title: Aging time course - Day 4 - 3

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69438.gif
Measurement: time(relative) 4 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 18220; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.49; Parameter Scan Time = 11:10:54; Parameter PMT Volts = 620; Parameter Scan Date = 2006-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 134203; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.49; Parameter Scan Time = 11:10:54; Parameter PMT Volts = 570; Parameter Scan Date = 2006-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 133744; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.15; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: Aging time course - Day 13 - 2

status: Public on Jul 29 2008

type: RNA

city: Stanford

first: Stuart

last: Kim

state: CA

department: Department of Developmental Biology

country: USA

institute: Stanford University Medical Center

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69449.gif
Measurement: time(relative) 13 d

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1140, 18650; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang 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 = 38.38; Parameter Scan Time = 11:02:58; Parameter PMT Volts = 590; Parameter Scan Date = 2006-03-29; Parameter Pixel Size = 10; Parameter Laser on time = 134731; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.81; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang 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 = 38.38; Parameter Scan Time = 11:02:58; Parameter PMT Volts = 670; Parameter Scan Date = 2006-03-29; Parameter Pixel Size = 10; Parameter Laser on time = 134272; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.14; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang

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

molecule: total RNA

organism: Caenorhabditis elegans

source_name: N2 ref.

label_protocol: not provided

extract_protocol: not provided

tag: N2 ref.

source_name: Day 13

tag: Day 13


title: hog1Dmsn2/4D vs  msn2/4D +KCl rep2

city: Cambridge

first: Andrew

middle: P

last: Capaldi

state: MA

address: Bauer 307, 7 Divinity Ave

department: MCB

institute: Harvard University

description:
hog1Dmsn2/4D vs  msn2/4D +KCl rep2
251338410837b.gpr

hyb_protocol: Labelled cDNA was hybridized and the arrays washed following the Agilent protocols with 200ng of cDNA in each channel

scan_protocol: Arrays were scanned on an Axon 4000b and the images quantified in Genepix 5

data_processing: Data in table were normalized using the LOWESS like function in Rosetta Resolver.  Genes were included in the table if one channel (Cy3 or Cy5) was 1.5 fold above that of the negative control spots

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: hog1Dmsn2/4D + 0.375M KCl (20min)

label_protocol: polyA RNA was converted into cDNA using reverse transcription with amino allyl UTP in the mix.  The sample was then labelled with Cy5 or Cy3 by incubation with the N-terminal ester of the appropriate dye.

growth_protocol: An overnight culture of cells was used to innoculate a culture to OD 0.05 in YEPD media and then grown to OD =0.58-0.60 (at 30 C shaking at 200 rpm) before harvesting (250ml) by filtration and snap freezing or treatment with stress and then filtration and snap freezing.

extract_protocol: Total RNA was isolated using Hot Phenol/Chloroform followed by NaAC, Isoproponal ppt.  Poly A RNA was then isolated using oligodT cellulose.  See manuscript for further details

treatment_protocol: Cells treated with KCl stress had YEPD at 30 C +KCl (or Glucose) added to the medium to a final concentration of 0.375M (0.75M) for 20min.

tag: strain EY0690 (w303)


title: hog1Dmsn2/4D vs  msn2/4D +KCl rep1

description:
hog1Dmsn2/4D vs  msn2/4D +KCl rep1
251144713624b.gpr


title: hog1Dmsn2/4D vs  msn2/4D +KCl rep3

description:
hog1Dmsn2/4D vs  msn2/4D +KCl rep3
251338410839b.gpr


title: Aging time course - Day 10 - 3

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69446.gif
Measurement: time(relative) 10 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 18160; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.51; Parameter Scan Time = 10:06:49; Parameter PMT Volts = 640; Parameter Scan Date = 2006-03-29; Parameter Pixel Size = 10; Parameter Laser on time = 134675; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.70; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.51; Parameter Scan Time = 10:06:49; Parameter PMT Volts = 630; Parameter Scan Date = 2006-03-29; Parameter Pixel Size = 10; Parameter Laser on time = 134216; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang

source_name: Day 10

tag: Day 10


title: Aging time course - Day 10 - 4

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69447.gif
Measurement: time(relative) 10 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 18240; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.06; Parameter Scan Time = 10:33:21; Parameter PMT Volts = 600; Parameter Scan Date = 2006-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 136058; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.28; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.06; Parameter Scan Time = 10:33:21; Parameter PMT Volts = 560; Parameter Scan Date = 2006-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 135660; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 0.86; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: Aging time course - Day 4 - 2

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69437.gif
Measurement: time(relative) 4 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1280, 18280; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang 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 = 34.88; Parameter Scan Time = 10:16:17; Parameter PMT Volts = 620; Parameter Scan Date = 2006-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 136042; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.78; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang 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 = 34.88; Parameter Scan Time = 10:16:17; Parameter PMT Volts = 550; Parameter Scan Date = 2006-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 135644; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 0.84; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang

source_name: Day 4

tag: Day 4


title: Aging time course - Day 13 - 1

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69448.gif
Measurement: time(relative) 13 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 17930; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang 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 = 38.07; Parameter Scan Time = 10:35:15; Parameter PMT Volts = 630; Parameter Scan Date = 2006-03-29; Parameter Pixel Size = 10; Parameter Laser on time = 134702; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang 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 = 38.07; Parameter Scan Time = 10:35:15; Parameter PMT Volts = 630; Parameter Scan Date = 2006-03-29; Parameter Pixel Size = 10; Parameter Laser on time = 134243; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.13; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: hog1Dmsn2/4D vs  hog1D +KCl rep3

description:
hog1Dmsn2/4D vs  hog1D +KCl rep3
251338410839t.gpr

source_name: hog1D +0.375M KCl (20min)


title: Aging time course - Day 10 - 2

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69445.gif
Measurement: time(relative) 10 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 830, 18200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.31; Parameter Scan Time = 12:09:22; Parameter PMT Volts = 580; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 134268; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.66; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.31; Parameter Scan Time = 12:09:22; Parameter PMT Volts = 660; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 133809; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.16; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: Aging time course - Day 4 - 1

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69436.gif
Measurement: time(relative) 4 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1080, 17920; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.36; Parameter Scan Time = 10:52:08; Parameter PMT Volts = 620; Parameter Scan Date = 2006-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 134185; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.79; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.36; Parameter Scan Time = 10:52:08; Parameter PMT Volts = 590; Parameter Scan Date = 2006-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 133726; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.14; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang

source_name: day 4

tag: day 4


title: hog1Dmsn2/4D vs  hog1D +KCl rep2

description:
hog1Dmsn2/4D vs  hog1D +KCl rep2
251338410837t.gpr


title: Aging time course - Day 7 - 4

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69443.gif
Measurement: time(relative) 7 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 18240; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.44; Parameter Scan Time = 10:47:28; Parameter PMT Volts = 660; Parameter Scan Date = 2006-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 136072; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.54; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.44; Parameter Scan Time = 10:47:28; Parameter PMT Volts = 660; Parameter Scan Date = 2006-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 135675; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 0.89; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang

source_name: Day 7

tag: Day 7


title: 4hr after shift, biological rep4

city: Houston

first: Jung Hyeob

last: Roh

state: TX

address: 6431 Fannin St.

department: Microbiology & Molecular Genetics

institute: The University of Texas

description: Gene expression data from aerobic condition

hyb_protocol: Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix

scan_protocol: Agilent GeneArray scanner under the control of the Affymetrix GCOS

data_processing: .CEL file converted to MAS5 format and analyzed using Affymetrix MAS5 default analysis settings and global scaling as normalization method.

label: biotin

organism: Cereibacter sphaeroides 2.4.1

source_name: R. sphaeroides 2.4.1, 4hr after shift

label_protocol: cDNA synthesized from total RNA was fragmented and labeled using the Enzo BioArray terminal labeling kit

growth_protocol: R. sphaeroides 2.4.1 was grown in 800 ml of medium in 1-liter glass bottles under anaerobic photosynthesis conditions (bubbled with a gas mixture of 95% N2 and 5% CO2). When the optical density at 600 nm (OD600) reached approximately 0.2 to 0.3, the light was turned off and the composition of the gas mixture was abruptly changed for aerobic growth conditions (gas mixture of 30% O2, 69% N2, and 1% CO2). RNA was isolated from a 50-ml aliquot of the culture prior to the shift to aerobic conditions (0 min) and at 15 min, 30 min, 1 h, 2 h, and 4 h after the shift.

extract_protocol: Total RNA was extracted by a modified hot-phenol method described in J. Biol. Chem. 279:9146-9155, 2004

treatment_protocol: Total RNA was extracted directly from the culture.

tag: wild type


title: hog1Dmsn2/4D vs  hog1D +KCl rep1

description:
hog1Dmsn2/4D vs  hog1D +KCl rep1
251144713624t.gpr


title: Aging time course - Day 7 - 3

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69442.gif
Measurement: time(relative) 7 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1050, 18000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.44; Parameter Scan Time = 12:26:33; Parameter PMT Volts = 590; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 134285; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.69; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.44; Parameter Scan Time = 12:26:33; Parameter PMT Volts = 680; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 133826; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.17; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: Aging time course - Day 10 - 1

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69444.gif
Measurement: time(relative) 10 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 18640; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.79; Parameter Scan Time = 10:57:13; Parameter PMT Volts = 650; Parameter Scan Date = 2006-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 136082; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.51; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 35.79; Parameter Scan Time = 10:57:13; Parameter PMT Volts = 670; Parameter Scan Date = 2006-07-21; Parameter Pixel Size = 10; Parameter Laser on time = 135685; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 0.88; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: daf-16; fer-15 (Tedesco #130E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30701.gif
Place of growth: Colorado
Genotype: daf-16; fer-15

scan_protocol: not provided

source_name: N2 mixed stage ref

tag: N2 mixed stage ref


title: daf-16; fer-15 (Tedesco #133E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30702.gif
Place of growth: Colorado
Genotype: daf-16; fer-15


title: Aging time course - Day 13 - 4

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69451.gif
Measurement: time(relative) 13 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 17880; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.52; Parameter Scan Time = 14:39:11; Parameter PMT Volts = 600; Parameter Scan Date = 2006-03-21; Parameter Pixel Size = 10; Parameter Laser on time = 134661; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.68; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.52; Parameter Scan Time = 14:39:11; Parameter PMT Volts = 630; Parameter Scan Date = 2006-03-21; Parameter Pixel Size = 10; Parameter Laser on time = 134202; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.11; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: 2hr after shift, biological rep4

source_name: R. sphaeroides 2.4.1, 2hr after shift


title: Aging time course - Day 13 - 3

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69450.gif
Measurement: time(relative) 13 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 18440; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.58; Parameter Scan Time = 10:08:28; Parameter PMT Volts = 630; Parameter Scan Date = 2006-03-21; Parameter Pixel Size = 10; Parameter Laser on time = 134601; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.68; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.58; Parameter Scan Time = 10:08:28; Parameter PMT Volts = 630; Parameter Scan Date = 2006-03-21; Parameter Pixel Size = 10; Parameter Laser on time = 134142; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.12; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: hog1Dmsn2/4D +KCl rep2

description:
hog1Dmsn2/4D +KCl rep2
251144713626t.gpr

source_name: wt in 0.375M KCl (20min)


title: 1hr after shift, biological rep4

source_name: R. sphaeroides 2.4.1, 1hr after shift


title: msn2/4D +KCl rep3

description:
msn2/4D +KCl rep3
251338410836b.gpr


title: hog1D +KCl rep3

description:
hog1D +KCl rep3
251338410836t.gpr

source_name: hog1D + 0.375M KCl (20min)


title: msn2/4D +KCl rep1

description:
msn2/4D +KCl rep1
251144713625b.gpr


title: 30min after shift, biological rep4

source_name: R. sphaeroides 2.4.1, 30min after shift


title: hog1D +KCl rep2

description:
hog1D +KCl rep2
251144714296b.gpr


title: 15min after shift, biological rep4

source_name: R. sphaeroides 2.4.1, 15min after shift


title: msn2/4D +KCl rep2

description:
msn2/4D +KCl rep2
251144714296t.gpr


title: daf-16; fer-15 (Tedesco #132E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30696.gif
Place of growth: Colorado
Genotype: daf-16; fer-15


title: hog1D +KCl rep1

description:
hog1D +KCl rep1
251144713625t.gpr


title: before shift, biological rep4

source_name: R. sphaeroides 2.4.1, before shift


title: hog1Dmsn2/4D +KCl rep3

description:
hog1Dmsn2/4D +KCl rep3
251144714137t.gpr


title: wt +KCl rep2

description:
wt +KCl rep2
251144713626b.gpr

source_name: wt in YEPD


title: age-1; fer-15 (Tedesco #128E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30704.gif
Place of growth: Colorado
Genotype: age-1; fer-15

source_name: age-1; fer-15

tag: age-1; fer-15


title: age-1; fer-15 (Tedesco #131E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30703.gif
Place of growth: Colorado
Genotype: age-1; fer-15


title: wt +KCl rep3

description:
wt +KCl rep3
251144714138t.gpr


title: wt +KCl rep1

description:
wt +KCl rep1
251144714105b.gpr


title: 2hr after shift, biological rep3


title: hog1Dmsn2/4D +KCl rep1

description:
hog1Dmsn2/4D +KCl rep1
251144713622t.gpr

source_name: hog1Dmsn2/4D + 0.375M KCl (20min)


title: 1hr after shift, biological rep3


title: fer-15 (Tedesco #124E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30699.gif
Place of growth: Colorado
Genotype: fer-15


title: fer-15 (Tedesco #125E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30700.gif
Place of growth: Colorado
Genotype: fer-15


title: fer-15 (Tedesco #134E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30698.gif
Place of growth: Colorado
Genotype: fer-15


title: 4hr after shift, biological rep3

description: Gene expression data from aerobic condition


title: 30min after shift, biological rep3


title: fer-15 (Tedesco #127E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30697.gif
Place of growth: Colorado
Genotype: fer-15


title: 15min after shift, biological rep3


title: daf-16; fer-15 (M) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30514.gif
Place of growth: Stanford
Genotype: daf-16; fer-15


title: daf-16; fer-15 (Tedesco #122E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24249.gif
Place of growth: Colorado
Genotype: daf-16; fer-15

source_name: daf-16; fer-15 day 4 adults (Tedesco #122E)

source_name: N2 mixed stage reference

tag: N2 mixed stage reference


title: CD34+ cell RNA from Primary Myelofibrosis patient number 7 replicate 1 (Jak2 V617F-V617F)

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: raw data requested but not available

hyb_protocol: dual hybridization on glass slide in Agilent hybridzation chamber.

scan_protocol: Agilent Scanner Software Feature extraction from Agilent Plateform Agilent of Gustave Roussy Institute (Villejuif, France)

data_processing: Extraction intensities, Background subtraction, normalization (LOWESS) by software Feature extraction (Agilent)

organism: Homo sapiens

source_name: Reference probe: mixture of all RNAs tested in the experimental map

label_protocol: direct labeling during in vitro transcription

growth_protocol: no culture Day 0

extract_protocol:
total RNA trizol extraction
Quality control on bioanalyser 2100
Mix of all RNAs tested in the experimental map to realized reference probe before amplification and labeling protocol

tag: Reference probe

treatment_protocol: immunomagnetic positive selection of CD34+ cells from peripheral blood of patient number 7 reached of Primary Myelofibrosis (JAK2 V617F-V617F)


title: CD34+ cell RNA from Primary Myelofibrosis patient number 6 replicate 2 (Jak2 v617f-v617f)

description: raw data requested but not available

value: mixture of all RNAs tested in the experimental map

extract_protocol:
total RNA trizol extraction
Quality control on bioanalyser 2100

treatment_protocol: immunomagnetic positive selection of CD34+ cells from peripheral blood of patient number 6 reached of Primary Myelofibrosis (JAK2 V617F-V617F)


title: age-1; fer-15 (A) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30513.gif
Place of growth: Stanford
Genotype: age-1; fer-15


title: CD34+ cell RNA from Primary Myelofibrosis patient number 7 replicate 2 (Jak2 V617F-V617F)

description: raw data requested but not available

treatment_protocol: immunomagnetic positive selection of CD34+ cells


title: 4hr after shift, biological rep2


title: before shift, biological rep3


title: fer-15 (M) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30517.gif
Place of growth: Stanford
Genotype: fer-15


title: fer-15; age-1 (Tedesco #129E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31860.gif
Place of growth: Colorado
Genotype: age-1; fer-15

source_name: fer-15; age-1

tag: fer-15; age-1


title: CD34+ cell RNA from Primary Myelofibrosis patient number 5 (Jak2 WT-V617F)

description: raw data requested but not available

treatment_protocol: immunomagnetic positive selection of CD34+ cells from peripheral blood of patient number 5 reached of Primary Myelofibrosis (JAK2 WT-V617F)


title: fer-15 (A) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30518.gif
Place of growth: Stanford
Genotype: fer-15


title: daf-16; fer-15 (12/01/01) vs. Mixed Stage N2 Ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24337.gif
Place of growth: Stanford
Genotype: daf-16; fer-15

source_name: N2 Mixed Stage Ref

tag: N2 Mixed Stage Ref


title: 1hr after shift, biological rep2


title: 2hr after shift, biological rep2


title: CD34+ cell RNA from Primary Myelofibrosis patient number 6 replicate 1 (Jak2 V617F-V617F)

description: raw data requested but not available


title: daf-16; fer-15 (11/16/01) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24253.gif
Place of growth: Stanford
Genotype: daf-16; fer-15


title: daf-16; fer-15 (10/18/01) vs. Mixed Stage N2 Ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24336.gif
Place of growth: Stanford
Genotype: daf-16; fer-15


title: fer-15 (Tedesco #113E) vs. N2 ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24240.gif
Place of growth: Colorado
Genotype: fer-15

source_name: fer-15 (Tedesco #113E)

tag: fer-15 (Tedesco #113E)


title: CD34+ cell RNA from Primary Myelofibrosis patient number 3 replicate 2 (Jak2 WT-V617F)

description: raw data requested but not available

treatment_protocol: immunomagnetic positive selection of CD34+ cells from peripheral blood of patient number 4 reached of Primary Myelofibrosis (JAK2 WT-V617F)


title: 30min after shift, biological rep2


title: 15min after shift, biological rep2


title: daf-16; fer-15 (Tedesco #121E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24251.gif
Place of growth: Colorado
Genotype: daf-16; fer-15

source_name: daf-16; fer-15 day 4 adults (Tedesco #121E)


title: age-1; fer-15 (M) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30348.gif
Place of growth: Stanford
Genotype: age-1; fer-15

source_name: N2 mixed stage ref


title: CD34+ cell RNA from Primary Myelofibrosis patient number 4 replicate 1 (Jak2 WT-V617F)

description: raw data requested but not available


title: before shift, biological rep2


title: 4hr after shift, biological rep1

source_name: R. sphaeroides 2.4.1, 4hr after shift


title: 2hr after shift, biological rep1

source_name: R. sphaeroides 2.4.1, 2hr after shift


title: CD34+ cell RNA from Primary Myelofibrosis patient number 2 replicate 1 (Jak2 wild type)

description: raw data requested but not available

treatment_protocol: immunomagnetic positive selection of CD34+ cells from peripheral blood of patient number 2 reached of Primary Myelofibrosis (JAK2 WT)


title: age-1; fer-15 (12/01/01) vs. Mixed Stage N2 Ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24338.gif
Place of growth: Stanford
Genotype: age-1; fer-15


title: CD34+ cell RNA from Primary Myelofibrosis patient number 4 replicate 2 (Jak2 WT-V617F)

description: raw data requested but not available


title: CD34+ cell RNA from Primary Myelofibrosis patient number 3 replicate 1 (jak2 WT-V617F)

description: raw data requested but not available

source_name: CD34+ cell RNA from Primary Myelofibrosis patient number 3 replicate 1 (Jak2 WT-V617F)

treatment_protocol: immunomagnetic positive selection of CD34+ cells from peripheral blood of patient number 3 reached of Primary Myelofibrosis (JAK2 WT-V617F)


title: 1hr after shift, biological rep1

source_name: R. sphaeroides 2.4.1, 1hr after shift


title: fer-15 (Tedesco #111E) vs. N2 ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24239.gif
Place of growth: Colorado
Genotype: fer-15

source_name: fer-15 (Tedesco #111E)

tag: fer-15 (Tedesco #111E)


title: CD34+ cell RNA from Primary Myelofibrosis patient number 2 replicate 2 (Jak2 wild type)

description: raw data requested but not available


title: CD34+ cells from Primary Myelofibrosis Patient 1 (Jak2 WT)

description: raw data requested but not available

source_name: CD34+ cell RNA from Primary Myelofibrosis patient number 1 (Jak2 wild type)

treatment_protocol: immunomagnetic positive selection of CD34+ cells from peripheral blood of patient number 1 reached of Primary Myelofibrosis (JAK2 WT)


title: CD34+CD42- sorted cells from Unmobilized normal peripheral blood

description: raw data requested but not available

source_name: pooled RNAs from 42 normal peripheral blood CD34+CD42b- sorted cells

extract_protocol:
total RNA trizol extraction
Quality control on bioanalyser 2100
Mix of RNAs from 42 normal peripheral blood after sorting CD34+CD42b- cells

treatment_protocol: immunomagnetic positive selection of CD34+ cells from normal peripheral blood  (42 healthy donors). CD34+ CD42b- sorting on FACS DIVA (Becton Dickinson) to avoid platelet aggregation at surface of hematopoietic progenitors


title: 30min after shift, biological rep1

source_name: R. sphaeroides 2.4.1, 30min after shift


title: 15min after shift, biological rep1

source_name: R. sphaeroides 2.4.1, 15min after shift


title: fer-15 (11/09/02) vs. N2 ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24238.gif
Place of growth: Stanford
Genotype: fer-15


title: CD34+ cells from Normal Bone Marrows replicate 2

description: raw data requested but not available

source_name: pooled RNAs from 6 normal bone marrow CD34+ cells

extract_protocol:
total RNA trizol extraction
Quality control on bioanalyser 2100
Mix of RNAs from 6 normal bone marrows

treatment_protocol: immunomagnetic positive selection of CD34+ cells from normal bone marrow (6 healthy donors)


title: age-1; fer-15 (Tedesco #120E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24244.gif
Place of growth: Colorado
Genotype: age-1; fer-15

source_name: age-1; fer-15 (Tedesco #120E)

tag: age-1; fer-15 (Tedesco #120E)


title: age-1; fer-15 (Tedesco #114E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24246.gif
Place of growth: Colorado
Genotype: age-1; fer-15

source_name: age-1; fer-15 day 4 adults

tag: age-1; fer-15 day 4 adults

source_name: N2 mixed stage reference


title: age-1; fer-15 (Tedesco #115E) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24248.gif
Place of growth: Colorado
Genotype: age-1; fer-15

source_name: age-1; fer-15 day 4 adults (Tedesco #115E)


title: fer-15 (11/24/01) vs. Mixed Stage N2 Ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24335.gif
Place of growth: Stanford
Genotype: fer-15

source_name: N2 Mixed Stage Ref


title: age-1; fer-15 (10/26/01) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24243.gif
Place of growth: Stanford
Genotype: age-1; fer-15


title: fer-15 (12/03/01) vs. N2 mixed stage ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24242.gif
Place of growth: Stanford
Genotype: fer-15


title: 2h Phagocytosis by RAW Cells Replicate 3

status: Public on Jul 28 2008

city: Montreal

first: Andre

last: Nantel

state: QC

address: 6100 Royalmount

department: Biotechnology Research Institute

country: Canada

institute: National Research Council of Canada

hyb_protocol: The microarray slides were diped sequentially in 0.2% SDS and water and immediately pre-hybridized for 1 hour at 42°C with 5X SSC, 0.1% SDS and 0.1% BSA and subsequently washed twice for 5 min with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer (Roche) with yeast tRNA (Invitrogen) and salmon sperm DNA (Sigma) in a SlideBooster hybridization chamber (Advalytix). The slides were washed twice with SSC-0.1% SDS, once with 1X SSC and once with 0.1X SSC. Slides were dried by centrifugation.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: Co-cultured with RAW264.7

label_protocol: 7.5 to 20 µg of total RNA was reverse transcribed using oligo(dT)20 in the presence of Cy5-dCTP or Cy3-dCTP (Amersham) and Superscript III reverse transcriptase (Invitrogen) . Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 30 min at 37°C. The labeled cDNAs were purified with Illustra Cyscribe GFX purification kit (GE Healthcare).

growth_protocol: Candida cells were grown overnight at 30°C in yeast extract-peptone-dextrose medium (YPD), washed twice in PBS, counted with a hemacymeter and resuspended just before the interaction at 10e8 cells / 30 ml of warm DMEM supplemented with 10% FBS (D-10). The macrophage cell lines were maintained in D-10 medium. For the interaction assays, 150 mm or 60 mm Petri dishes were seeded 24 hours before with 33X10e7/30 ml or 14X10e7/10 ml of macrophage cells respectively and medium was replaced with 30 ml or 10 ml respectively of a Candida suspension to give a final MOI of 1.

extract_protocol: 1 to 4 X 150 mm dishes were harvested by a quick wash in D-PBS, followed by addition of 10 ml/plate (Candida only) or 15 ml/plate (Candida with macrophages) of Trizol reagent. Cells were collected and centrifuged at 12000 X g. Pellets contained intact Candida cells, and the pellet containing Candida with macrophages was washed 2 more times with Trizol to remove contaminating macrophage DNA and RNA. Intact Candida cell pellets were quickly frozen at –80°C. Total RNA was isolated using the hot phenol extraction protocol repeated three times (Kohrer, K., and H. Domdey. 1991. Preparation of high molecular weight RNA. Methods Enzymol 194:398-405). Total RNA was further purified using RNeasy mini kit (Qiagen) according to the manufacturer instructions. RNA quantification was assessed by absorbance reading at 260 nm (Nanodrop) and its quality was assessed using an Agilent 2100 Bioanalyzer (Santa Clara, CA).

treatment_protocol: Co-cultured with RAW264.7

tag: Time

source_name: No macrophage control

treatment_protocol: No macrophage control


title: 2h Phagocytosis by RAW Cells Replicate 4


title: 4h Phagocytosis by RAW Cells Replicate 1


title: before shift, biological rep1

description: Gene expression data from anaerobic photosynthesis condition, i.e. before shift to aerobic condition

source_name: R. sphaeroides 2.4.1, before shift


title: 4h Phagocytosis by RAW Cells Replicate 2


title: 1h Phagocytosis by RAW Cells Replicate 2


title: CD34+ cells from Normal Bone Marrows replicate 3

description: raw data requested but not available

source_name: Reference probe: mixture of all RNAs tested in the experimental map

tag: pooled RNAs from 6 normal bone marrow CD34+ cells


title: 4h Phagocytosis by BMDM Cells Replicate 4

source_name: Co-cultured with BMDM

treatment_protocol: Co-cultured with BMDM


title: 4h Phagocytosis by RAW Cells Replicate 3


title: 4h Phagocytosis by RAW Cells Replicate 4


title: 1h Phagocytosis by RAW Cells Replicate 1


title: 2h Phagocytosis by RAW Cells Replicate 1


title: 4h Phagocytosis by BMDM Cells Replicate 3


title: 1h Phagocytosis by RAW Cells Replicate 3


title: 1h Phagocytosis by RAW Cells Replicate 4


title: 2h Phagocytosis by RAW Cells Replicate 2


title: 4h Phagocytosis by BMDM Cells Replicate 2


title: CD34+ cells from Normal Bone Marrows replicate 1

description: raw data requested but not available


title: fer-15 (Tedesco #112E) vs. N2 ref

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24241.gif
Place of growth: Colorado
Genotype: fer-15

source_name: fer-15 (Tedesco #112E)

tag: fer-15 (Tedesco #112E)

source_name: N2 mixed stage ref


title: 4h Phagocytosis by BMDM Cells Replicate 1


title: 2h Phagocytosis by BMDM Cells Replicate 4


title: 2h Phagocytosis by BMDM Cells Replicate 3


title: 1h Phagocytosis by BMDM Cells Replicate 3


title: 1h Phagocytosis by BMDM Cells Replicate 2


title: 2h Phagocytosis by BMDM Cells Replicate 2


title: 2h Phagocytosis by BMDM Cells Replicate 1


title: 1h Phagocytosis by BMDM Cells Replicate 4


title: 1h Phagocytosis by BMDM Cells Replicate 1


title: MS_HCT116_p53-_48h_50uM_AAI_R3

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: 50% formamide, amersham hyb buffer, 3 nights, 42 degrees

hyb_protocol: Corresponding control and treated samples labelled with different fluorophores were combined in a 50 ul hybridisation mix (19 ul Microarray Hybridisation Solution purchased from GE Healthcare and 50% deionised formamide) and heated at 70°C for 2 min and then at 37°C for 10 min. Sample was pipetted onto a microarray slide and covered with a glass cover slip. A 150ul aliquot of 6 X SSPE was pipetted underneath the slide to prevent dehydration. The hybridisation chamber was sealed and incubated at 42°C for 72 h. Type 7* slides were washed three times in 4 X SSPE, 10 mM EDTA pH 8.0 as above, followed by a 10 s wash in 50% deionised formamide, 6 X SSPE, before a brief rinse in HPLC grade water and drying with nitrogen gas.

scan_protocol: Scanner: Axon4000A. Voltage: 3.58 3.52. Resolution (micrometers): 10.

data_processing: Regions were used for normalizing samples 1-54. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

label_protocol: Total RNA (4 ug) was reversed transcribed into cDNA and fluorescently labelled with Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences, UK) using the Invitrogen Indirect cDNA Labelling Kit protocol (Invitrogen, UK) according to the manufacturer's instructions. After labelling, repetitive sequences within the cDNA samples were blocked with 16 ug Human Cot-1 DNA (Invitrogen, UK) to prevent non-specific sequences binding to the cDNA probes.

extract_protocol: Cell pellets were collected and total RNA extracted using the Qiagen RNeasy Mini Kit protocol (RNeasy Mini Handbook, Qiagen, UK). After addition of lysis buffer (RLT, Qiagen) samples were homogenized using QIAshredders (Qiagen).

tag: tissue type

value: tumor


title: MS_HCT116_p53-_6h_100uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.34 3.69. Resolution (micrometers): 10.


title: MS_HCT116_p53-_6h_100uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage:3.2 2.79 . Resolution (micrometers): 10.


title: MS_HCT116_p53-_24h_50uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage: 3.38 3.43. Resolution (micrometers): 10.


title: MS_HCT116_p53-_6h_100uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.16 2.79 . Resolution (micrometers): 10.


title: MS_HCT116_p53-_6h_50uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage:3.07 3.2 . Resolution (micrometers): 10.


title: MS_HCT116_p53-_24h_50uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.53 3.83. Resolution (micrometers): 10.


title: MS_HCT116_p53-_48h_100uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.67 3.66. Resolution (micrometers): 10.


title: MS_HCT116_p53-_48h_100uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.29 3.62. Resolution (micrometers): 10.


title: MS_HCT116_p53-_6h_50uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage: 3.19 3.65. Resolution (micrometers): ?.


title: MS_HCT116_p53-_48h_50uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage:3.51 3.61 . Resolution (micrometers): ?.


title: MS_HCT116_p53-_24h_50uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.54 3.96. Resolution (micrometers): 10.


title: MS_HCT116_p53-_48h_100uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage:3.68 3.61. Resolution (micrometers): ?.


title: MS_HCT116_p53-_24h_100uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.42 3.02. Resolution (micrometers): 10.


title: MS_HCT116_p53-_6h_50uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage:3.18 3.75 . Resolution (micrometers): 10.


title: MS_HCT116_p53+_6h_50uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage: 3.2 3.47. Resolution (micrometers): 10.


title: MS_HCT116_p53-_24h_100uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage: 3.37 3.02. Resolution (micrometers): 10.


title: MS_HCT116_p53-_24h_100uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.33 3.57. Resolution (micrometers): ?.


title: MS_HCT116_p53+_6h_50uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.22 3.61. Resolution (micrometers): 10.


title: MS_HCT116_p53-_48h_50uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage:3.56 3.52 . Resolution (micrometers): 10.


title: UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP2_array1

type: genomic

city: Chapel Hill

first: Christina

middle: M

last: Whittle

state: NC

address: 406 Fordham Hall, CB#3280

department: Biology

institute: University of North Carolina-Chapel Hill

hyb_protocol: Samples were hybridized by Nimblegen Systems, Inc. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697

scan_protocol: Samples were scanned by Nimblegen Systems, Inc. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697

data_processing: Data was normalized by median centering log2 ratios (IP/input). Log ratios from each experiment were converted to z-scores.

molecule: genomic DNA

source_name: gDNA from HTZ-1 ChIP in N2 embryos, labeled with Cy5.

growth_protocol: Standard C. elegans growth in liquid culture for N2 wildtype.

extract_protocol: Extracts were prepared by resuspending embryo pellets in 1 volume ChIP Buffer (50mM HEPES-KOH pH 7.5, 300mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100, 0.1% sodium deoxycholate, 10% glycerol, protease inhibitors (Calbiochem)), followed by dounce homogenization (50X) and sonication (4X, 1s on, 0.5s off, at 20% amplitude on ice) using a Branson Sonifier. In a volume of 500uL, 2mg extract was used for each ChIP with 5% taken as Input directly into 400uL elution buffer (0.1M NaHCO3, 1% SDS). 2-6ug antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were pulled down with 10uL protein-A or protein G sepharose (Amersham) and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer with 500mM or 1M NaCl, LiCl solution (10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA), and TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were treated with 20ug RNAse for 30 minutes at 37C. IP samples were eluted twice with 200uL elution buffer. 16ul NaCl (200mM final) was added to each sample and crosslinks were reversed by incubation overnight at 65C. DNA was cleaned up using Zymo (Zymo Research) DNA purification columns.

treatment_protocol: Embryos were prepared by bleaching from gravid N2 adults grown in S-basal media liquid culture. Live embryos were cross-linked using 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 15 minutes. Embryos were then washed twice with M9 Buffer and once by ChIP buffer. Pellets were frozen at -80C.

tag: Strain

tag: Stage

value: Mixed Embryos

tag: Fix

value: 2% Formaldehyde, 30 minutes

source_name: Input gDNA from ChIP in N2 embryos, labeled with Cy3

label_protocol: Samples were amplified and labeled using LM-PCR as described in Ercan et al. (2007) Nat Genet. 2007 Mar;39(3):403-8. PMID: 17293863


title: MS_HCT116_p53+_6h_100uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.22 3.42. Resolution (micrometers): 10.


title: UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP4_array1

source_name: gDNA from HTZ-1 ChIP in N2 embryos, labeled with Cy3.

label_protocol: Samples were amplified and labeled using LM-PCR as described in Ercan et al. (2007) Nat Genet. 2007 Mar;39(3):403-8.

source_name: Input gDNA from ChIP in N2 embryos, labeled with Cy5


title: 13130784_sce15cy3_sce14cy5

city: Mississauga

first: James

middle: B

last: Anderson

state: Ontario

address: 3359 Mississauga Road N.

institute: University of Toronto

description:
Isopropanol precipitation
_ Add 1 volume (I added 120 µL) of isopropanol.
_ Precipitate the DNA on at -20C for 30 minutes (or place at –20°C); spin 10 minutes at 4°C. _ Remove isopropanol from pellet; rinse pellet with ice cold 70% ethanol (200ul). Scott rinses twice in 70% EtOH, the second time with EtOH that has been sitting at RT.
_ Pulse centrifuge the samples, and remove all remaining alcohol by pipetting.
_ Do not allow the labeled cDNA to dry completely.
Resuspend the pellet in 5 ul of dH2O (SigmaW4502).
Often, some colour can be observed in the resuspended pellet; however, lack of colour does not necessarily indicate a failed reaction.

hyb_protocol: Hybridization A prehybridization step is not required. Although the best results are generally obtained from using the cDNA immediately after labeling, it can be stored in the dark at –20°C for several days. _ To each 100 µL of DIG Easy Hyb solution (Roche), add 5 µL of yeast tRNA (Invitrogen; 10 mg/ml) and 5 µL of calf thymus DNA (Sigma; 10 mg/ml). (I used ss salmon sperm DNA 10mg/ml). _Incubate the mixture at 65°C for 2 minutes and cool to room temperature. Add 77.5ul of DIG easy Hyb soln to each pooled pair of Cyanine 5 and Cyanine 3-labeled cDNA (about 5 µL). Pipette well to mix. _Incubate at 65°C for 3 minutes, and cool to room temperature. Vortex and quick spin. _prewarm the hyb chamber and container with SDW.37C. _ For the hybridizations involving the use of coverslips, the hyb mixture should be pipetted directly onto the coverslip. Place coverslip onto a reliable surface (the corner of a tip box works well) and add the hyb mixture. Lay the slide “array-side” down on top of the coverslip. Use a 24 x 50 mm coverslip for the yeast arrays. _ Carefully place the slide(s) into hybridization chamber(s). The hybridization chambers that we use are plastic microscope slide boxes containing a small amount of DIG Easy Hyb solution in the bottom (to keep a humid environment). Clean plain microscope slides are placed at every second or third slide position in the slide box to create rails or a platform onto which the hybridization arrays can be placed. Each hybridization chamber can hold two or three hybridization slides (depending on which direction the slides are placed). The lid is carefully placed onto the box and the box is then wrapped with plastic wrap. _ Incubate on a level surface in a 37 °C incubator overnight (about 18 hours). Washing _ Critical that gloves be worn during this procedure _Disassemble the hybridization chamber and remove the coverslip by quickly but gently dipping the array in 1X SSC (let the coverslip slide off gently, let the CV slide off gently). _ When all of the arrays have been removed from the hybridization chambers, wash 3 times for 15 minutes each at 50°C in 50 ml Falcon tubes containing pre-warmed (at 50oC) 1X SSC/0.1% SDS with gentle occasional agitation. I wash 2 slides per falcon tube back to back for all washes except the very last one before scanning. _After the washes are complete, rinse the slides twice in room temperature 1X SSC (plunging 4-6 times) and then in 0.1X SSC. The last wash is the most stringent for the array so do this wash at the last minute before scanning. Shake vigorously in this wash, do not be afraid of washing off the dyes in this step, it is critical for removing background. Also must use fresh 0.1X SSC for each slide. _ I dry the slides from the last wash in the Westwood lab with the pressurized air sprayer. _ Arrays should be stored in the dark. It is recommended that arrays be scanned as soon as possible after they are washed.

scan_protocol: Scanning and data analysis Microarrays were scanned at a 10-µm resolution with a ScanArray 4000 system (GSI Lumonics/Perkin Elmer), using both blue and red lasers. The 16-bit TIFF images were saved and quantified with QuantArray software (v3.0, Perkin Elmer). The adaptive quantification algorithm was used. Further analysis, including data normalization, was performed with GeneTraffic Duo 2.5 (Iobion Informatics LLC, La Jolla, Calif.). The quantification data were exported from QuantArray and uploaded into GeneTraffic analysis software, where Lowess (Locally Weighted Scatter Plot Smoother) normalization was applied on a subgrid basis. Software filters were applied to flag additional spots whose intensities were less than twice the average background, as well as those with absolute fluorescence intensities less than 100.

data_processing:
Normalization
This method normalizes the data to the intensity for each spot and its surrounding area. This method compensates for the effects of dim spots and ensures that normalization is not influenced by the absolute values or the distribution of the bright spots. This method compares the channel 2 intensity /channel 1 intensity normalized (treated/over normalized reference sample) for all non flagged spots in each sub grid (Reference Gene traffic 2.8 Duo Manual Rev. C).
Once the data was normalized the criteria used for filtering the microarray data and selection of significantly unregulated or down regulated genes were for each gene the mean log 2 ratio up 0.67 for all valid spots of that gene. Coefficient of variance for all valid spots of that gene less than 1, Number of valid spots greater at 75% for the gene. The covariance of Variance is the standard deviation expressed as a percentage of the mean. This is a measure of the precision of the outcome over several replications. The higher the precision the lower the covariance so that outliers are not counted in the results as valid data spots.
Usable spot pairs were identified. (Usable spot pairs were defined as having the signal intensities of each channel greater than twice the average background for that channel and having the fluorescence intensity of at least one channel greater than the average intensity of the background.) The quantification data were exported from QuantArray and uploaded into GeneTraffic analysis software, where Lowess normalization was applied on a subgrid basis. Software filters were applied to flag additional spots whose intensities were less than twice the average background, as well as those with absolute fluorescence intensities less than 100. The three hybridizations were treated as replicates, and a distribution of the mean log2-transformed ratios of the Cy5/Cy3 intensities was plotted (Fig. 4, dotted line). For replicate experiments, at least two-thirds of the spots for a 4) had to meet the aforementioned validation criteria for thegiven gene (n ≥ ratio to be included in the distribution. For 95% of the data, the average fold change between the two channels was less than 1.2. Over 99% of the spots exhibited Cy3 and Cy5 signal intensities within ±1.3-fold of each other. The average number of usable spot pairs per slide in these trials was 5542.
Genes were considered in the analysis only if the covariance of the aggregate data from all six arrays was less than 100%.

source_name: Sce15, reference

label_protocol:
Protocols from the UHN Microarray Centre 2003.05.15 ©2003 University Health Network/Ontario Cancer Institute
Direct Labeling Protocol from the University Health Network (UHN) Microarray Centre
RNA Isolation
There are a variety of protocols available that will yield RNA of sufficient quality for microarrays. Many microarray users rely on the Qiagen RNeasy kit for the isolation or cleanup of total RNA. We have not observed any appreciable difference between images derived from the use of total RNA versus mRNA.
Determine the final concentration of purified RNA by measuring A260 and A280. Prepare RNA to a final concentration of at least 1 µg/µL.
I used the hot phenol/chloroform protocol from this website site: http://transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php
Reverse Transcription
For 10-20 µg of Qiagen purified total RNA or 0.1-0.5 µg of mRNA, the RT reaction volume is 40 µl. I aimed for 20ug.
Combine the following on ice:
8.0 µL 5X First Strand reaction buffer (Superscript II, Invitrogen)
1.5 µL AncT mRNA primer (5’-T20VN, 100 pmol/_l)
3.0 µL dNTP (-dCTP) (6.67 mM each of dATP, dGTP, dTTP)
1.0 µL 2 mM dCTP
1.0 µL 1 mM Cyanine 3 or Cyanine 5-dCTP (NEN)
4.0 µL 0.1 M DTT
0.1 – 20 µg RNA (0.1-0.5 µg mRNA or 10-20 µg total RNA)
to 40 µL dH20 (Sigma)
_ Label the two different samples to be analyzed (i.e. control and experimental) on an array with different fluors (i.e. Cyanine 3 or Cyanine 5). It is also suggested that you perform reciprocal labeling (For more information on reciprocal labeling see the microFAQ).
_ Incubate the labeling reaction at 65°C for 5 minutes, then at 42°C for 5 minutes. Ensure that the reactions are kept in the dark as the dyes are light sensitive. If the incubator is not covered use aluminum foil to create a cover preventing light from photo bleaching the fluors.
_ Add 2 µL of reverse transcriptase (Superscript II, Invitrogen). Incubate at 42 °C for 3 hours.
Stop Reaction
_ Briefly centrifuge the reaction and place on ice.
_ Add 5 µL of 50 mM EDTA (pH 8.0), and 4 µL of 5 N NaOH. Mix well by pipetting
_ Incubate at 65°C for 20 minutes to hydrolyse the RNA.
_ Add 4.5 µL of 5 M acetic acid. (A small aliquot of the reaction can be pipetted onto pH paper to ensure the solution is neutralized. Checking the pH is also an optional step that is not necessary for every reaction.)
_ Combine the two reactions that will be hybridized to the same slide (i.e. control and experimental). (I added Cy5 to Cy3).

growth_protocol: Evolved in 0.5x YPD. 57 days of growth, 1 transfer per day, No drug

extract_protocol:
Reference for this protocol: http://transcriptome.ens.fr/sgdb/protocols/preparation_yeast.php
This is a standard Yeast hot acid phenol/chloroform RNA extraction protocol followed by a total RNA clean up using Qiagen RNeasy mini spin columns. The RNA is then quantified by measuring A260 and A280 and then checked by running a DEPC 1% Agarose gel.
RNA extraction:
1. Centrifuge cells at room temperature, wash with sterile water and centrifuge again. Usually, 50ml of culture at OD 0.6-0.8 are enough.
2. If necessary, store cell pellets at -80°C.
3. Resuspend cell pellets in TES buffer (10mM Tris pH 7.5, 10mM EDTA, 0.5%SDS, autoclaved) (1.2ml buffer for 50 OD of cells).
4. Transfer 400ul aliquots of the resuspended cells in three 1.5ml eppendorf tubes.
5. Add 400ul of Phenol:Chloroform 5:1 (from Sigma ref: P-1944).
6. Incubate at 65°C for 20min and vortex 30sec every 5min (be very careful with hot phenol!!).
7. Cool at -80°C for 30min.
8. Centrifuge at room temperature for 15min at 15000rpm.
9. Keep the aqueous phase and add 400ul of Phenol:Chlorofom 5:1.
10. Vortex tubes three times for 30sec then centrifuge.
Repeat steps 8 to 10 one more time.
11. Add 300µl of Chloroform (ready red from Sigma) to the aqueous phase.
12. Vortex tubes three times 20sec.
13. Centrifuge 2' at 15000rpm.
14. Transfer aqueous phase in tubes containing 30µl of 3M Na Ac pH 5.3 (autoclaved).
15. Add 600µl Ethanol absolute.
16. Incubate one hour at -20°C.
17. Centrifuge 15min at 15000rpm at 4°C.
18. Dry pellets and resuspend the three pellets in the same 100µl of bidistilled autoclaved water (Sigma W4502).
19. Carefully quantify RNA and use 100µg for RNA clean up.
RNA clean up:
1. The RNA clean up is an essential step for the quality of the Reverse Transcription. Use a Rneasy minikit (Qiagen, ref : 74106) for RNA clean up. Just follow the recommendations of Qiagen.
2. Elute the column with 50µl of water a first time, then re-elute a second time with the same 50µl.
3. Quantify your purified RNA. You will need 20µg for cDNA synthesis.

tag: Wild-type, ura-, G418, no drug mat a

source_name: Sce14, reference


title: MS_HCT116_p53+_6h_100uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.17 3.47. Resolution (micrometers): 10.


title: 13130785_sce16cy3_sce14cy5

source_name: Sce16, reference

growth_protocol: Evolved in 0.5x YPD. 57 days of exposure to drug in increasing concentrations of Amphotericin B from 0 to 128ug/ml. One transfer per day


title: MS_HCT116_p53+_6h_100uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage: 3.1 2.86. Resolution (micrometers): 10.


title: MS_HCT116_p53+_6h_50uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.22 3.37. Resolution (micrometers): 10.


title: UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP3_array1


title: UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP1_array1

extract_protocol: Extracts were prepared by resuspending embryo pellets in 1 volume ChIP Buffer (50mM HEPES-KOH pH 7.5, 300mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100, 0.1% sodium deoxycholate, 10% glycerol, protease inhibitors (Calbiochem)), followed by dounce homogenization (50X) and sonication (4X, 1s on, 0.5s off, at 20% amplitude on ice) using a Branson Sonifier. In a volume of 500uL, 2mg extract was used for each ChIP with 5% taken as Input directly into 400uL elution buffer (0.1M NaHCO3, 1% SDS). 2-6ug antibody was added to each IP sample and incubated overnight at 4C. Immune complexes were pulled down with 10uL protein-A or protein G sepharose (Amersham) and washed 5 minutes with 1.5mL of each of the following solutions: ChIP Buffer, ChIP Buffer with 500mM or 1M NaCl,  LiCl solution (10mM Tris-HCl pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA), and TE (10mM Tris-HCl pH 8.0, 1mM EDTA). Samples were treated with 20ug RNAse for 30 minutes at 37C. IP samples were eluted twice with 200uL elution buffer. 16ul NaCl (200mM final) was added to each sample and crosslinks were reversed by incubation overnight at 65C. DNA was cleaned up using Zymo (Zymo Research) DNA purification columns.


title: 13133846_sce15cy5_sce2542cy3_Rep2

source_name: Sce2542, treated

tag: Evolved in 0.5x YPD plus Amphotericin B. 57 days of growth, 1 transfer per day, single colony (Wild-type, ura-, G418, mat a)


title: 13133848_sce15cy5_sce2542cy3_Rep4


title: 13133845_sce15cy3_sce2542cy5_Rep1


title: UNC_lieb_cwhittle_N2_embryo_RNAPII_CHIP2_array1

source_name: gDNA from RNA Polymerase II ChIP in N2 embryos, labeled with Cy3


title: 13133843_sce14cy3_sce2539cy5_Rep3

source_name: Sce2539, treated


title: 13133844_sce14cy5_sce2539cy3_Rep4


title: MS_HCT116_p53+_48h_100uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage: 3.45 3.63. Resolution (micrometers): 10.


title: MS_HCT116_p53+_48h_100uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.67 3.57. Resolution (micrometers): 10.


title: 13133842_sce16cy5_sce2470cy3_Rep4

growth_protocol: Evolved in 0.5x YPD. 1100 generations, No drug

source_name: Sce2470, treated

growth_protocol: Evolved in 0.5x YPD. 1100 generations: Amphotercin B increasing concentrations from 0,0.125,0.25,0.5,1.0,0,4.0,8.0,16.0,32.0,64.0 through to 128.0 micrograms per ml

tag: single colony (Wild-type, ura-, G418, mat a) from endpoint of evolution 1100 generations in increasing concentrations of Amphotericin B from 0 to 128ug/ml


title: MS_HCT116_p53+_48h_50uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.1 3.59. Resolution (micrometers): 10.


title: UNC_lieb_cwhittle_N2_embryo_RNAPII_CHIP1_array1

source_name: gDNA from RNA Polymerase II (8WG16) ChIP in N2 embryos, labeled with Cy5.


title: MS_HCT116_p53+_48h_100uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.37 3.81. Resolution (micrometers): 10.


title: 13133839_sce14cy3_sce2539cy5_Rep1

tag: single colony (Wild-type, ura-, G418, mat a) from endpoint of evolution over 57 days of exposure to drug in increasing concentrations of Amphotericin B from 0 to 128ug/ml


title: 13133840_sce14cy5_sce2539cy3_Rep2


title: MS_HCT116_p53+_48h_50uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.46 3.91. Resolution (micrometers): 10.


title: MS_HCT116_p53+_24h_50uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.29 3.63. Resolution (micrometers): 10.


title: 13133841_sce16cy3_sce2470cy5_Rep3


title: 13133836_sce16cy3_sce2470cy5_Rep1


title: MS_HCT116_p53+_24h_50uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.38 3.68. Resolution (micrometers): 10.


title: 13133832_sce15cy3_sce2469cy5_Rep1

source_name: Sce2469, treated

tag: single colony (Wild-type, ura-, G418 mat a) from endpoint of evolution 1100 generations in increasing concentrations of Amphotericin B from 0 to 128ug/ml


title: 13133834_sce15cy3_sce2469cy5_Rep3


title: 13133830_sce14cy3_sce2468cy5_Rep3

tag: Wild-type, ura-, G418, no drug

source_name: Sce2468, treated

tag: single colony (Wild-type, ura-, G418, no drug) from endpoint of evolution 1100 generations in increasing concentrations of Amphotericin B from 0 to 256ug/ml


title: 13133829_sce14cy5_sce2468cy3_Rep2

tag: single colony (Wild-type, ura-, G418, mat a) from endpoint of evolution over 57 days generations in increasing concentrations of Amphotericin B from 0 to 128ug/ml


title: 13133831_sce14cy5_sce2468cy3_Rep4


title: 13133835_sce15cy5_sce2469cy3_Rep4


title: 13133828_sce14cy3_sce2468cy5_Rep1


title: MS_HCT116_p53+_24h_100uM_AAI_R3

scan_protocol: Scanner: Axon4000A. Voltage: 3.41 3.74. Resolution (micrometers): 10.


title: MS_HCT116_p53+_24h_100uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage: 30.37 3.07.Resolution (micrometers): 10.


title: MS_HCT116_p53+_24h_100uM_AAI_R1

scan_protocol: Scanner: Axon4000A. Voltage: 3.29 3.19. Resolution (micrometers): 10.


title: Exp 1 TP3 (12 hr)

city: College Station

first: Gus

middle: John

last: Menger

department: Anatomy and Neurobiology

institute: Texas A&M Health Science Center

description: As per Menger et al. 2007 - Physiological Genomics

hyb_protocol: Fragmented biotinylated cRNA (15 µg) was hybridized on Affymetrix GeneChip mouse U74 version 2 arrays at 45°C and 60 rpm in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 h.

scan_protocol: Following hybridization, arrays were washed and stained using Affymetrix protocols for antibody amplification staining on a GeneChip Fluidics Station 400 in conjunction with Affymetrix Microarray Suite 5.0 software. After a brief wash with a nonstringent buffer, the stained signals on the array were then amplified with a solution containing 3 µg/ml antistreptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA), 1x morpholine ethane sulfonic buffer, 2 mg/ml acetylated BSA, and 0.1 mg/ml normal goat IgG for 10 min followed by a second staining with streptavidin phycoerythrin for 10 min at 25°C. After a final wash with a stringent buffer, the probe array was scanned at the excitation wavelength of 570 nm using an Agilent GeneArray Scanner (Palo Alto, CA). After scanning, each image was first checked for major chip defects or abnormalities during hybridization as a quality control. Arrays were scanned using a global scaling strategy in which the average absolute signal intensity of all arrays was set to an arbitrary target signal intensity of 500 prior to uploading into GeneSpring 7.3 software (Agilent Technologies, Palo Alto, CA).

data_processing: GeneChip signal intensity data from three biological replicates of NIH/3T3 cells were uploaded into GeneSpring 7.2 for additional processing/filtering [Physiol Genomics. 2007 May 11;29(3):280-9]

organism: Mus musculus

source_name: Circadian profiling of NIH fibroblasts - 6hour intervals

label_protocol: Prior to analysis, the quality of all NIH/3T3 RNA samples was assessed by electrophoresis on 1% agarose gels containing 0.1 µg/ml ethidium bromide. Labeled cRNAs were produced from purified RNA collected at each time point and hybridized on mouse U74v2 GeneChips. Experimental procedures including double-stranded cDNA synthesis and biotinylated cRNA preparation were conducted according to recommended protocols described in Affymetrix GeneChip Expression Analysis Technical Manual. To assure the quality of labeling and fragmentation efficiency, unfragmented and fragmented cRNA products were analyzed on an Agilent 2100 bioanalyzer prior to hybridization on arrays.

growth_protocol: For each of three biological replicates, NIH/3T3 cells (passages 4 and 5) were seeded on culture dishes (60 mm; Corning, Corning, NY) and maintained at 37°C and 5% CO2 in Dulbecco's minimum essential medium (DMEM; Invitrogen, Carlsbad, CA) supplemented with 20% fetal bovine serum (FBS; HyClone, Logan, UT), 3,000 µg/ml glucose and 292 µg/ml L-glutamine. At 48-h intervals, the medium was changed and cultures were expanded 1:3 or 1:4. Prior to experimental analysis, cultures were plated in multiple T-75 flasks. At ~24 and 44 h after plating, the culture medium was changed so as to respectively lower the FBS concentration to 10% and then to 5%. To facilitate cell cycle and circadian oscillation synchronization across cultures, cells were subjected to medium replacement and exposed to serum-free medium (DMEM) containing 15 µM forskolin (Calbiochem, La Jolla, CA) for 2 h. Cultures were rinsed and thereafter maintained in serum-free DMEM.

extract_protocol: Immediately after forskolin treatment, cells were harvested from individual flasks (approximate density: 1.3 x 106 cells/cm2) at 6-h intervals for 48 h and total cellular RNA was extracted using RNeasy Midi-Kit protocols (Qiagen, Valencia, CA). RNA extracts from individual samples were treated with on-column DNase-I digestion and concentrated with ethanol precipitations.

tag: Forskolin-pulsed NIH3T3 fibroblasts


title: Exp 3 TP3 (12 hr)

source_name: circadian profiling of NIH3T3 fibroblasts - 6 hour intervals


title: Math2 2

status: Public on Jul 27 2008

city: Tokyo

first: Kou

last: Takahashi

address: 4-1-1 Ogawahigashimachi, Kodaira

country: Japan

institute: NCNP

description: Primary cortical cells were transfected with control or math2 vector

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45ºC on Affymetrix GeneChip Rat Genome 230 2.0 array.

scan_protocol: Gene chips were scanned using Affymetrix High Resolution Genechip scanner 3000

data_processing: Data was processed using Affymetrix Microarray Suite 5.0 software. The trimmed mean signal of all probe sets was adjusted to a user specific target signal value for each array for global scaling.

label: Biotin

organism: Rattus norvegicus

source_name: Rat brain

label_protocol: 50 ng of total RNA was used for cDNA synthesis with a Two-Cycle Target Labeling Kit

growth_protocol: The culture medium used was Eagle MEM  supplemented with 10% fetal calf serum; 5 % glucose ; 2 mM L-glutamine ; and 0.02mg/ml gentamycin .

extract_protocol: After separation of the transfected cultured cortical cells, total RNA was extracted with Isogen reagent .

treatment_protocol: Using TransFectin transfection reagent , we co-transfected cortical cells cultured in a 10-cm dish with 13.3 µg of Math2 expression vector or control vector and 2.7 µg of low-affinity nerve growth factor receptor (LNGFR) expression vector that encoded a cytoplasmically truncated cell surface marker. After incubation for 24 h, the cells were separated with a MACSelect LNGFR Transfected Cell Selection Kit  according to the manufacturer's protocol.

tag: Cerebral cortices from 19-day-old fetal SD rats (E19)


title: MS_HCT116_p53+_24h_50uM_AAI_R2

scan_protocol: Scanner: Axon4000A. Voltage: 3.31 3.68. Resolution (micrometers): 10.


title: Math2 3


title: UNC_lieb_cwhittle_N2_embryo_RNAPII_CHIP2_array2

scan_protocol: Samples were scanned by Nimblegen Systems, Inc. Singh-Gasson S, Green RD, Yue Y, Nelson C, Blattner F, Sussman MR, Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol. 1999 Oct;17(10):974-8. PMID: 10504697

source_name: gDNA from RNA Polymerase II (8WG16) ChIP in N2 embryos, labeled with Cy3


title: UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP4_array2


title: UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP3_array2

source_name: gDNA from HTZ-1 ChIP in N2 embryos, labeled with Cy5.

source_name: Input gDNA from ChIP in N2 embryos, labeled with Cy3


title: UNC_lieb_cwhittle_N2_embryo_RNAPII_CHIP1_array2

source_name: gDNA from RNA Polymerase II ChIP in N2 embryos, labeled with Cy5.


title: Alveolar macrophages, non-smoker 014, B. cepacia BC treatment

status: Public on Jul 26 2008

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HuGeneFL. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneArray 2500.

data_processing: MAS 4

source_name: alveolar macrophages obtained from bronchoalveolar lavage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA for HuGeneFL (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: Age

tag: Sex

value: M

tag: Ethnic group

value: other

tag: Smoking status

value: smoker, 20 pack-years


title: Alveolar macrophages, non-smoker 014, lab strain PAK treatment


title: Alveolar macrophages, non-smoker 014, control


title: Alveolar macrophages, non-smoker 013, early clinical isolate AD2A treatment

value: white


title: Alveolar macrophages, non-smoker 013, control


title: Alveolar macrophages, non-smoker 013, late clinical isolate AD15B treatment


title: Alveolar macrophages, non-smoker 013, B. cepacia BC treatment


title: Alveolar macrophages, non-smoker 013, lab strain PAK treatment


title: control 3

source_name: rat brain


title: Alveolar macrophages, non-smoker 011, control

value: F

value: smoker, 11 pack-years


title: UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP2_array2

tag: Strain


title: Alveolar macrophages, non-smoker 011, lab strain PAK treatment


title: UNC_lieb_cwhittle_N2_embryo_HTZ-1_CHIP1_array2

tag: Stage


title: Alveolar macrophages, non-smoker 011, B. cepacia BC treatment


title: control 2


title: Alveolar macrophages, non-smoker 010, late clinical isolate AD15B treatment

value: smoker, 14 pack-years


title: Math2 1


title: control 1


title: Alveolar macrophages, non-smoker 010, B. cepacia BC treatment


title: Alveolar macrophages, non-smoker 010, early clinical isolate AD2A treatment


title: Alveolar macrophages, non-smoker 007, B. cepacia BC treatment

value: black


title: Alveolar macrophages, non-smoker 010, control


title: Alveolar macrophages, non-smoker 010, lab strain PAK treatment


title: Alveolar macrophages, non-smoker 002, control

value: non-smoker


title: Alveolar macrophages, non-smoker 004, control


title: Alveolar macrophages, non-smoker 007, control


title: Alveolar macrophages, non-smoker 009, lab strain PAK treatment

value: smoker, 30 pack-years


title: Alveolar macrophages, non-smoker 009, control


title: Alveolar macrophages, non-smoker 001, lab strain PAK treatment

tag: Ethnic group:white


title: Alveolar macrophages, non-smoker 001, control


title: Alveolar macrophages, non-smoker 009, B. cepacia BC treatment


title: Alveolar macrophages, non-smoker 004, lab strain PAK treatment


title: Alveolar macrophages, non-smoker 007, lab strain PAK treatment


title: Alveolar macrophages, non-smoker 002, lab strain PAK treatment


title: LEC 8h VEGFC - trial 3

status: Public on Jul 25 2008

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

country: Switzerland

institute: ETH Zurich

hyb_protocol: Hybridization protocol Array hybridization, array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.

scan_protocol: Scan protocol Chemiluminescent Detection Kit (P/N 4339627) and Chemiluminescent Microarray Analyzer User Guide (P/N 4338852B).

data_processing: Data processing The Expression Array System Software suite performs the auto-gridding, feature extraction, fluorescence normalization, and signal data generation. The quantification data contain many distinct measurements for each probe, including the three basic measurements: Signal, S/N, and Flag values. The Signal value is the fully corrected, background subtracted measurement of chemiluminescent signal for gene expression values. The S/N value represents the ratio of signal above noise, or the measurement uncertainty of the probe signal, and can be used as a confidence level for the probe measurement. An S/N of 3 represents approximately a 99.95% confidence that the probe is detected above the background noise. In situations where the probe showed S/N < 1, the signal measurement is replaced with a 1 SDEV upper limit based on its probe signal SDEV.

label: Chemiluminescent Digoxigenin-UTP labeled cRNA

source_name: Human primary dermal microvascular lymphatic endothelial cell (LEC) isolated from neonatal human foreskin

label_protocol: Digoxigenin-UTP labeled cRNA was generated from 0.5 µg of total RNA for each sample using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit (P/N 4363105) according to the manufacturer’s protocol.

growth_protocol: LEC were seeded onto fibronectin-coated culture dishes (10 µg/ml; BD Biosciences, Bedford, MA) and were cultured in endothelial cell basal medium (EBM; Cambrex Bio Science, Walkersville, MD) supplemented with 20% fetal bovine serum (FBS; Invitrogen, Grand Island, NY), 2 mM L glutamine, antibiotic-antimycotic solution, 10 µg/ml hydrocortisone  and N6,2'-O-dibutyryl-adenosine 3',5'-cyclic monophosphate (25 µg/ml; all from Fluka, Buchs, Switzerland) for up to 7 passages.

extract_protocol: Isolate total cellular RNA with 1 ml of the Trizol reagent (Invitrogen) after washing one 80-90 % confluent 10 cm culture dish with PBS. Homogenize the sample using a cell scraper and add 0.2 ml of chloroform in a 1.5 ml tube. Shake the sample vigorously for 15 seconds and allow standing for 5 minutes. Centrifuge the resulting mixture at 12,000 x g for 15 minutes at 4 degree Celsius. Transfer the aqueous phase to a fresh tube and add 0.5 ml of iso-propanol and mix. Allow the sample to stand for 5 minutes at room temperature and centrifuge at 12,000 x g for 10 minutes at 4 degrees Celsius. Remove the supernatant and wash the RNA pellet by adding 1 ml of 75% ethanol. Vortex the sample and then centrifuge at 12,000 x g for 5 minutes at 4 degrees Celsius. Remove the ethanol and briefly dry the RNA pellet for 5 minutes and add 50 micro-liter of RNAase/DNAase free water and mix by repeated pipetting until RNA pellet is fully dissolved.

treatment_protocol: Primary LEC were serum starved overnight in EBM supplemented with 0.2% bovine serum albumin. Cells were treated or not for 1h, 4h, 8h or 24h with recombinant human VEGF-A165 (R&D Systems; 20 ng/ml) or mature human VEGF-C (R&D Systems; 500 ng/ml).

tag: CD45-/CD34-/CD31+ Human Lymphatic Endothelial Cell (LEC)


title: LEC 8h VEGFC - trial 2


title: LEC 24h VEGFC - trial 2


title: LEC 24h VEGFC - trial 1


title: LEC 8h VEGFC - trial 1


title: LEC 4h VEGFC - trial 1


title: LEC 4h VEGFC - trial 2


title: LEC 4h VEGFC - trial 3


title: Mutant strain VC10020 vs. Wild-type N2 (gk488_oligotest)

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

institute: University of British Columbia

scan_protocol: The scanner used was an Axon Scanner (Model # 4000B) . see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: The raw log2 intensity ratio were normalized with the LOESS regression

label_protocol: Cy3 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

extract_protocol: DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using the solid tissue protocol.

tag: mutant strain VC10020 (gk488/mIn1), hermaphrodites, whole animals

source_name: Wild-type N2

label_protocol: Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.

tag: Wild-type N2 strain, hermaphrodites, whole animals


title: Male vs. Female (human_oligotest)

hyb_protocol: ee Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

source_name: Male

tag: Pool of 6 male donors provided by Promega Corporation

source_name: Female

tag: Pool of 6 female donors provided by Promega Corporation


title: LEC 1h VEGFC - trial 3


title: LEC 24h VEGFA - trial 3


title: LEC 24h VEGFA - trial 2


title: LEC 8h VEGFA - trial 3


title: Mutant strain VC10019 vs. Wild-type N2 (gk487_oligotest)

tag: mutant strain VC10019 (gk487/mIn1), hermaphrodites, whole animals


title: LEC 24h VEGFA - trial 1


title: LEC 8h VEGFA - trial 2


title: LEC 1h VEGFC - trial 1


title: LEC 24h VEGFC - trial 3


title: LEC 4h VEGFA - trial 3


title: Rhodopseudomonas palustris cells grown in the presence of pC-HSL #2

city: Seattle

first: Yasuhiro

last: Oda

state: WA

address: Box 357242, 1705 N.E. Pacific Street, HSB K-354

department: Department of Microbiology

institute: University of Washington

description: A high-density oligonucleotide microarray (Affymetrix GeneChip) was custom designed and manufactured by Affymetrix based on the sequences of ORFs and intergenic regions. cDNA synthesis, fragmentation, labeling, hybridization, and processing of custom designed Rhodopseudomonas palustris GeneChips were carried out as recommended by the manufacturer. Experiments were performed in duplicate with independently prepared samples.

hyb_protocol: As recommended by the manufacturer (Affymetrix)

data_processing: The Affymetrix GeneChip Operating Software Version 1.4 was used for initial data acquisition and processing.

label: Biotinylated GeneChip reagent

organism: Rhodopseudomonas palustris CGA009

source_name: Photosynthetic bacterium Rhodopseudomonas palustris

extract_protocol: Rhodopseudomonas palustris cells were disrupted by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.


title: Rhodopseudomonas palustris cells grown in the presence of pC-HSL #1

scan_protocol: As recommended by the manufacturer (Affymetrix)


title: LEC 1h VEGFA - trial 3


title: LEC 4h VEGFA - trial 2


title: LEC 1h VEGFA - trial 1


title: LEC 0h control - trial 1


title: LEC 4h VEGFA - trial 1


title: LEC 0h control - trial 3


title: LEC 1h VEGFA - trial 2


title: Rhodopseudomonas palustris cells grown in the absence of pC-HSL #2

label_protocol: As recommended by the manufacturer (Affymetrix)


title: LEC 0h control - trial 2


title: LEC 8h VEGFA - trial 1


title: E. coli NaCl hyperosmotic treatment (biological replicate 2)

city: Hobart

first: John

middle: Phillip

last: Bowman

state: Tasmania

address: College Road, Sandy Bay

department: School of Agricultural Science

country: Australia

institute: University of Tasmania

description: The sucrose and NaCl hyperosmotic treatment data were compared to the no treatment control data separately.

hyb_protocol: Hybridization of the fragmented, biotinylated cDNA to a chip, washing, and staining of the chip was done on an Affymetrix workstation as described previously (Expression Analysis Technical Manual; Affymetrix, Inc., Santa Clara, Calif.). Detailed method is equivalent to that described by Soupene and colleagues: http://nature.berkeley.edu/%7eopaliy/papers/MG1655/MAprotocol.pdf

scan_protocol: Scanning of the chip were done on an Affymetrix workstation as described previously (Expression Analysis Technical Manual; Affymetrix, Inc., Santa Clara, Calif.).

data_processing: Background correction, normalization and calculation of the expression measures were performed using RMA procedure with the WebArray platform (http://bioinformatics.skcc.org/webarray/). Subsequently the program EDGE (http://www.biostat.washington.edu/software/jstorey/edge/) was used to estimate the conditional false discovery rate (FDR), the expected proportion of false positives conditioned on having k 'significant' findings.

organism: Escherichia coli

source_name: E. coli Frag1, NaCl hyperosmotic treatment (biological replicate 2)

label_protocol: Gene expression was assessed on Affymetrix E. coli Genome GeneChip arrays (Affymetrix, Inc., Santa Clara, Calif.). Briefly, total RNA was prepared from E. coli cells by phenol-chloroform extraction, and ~10 µg of total RNA was used to synthesize cDNA. After purification with a Qiagen cDNA purification kit (Qiagen, Inc.), the cDNA was fragmented with DNase I. The fragmented cDNA was end biotinylated by terminal transferase with biotinylated ddATP.

growth_protocol: Grown in Davis's Mineral Salts medium (Gibco BRL Life Technologies Inc.) with 0.1% D-glucose at 25 C (100 r.p.m. shaking) until an OD (550 nm) of 0.6.

extract_protocol: RNA was obtained using the RNAeasy MIDI RNA extraction kit (Qiagen) using lysis buffer containing 0.1% beta-mercaptoethanol. RNA was extracted from lysates and purified according to the manufacturer’s standard protocol and subsequently stored at -80°C. RNA quality was assessed with electrophoresis using a RNA bioanalyser 2100 and Lab RNAChip (Agilent Technologies) before progression to microarray hybridization.

treatment_protocol: Cell suspension was ammended with 1.37 M NaCl to obtain an osmotic pressure of 2.7 Os kg-1 for 10 minutes. The biomass was centrifuged at 4000 rpm and the pellet treated with RNAProtect (Qiagen) following the manufacturer's protocol.

tag: E. coli, strain Frag1


title: Rhodopseudomonas palustris cells grown in the absence of pC-HSL #1


title: E. coli sucrose hyperosmotic treatment (biological replicate 2)

source_name: E. coli Frag1, sucrose hyperosmotic treatment (biological replicate 2)

treatment_protocol: Cell suspension was ammended with 1.25 M sucrose to an osmotic pressure of 2.7 Os kg-1 for 10 minutes. The biomass was centrifuged at 4000 rpm and the pellet treated with RNAProtect (Qiagen) following the manufacturer's protocol.


title: E. coli control, biological replicate 1

source_name: E. coli Frag1 (control sample 1)

treatment_protocol: No treatment (control sample).


title: D20_B9

city: Piscataway

first: Minjie

last: Luo

state: NJ

address: 675 Hoes Lane

institute: University of Medicine and Dentistry of New Jersey

description:
D20_B9ag_R600G500_50320.gpr
Single sperm from donor#D20

hyb_protocol: Hybridization was done with 1x hybridization solution (5x Denhart's solution, 0.5% SDS, 5x SSC, 20 µL of ssDNA/1000 microarray spots) in a Hybridization Chamber (Corning) at 56°C for 2.5-4 h. After hybridization, the slide was washed at 56°C with 1x SSC and 0.1% SDS for 10 min, twice with 0.5x SSC for 30 sec, and twice with 0.2x SSC for 30 sec.

scan_protocol: Microarrays were scanned with GenePix 4000B (Axon Instruments)

data_processing: The resulting images were analyzed with either the GenePix Pro (Axon Instruments) or ImaGene (BioDiscovery) software.

source_name: Semen donor #D20

label_protocol: Probes were labeled in 25 µL of labeling solution containing  Sequenase buffer), 0.5 units/µL Sequenase (Amersham Pharmacia Biosciences), Cy3-ddATP and Cy5-ddGTP (PE Biosystems) for AG probes, and Cy3-ddUTP and Cy5-ddCTP for CT probes (750 nM each). The reaction was incubated at 70°C for 10 min. The slide was washed under conditions as described above.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The procedures for multiplex amplification and genotype determination are illustrated in Figure 1. First, multiplex PCR (Fig. 1A) was performed in 30 µL of PCR mix containing 1x PCR buffer (50 mM KCl, 100 mM Tris-HCl at pH 8.3, 1.5 mM MgCl2, and 100 µg/mL gelatin), four dNTPs (200 µM each; Invitrogen), primers (20 nM each) for all SNPs in the multiplex group, 6 units of HotStar Taq DNA polymerase (QIAGEN), and 5 ng of DNA or single sperm. The samples were first heated to 94°C for 15 min to activate the Taq DNA polymerase followed by 40 PCR cycles. Each PCR cycle consisted of 40 sec at 94°C for denaturation and 2 min at 55°C followed by 5 min of ramping from 55°C to 70°C for annealing and extension. A final extension step was carried out at 72°C for 3 min at the end of the 40-th cycle. PCR amplifications were performed with thermal cyclers capable of ramping as slow as 0.01°C/sec. ssDNA was generated in both directions by using the same conditions for multiplex PCR except: (1) 1-2 µL of product from the multiplex PCR was used as templates, (2) only one primer for each SNP; and (3) 45 PCR cycles.

tag: Single sperm prepared by flow cytometry


title: D20_B7

description:
D20_B7ag_R600G500_50320.gpr
Single sperm from donor#D20


title: D20_B11

description:
D20_B11ag_R650G550_50320.gpr
Single sperm from donor#D20


title: E. coli NaCl hyperosmotic treatment (biological replicate 1)

source_name: E. coli Frag1, hyperosmotic NaCl treatment (biological replicate 1)


title: D20_B2

description:
D20_B2_R620G520_50313.gpr
Single sperm from donor#D20


title: D20_A7

description:
D20_A7_R610G510_50313.gpr
Single sperm from donor#D20


title: D20_B10

description:
D20_B10ag_R650G550_50320.gpr
Single sperm from donor#D20


title: D20_B8

description:
D20_B8ag_R600G500_50320.gpr
Single sperm from donor#D20