title: MOCK RIP N.2A

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74172.gif
Antibody used in RIP: no

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 4600; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 25.44; Parameter Scan Time = 10:31:39; Parameter PMT Volts = 360; Parameter Scan Date = 2007-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 24840; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.03; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 25.44; Parameter Scan Time = 10:31:39; Parameter PMT Volts = 380; Parameter Scan Date = 2007-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 24839; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

data_processing:
Arrays were normalized computationally by the Stanford Microarray Database (SMD). The data were filtered for signal over background of greater than 1.5 in the channel measuring aaRNA from extract, and only features that met these criteria in > 50% of the arrays were included for further analysis. Log2 median ratios were retrieved and exported into Microsoft Excel.To identify transcripts that were specifically enriched by association with PUM1, we performed two class Significance Analysis of Microarrays (SAM) on median centered arrays.
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)


title: PUM2 RIP N.4A

status: Public on Sep 08 2008

type: RNA

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2008-03/78967.gif
Antibody used in IP: yes

hyb_protocol: Cy3- and Cy5-labeled aaRNA probes were mixed and applied to arrays in hybridization solution (3x SSC, 20 ug poly(A) RNA [Invitrogen], 20 ug yeast tRNA [Invitrogen], 20 ug Human Cot-1 DNA [Invitrogen], 20 mM HEPES [pH 7.0] and 0.3% SDS) for 18 h at 65°C. The arrays were then washed sequentially in 400 ml of 2x SSC with 0.1% SDS, 1x SSC, and 0.2x SSC. The first wash was performed for 5 min at 65°C, the subsequent washes were performed for 5 min at RT. The arrays were dried by centrifugation and immediately scanned.

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). FeatureExtraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 920, 4800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 23.81; Parameter Scan Time = 10:31:46; Parameter PMT Volts = 380; Parameter Scan Date = 2008-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 33107; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 23.81; Parameter Scan Time = 10:31:46; Parameter PMT Volts = 400; Parameter Scan Date = 2008-03-07; Parameter Pixel Size = 10; Parameter Laser on time = 33106; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.39; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

data_processing: The data were filtered for signal over background of greater than 1.5 in the channel measuring aaRNA from extract, and only features that met these criteria in > 50% of the arrays were included for further analysis. Log2 median ratios were retrieved and exported into Microsoft Excel. To identify transcripts that were specifically enriched by association with PUM2, we performed two class Significance Analysis of Microarrays (SAM) on median centered arrays. VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Homo sapiens

source_name: aaRNA from extract

label_protocol: Poly-adenylated RNAs were amplified in the presence of aminoallyl-UTP with Amino Allyl MessageAmp II aRNA kit (Ambion). For this purpose, 500 ng total RNA from extracts and half (50-100 ng) of the immunopurified RNAs were used for amplification. 8 ug of the amplified RNAs (aaRNA) were fluorescently labeled with NHS-monoester Cy3 and Cy5 dyes (GE HealthSciences), except for mock RNA samples, where an aaRNA amount proportional to the yield obtained from corresponding PUM affinity isolates was used.

extract_protocol: Total RNA was isolated from cell extracts and immunopurified samples with the mirVanaTM PARISTM kit (Ambion). RNA was quantified with a NanoDrop device (Witeg AG).

tag: aaRNA from extract

source_name: aaRNA from PUM2 RIP

tag: aaRNA from PUM2 RIP


title: MOCK RIP N.3B

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76041.gif
Antibody used in RIP: no

hyb_protocol: Cy3- and Cy5-labeled aaRNA probes were mixed and applied to arrays in hybridization solution (3x SSC, 20 ug poly(A) RNA [Invitrogen], 20 ug yeast tRNA [Invitrogen], 20 ug Human Cot-1 DNA [Invitrogen], 20 mM HEPES [pH 7.0] and 0.3% SDS) for 18 h at 65 degree C. The arrays were then washed sequentially in 400 ml of 2x SSC with 0.1% SDS, 1x SSC, and 0.2x SSC. The first wash was performed for 5 min at 65 degree C, the subsequent washes were performed for 5 min at RT. The arrays were dried by centrifugation and immediately scanned.

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 25.25; Parameter Scan Time = 10:31:21; Parameter PMT Volts = 380; Parameter Scan Date = 2007-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 26633; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.92; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 25.25; Parameter Scan Time = 10:31:21; Parameter PMT Volts = 380; Parameter Scan Date = 2007-07-20; Parameter Pixel Size = 10; Parameter Laser on time = 26632; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

source_name: aaRNA from MOCK RIP

tag: aaRNA from MOCK RIP


title: Colon_NonTreated_rep1

city: Amsterdam

first: Antonie

last: Zwiers

address: Van der Boechorststraat 7

department: MCBI

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Biological replicate 1 of 4 Non-treated

hyb_protocol: Hybridization protocol available via www.vumc.nl/microarrays. Also described in Bergman et al, Cancer Res 2005; 65: (20). October 15, 2005

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner (Agilent Technologies). Spots were quantified by Imagene 5.5.4 software (Biodiscovery Ltd, Marina del Rey, CA, USA), using the default settings.

data_processing: The BioConductor package Limma (Smyth and Speed 2003) version 2.6.0 was used to perform data processing. Background correction according to 'Edwards' was applied with an offset of 30. Intensity-dependent normalization using local estimation (‘Loess’) was performed separately on each sector of the array. In addition, ‘scale’ (or ‘quantile’) normalization was applied, which makes the data more comparable across different arrays. Spots were included in the analysis when in at least 80% of the microarrays a reliable data point was obtained for that element (defined by a minimal signal intensity > 50 for both Cy3 and Cy5). Data are expressed as normalized log2 ratios of fluorescence intensities of the experimental over the reference sample. The use of a common reference sample allows comparison of the relative expression levels across all samples. Therefore, the expression levels were median centered, i.e. each spotted element was expressed relative to the median expression level of that element across all samples. Genes represented more than once on the microarrays were averaged from sequences with the same Unigene cluster ID.

organism: Mus musculus

source_name: Colon Non-treated

label_protocol: RNA labeling protocol available via www.vumc.nl/microarrays. Also described in Bergman et al, Cancer Res 2005; 65: (20). October 15, 2005

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: Strain

value: SJL/J

tag: Gender

value: male

tag: Age

value: 6 weeks

tag: Tissue

value: Colon

source_name: Common reference pool from pooled colon derived total RNA of treated and non-treated mice

value: pooled colon


title: PUM1 RIP N.2A

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74170.gif
Antibody used in RIP: yes

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1040, 4320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 25.13; Parameter Scan Time = 10:12:18; Parameter PMT Volts = 370; Parameter Scan Date = 2007-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 24821; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.03; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 25.13; Parameter Scan Time = 10:12:18; Parameter PMT Volts = 370; Parameter Scan Date = 2007-05-04; Parameter Pixel Size = 10; Parameter Laser on time = 24820; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

source_name: aaRNA from PUM1 RIP

tag: aaRNA from PUM1 RIP


title: PUM1 RIP N.1B

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74298.gif
Antibody used in RIP: yes

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 24.75; Parameter Scan Time = 12:24:51; Parameter PMT Volts = 380; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 25321; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.91; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 24.75; Parameter Scan Time = 12:24:51; Parameter PMT Volts = 370; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 25321; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: UF436_Xylem-Rep1

status: Public on Sep 06 2008

city: Gainesville

first: Matias

last: Kirst

state: FL

country: USA

institute: University of Florida

hyb_protocol: 1.5ug labeled ds-cDNA was denatured at 95░C for 5min and hybridized to custom in situ synthesized oligonucleotide microarrays (produced by NimbleGen, Madison, WI) at 42░C overnight (16-20h).  Hybridization and wash buffers are described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf)

scan_protocol: As described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf).

data_processing: Raw intensity data was background corrected (Irizarry et al. 2003, Exploration, normalization, and summaries of high density oligonucleotide array probe level data.  Biostatistics 4: 249-264) and normalized using the Quantile normalization method (Bolstad et al. 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193).

organism: Populus trichocarpa x Populus deltoides

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, secondary xylem tissue

label_protocol: RNA extracted from each progeny was converted to double-stranded (ds-) cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturerÆs protocol, except that synthesis of first and second strands were extended to 16h. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37░C.

growth_protocol: A pseudo-backcross population (Family 52-124) derived from the cross of a female P. trichocarpa X P. deltoides hybrid (genotype æ52-225Æ) and a male P. deltoides (genotype æD124Æ) was obtained from the Department of Forestry at the University of Minnesota-Duluth as hardwood cuttings. After rooting, bud break and shoot elongation, fresh softwood terminal cuttings were harvested and placed in rooting media pellets (Jiffy Forestry Products, Lorain, OH) for two weeks. Rooted cuttings were planted in two gallon pots and grown for six weeks in ebb-and-flow benches in a greenhouse under long day conditions (16h light:8hr dark) and standard nutrient regime (HockingÆs Modified Complete Fertilizer, Cooke et al. 2003, Plant Cell and Environment 26: 757-770) supplemented with 25mM nitrogen (NH4NO3). Plants were distributed in the greenhouse in a partially balanced incomplete block design with three biological replications per genotype.

extract_protocol: At harvest, the main plant organs (stems, roots, leaves and sylleptic branches) were collected separately. Stems were further dissected into secondary xylem tissue and phloem/bark/immature xylem. Leaf, secondary xylem, and root tissue from two biological replicates of each genotype were selected for gene expression analysis. All tissue was flash-frozen in liquid nitrogen immediately after harvest and stored at -80░ Celsius (C) prior to lyophilization and subsequent RNA isolation.  RNA was isolated by a standard protocol described previously (Chang S, J. Puryear, J. Cairney 1993, A simple and efficent method for isolating RNA from pine trees. Plant Mol Biol Rep 11: 113-116).

tag: 25mM supplemental N, long day conditions


title: UF435_Xylem-Rep1


title: UF452_Xylem-Rep1


title: PUM1 RIP N.2B

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74299.gif
Antibody used in RIP: yes

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 4760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 24.94; Parameter Scan Time = 12:42:37; Parameter PMT Volts = 380; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 25339; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.91; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 24.94; Parameter Scan Time = 12:42:37; Parameter PMT Volts = 370; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 25338; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.53; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: UF453_Xylem-Rep1


title: MOCK RIP N.1A

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73933.gif
Antibody used in RIP: no

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 24.19; Parameter Scan Time = 11:05:21; Parameter PMT Volts = 360; Parameter Scan Date = 2007-04-26; Parameter Pixel Size = 10; Parameter Laser on time = 24717; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.00; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 24.19; Parameter Scan Time = 11:05:21; Parameter PMT Volts = 380; Parameter Scan Date = 2007-04-26; Parameter Pixel Size = 10; Parameter Laser on time = 24717; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: UF441_Xylem-Rep1


title: UF437_Xylem-Rep1


title: UF409_Xylem-Rep1


title: MOCK RIP N.3A

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76038.gif
Antibody used in RIP: no

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 25.81; Parameter Scan Time = 11:51:10; Parameter PMT Volts = 360; Parameter Scan Date = 2007-07-18; Parameter Pixel Size = 10; Parameter Laser on time = 26526; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.93; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 25.81; Parameter Scan Time = 11:51:10; Parameter PMT Volts = 380; Parameter Scan Date = 2007-07-18; Parameter Pixel Size = 10; Parameter Laser on time = 26526; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.51; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: UF372_Xylem-Rep1


title: UF457_Xylem-Rep1


title: UF402_Xylem-Rep1


title: UF406_Xylem-Rep1


title: UF456_Xylem-Rep1


title: UF381_Xylem-Rep1


title: UF352_Xylem-Rep1


title: UF392_Xylem-Rep1


title: UF326_Xylem-Rep1


title: UF36_Xylem-Rep1


title: MOCK RIP N.1B

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74301.gif
Antibody used in RIP: no

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 24.63; Parameter Scan Time = 10:12:22; Parameter PMT Volts = 370; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 25271; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.88; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 24.63; Parameter Scan Time = 10:12:22; Parameter PMT Volts = 350; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 25271; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: UF325_Xylem-Rep1


title: UF320_Xylem-Rep1


title: UF309_Xylem-Rep1


title: UF300_Xylem-Rep1


title: UF290_Xylem-Rep1


title: UF299_Xylem-Rep1


title: UF337_Xylem-Rep1


title: PUM1 RIP N.3A

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/76037.gif
Antibody used in RIP: yes

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 5240; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 26.06; Parameter Scan Time = 12:13:50; Parameter PMT Volts = 340; Parameter Scan Date = 2007-07-18; Parameter Pixel Size = 10; Parameter Laser on time = 26551; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.94; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 26.06; Parameter Scan Time = 12:13:50; Parameter PMT Volts = 400; Parameter Scan Date = 2007-07-18; Parameter Pixel Size = 10; Parameter Laser on time = 26551; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

tag: aaRNA fromPUM1 RIP


title: UF237_Xylem-Rep1


title: UF254_Xylem-Rep1


title: UF246_Xylem-Rep1


title: UF247_Xylem-Rep1


title: UF270_Xylem-Rep1


title: UF285_Xylem-Rep1


title: UF266_Xylem-Rep1


title: UF241_Xylem-Rep1


title: UF272_Xylem-Rep1


title: UF284_Xylem-Rep1


title: UF269_Xylem-Rep1


title: Wild-type cell biological rep2

city: Boston

first: Miriam

middle: E

last: Bucheli

state: MA

address: 240 Longwood Ave.,

department: BCMP

institute: Harvard Medical School

hyb_protocol: GeneChip® Hybridization, Wash and Stain Kit (Affymetrix, HMS Biopolymers Facility)

scan_protocol: The GeneChip® Scanner 3000 7G controlled by GeneChip® Operating Software (Affymetrix, HMS Biopolymers Facility)

data_processing: The data were analyzed using Tiling Analysis Software (TAS) from Affymetrix. We used quantile normalization and scaled to a target intensity of 100. For analysis of individual chips, we used a bandwidth of 50 bp and 1-sided upper p-value. For comparisons of strains to wild-type, which compared 2 mutant replicates to the 2 wild-type replicates, we used a bandwidth of 100 bp and a 2-sided p-value.

label: biotin

organism: Saccharomyces cerevisiae

source_name: Strain: NPL3

label_protocol: Sense RNA was synthesized using whole transcript sense target labeling assay (Affymetrix, HMS Biopolymers Facility)

growth_protocol: Strains were grown at 30°C.

extract_protocol: RNA extracted with hot phenol extraction as described in Kim M, et al. (2006) Mol Cell 24: 723-734.

treatment_protocol: Strains npl3-120, npl3-S411A and rna15-2 containining point mutations  have been described before (Bucheli ME, Buratowski S (2005) Embo J 24: 2150-2160, Lund MK, et al (2008) MCB, Amrani N et al (1997) MCB 17: 3694-701.


title: Wild-type cell biological rep1


title: rna15-2 cell biological rep2

source_name: Strain: rna15-2


title: npl3-s411a cell biological rep1

source_name: Strain: npl3-S411A


title: UF32_Xylem-Rep1


title: rna15-2 cell biological rep1


title: npl3-120 cell biological rep2

source_name: Strain: npl3-120


title: MOCK RIP N.2B

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2007-05/74297.gif
Antibody used in RIP: no

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1160, 5120; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 24.63; Parameter Scan Time = 10:39:42; Parameter PMT Volts = 370; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 25299; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 2.90; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 24.63; Parameter Scan Time = 10:39:42; Parameter PMT Volts = 350; Parameter Scan Date = 2007-05-16; Parameter Pixel Size = 10; Parameter Laser on time = 25298; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.54; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano


title: SD1522_PMT_AcH3_B

type: genomic

city: Muenster

first: Carsten

last: Müller-Tidow

address: Domagkstrasse 3

country: Germany

institute: University Hopital Muenster

hyb_protocol: Hoemme C et al., Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip. Blood. 2008 Mar 1;111(5):2887-95.

molecule: genomic DNA

source_name: U937-empty vector cells (PMT), ChIP DNA

tag: U937 PMT cells, ChIP DNA

source_name: U937-empty vector cells (PMT), input DNA

tag: U937 PMT cells, input DNA


title: npl3-120 cell biological rep1


title: SD1521_PML_AcH3_B

scan_protocol: Hoemme C et al., Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip. Blood. 2008 Mar 1;111(5):2887-95.


title: SD1524_Pr9_AcH3_B

data_processing: Hoemme C et al., Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip. Blood. 2008 Mar 1;111(5):2887-95.

source_name: U937-PML-RAR{alpha} cells (Pr9), ChIP DNA

tag: U937 Pr9 cells, ChIP DNA

source_name: U937-PML-RAR{alpha} cells (Pr9), input DNA

tag: U937 Pr9 cells, input DNA


title: SD1587_PMT_diLys4_B

label_protocol: Hoemme C et al., Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip. Blood. 2008 Mar 1;111(5):2887-95.


title: npl3-s411a cell biological rep2


title: UF240_Xylem-Rep1


title: UF229_Xylem-Rep1


title: UF223_Xylem-Rep1


title: UF214_Xylem-Rep1


title: UF209_Xylem-Rep1


title: UF201_Xylem-Rep1


title: UF401_Xylem-Rep1


title: SD1437_Pr9_AcH3_B

extract_protocol: Hoemme C et al., Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip. Blood. 2008 Mar 1;111(5):2887-95.


title: PUM1 RIP N.1A

description:
Simple annotation: RNA coimmunoprecipitation, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2007-04/73932.gif
Antibody used in RIP: yes

scan_protocol: Scanned with an AxonScanner 4200A (Molecular Devices). Data were collected using GENEPIX 5.1 (Molecular Devices). Feature; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1440, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alessia,,Galgano 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 = 23.56; Parameter Scan Time = 10:37:48; Parameter PMT Volts = 380; Parameter Scan Date = 2007-04-26; Parameter Pixel Size = 10; Parameter Laser on time = 24689; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.02; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano 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 = 23.56; Parameter Scan Time = 10:37:48; Parameter PMT Volts = 380; Parameter Scan Date = 2007-04-26; Parameter Pixel Size = 10; Parameter Laser on time = 24689; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Laser Power = 3.52; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alessia,,Galgano

data_processing:
Arrays were normalized computationally by the Stanford Microarray Database (SMD). The data were filtered for signal over background of greater than 1.5 in the channel measuring aaRNA from extract, and only features that met these criteria in > 50% of the arrays were included for further analysis. Log2 median ratios were retrieved and exported into Microsoft Excel.To identify transcripts that were specifically enriched by association with PUM1, we performed two class Significance Analysis of Microarrays (SAM) on median centered arrays.
VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm


title: 5651_B_Pr9_AcH3


title: 5649_B_Pr9_AcH3


title: SD1435_Pr9_diLys4_B


title: 5535_Pr9_diLys4_B


title: UF35_Xylem-Rep1


title: UF909_Xylem-Rep1


title: UF936_Xylem-Rep1


title: 5510_Pr9_dL9_B


title: UF881_Xylem-Rep1


title: UF861_Xylem-Rep1


title: 5533_PMT_diLys4_B


title: UF911_Xylem-Rep1


title: UF925_Xylem-Rep1


title: UF883_Xylem-Rep1


title: UF844_Xylem-Rep1


title: UF419_Xylem-Rep1


title: UF850_Xylem-Rep1


title: 5507_Pr9_PML_B


title: UF805_Xylem-Rep1


title: 5505_Pr9_triLys4_B


title: 5506_Pr9_triLys9_B


title: UF852_Xylem-Rep1


title: 5508_Pr9_AcH3_B


title: UF66_Xylem-Rep1


title: 5430_B_Pr9_PML


title: UF907_Xylem-Rep1


title: UF293_Xylem-Rep1


title: UF280_Xylem-Rep1


title: UF407_Xylem-Rep1


title: UF546_Xylem-Rep1


title: 5428_B_Pr9_PML


title: UF539_Xylem-Rep1


title: 5427_B_PMT_AcH3


title: UF477_Xylem-Rep1


title: UF40_Xylem-Rep1


title: 5426_B_PMT_AcH3


title: UF287_Xylem-Rep1


title: UF217_Xylem-Rep1


title: UF934_Xylem-Rep1


title: UF383_Xylem-Rep1


title: UF939_Xylem-Rep1


title: UF231_Xylem-Rep1


title: UF224_Xylem-Rep1


title: 2179_B_PMT_PML


title: 1785_PMT_dL9_B


title: UF931_Xylem-Rep1


title: 2177_B_PMT_PML


title: UF929_Xylem-Rep1


title: UF927_Xylem-Rep1


title: 1784_PMT_triLys4_B


title: UF924_Xylem-Rep1


title: 1783_PMT_triLys9_B


title: UF926_Xylem-Rep1


title: UF922_Xylem-Rep1


title: 1725_PMT_PML_B


title: UF915_Xylem-Rep1


title: 9876_PMT_A

source_name: U937 PMT cells, ChIP DNA

source_name: U937 PMT cells, input DNA


title: SD1587_PMT_diLys4


title: 1724_PMT_AcH3_B


title: UF923_Xylem-Rep1


title: UF919_Xylem-Rep1


title: 9082_PMT_A


title: 9781_AE_A

source_name: U937 AE cells, ChIP DNA

tag: U937 AE cells, ChIP DNA

source_name: U937 AE cells, input DNA

tag: U937 AE cells, input DNA


title: UF917_Xylem-Rep1


title: UF921_Xylem-Rep1


title: UF914_Xylem-Rep1


title: 9081_PMT_A


title: UF912_Xylem-Rep1


title: UF913_Xylem-Rep1


title: SD1524_Pr9_AcH3


title: UF906_Xylem-Rep1


title: SD1522_PMT_AcH3


title: UF897_Xylem-Rep1


title: UF902_Xylem-Rep1


title: 9079_PMT_A


title: UF894_Xylem-Rep1


title: SD1435_Pr9_diLys4


title: 9070_Pr9_A

source_name: U937 Pr9 cells, ChIP DNA

source_name: U937 Pr9 cells, input DNA


title: UF892_Xylem-Rep1


title: 8892_AE_dL4


title: SD1437_Pr9_AcH3


title: UF886_Xylem-Rep1


title: UF891_Xylem-Rep1


title: UF888_Xylem-Rep1


title: SD1521_PML_AcH3


title: 5651_Pr9_AcH3


title: 5649_Pr9_AcH3


title: UF884_Xylem-Rep1


title: UF877_Xylem-Rep1


title: UF879_Xylem-Rep1


title: 4707_Pr9_A


title: UF380_Xylem-Rep1


title: UF873_Xylem-Rep1


title: UF871_Xylem-Rep1


title: 5535_Pr9_diLys4


title: 8875_Pr9_A


title: 4698_AE_A


title: UF867_Xylem-Rep1


title: UF882_Xylem-Rep1


title: UF859_Xylem-Rep1


title: 4689_Pr9_A


title: 5533_PMT_diLys4


title: 4488_PMT_A


title: 5510_Pr9_dL9


title: 5508_Pr9_AcH3


title: UF863_Xylem-Rep1


title: UF865_Xylem-Rep1


title: UF840_Xylem-Rep1


title: UF846_Xylem-Rep1


title: UF848_Xylem-Rep1


title: UF847_Xylem-Rep1


title: 4595_AE_A


title: 5507_Pr9_PML


title: UF836_Xylem-Rep1


title: UF856_Xylem-Rep1


title: 4478_AE_A


title: UF820_Xylem-Rep1


title: 5506_Pr9_triLys9


title: UF831_Xylem-Rep1


title: UF833_Xylem-Rep1


title: UF824_Xylem-Rep1


title: 4324_AE_dL4


title: 5505_Pr9_triLys4


title: 5430_Pr9_PML


title: 5428_Pr9_PML


title: 8888_PMT_A


title: 4481_PMT_A


title: 9080_PMT_tL9

source_name: 9080_PMT_tL9, ChIP DNA

tag: 9080_PMT_tL9, ChIP DNA


title: UF819_Xylem-Rep1


title: 5426_PMT_AcH3


title: 9074_PMT_dL4

source_name: 9074_PMT_dL4, ChIP DNA

tag: 9074_PMT_dL4, ChIP DNA


title: UF816_Xylem-Rep1

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, secondary xylem tissue


title: UF814_Xylem-Rep1


title: UF808_Xylem-Rep1


title: 4307_AE_A


title: 9072_PMT_tL4

source_name: 9072_PMT_tL4, ChIP DNA

tag: 9072_PMT_tL4, ChIP DNA


title: 5427_PMT_AcH3


title: UF810_Xylem-Rep1


title: UF813_Xylem-Rep1


title: 2179_PMT_PML


title: UF807_Xylem-Rep1


title: UF802_Xylem-Rep1


title: UF800_Xylem-Rep1


title: UF803_Xylem-Rep1


title: UF812_Xylem-Rep1


title: 8882_PMT_HDAC

source_name: 8882_PMT_HDAC, ChIP DNA

tag: 8882_PMT_HDAC, ChIP DNA


title: UF79_Xylem-Rep1


title: 8890_PMT_dL9

source_name: 8890_PMT_dL9, ChIP DNA

tag: 8890_PMT_dL9, ChIP DNA


title: 9071_PMT_HDAC

source_name: 9071_PMT_HDAC, ChIP DNA

tag: 9071_PMT_HDAC, ChIP DNA


title: UF755_Xylem-Rep1


title: 1725_PMT_PML

source_name: U937-empty vector cells (PMT), ChIP DNA


title: 8881_Pr9_dL4

source_name: 8881_Pr9_dL4, ChIP DNA

tag: 8881_Pr9_dL4, ChIP DNA


title: 1784_PMT_triLys4

source_name: U937-empty vector cells (PMT), input DNA


title: 2177_PMT_PML


title: 1785_PMT_dL9


title: UF806_Xylem-Rep1


title: UF748_Xylem-Rep1


title: 8877_PMT_dL4

source_name: 8877_PMT_dL4, ChIP DNA

tag: 8877_PMT_dL4, ChIP DNA


title: UF743_Xylem-Rep1


title: UF734_Xylem-Rep1


title: UF729_Xylem-Rep1


title: UF722_Xylem-Rep1


title: UF724_Xylem-Rep1


title: 8869_PMT_dL4

source_name: 8869_PMT_dL4, ChIP DNA

tag: 8869_PMT_dL4, ChIP DNA


title: UF720_Xylem-Rep1

tag: 25mM supplemental N, long day conditions


title: 1724_PMT_AcH3


title: 1783_PMT_triLys9


title: 8661_PMT_dL4

source_name: 8661_PMT_dL4, ChIP DNA

tag: 8661_PMT_dL4, ChIP DNA

source_name: U937 PMT cells, input DNA


title: 8660_PMT_PML

source_name: 8660_PMT_PML, ChIP DNA

tag: 8660_PMT_PML, ChIP DNA


title: 4703_Pr9_dL4

source_name: 4703_Pr9_dL4, ChIP DNA

tag: 4703_Pr9_dL4, ChIP DNA


title: Primary ovine microglia PrPC bio repC tech rep3 (Mock12C.3)

city: Pullman

first: James

last: Stanton

state: WA

institute: Washington State University

description: Mock infected primary ovine microglial cells

hyb_protocol: Affymetrix hybridization protocols; Affymetrix GeneChip Fluidics Station 450

scan_protocol: Affymetrix GeneChip Scanner 300 7G

data_processing: All analyses of microarray data were conducted using Bioconductor for R (www.R-project.org). Data were normalized using the Micro Array Suite 5.0 (MAS5) algorithm.  The ComBat algorithm (http://statistics.byu.edu/johnson/ComBat/) was used to correct for batch effect.

organism: Ovis aries

source_name: primary ovine microglial cells sham inoculated with PrPC

label_protocol: 10ug total RNA labelled according to Affymetrix one cycle labelling protocol

growth_protocol: Microglial cells were cultured using standard techniques, in OPTI-MEM I Reduced Serum Medium (Invitrogen, Carlsbad, CA) supplemented with 10% heat-inactivated FBS, 2 mM L-glutamine, 10 IU/ml of penicillin, and 10 mg/ml of streptomycin.

extract_protocol: QIAshredder spin columns (Qiagen, Valencia, CA) followed by Qiagen RNeasy mini spin columns

treatment_protocol: Primary microglia were passed into 6-well plates and grown to approximately 60% confluency.  Microglia were rinsed once with PBS and then overlaid with 200 μl of a 1/20 dilution of either the Rov9Sc lysate (Inoc A, B, and C) or the Rov9C lysate (Mock A, B, and C) in OPTI-MEM.  All replicates (A, B, and C) of both treatment groups (Inoc and Mock) were incubated for six hours and then 200 μl of OMEM were added to each well.  Following an additional two days of incubation, 0.5 ml of OMEM was added to each well, and microglia were incubated for four days at which time they were expanded into 25-cm2 tissue culture flasks.  Microglia were fed every three to four days with OMEM as necessary and serially passed 1/5 after reaching confluence.

tag: Primary ovine microglia


title: UF716_Xylem-Rep1


title: UF715_Xylem-Rep1


title: UF717_Xylem-Rep1


title: UF710_Xylem-Rep1


title: UF705_Xylem-Rep1


title: UF706_Xylem-Rep1


title: Primary ovine microglia PrPC bio repC tech rep2 (Mock12C.2)


title: Primary ovine microglia PrPC bio repC tech rep1 (Mock12C.1)


title: UF69_Xylem-Rep1


title: Primary ovine microglia PrPC bio repB tech rep3 (Mock12B.2.3)


title: UF701_Xylem-Rep1


title: 4487_Pr9_tL4

source_name: 4487_Pr9_tL4, ChIP DNA

tag: 4487_Pr9_tL4, ChIP DNA

source_name: U937 Pr9 cells, input DNA

tag: U937 Pr9 cells, input DNA


title: 4497_Pr9_PML

source_name: 4497_Pr9_PML, ChIP DNA

tag: 4497_Pr9_PML, ChIP DNA


title: 4688_Pr9_tL4

source_name: 4688_Pr9_tL4, ChIP DNA

tag: 4688_Pr9_tL4, ChIP DNA


title: Primary ovine microglia PrPC bio repB tech rep2 (Mock12B.2.2)


title: 4486_Pr9_dL9

source_name: 4486_Pr9_dL9, ChIP DNA

tag: 4486_Pr9_dL9, ChIP DNA


title: UF700_Xylem-Rep1

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, secondary xylem tissue


title: UF7_Xylem-Rep1


title: 4479_PMT_PML

source_name: 4479_PMT_PML, ChIP DNA

tag: 4479_PMT_PML, ChIP DNA

tag: U937 PMT cells, input DNA


title: UF718_Xylem-Rep1


title: UF62_Xylem-Rep1


title: Primary ovine microglia PrPC bio repA tech rep3 (Mock12A.3)


title: UF61_Xylem-Rep1


title: Primary ovine microglia PrPC bio repB tech rep1 (Mock12B.2.1)


title: UF590_Xylem-Rep1


title: UF703_Xylem-Rep1


title: Primary ovine microglia PrPC bio repA tech rep2 (Mock12A.2)


title: UF58_Xylem-Rep1


title: UF570_Xylem-Rep1


title: UF565_Xylem-Rep1


title: 4477_Pr9_dL9

source_name: 4477_Pr9_dL9, ChIP DNA

tag: 4477_Pr9_dL9, ChIP DNA


title: 4413_Pr9_HDAC

source_name: 4413_Pr9_HDAC, ChIP DNA

tag: 4413_Pr9_HDAC, ChIP DNA


title: UF561_Xylem-Rep1


title: 4412_Pr9_tL9

source_name: 4412_Pr9_tL9, ChIP DNA

tag: 4412_Pr9_tL9, ChIP DNA


title: UF547_Xylem-Rep1


title: UF544_Xylem-Rep1


title: 4317_Pr9_HDAC

source_name: 4317_Pr9_HDAC, ChIP DNA

tag: 4317_Pr9_HDAC, ChIP DNA


title: Primary ovine microglia PrPC bio repA tech rep1 (Mock12A.1)


title: 4316_PMT_tL4

source_name: 4316_PMT_tL4, ChIP DNA

tag: 4316_PMT_tL4, ChIP DNA


title: UF541_Xylem-Rep1

tag: 25mM supplemental N, long day conditions


title: Primary ovine microglia PrPSc bio repC tech rep3 (Inoc12C.3)

description: PrPSc infected primary ovine microglial cells

source_name: primary ovine microglial cells inoculated with PrPSc


title: UF534_Xylem-Rep1


title: Primary ovine microglia PrPSc bio repC tech rep2 (Inoc12C.2)


title: 4314_PMT-dL4

source_name: 4314_PMT-dL4, ChIP DNA

tag: 4314_PMT-dL4, ChIP DNA

source_name: U937 PMT cells, input DNA


title: UF552_Xylem-Rep1


title: UF503_Xylem-Rep1


title: UF513_Xylem-Rep1


title: 4318_Pr9_tL9

source_name: 4318_Pr9_tL9, ChIP DNA

tag: 4318_Pr9_tL9, ChIP DNA


title: Primary ovine microglia PrPSc bio repB tech rep3 (Inoc12B.2.3)


title: Primary ovine microglia PrPSc bio repB tech rep2 (Inoc12B.2.2)


title: UF532_Xylem-Rep1


title: UF526_Xylem-Rep1


title: UF529_Xylem-Rep1


title: 8873_PMT_tL9

source_name: 8873_PMT_tL9, ChIP DNA

tag: 8873_PMT_tL9, ChIP DNA


title: UF533_Xylem-Rep1


title: UF585_Xylem-Rep1


title: Primary ovine microglia PrPSc bio repC tech rep1 (Inoc12C.1)

tag: Primary ovine microglia


title: 4311_Pr9_PML

source_name: 4311_Pr9_PML, ChIP DNA

tag: 4311_Pr9_PML, ChIP DNA


title: UF500_Xylem-Rep1


title: UF498_Xylem-Rep1


title: UF494_Xylem-Rep1


title: UF723_Xylem-Rep1


title: 4309_PMT_dL9

source_name: 4309_PMT_dL9, ChIP DNA

tag: 4309_PMT_dL9, ChIP DNA


title: 4310_Pr9_dL4

source_name: 4310_Pr9_dL4, ChIP DNA

tag: 4310_Pr9_dL4, ChIP DNA

source_name: U937 Pr9 cells, input DNA

tag: U937 Pr9 cells, input DNA


title: Primary ovine microglia PrPSc bio repA tech rep3 (Inoc12A.3)


title: Primary ovine microglia PrPSc bio repA tech rep1 (Inoc12A.1)


title: UF490_Xylem-Rep1


title: UF481_Xylem-Rep1


title: YPS1009 vs DBY8268 CGH #2

status: Public on Sep 05 2008

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

institute: University of Wisconsin Madison

description:
CGH array comparing strains
yG9-70A

hyb_protocol: As indicated in Gasch AP Methods in Enzymology 350: 393-414

scan_protocol: Arrays were scanned on an Axon 4000B scanner

data_processing: Data were extracted using GenePix 6.0.  Data were normalized by regional mean-centering as described by Lyne et al. 2003 BMC Genomics

label: Oyster 500 cyanine dye

source_name: DBY8268 genomic DNA

label_protocol: Indirect labeling using random hexmaer primers, amino-allyl-dUTP, and cyanine dyes from Flownamics (Madison, Wi) as described in Pollak et al. Nature Genetics 1999

growth_protocol: Unless otherwise noted, cells were grown 3 doublings in YPD  at 30C to OD600 ~0.5

extract_protocol: Yeast Genomic DNA prep columns from Zymo Research

treatment_protocol: No treatment

tag: DBY8268 (ura3-52/ura3-deletion, ho/ho, GAL2/GAL2)

label: Oyster 650 cyanine dye

source_name: YPS1009 genomic DNA

tag: Strain YPS1009


title: YJM789 vs DBY8268 CGH #2

description:
CGH array comparing strains
yG9-70B

source_name: YJM789 genomic DNA

tag: Strain YJM789


title: YJM789 vs DBY8268 #1

description:
CGH array comparing strains
yG9-64B


title: YPS1009 vs DBY8268 #1

description:
CGH array comparing strains
yG9-64A


title: RM11-1a vs DBY8268 CGH #1

description:
CGH array comparing strains
yG9-55A

source_name: RM11-1a genomic DNA

tag: Strain RM11-1a


title: Primary ovine microglia PrPSc bio repA tech rep2 (Inoc12A.2)


title: Y10 vs DBY8268 #1

description:
CGH array comparing strains
yG9-63B

source_name: Y10 genomic DNA

tag: Strain Y10


title: UF468_Xylem-Rep1

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, secondary xylem tissue


title: RM11-1a vs DBY8268 #2

description:
CGH array comparing strains
yG9-71A


title: M22 vs DBY8268 CGH #2

description:
CGH array comparing strains
yG9-71B

source_name: M22 genomic DNA

tag: Strain M22


title: Y10 vs DBY8268 #2

description:
CGH array comparing strains
yG9-74B


title: M22 vs DBY8268 #1

description:
CGH array comparing strains
yG9-55B


title: DBY8268 vs DBY8268 CGH #2

description:
CGH array comparing strains
yG9-34B


title: K9 vs DBY8268 #1

description:
CGH array comparing strains
yG9-63A

source_name: K9 genomic DNA

tag: Strain K9


title: DBY8268 vs DBY8268 CGH #1

description:
CGH array comparing strains
yG9-34A


title: Prohibitin transfected Caco2-BBE

city: Atlanta

first: Arianne

last: Theiss

state: GA

address: 615 Michael St

institute: Emory University

description: Baseline comparison of global gene expression in vector and prohibitin transfected Caco2-BBE intestinal epithelial cells to determine the effect of prohibitin overexpression.

hyb_protocol: After the addition of 1 ug of Poly A RNA (Sigma, P9403) the probes were hybridized to the arrays at 42ºC for 16 hours, and washed.

scan_protocol: The microarrays were scanned with a GenePix4000A scanner (Axon Instruments, Union City, CA).

data_processing: Any Cy3 or Cy5 fluorescence level below background or smaller than 60% of the original spotting area was defined as “absent”.  Background values below 1000 were set to 1000.  The data in the VALUE column is expressed as the natural log of the ch1/ch2 ratios.

source_name: Prohibitin transfected Caco2-BBE

label_protocol: Equal amounts of total RNA from four individual wells of Caco2-BBE cells transfected with prohibitin expression contructs (pcDNA4+Prohibitin coding region) were pooled together.   20 µg of total RNA was combined with 5X 1st Strand Buffer, 1 µg Oligo dT20mer, 0.1M DTT (Gibco Invitrogen, Carlsbad, CA), low dTTP/dNTP mix (Amersham Biosciences, Piscataway, NJ), RNasin (Promega Biosciences, San Luis Obispo, CA), and Cyanine 5-dUTP (PerkinElmer, Torrance, CA) in 500 µL tubes. The reactions were heated to 65ºC for 5 minutes and reverse transcribed with SuperScript II RNase H- Reverse Transcriptase (Gibco) at 42ºC for 90 min. Five µL of 0.5 M EDTA was added to stop the reaction and then the mixture was heated to 65ºC for 30 min with 10 µL of 1 M NaOH to hydrolyze the RNA, followed by the addition of 25 µL of 1 M Tris to neutralize the NaOH. The Cy-3 and Cy-5 labeled probes were combined and isolated by running through a Microcon YM-30 size-exclusion column (Millipore), washed with TE buffer, and resuspended in 11 µL of TE.

extract_protocol: RNeasy Mini Kit (Qiagen) was used to extract total RNA according to the manufacturer's protocol.

tag: Caco2-BBE cells passage 41 transfected with pcDNA4 (Invitrogen) vector containing prohibitin coding region for 72 hours.

source_name: Universal human reference RNA

label_protocol: Universal human reference RNA was combined with 5X 1st Strand Buffer, 1 µg Oligo dT20mer, 0.1M DTT (Gibco Invitrogen, Carlsbad, CA), low dTTP/dNTP mix (Amersham Biosciences, Piscataway, NJ), RNasin (Promega Biosciences, San Luis Obispo, CA), and Cyanine 3-dUTP (PerkinElmer, Torrance, CA) in 500 µL tubes. The reactions were heated to 65ºC for 5 minutes and reverse transcribed with SuperScript II RNase H- Reverse Transcriptase (Gibco) at 42ºC for 90 min. Five µL of 0.5 M EDTA was added to stop the reaction and then the mixture was heated to 65ºC for 30 min with 10 µL of 1 M NaOH to hydrolyze the RNA, followed by the addition of 25 µL of 1 M Tris to neutralize the NaOH. The Cy-3 and Cy-5 labeled probes were combined and isolated by running through a Microcon YM-30 size-exclusion column (Millipore), washed with TE buffer, and resuspended in 11 µL of TE.

tag: Universal human reference RNA


title: K9 vs DBY8268 #2

description:
CGH array comparing strains
yG9-74A


title: DBY8268 vs DBY8268 #3

description:
CGH array comparing strains
yG9-73A


title: Empty vector transfected Caco2-BBE

source_name: Empty vector transfected Caco2-BBE

label_protocol: Equal amounts of total RNA from four individual wells of Caco2-BBE cells transfected with empty vector were pooled together.   20 µg of total RNA was combined with 5X 1st Strand Buffer, 1 µg Oligo dT20mer, 0.1M DTT (Gibco Invitrogen, Carlsbad, CA), low dTTP/dNTP mix (Amersham Biosciences, Piscataway, NJ), RNasin (Promega Biosciences, San Luis Obispo, CA), and Cyanine 5-dUTP (PerkinElmer, Torrance, CA) in 500 µL tubes. The reactions were heated to 65ºC for 5 minutes and reverse transcribed with SuperScript II RNase H- Reverse Transcriptase (Gibco) at 42ºC for 90 min. Five µL of 0.5 M EDTA was added to stop the reaction and then the mixture was heated to 65ºC for 30 min with 10 µL of 1 M NaOH to hydrolyze the RNA, followed by the addition of 25 µL of 1 M Tris to neutralize the NaOH. The Cy-3 and Cy-5 labeled probes were combined and isolated by running through a Microcon YM-30 size-exclusion column (Millipore), washed with TE buffer, and resuspended in 11 µL of TE.

tag: Caco2-BBE cells passage 41 transfected with pcDNA4 (Invitrogen) vector for 72 hours.


title: UF489_Xylem-Rep1

tag: 25mM supplemental N, long day conditions


title: AGY0249 Heat 15 min rep 3 (v1.1)

first: David

middle: B

last: Berry

address: 3456 Genetics Biotech. Building

institute: University of Wisconsin: Madison

description: no additional information

hyb_protocol: As in Gasch, Methods in Enzymology, 2002

scan_protocol: Arrays were scanned using GenePix (4000B from Axon Instruments)

data_processing: Bahler normalized, background subtracted VALUE determined by a moving window local to the spot normalized

label: Oyster 556

source_name: AGY0249 grown 3 doublings in YPD and collected

label_protocol: Cyanine dyes (Flownamics, Madison, WI) were used; otherwise, as in Gasch, Methods in Enzymology, 2002

growth_protocol: Grown three doublings in YPD to an OD600 of 0.3, and exposed to stress in YPD.

extract_protocol: Hot phenol extraction as in Gasch, Methods in Enzymology, 2002

treatment_protocol: Stressors were added to the final concentrations of 0.7M NaCl for 45 min or 37˚C Heat Shock for 15 min

tag: Strain AGY0249 (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 msn2::KanMX msn4::URA3)

label: Oyster 645

source_name: AGY0249 grown 3 doublings and exposed to 30-37˚C Heat Shock 15 min


title: AGY0249 Heat 15 min rep 5 (v1.1)

description: no additional information


title: MCF-7 nuclease hypersensitive

city: Taipei

first: Ming-Ta

last: Hsu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang Ming University

description: Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) and 0units (control) or 5units of MNase at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. DNA was then phenol/chloroform extracted and ethanol precipitate.

hyb_protocol: According to the manual of Agilent protocol (http://www.agilent.com)

scan_protocol: Scanning was performed as the manual of Agilent protocol (http://www.agilent.com)

data_processing: The Cy3 hybridization intensity was normalized to Cy5 for comparison among samples. The log2 ratio(log2 Cy5/Cy3) were calculated and compared. Agilent software was used.

source_name: MCF-7 total genomic DNA

label_protocol: According to the manual of Agilent Oligo Microarray Kit.

extract_protocol: Cells were grown to 90 % confluence in 6 well tissue culture dish. Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. Suspensions were collected in a 1.5ml eppendorf tube and treated with 0.1 mg/ml of RNase A for an hour at 37 ℃ and then with 0.3 mg/ml of proteinase K for 12-16 hours at 55 ℃. An equal volume of phenol/chloroform/isoamyl alcohol mixture (24:25:1) was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. The aqueous phase was collected carefully, and then repeated the extraction procedure until the interface is clean. The aqueous phase again was collected and an equal volume of chloroform was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. This procedure was repeated until the interface was clean. Finally, total genomic DNA in the aqueous phase was precipitated by the addition of 1/10 volume of 7.5 M ammonium acetate (pH: 5.2) and two volume of absolute ethanol. The mixture was incubated at -70℃ overnight and centrifuged at 13000 rpm, 4℃ for 30 min. Supernatant was removed and the pellet was washed by proper amount of 70 % ethanol and then centrifuged. In the end, the pellet was redissolved in d3H20 and then stored at -20℃. The integrity of the DNA extracted was checked by 1.2 % (w/v) agarose gel electrophoresis. The concentration of DNA was estimated by ultraviolet spectrophotometry.

treatment_protocol: Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. Genomic DNA was extracted and labeled with Cy3 fluorescence dye.

tag: Cell line

tag: Gender

value: Female

tag: Age

tag: Tissue

value: Breast tumor

source_name: MCF-7 nuclease released small DNA fragments

extract_protocol: Cells were grown to 90 % confluence in 6 well tissue culture dish. Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) and 5units of MNase at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. Suspensions were collected in a 1.5ml eppendorf tube and treated with 0.1 mg/ml of RNase A for an hour at 37 ℃ and then with 0.3 mg/ml of proteinase K for 12-16 hours at 55 ℃. An equal volume of phenol/chloroform/isoamyl alcohol mixture (24:25:1) was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. The aqueous phase was collected carefully, and then repeated the extraction procedure until the interface is clean. The aqueous phase again was collected and an equal volume of chloroform was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. This procedure was repeated until the interface was clean. Finally, total genomic DNA in the aqueous phase was precipitated by the addition of 1/10 volume of 7.5 M ammonium acetate (pH: 5.2) and two volume of absolute ethanol. The mixture was incubated at -70℃ overnight and centrifuged at 13000 rpm, 4℃ for 30 min. Supernatant was removed and the pellet was washed by proper amount of 70 % ethanol and then centrifuged. In the end, the pellet was redissolved in d3H20 and then stored at -20℃. The integrity of the DNA extracted was checked by 1.2 % (w/v) agarose gel electrophoresis. The concentration of DNA was estimated by ultraviolet spectrophotometry. Nuclease-released small DNA fragments with molecular lower than 200bp is purified by gel extraction.

treatment_protocol: Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) and 5units of MNase at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. Genomic DNA was extracted. Nuclease-released small DNA fragments with molecular lower than 200bp was purified by gel extraction and labeled with Cy5 fluorescence dye.


title: MCF-7 nuclease hypersensitive (10ug/ml alpha-amanitin)

description: Cells were grown to 90 % confluence in 6 well tissue culture dish. Cells were treated with 10μg/ml alpha-amanitin for 48hrs. Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) and 0units (control) or 5units of MNase at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. DNA was then phenol/chloroform extracted and ethanol precipitate.

source_name: MCF-7 total genomic DNA (10ug/ml alpha-amanitin treated)

extract_protocol: Cells were grown to 90 % confluence in 6 well tissue culture dish. Cells were treated with 10μg/ml alpha-amanitin for 48hrs. Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. Suspensions were collected in a 1.5ml eppendorf tube and treated with 0.1 mg/ml of RNase A for an hour at 37 ℃ and then with 0.3 mg/ml of proteinase K for 12-16 hours at 55 ℃. An equal volume of phenol/chloroform/isoamyl alcohol mixture (24:25:1) was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. The aqueous phase was collected carefully, and then repeated the extraction procedure until the interface is clean. The aqueous phase again was collected and an equal volume of chloroform was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. This procedure was repeated until the interface was clean. Finally, total genomic DNA in the aqueous phase was precipitated by the addition of 1/10 volume of 7.5 M ammonium acetate (pH: 5.2) and two volume of absolute ethanol. The mixture was incubated at -70℃ overnight and centrifuged at 13000 rpm, 4℃ for 30 min. Supernatant was removed and the pellet was washed by proper amount of 70 % ethanol and then centrifuged. In the end, the pellet was redissolved in d3H20 and then stored at -20℃. The integrity of the DNA extracted was checked by 1.2 % (w/v) agarose gel electrophoresis. The concentration of DNA was estimated by ultraviolet spectrophotometry.

treatment_protocol: Cells were treated with 10μg/ml alpha-amanitin for 48hrs. Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. Genomic DNA was extracted and labeled with Cy3 fluorescence dye.

source_name: MCF-7 nuclease-released small DNA fragments (10ug/ml alpha-amanitin treated)

extract_protocol: Cells were grown to 90 % confluence in 6 well tissue culture dish. Cells were treated with 10μg/ml alpha-amanitin for 48hrs. Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) and 5units of MNase at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. Suspensions were collected in a 1.5ml eppendorf tube and treated with 0.1 mg/ml of RNase A for an hour at 37 ℃ and then with 0.3 mg/ml of proteinase K for 12-16 hours at 55 ℃. An equal volume of phenol/chloroform/isoamyl alcohol mixture (24:25:1) was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. The aqueous phase was collected carefully, and then repeated the extraction procedure until the interface is clean. The aqueous phase again was collected and an equal volume of chloroform was added, mixed thoroughly, and centrifuged at 13000 rpm for 10 min. This procedure was repeated until the interface was clean. Finally, total genomic DNA in the aqueous phase was precipitated by the addition of 1/10 volume of 7.5 M ammonium acetate (pH: 5.2) and two volume of absolute ethanol. The mixture was incubated at -70℃ overnight and centrifuged at 13000 rpm, 4℃ for 30 min. Supernatant was removed and the pellet was washed by proper amount of 70 % ethanol and then centrifuged. In the end, the pellet was redissolved in d3H20 and then stored at -20℃. The integrity of the DNA extracted was checked by 1.2 % (w/v) agarose gel electrophoresis. The concentration of DNA was estimated by ultraviolet spectrophotometry. Nuclease-released small DNA fragments with molecular lower than 200bp is purified by gel extraction.

treatment_protocol: Cells were treated with 10μg/ml alpha-amanitin for 48hrs. Cells were washed three times with ice-cold 1X PBS. The cells were lysed with 700 μl of ice-cold MNase lysis buffer on ice for 15 min. The lysate was removed by suction, and then gently rinse the nuclei with 700 μl of MNase digestion buffer (without CaCl2). The reaction was performed by incubating cell nuclei in 650 μl of MNase digestion buffer (with CaCl2) and 5units of MNase at 25 ℃ for 5 min. The reaction was terminated by adding 40 μl MNase stop buffer and 20 μl of 20 % SDS. Genomic DNA was extracted. Nuclease-released small DNA fragments with molecular lower than 200bp was purifed by gel extraction and labeled with Cy5 fluorescence dye.


title: AGY0249 Heat 15 min rep 2 (v1.1)

description: no additional information


title: Primary ovine microglia PrPSc bio repB tech rep1 (Inoc12B.2.1)

source_name: primary ovine microglial cells inoculated with PrPSc

tag: Primary ovine microglia


title: AGY0249 NaCl 45 min rep 5 (v1.1)

description: no additional information

source_name: AGY0249 grown 3 doublings and exposed to 0.7M NaCl 45 min


title: AGY0249 NaCl 45 min rep 3 (v1.1)

description: no additional information


title: AGY0235 Heat 15 min rep 3 (v1.1)

description: no additional information

source_name: AGY0235 grown 3 doublings in YPD and collected

tag: Strain AGY0235 (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0  msn4::URA3)

source_name: AGY0235 grown 3 doublings and exposed to 30-37˚C Heat Shock 15 min


title: AGY0249 NaCl 45 min rep 4 (v1.1)

description: no additional information


title: AGY0235 Heat 15 min rep 4 (v1.1)

description: no additional information


title: AGY0235 Heat 15 min rep 5 (v1.1)

description: no additional information


title: AGY0249 Heat 15 min rep 1 (v1.1)

description: no additional information


title: AGY0249 NaCl 45 min rep 1 (v1.1)

description: no additional information


title: AGY0249 NaCl 45 min rep 2 (v1.1)

description: no additional information


title: AGY0235 Heat 15 min rep 1 (v1.1)

description: no additional information


title: AGY0249 Heat 15 min rep 4 (v1.1)

description: no additional information


title: AGY0235 NaCl 45 min rep 5 (v1.1)

description: no additional information

source_name: AGY0235 grown 3 doublings and exposed to 0.7M NaCl 45 min


title: AGY0235 NaCl 45 min rep 1 (v1.1)

description: no additional information


title: AGY0235 Heat 15 min rep 2 (v1.1)

description: no additional information


title: AGY0235 NaCl 45 min rep 3 (v1.1)

description: no additional information


title: AGY0050 Heat 15 min rep 5 (v1.1)

description: no additional information

source_name: AGY0050 grown 3 doublings in YPD and collected

tag: Strain AGY0050 (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 msn2::KanMX)

source_name: AGY0050 grown 3 doublings and exposed to 30-37˚C Heat Shock 15 min


title: AGY0235 NaCl 45 min rep 4 (v1.1)

description: no additional information


title: AGY0050 Heat 15 min rep 4 (v1.1)

description: no additional information


title: AGY0050 Heat 15 min rep 2 (v1.1)

description: no additional information


title: AGY0050 Heat 15 min rep 1 (v1.1)

description: no additional information


title: AGY0235 NaCl 45 min rep 2 (v1.1)

description: no additional information


title: MCF-7 RNA

description:
Array Image: Without seriously artifacts
Background: 20-100
Noise: <10
Hybridization controls: BioB: 50%A; 50%P
bioC, bioD, and cre: P
internal control genes: Either 3'/5' probe set of GAPDH or 3'/5' probe set of actin <3

hyb_protocol: Affymetrix microarray was performed using Human U133 2.0 (Affymetrix). Details of the methods for RNA quality, sample labeling, hybridization and expression analysis are according to the manual of Affymetrix Microarray Kit and Affymetrix website.

data_processing: Using scaling factor. The default settings are "scaling all probe sets to target signal: 500" and "normalization by user defined in value: 1

source_name: MCF7 cell line

extract_protocol: Cells were grown to 85 % confluence in 10 cm tissue culture dish. Each 10 cm dish was washed with 1x PBS for three times. Total RNA was extracted according to the RNeasy® Mini Kit Spin Protocol (QIAGEN). The integrity of the RNA extract was checked by 1.2 % (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry.


title: AGY0050 NaCl 45 min rep 4 (v1.1)

description: no additional information

source_name: AGY0050 grown 3 doublings and exposed to 0.7M NaCl 45 min


title: AGY0050 Heat 15 min rep 3 (v1.1)

description: no additional information


title: BY4741 Heat 15 min rep 4 (v1.1)

description: no additional information

source_name: BY4741 grown 3 doublings in YPD and collected

tag: Strain BY4741 (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0)

source_name: BY4741 grown 3 doublings and exposed to 30-37˚C Heat Shock 15 min


title: BY4741 Heat 15 min rep 5 (v1.1)

description: no additional information


title: AGY0050 NaCl 45 min rep 3 (v1.1)

description: no additional information


title: BY4741 NaCl 45 min rep 6 (v1.1)

description: no additional information

source_name: BY4741 grown 3 doublings and exposed to 0.7M NaCl 45 min


title: AGY0050 NaCl 45 min rep 2 (v1.1)

description: no additional information


title: AGY0050 NaCl 45 min rep 1 (v1.1)

description: no additional information


title: BY4741 Heat 15 min rep 1 (v1.1)

description: no additional information


title: AGY0050 NaCl 45 min rep 5 (v1.1)

description: no additional information


title: BY4741 Heat 15 min rep 3 (v1.1)

description: no additional information


title: BY4741 NaCl 45 min rep 5 (v1.1)

description: no additional information


title: BY4741 NaCl 45 min rep 4 (v1.1)

description: no additional information


title: BY4741 Heat 15 min rep 2 (v1.1)

description: no additional information


title: BY4741 NaCl 45 min rep 3 (v1.1)

description: no additional information


title: BY4741 NaCl 45 min rep 2 (v1.1)

description: no additional information


title: BY4741 NaCl 45 min rep 1 (v1.1)

description: no additional information


title: Normal triceps 2

status: Public on Sep 04 2008

city: Jerusalem

first: Noa

last: Novershtern

address: Admond Safra Campus

department: School of Computer Science and Engineering

country: Israel

institute: The Hebrew University

description: Gene expression data from normal unaffected muscle specimen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133A GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Affymetrix Microarray Software Suite 5.0 and RMA normalization (using RMAExpress software)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Tissues were disrupted in dry ice and homogeneized and total RNA was isolated using TriReagent (Molecular Research Center,  Cincinnati, OH) according to the manufacturer’s recommended protocol. Integrity of the isolated RNA was analyzed using a standard 1% agarose gel electrophoresis and purified total RNA was quantified using Nanodrop ND1000.

treatment_protocol: All muscle biopsies were collected and immediately frozen in liquid nitrogen untill used for RNA extraction.

tag: Normal, tissue

value: triceps, age:48, gender:female


title: BY4741 NaCl 15 min rep 1 (v1.0)

source_name: BY4741 grown 2 doublings in YPD and collected

growth_protocol: Grown two or more doublings in YPD to an OD600 of 0.3, and exposed to stress in YPD.

treatment_protocol: Stressors were added to the final concentrations of 0.7M NaCl or 0.5mM H2O2, for 60 and 40 minutes respectively

source_name: BY4741 grown 2 doublings and exposed to 0.7M NaCl 15 min


title: Normal quadriceps 3

value: quadriceps, age:21, gender:male


title: Normal deltoid 1

value: deltoid, age:26, gender:male


title: Normal quadriceps 2

value: quadriceps, age:52, gender:female


title: Normal gluteus

value: gluteus, age:56, gender:male


title: Affected deltoid 6

description: Gene expression data from HIBM affected muscle

tag: Affected, tissue

value: deltoid, age:46, gender:female


title: Normal quadriceps 1

value: quadriceps, age:18, gender:male


title: Normal deltoid 2

value: deltoid, age:19, gender:male


title: Affected biceps 2

value: biceps, age:25, gender:female


title: Normal triceps 1

value: triceps, age:31, gender:female


title: Affected deltoid 4

value: deltoid, age:29, gender:male


title: Normal paraspinal

value: paraspinal, age:73, gender:female


title: Affected tibialis anterior

value: tibialis, age:26, gender:male


title: Normal deltoid 3

value: deltoid, age:74, gender:female


title: Affected quadriceps

value: quadriceps, age:59, gender:female


title: Affected deltoid 2

value: deltoid, age:55, gender:female


title: Affected deltoid 5

value: deltoid, age:40, gender:male


title: Affected deltoid 3

value: deltoid, age:45, gender:male


title: Affected deltoid 1


title: Xenopus muelleri genomic DNA

city: Hamilton

first: Frederic

last: Chain

state: Ontario

address: 1280 Main Street West

department: Biology

country: Canada

institute: McMaster University

description: gDNA hybridization intensities for a non-target organism

hyb_protocol: After completion of the Klenow Pol I catalyzed reaction, the distribution of PCR products was examined on Agilent Bioanalyzer with the DNA 1000 kit.  The entire volume of the product (~50 μl) was used in the hybridization reaction on the Affymetrix Xenopus laevis Gene Chip following manufacturers instructions

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Normalization was not performed due to the nature of our experiment (because we are using genomic DNA, essentially all probes should hybridize well in target species).  The goal was to identify probes that do not hybridize well in non-target species.

organism: Xenopus muelleri

source_name: Xenopus muelleri female adult blood

label_protocol: 50-100 nanograms of fragmented gDNA were then amplified using the BioPrime Labeling System (Invitrogen) following the manufacturers instructions.

extract_protocol: Five micrograms of gDNA from each species was fragmented with Dpn I at 37°C for 3 hours.  Fragmented gDNA was purified with Qiagen PCR clean-up kit and the fragment distribution was checked on Agilent Bioanalyzer (Agilent) using the DNA 1000 assay.

treatment_protocol: Animal was immersed in MS222 and blood was immediately extracted

tag: Adult


title: breast cancer patient sample #7678

city: Baltimore

first: Wayne

last: Yu

state: MD

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

description: individual patient sample

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5) array CGH data extraction protocol.

data_processing: Linear normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: breast cancer patient sample #7678

label_protocol: 10 ng of genomic DNA was amplified with phi29 DNA polymerase at 30°C for 16 hours. Amplified DNA was then digested with 50 units of Alu I and Rsa I at 37° for 2 hours and purified by using QIAQuick PCR clean-up kit. Labeling reactions were performed with 7 ug aliquots of this DNA at 37C for 3 hours using BioPrime Array CGH Genomic Labeling Module with 3 umol Cy5- or Cy3-dUTP, Invitrogen. Labeled samples were purified , concentrated on a Centricon YM-30 column, Millipore.

extract_protocol: Genomic DNA extracted using Qiagen Dneasy mini kit following manufacturer's instructions

tag: human breast cancer with basal-like feature

source_name: human female blood pooled genomic DNA, Promega

tag: human female pooled genomic DNA, Promega


title: breast cancer patient sample #2062

description: individual patient sample

source_name: breast cancer patient sample #2062


title: Xenopus laevis genomic DNA

description: gDNA hybridization intensities for the target organism

organism: Xenopus laevis

source_name: Xenopus laevis male and female adult blood


title: breast cancer patient sample #12668

description: individual patient sample

source_name: breast cancer patient sample #12668


title: breast cancer patient sample #65244

description: individual patient sample

source_name: breast cancer patient sample #65244


title: breast cancer patient sample #37958

description: individual patient sample

source_name: breast cancer patient sample #37958


title: Xenopus borealis genomic DNA

organism: Xenopus borealis

source_name: Xenopus borealis male and female adult blood


title: breast cancer patient sample #21923-1

description: individual patient sample

source_name: breast cancer patient sample #21923-1


title: breast cancer patient sample #3763

description: individual patient sample

source_name: breast cancer patient sample #3763


title: breast cancer patient sample #40387

description: individual patient sample

source_name: breast cancer patient sample #40387


title: UF491_Xylem-Rep1

scan_protocol: As described elsewhere (http://www.nimblegen.com/products/lit/exp_userguide_2008_05_21.pdf).

source_name: (P. trichocarpa X P. deltoides) X P. deltoides segregating progeny, secondary xylem tissue


title: breast cancer patient sample #6275

description: individual patient sample

source_name: breast cancer patient sample #6275


title: breast cancer patient sample #39693

description: individual patient sample

source_name: breast cancer patient sample #39693


title: breast cancer patient sample #5100-2

description: individual patient sample

source_name: breast cancer patient sample #5100-2


title: breast cancer patient sample #4092

description: individual patient sample

source_name: breast cancer patient sample #4092


title: bipolar disorder, BA46-104

status: Public on Sep 03 2008

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

country: Japan

institute: RIKEN

description: Gene expression data in human prefrontal cortex

hyb_protocol: Biotin-labeled cRNA sample was hybridized according to manufacture's instruction.

scan_protocol: Hybridization signal on the chip was scanned using an HP GeneArray scanner (Hewlett-Packard).

data_processing: The data were normalized by median centering by GeneSpring software (Agilent)

source_name: bipolar disorder

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

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

tag: prefrontal cortex (BA46)

tag: bipolar disorder


title: control, BA46-105

source_name: control

tag: control


title: control, BA46-103


title: bipolar disorder, BA46-102


title: schizophrenia, BA46-101

source_name: schizophrenia

tag: schizophrenia


title: control, BA46-99


title: breast cancer patient sample #15502

description: individual patient sample

source_name: breast cancer patient sample #15502

source_name: human female blood pooled genomic DNA, Promega


title: breast cancer patient sample #9997

description: individual patient sample

source_name: breast cancer patient sample #9997


title: control, BA46-96


title: schizophrenia, BA46-97


title: breast cancer patient sample #30995

description: individual patient sample

source_name: breast cancer patient sample #30995


title: control, BA46-95


title: bipolar disorder, BA46-98


title: schizophrenia, BA46-100


title: control, BA46-91


title: schizophrenia, BA46-92


title: schizophrenia, BA46-94


title: schizophrenia, BA46-88


title: control, BA46-90


title: schizophrenia, BA46-85


title: control, BA46-86


title: control, BA46-84


title: schizophrenia, BA46-82


title: schizophrenia, BA46-93


title: control, BA46-80


title: breast cancer patient sample #20802

description: individual patient sample

source_name: breast cancer patient sample #20802


title: schizophrenia, BA46-81


title: schizophrenia, BA46-78


title: control, BA46-83


title: schizophrenia, BA46-75


title: control, BA46-70


title: bipolar disorder, BA46-74


title: bipolar disorder, BA46-76


title: schizophrenia, BA46-87


title: bipolar disorder, BA46-69


title: control, BA46-79


title: schizophrenia, BA46-66


title: control, BA46-71


title: schizophrenia, BA46-73


title: bipolar disorder, BA46-64


title: control, BA46-65


title: schizophrenia, BA46-68


title: bipolar disorder, BA46-57


title: bipolar disorder, BA46-62


title: control, BA46-59


title: bipolar disorder, BA46-58


title: control, BA46-77


title: control, BA46-67


title: control, BA46-60


title: bipolar disorder, BA46-61


title: bipolar disorder, BA46-72


title: control, BA46-56


title: schizophrenia, BA46-55


title: control, BA46-54


title: control, BA46-53


title: bipolar disorder, BA46-46


title: control, BA46-52


title: schizophrenia, BA46-45


title: bipolar disorder, BA46-48


title: schizophrenia, BA46-47


title: bipolar disorder, BA46-50


title: control, BA46-49


title: bipolar disorder, BA46-63


title: schizophrenia, BA46-44


title: bipolar disorder, BA46-34


title: bipolar disorder, BA46-42


title: bipolar disorder, BA46-36


title: schizophrenia, BA46-41


title: control, BA46-43


title: bipolar disorder, BA46-32


title: schizophrenia, BA46-37


title: control, BA46-38


title: bipolar disorder, BA46-28


title: schizophrenia, BA46-40


title: schizophrenia, BA46-39


title: control, BA46-29


title: control, BA46-35


title: schizophrenia, BA46-26


title: schizophrenia, BA46-31


title: schizophrenia, BA46-25


title: control, BA46-27


title: control, BA46-30


title: bipolar disorder, BA46-23


title: control, BA46-24


title: schizophrenia, BA46-22


title: control, BA46-19


title: bipolar disorder, BA46-21


title: control, BA46-33


title: Xenopus borealis Testis, biological rep 3

description: 1 of 3 biological replicates of gene expression data from sexually mature testis.

hyb_protocol: Hybridization to Affymetrix Xenopus laevis Genome expression array followed the manufacturer's (Affymetrix) protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data were RMA normalized using RMA Express and a probemask (based on perfect match probes for X.laevis and X.borealis).
Normalization of 3 biological replicates were performed with 3 biological replicates of X.borealis brain

source_name: Xenopus borealis, sexually mature testis

label_protocol: Two micrograms of total RNA was used to prepare biotin labeled cRNA probes following the manufacturer’s (Affymetrix) protocol.

extract_protocol: Total RNA was isolated using TRIzol® Reagent (Invitrogen Life Technologies) according to the manufacturer’s protocol and purified with RNeasy Mini Kit (Qiagen).

treatment_protocol: Animal was immersed in MS222 and gonad was immediately extracted

tag: Adult male Xenopus borealis (Kenya)


title: schizophrenia, BA46-17


title: Xenopus borealis Testis, biological rep 1


title: control, BA46-15


title: Xenopus borealis Testis, biological rep 2


title: schizophrenia, BA46-11


title: bipolar disorder, BA46-18


title: bipolar disorder, BA46-16


title: schizophrenia, BA46-9


title: bipolar disorder, BA46-14


title: bipolar disorder, BA46-13


title: bipolar disorder, BA46-8


title: schizophrenia, BA46-12


title: bipolar disorder, BA46-4


title: schizophrenia, BA46-7


title: bipolar disorder, BA46-6


title: bipolar disorder, BA46-2


title: schizophrenia, BA46-10


title: bipolar disorder, BA46-20


title: Normal, synovial membrane patient J12 (U133A)

status: Public on Sep 02 2008

city: Hannover

first: René

last: Huber

state: Lower Saxony

address: Carl-Neuberg-Str. 1

department: Institute for Clinical Chemistry

institute: Hannover Medical School

description: see publication for details

hyb_protocol: according to supplier´s instructions, Affymetrix

scan_protocol: by laser scanning (Hewlett Packard gene scanner)

data_processing: background corrected signal intensities were determined using the MAS 5.0 software (Affymetrix)

source_name: synovial membrane patient J12 (normal control)

extract_protocol: according RNeasy Kit, Qiagen

tag: sex

value: m

tag: age

tag: normal control


title: bipolar disorder, BA46-1


title: Normal, synovial membrane patient J2 (U133B)

description: see publication for details

data_processing: background corrected signal intensities were determined using the MAS 5.0 software (Affymetrix

source_name: synovial membrane patient J2 (normal control)

label_protocol: according to supplier´s instructions, Affymetrix

value: f

tag: normal controls


title: Normal, synovial membrane patient J7 (U133B)

description: see publication for details

source_name: synovial membrane patient J7 (normal control)


title: Rheumatoid arthritis, synovial membrane patient EB141 (U133B)

description: see publication for details

source_name: synovial membrane patient EB141 (rheumatoid arthritis)

treatment_protocol:
NSAID,
prednisolone,
Tilidin

tag: disease

value: rheumatoid arthritis


title: Normal, synovial membrane patient J19 (U133A)

description: see publication for details

source_name: synovial membrane patient J19 (normal control)


title: Rheumatoid arthritis, synovial membrane patient EB141 (U133A)

description: see publication for details


title: Rheumatoid arthritis, synovial membrane patient EB124 (U133A)

description: see publication for details

source_name: synovial membrane patient EB124 (rheumatoid arthritis)

treatment_protocol:
COX-2 inhibitor,
prednisolone,
quensyl


title: Normal, synovial membrane patient J7 (U133A)

description: see publication for details


title: Rheumatoid arthritis, synovial membrane patient EB108 (U133B)

description: see publication for details

source_name: synovial membrane patient EB108 (rheumatoid arthritis)

treatment_protocol:
NSARD,
prednisolone

tag: age 73


title: Osteoarthritis, synovial membrane patient EB100 (Affymetrx U133B)

description: see publication for details

source_name: synovial membrane patient EB100 (osteoarthritis)

treatment_protocol: NSARD

value: osteoarthritis


title: Osteoarthritis, synovial membrane patient EB140 (U133B)

description: see publication for details

source_name: synovial membrane patient EB149 (osteoarthritis)

treatment_protocol: NSAID


title: Normal, synovial membrane patient J2 (U133A)

description: see publication for details


title: schizophrenia, BA46-3


title: Normal, synovial membrane patient J12 (U133B)

description: see publication for details


title: Normal, synovial membrane patient J6 (U133A)

description: see publication for details

source_name: synovial membrane patient J6 (normal control)

tag: age :17


title: Osteoarthritis, synovial membrane patient EB140 (U133A)

description: see publication for details

source_name: synovial membrane patient EB140 (osteoarthritis)


title: Rheumatoid arthritis, synovial membrane patient EB110 (U133B)

description: see publication for details

source_name: synovial membrane patient EB110 (rheumatoid arthritis)


title: Normal, synovial membrane patient J6 (U133B)

description: see publication for details


title: Osteoarthritis, synovial membrane patient EB97 (U133B)

description: see publication for details

source_name: synovial membrane patient EB97 (osteoarthritis)

treatment_protocol:
NSARD,
prednisolone,
MTX


title: Rheumatoid arthritis, synovial membrane patient EB110 (U133A)

description: see publication for details


title: Rheumatoid arthritis, synovial membrane patient EB108 (U133A)

description: see publication for details


title: Rheumatoid arthritis, synovial membrane patient EB124 (U133B)

description: see publication for details


title: Osteoarthritis, synovial membrane patient EB104 (Affymetrx U133A)

description: see publication for details

source_name: synovial membrane patient EB104 (osteoarthritis)


title: Osteoarthritis, synovial membrane patient EB104 (U133B)

description: see publication for details


title: Osteoarthritis, synovial membrane patient EB99 (Affymetrx U133B)

description: see publication for details

source_name: synovial membrane patient EB99 (osteoarthritis)


title: Osteoarthritis, synovial membrane patient EB99 (Affymetrx U133A)

description: see publication for details


title: Osteoarthritis, synovial membrane patient EB94 (U133B)

description: see publication for details

source_name: synovial membrane patient EB94 (osteoarthritis)


title: Rheumatoid arthritis, synovial membrane patient EB74 (U133A)

description: see publication for details

source_name: synovial membrane patient EB74 (rheumatoid arthritis)


title: Osteoarthritis, synovial membrane patient EB90 (U133B)

description: see publication for details

source_name: synovial membrane patient EB90 (osteoarthritis)


title: Osteoarthritis, synovial membrane patient EB100 (Affymetrx U133A)

description: see publication for details


title: Osteoarthritis, synovial membrane patient EB97 (Affymetrx U133A)

description: see publication for details


title: Osteoarthritis, synovial membrane patient EB94 (U133A)

description: see publication for details


title: Rheumatoid arthritis, synovial membrane patient EB56 (U133B)

description: see publication for details

source_name: synovial membrane patient EB56 (rheumatoid arthritis)

treatment_protocol:
prednisolone,
MTX


title: Rheumatoid arthritis, synovial membrane patient EB56 (U133A)

description: see publication for details


title: Osteoarthritis, synovial membrane patient EB90 (U133A)

description: see publication for details

tag: diesease


title: Osteoarthritis, synovial membrane patient EB54 (U133B)

description: see publication for details

source_name: synovial membrane patient EB54 (osteoarthritis)


title: Rheumatoid arthritis, synovial membrane patient EB41 (U133B)

description: see publication for details

source_name: synovial membrane patient EB41 (rheumatoid arthritis)

treatment_protocol:
NSARD,
azulfidine,
prednisolone


title: Rheumatoid arthritis, synovial membrane patient EB40 (U133B)

description: see publication for details

source_name: synovial membrane patient EB40 (rheumatoid arthritis)

value: rheumatoid arthrits


title: Osteoarthritis, synovial membrane patient EB54 (U133A)

description: see publication for details


title: Rheumatoid arthritis, synovial membrane patient EB27 (U133B)

description: see publication for details

source_name: synovial membrane patient EB27 (rheumatoid arthritis)


title: Rheumatoid arthritis, synovial membrane patient EB35 (U133A)

description: see publication for details

source_name: synovial membrane patient EB35 (rheumatoid arthritis)

treatment_protocol:
NSARD,
azulfidine,
prednisolone,
MTX


title: Osteoarthritis, synovial membrane patient EB21 (U133B)

description: see publication for details

source_name: synovial membrane patient EB21 (oateoarthritis)


title: Rheumatoid arthritis, synovial membrane patient EB20 (U133B)

description: see publication for details

source_name: synovial membrane patient EB20 (rheumatoid arthritis)


title: Rheumatoid arthritis, synovial membrane patient EB74 (U133B)

description: see publication for details


title: Rheumatoid arthritis, synovial membrane patient EB41 (U133A)

description: see publication for details


title: Osteoarthritis, synovial membrane patient EB24 (U133B)

description: see publication for details

source_name: synovial membrane patient EB24 (osteoarthritis)


title: Rheumatoid arthritis, synovial membrane patient EB27 (U133A)

description: see publication for details


title: Rheumatoid arthritis, synovial membrane patient EB35 (U133B)

description: see publication for details

treatment_protocol:
NSARD,
prednisolone,
azulfidine,
MTX


title: Osteoarthritis, synovial membrane patient EB24 (U133A)

description: see publication for details


title: Osteoarthrisits, synovial membrane patient EB21 (U133A)

description: see publication for details

source_name: synovial membrane patient EB21 (osteoarthrisits)


title: Post-irradiated at 2.0Gy 24hrs Rep3

city: Montreal

first: Olivier

middle: Charles

last: Maes

state: Quebec

address: 3999 Cote Ste Catherine

department: Bloomfield Centre for Research in Aging

institute: Lady Davis Institute for Medical Research

description: A broad coverage of the human genome (approximately 6424 unique genes) was analyzed using the NIA Human MGC cDNA microarray, which consist of full-length cDNA clones generated by the National Cancer Institute’s Mammalian Gene Collection (http://mgc.nci.nih.gov/).

hyb_protocol: Nadon NL, Mohr D, Becker KG. National Institute on Aging microarray facility--resources for gerontology research. Journals of Gerontology Series A-Biological Sciences & Medical Sciences 2005;60(4):413-5 (PMID: 15933377)

scan_protocol: Hybridization intensities were measured using a Storm PhosphorImager (Amersham BioSciences, USA).

data_processing:
Data acquisition and global background correction were obtained using the Array-Pro Analyzer 4.5 software (Media Cybernetics, MD, USA).  There has been no data processing or normalization of the background-corrected raw data prior to their analysis.
Net intensity was derived from whole cell area measurement and corrected with mean intensity from background cells, calculated using a biquadratic polynomial.

source_name: Foreskin fibroblasts (AG1522)

label_protocol: Three µg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and M-MLV reverse transcribed (Invitrogen) in the presence of 100 mCi of [32P]dCTP (Amersham Bioscience, Piscataway, NJ) according to Maes et al. 2007 (Neurobiol Aging. 28:1795-809).

growth_protocol: Cells and culture conditions were previously described by Wu et al. (2002)  Journal of radiation research 43 Suppl:S181-5.

extract_protocol: Total RNA was extracted by Trizol reagent.

treatment_protocol: Confluent cell cultures were irradiated with 250 kV X-rays at two dose levels, either 0.1 or 2 Gy, at NASA’s Johnson Space Center (JSC, Houston, TX, USA). The exposure at 2 Gy took 3.2 minutes; that at 0.1 Gy took 42 seconds.

tag: Low-LET irradiation of  2.0 Gy

tag: Expression after 24 hrs


title: Post-irradiated at 2.0Gy 24hrs Rep2


title: Post-irradiated at 2.0Gy 2hrs Rep3

tag: Expression after 2hrs


title: Post-irradiated at 2.0Gy 24hrs Rep1


title: Rheumatoid arthritis, synovial membrane patient EB20 (U133A)

description: see publication for details

treatment_protocol:
NSARD,
azulfidine,
prednisolone,

tag: disease:rheumatoid arthritis