 12:32:16; Parameter PMT Volts = 660; Parameter Scan Date = 2003-09-05; Parameter Pixel Size = 10; Parameter Laser on time = 161725; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.29; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: amygdala, central nucleus sprague2

status: Public on Jan 27 2004

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description:
amygdala, central nucleus sprague2
whole tissue, pool of 5 animals, 20 weeks old, male
Sprague Dawley amygdala, central nucleus
file:R3KJF02021180

organism: Rattus norvegicus


title: amygdala wistar ky 3946

description:
amygdala wistar ky 3946
whole tissue, individual animal, 10 weeks old, male
Wistar Kyoto amygdala
file:p3942w


title: amygdala, central nucleus sprague1

description:
amygdala, central nucleus sprague1
whole tissue, pool of 5 animals, 20 weeks old, male
Sprague Dawley amygdala, central nucleus
file:R3KJF02021179


title: UB stalk 1

status: Public on Jul 01 2005

city: Berlin

first: Kai

middle: Martin

last: Schmidt-Ott

address: Robert-Roessle-Str. 10

department: Differentiation and Regeneration of Kidney Epithelia

country: Germany

institute: Max-Delbrueck Center for Molecular Medicine

description:
Metanephric mesenchyme and ureteric buds were dissected from E12.5  mice.  At this stage of development, the ureteric buds have already initiated branching morphogenesis producing four or more tips attached to one stalk. To isolate the metanephric mesenchyme, ureteric bud tip and stalk for separate analysis, embryonic kidneys were dissected and treated with DNase (100 U/ml; Boehringer Mannheim) and trypsin (1 mg/ml; Sigma) for 10 min at 37C in L-15 media. The mesenchyme was freed with minutia pins (Fine Scientific) and the tissues were transferred to L-15 with soybean trypsin inhibitor (1 mg/ml). Cross-contamination between ureteric buds and metanephric mesenchymes was ruled out by visual inspection and staining with dolichos bifloris lectin, which selectively stains the ureteric bud at this stage. Ureteric bud tips were dissected from ureteric bud stalks using minutia pins. In all, approximately 1,000 mouse ureteric bud tips, 350 mouse ureteric bud stalks, and 300 mouse mesenchymes were harvested to prepare RNA. Total RNA from ureteric buds and metanephric mesenchymes was extracted using RNeasy mini kit (Qiagen, Valencia, CA) with on-column DNase digestion according to the manufacturer´s instructions. Targets were produced using standard Affymetrix procedures from 1 ug of total RNA.  2 replicates of the target labeling process were analyzed for each sample.
Keywords = Mus musculus, metanephric mesenchyme, ureteric bud tip, ureteric bud stalk, molecular screen for spatially restricted transcripts

source_name: E12.5 ureteric bud stalk


title: metanephric mesenchyme 2

source_name: E12.5 metanephric mesenchyme


title: UB stalk 2


title: metanephric mesenchyme 1


title: UB tip 1

source_name: E12.5 ureteric bud tip


title: amygdala sprague 3950

description:
amygdala sprague 3950
whole tissue, individual animal, 10 weeks old, male
Sprague Dawley amygdala
file:p3724w


title: UB tip 2