title: EPO+LY donor 3

description:
Simple annotation: Hematopoiesis, Normal tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/53417.gif
Compound Based Treatment: 1

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 0; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:48:04; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Agilent Technologies Scanner; Parameter Pixel Size = 10; Parameter Scan Time = 11:48:04; Parameter Scanner Model = G2505B; Parameter Scanning software version = A.6.3.1; Parameter Scanning software = ChipScan; Parameter Scan Date = 2004-05-05; Performer: Einar Andreas,,Sivertsen

source_name: Amplified Universal Human Reference RNA (Stratagene)

source_name: mplified RNA from early erythroid progenitors stimulated with EPO and LY


title: Case_19_2005061504

status: Public on Nov 08 2006

type: genomic

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Comparison between individual with Gastrointestinal stromal tumor (GIST) vs normal individual

hyb_protocol: Probe preparation and preblocking of the slide were performed as described by Fiegler et al. (2003). Equal amounts (200 pmol) of Cy5- and Cy3-labeled probe were combined with 100 ug Cot-1 DNA followed by an ethanol precipitation. Resuspension of the pellet was done in hybridization buffer (50% formamide, 10% dextran sulfate, 0.1% Tween 20, 2 x SSC, and 10 mM Tris HCl, pH 7.5) containing 400 ug yeast tRNA to hybridize a spotting area of 24 x 60 mm.  The slide was blocked with 50 ug Cot-1 DNA and 300 ug salmon sperm DNA dissolved in 60 ul hybridization buffer. Blocking solution and probe mixture were denaturated for 10 min in a water bath at 75C. Blocking solution was then placed on the slide covered with a coverslip (24 x 60 mm) and placed in a humid chamber. Meanwhile, the probe was placed at 37C for preannealing. After 1 hr of blocking, the coverslip was removed and probe was placed on the slide. After placing a coverslip (24 x 60 mm), the slide was placed in a humid chamber saturated with 20% formamide and 2 x SSC. Hybridization was allowed to take place for two nights at 37C. Posthybridization washes were performed as described by Fiegler et al. (2003). The coverslip was removed by placing the slide in PBS with 0.05% Tween 20, followed by a 10- min wash in a fresh solution of PBS/Tween 20 at room temperature, 30 min in 50% formamide/2 x SSC at 42C, and 10 min in PBS/0.05% Tween 20 at room temperature. Slides were spin dried at 1000 rpm for 5 min. See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

scan_protocol: Array slides were scanned with a GenePix 4000B scanner and hybridization signals were evaluated using GenePixPro 3.0 image analysis software.

data_processing: All data analysis was performed with Excel. Spot intensities were corrected for local background, and only spots with signal intensities at least two fold above background signal intensities were included in the final analysis. For each clone, a ratio of Cy5 to Cy3 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of the autosomes followed by the 2D normalization. Normalized ratios of the duplicates were averaged and a log2 value was calculated. Precise localizations of clones spotted on the array were obtained from the Ensemble database (www.ensembl.org/Homo_sapiens). The Normalized ratio is not included  in the submitted raw data.

molecule: genomic DNA

organism: Homo sapiens

source_name: control DNA

label_protocol: The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy5-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

extract_protocol: Genomic DNA was isolated from lymphocytes of normal individuals.

tag: normal individual, Tissue

value: lymphocyte

source_name: 68/F Rectum

label_protocol: The gDNA was labeled by a random prime labeling system (Bioprime DNA labeling System; Invitrogen) using Cy3-labeled dCTPs (Amersham Biociences). See also Vermeesch et al: Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2005, 53:413-22.

extract_protocol: Genomic DNA was extracted from a frozen fragment of the tumor, using a microdissection technique to reduce contamination with non-neoplastic tissue. DNA was extracted using a standard proteinase K digestion followed by phenol/chloroform extraction and ethanol precipitation.

tag: Age

value: 68, Gender:female, tissue :rectum


title: Case_43_2004070148

scan_protocol: Array slides were scanned with an Agilent G2565 scanner and hybridisation signals were evaluated using Array Vision V7 image analysis software.

source_name: 49/F Mesent.

value: 49, Gender:female, tissue :Mesent.


title: Case_35_2005061511

source_name: 44/F Stomach

value: 44, Gender:female, tissue :stomach


title: Case_46_2004070102

source_name: 77/M Stomach

value: 77, Gender:male, tissue :Stomach


title: Case_46_2004070103


title: Case_15_2005090103

source_name: 66/F Stomach

value: 66, Gender:female, tissue :stomach


title: Case_19_2005061503


title: Case_65_2005092904b

source_name: 57/M small intestin

value: 57, Gender:male, tissue :small intestin


title: Case_40_2004121333

source_name: 64/M Small intestin

value: 64, Gender:male, tissue :small intestin


title: Case_41_2004121317

source_name: 61/F Retro

value: 61, Gender:female, tissue :retro


title: Case_38_2004090152

source_name: 82/M Stomach

value: 82, Gender:male, tissue :stomach


title: Case_28_2005061523

source_name: 68/M Small intestin

value: 68, Gender:male, tissue :Small intestin


title: Case_43_2004070149


title: Case_15_2005090102


title: Case_61_2005101312b

source_name: 53/M duodenum

value: 53, Gender:male, tissue :duodenum


title: Case_65_2005092904a


title: Case_36_2004121318

source_name: 81/F Stomach

value: 81, Gender:female, tissue :stomach


title: Case_28_2005061524


title: Case_45_2005061505

source_name: 46/F small intestin

value: 46, Gender:female, tissue :small intestin


title: Case_34_2004090157

source_name: 55/F Duodenum

value: 55, Gender:female, tissue :duodenum


title: Case_33_2004070167

source_name: 82/F Stomach

value: 82, Gender:female, tissue :stomach


title: Case_1_2004042904

value: 77, Gender:male, tissue :stomach


title: Case_61_2005101312a

value: lymphocyte


title: Case_52_2005092905b

source_name: 69/M Mesent.

value: 69, Gender:male, tissue :Mesent.


title: Case_64_2005060866

source_name: 29/M small intestin

value: 29, Gender:male, tissue :small intestin

source_name: control DNA


title: Case_47_2005101303b


title: Case_52_2005092905a


title: Case_32_2004121328

source_name: 61/F small intestin

value: 61, Gender:female, tissue :small intestin


title: Case_64_2005060872


title: Case_47_2005101303a

value: 77, Gender:male, tissue :Stomach


title: Case_31_2004070114

source_name: 45/M Rectum

value: 45, Gender:male, tissue :rectum


title: Case_59_2005060109

source_name: 64/F Stomach

value: 64, Gender:female, tissue :Stomach


title: Case_58_2005060117

source_name: 73/F Stomach

value: 73, Gender:female, tissue :Stomach


title: Case_42_2005092908b


title: Case_59_2005060110


title: Case_58_2005060118


title: Case_44_2005060122

source_name: 71/M Stomach

value: 71, Gender:male, tissue :stomach


title: Case_3_2004090156

source_name: 55/M Stomach

value: 55, Gender:male, tissue :stomach


title: Case_37_2005031544

source_name: 78/F Stomach

value: 78, Gender:female, tissue :stomach


title: Case_1_2004042903

source_name: 77/M Stomach


title: Case_42_2005092908a


title: Case_27_2005092907b

source_name: 71/M Duodenum

value: 71, Gender:male, tissue :duodenum


title: Case_37_2005031543


title: Case_27_2005092907a


title: Case_30_2004090151

source_name: 62/M Stomach

value: 62, Gender:male, tissue :stomach


title: Case_49_2004121322

source_name: 60/M Stomach

value: 60, Gender:male, tissue :Stomach


title: Case_28_2004121310

source_name: 68/M Small intestin

value: 68, Gender:male, tissue :Small intestin


title: Case_44_2005060123


title: Case_23_2005060111

source_name: 64/M Small intestin

value: 64, Gender:male, tissue :small intestin


title: Case_24_2005092910b

source_name: 81/M Small intestin

value: 81, Gender:male, tissue :small intestin


title: Case_31_2004070113

value: lymphocyte


title: Case_23_2005060112


title: Case_29_2004121309

source_name: 34/M Stomach

value: 34, Gender:male, tissue :stomach


title: Case_2_2005033037

source_name: 75/M Stomach

value: 75, Gender:male, tissue :stomach


title: Gene expression profiling in zebrafish embryos exposed to 3,4-dichloroaniline (3,4-DCA), test 2, control cy3 labeled

type: RNA

city: Leipzig

first: Doris

last: Voelker

address: Permoser Str. 15

department: Cell Toxicology

country: Germany

institute: UFZ Centre for Environmental Research Leipzig-Halle

hyb_protocol: The two labelling reactions were combined, vacuum dried and resuspended in 32 µl hybridisation buffer (50% formamide, 5x SSC, 0.1% SDS and 0.1 mg/ml salmon sperm DNA). The samples were denaturised by heating to 95°C for 3 minutes. A volume of 30 µl of the reaction were hybridised to the 14 k zebrafish oligonucleotide slides. The slides were incubated for 14 hours at 42°C in a water bath. Washing was performed in 0.1% SDS, 2x SSC for 10 minutes, followed by three additional washes for 10 minutes in 0.2x SSC, 0.1x SSC and 0.05x SSC at room temperature. The slides were dried by centrifugation. Microarray hybridisations were performed for all replicates of samples treated with 12.4 µM 3,4-DCA (n = 3). For every single experiment, dye-swaps were performed.

scan_protocol: The hybridised slides were scanned at 10 µm resolution using the ScanArray Express Scanner (Perkin Elmer, USA) at 532 nm (Cy3) and 635 nm (Cy5). The laser power of the scanner was adjusted between 80% to 100% and PMT (photo multiplier value) was preset between 60 and 80, depending on the amount of background fluorescence and the saturation of signals.

data_processing: Microarray data were analyzed using the TM4 software package (http://www.tm4.org/) (Saeed et al., 2003). TIGR Spotfinder 3.0.0 beta was used to identify spots on the array and to assess the quality of spots for downstream analyses. TIGR MIDAS 2.19 was then used to adjust the data by applying LOWESS normalization (Quackenbush, 2002). A 30% quantile was used to remove data with weak fluorescence recordings for both Cy3 and Cy5 prior to subsequent statistical analyses. Genes with significantly altered expression patterns were identified by one-class SAM (significance analysis of microarrays) (Tusher et al., 2001).

molecule: total RNA

organism: Danio rerio

source_name: zebrafish embryos (48 hpf) exposed to control medium, test 2, cy3-labeled

label_protocol:
For indirect labelling of cDNA to the cyanine dyes, a reverse transcriptase labelling mixture including aminoallyl-UTP was added to the RNA. The reaction was incubated at 42°C for 14 hours to generate aminoallyl-labelled cDNA.
Unincorporated aa-dUTP and free amines were removed using the QIAquick PCR purification kit (Qiagen, Hilden, Germany). The samples were dried in a vacuum centrifuge. Aminoallyl-labelled cDNA was resuspended in 4.5 µl 0.1 M sodium carbonate buffer (pH 9.0) and mixed with 4,5 µl of Cy3 or Cy5 monoreactive dye (Amersham Biosciences, Munich, Germany) in DMSO. Dye coupling was performed for one hour at room temperature in the dark. Uncoupled dyes were removed using the QIAquick PCR purification kit (Qiagen).

extract_protocol: Total RNA was extracted from zebrafish embryos using Trizol Reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer`s instructions. Contaminations of genomic DNA were removed by treatment with DNAse I (Roche, Grenzach, Germany) for 15 min at 25° C.

treatment_protocol: Collection of zebrafish eggs and exposure of embryos were performed according to established protocols (Nagel, 1998; Schulte and Nagel, 1994). Control treatment was performed in 10 ml test medium (2 mM CaCl2, 0.5 mM MgSO4, 0.75 mM NaHCO3, 0.08 mM KCl) in triplicates starting on three different days.

tag: zebrafish embryos (48 hpf) exposed to control medium directly upon fertilization

tag: (hpf = hours post fertilization)

source_name: zebrafish embryos (48 hpf) exposed to 3,4-dichloroaniline, test 2, cy5-labeled

treatment_protocol: Collection of zebrafish eggs and exposure of embryos were performed according to established protocols (Nagel, 1998; Schulte and Nagel, 1994). Exposure was performed in 10 ml test medium (2 mM CaCl2, 0.5 mM MgSO4, 0.75 mM NaHCO3, 0.08 mM KCl) in triplicates starting on three different days. The concentration used for microarray analysis corresponded to the LOEC (lowest observed effect concentration) for survival (12.4 µM) of the embryo test. 100 zebrafish embryos were exposed from two hours post fertilization (hpf) for up to 48 h hpf. Control embryos were exposed in 10 ml test medium.


title: Case_22_2004121341

source_name: 65/M Small intestin

value: 65, Gender:male, tissue :small intestin

source_name: control DNA


title: Case_20_2004121323

source_name: 44/M Duodenum

value: 44, Gender:male, tissue :duodenum


title: Case_24_2005092910a


title: Case_26_2004121340

source_name: 68/F Colon

value: 68, Gender:female, tissue :colon


title: Case_12_2005060119

source_name: 46/M Stomach

value: 46, Gender:male, tissue :stomach


title: Case_18_2005101313a

source_name: 71/M Stomach


title: Gene expression profiling in zebrafish embryos exposed to 3,4-dichloroaniline (3,4-DCA), test 3, control cy5-labeled

source_name: zebrafish embryos (48 hpf) exposed to control medium, test 3, cy5-labeled

treatment_protocol: Collection of zebrafish eggs and exposure of embryos were performed according to established protocols (Nagel, 1998; Schulte and Nagel, 1994). Control treatment was performed in 10 ml test medium (2 mM CaCl2, 0.5 mM MgSO4, 0.75 mM NaHCO3, 0.08 mM KCl) in triplicates starting on three different days. The concentration used for microarray analysis corresponded to the LOEC (lowest observed effect concentration) for survival (12.4 µM) of the embryo test. 100 zebrafish embryos were exposed from two hours post fertilization (hpf) for up to 48 h hpf. Control embryos were exposed in 10 ml test medium.

source_name: zebrafish embryos (48 hpf) exposed to 3,4-dichloroaniline, test 3, cy3-labeled

extract_protocol: Total RNA was extracted from zebrafish embryos using Trizol Reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer`s instructions. Contaminations of genomic DNA were removed by treatment with DNAse I (Roche, Grenzach, Germany) for 15 min at 25° C


title: Case_18_2005101313b


title: Gene expression profiling in zebrafish embryos exposed to 3,4-dichloroaniline (3,4-DCA), test 3, control cy3-labeled

source_name: zebrafish embryos (48 hpf) exposed to control medium, test 1, cy3-labeled

source_name: zebrafish embryos (48 hpf) exposed to 3,4-dichloroaniline, test 3, cy5-labeled


title: Gene expression profiling in zebrafish embryos exposed to 3,4-dichloroaniline (3,4-DCA), test2, control cy5 labeled

source_name: zebrafish embryos (48 hpf) exposed to control medium, test 2, cy5-labeled

source_name: zebrafish embryos (48 hpf) exposed to 3,4-dichloroaniline, test 1, cy3-labeled


title: Case_11_2005031546

source_name: 49/M Stomach

value: 49, Gender:male, tissue :stomach


title: Case_2_2005033038


title: Case_17_2004090141

source_name: 69/M Stomach

value: 69, Gender:male, tissue :stomach


title: Gene expression profiling in zebrafish embryos (48 hpf) exposed to 3,4-dichloroaniline, test1, control cy3 labeled

source_name: pool of 100 zebrafish embryos (48 hpf) exposed to control medium, test 1, cy3-labeled

treatment_protocol: Collection of zebrafish eggs and exposure of embryos were performed according to established protocols (Nagel, 1998; Schulte and Nagel, 1994). 100 zebrafish embryos were exposed from two hours post fertilization (hpf) for up to 48 h hpf. Control embryos were exposed in 10 ml test medium (2 mM CaCl2, 0.5 mM MgSO4, 0.75 mM NaHCO3, 0.08 mM KCl).

source_name: pool of 100 zebrafish embryos (48 hpf) exposed to 3,4-dichloroaniline, test 1, cy5-labeled

treatment_protocol: Collection of zebrafish eggs and exposure of embryos were performed according to established protocols (Nagel, 1998; Schulte and Nagel, 1994). Exposure was performed in 10 ml test medium (2 mM CaCl2, 0.5 mM MgSO4, 0.75 mM NaHCO3, 0.08 mM KCl) in triplicates starting on three different days. The concentration used for microarray analysis corresponded to the LOEC (lowest observed effect concentration) for survival (12.4 µM) of the embryo test. 100 zebrafish embryos were exposed from two hours post fertilization (hpf) for up to 48 h hpf.

tag: zebrafish embryos (48 hpf) exposed to the LOEC (lowest observed effect concentration) of the environmental contaminant 3,4 dichloroaniline (12.4 µM) directly upon fertilization


title: Case_65_2005092026b

source_name: 57/M small intestin

value: 57, Gender:male, tissue :small intestin


title: Case_19_2004040112

source_name: 68/F Rectum

value: 68, Gender:female, tissue :rectum


title: Case_13_2005092903b

source_name: control DNA

source_name: 51/M Stomach

value: 51, Gender:male, tissue :stomach


title: Case_10_2005031548

source_name: 75/F Stomach

value: 75, Gender:female, tissue :stomach


title: Case_12_2005060120

source_name: 46/M Stomach


title: Case_13_2005092903a


title: Case_16_2004090140

source_name: 25/F Stomach

value: 25, Gender:female, tissue :stomach


title: Gene expression profiling in zebrafish embryos exposed to 3,4-dichloroaniline (3,4-DCA), test 1, control cy5 labeled

source_name: zebrafish embryos (48 hpf) exposed to control medium, test 1, cy5-labeled


title: Case_15_2004070118

source_name: 66/F Stomach

value: 66, Gender:female, tissue :stomach


title: Case_21_2004121324

source_name: 46/M Small Intestin

value: 46, Gender:male, tissue :small intestin


title: Case_11_2005031545


title: mouse kidney antisense U74A

status: Public on Nov 07 2006

city: Newcastle

first: Andreas

last: Werner

address: Framlington Place

department: Cell and Molecular Biosciences

country: United Kingdom

institute: Newcastle University

description: Antisense transcripts: Reversely annotated probesets identified using the mask provided by Affymetrix to distinguish beween reverse and forward probe sets.

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip? Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Mus musculus

source_name: total mouse kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6.75 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Kidneys were dissected, rinsed in ice cold PBS and directly used for RNA extraction with TRIzol (Invitrogen).

tag: Strain C57B6

tag: Male, age 2 weeks


title: mouse kidney antisense U74B


title: Case_19_2004040111


title: Case_65_2005092028a


title: SUP fraction for the analysis of Distibution of Scc1 on Chromosome VI

status: Public on Nov 06 2006

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: Sup fraction used for the normalization of Scc1 distribution data on chromosome VI.

data_processing: The protocol provided by Affymetrix (GCOS ver1.4) was used.

organism: Saccharomyces cerevisiae

source_name: Sup fraction (equal to Whole cell extract DNA)

tag: Benomyl arrested wild type yeast cell was used.


description: Distribution of hinge-substituted SMC on chromosome VI. No binding was detected.

source_name: Chromatin-immunoprecipitated DNA

tag: Strain K13585 (MATa,(Smc1p14, Smc3MP1-HA3)) was used. W303 back.


title: Scc1 distribution in G2 phase(Chromosome VI)

description: Distribution of Scc1 on chromosome VI.

tag: Scc1 was tagged by 6HA. Cells were arrested in G2 phase by benomyl. Wild type cells.


title: SUP fraction for the analysis of Distibution of hinge-substituted SMCs on Chromosome VI

description: SUP fraction for the normalization of distribution of hinge-substituted SMC on chromosome VI.

tag: Strain K13585 (MATa,(Smc1p14, Smc3MP1-HA3)), W303 back, was used.


title: mouse brain antisense U74B

source_name: total mouse brain

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: The brain was dissected, rinsed in ice cold PBS and directly used for RNA extraction with TRIzol (Invitrogen).

tag: Strain 129SvJ

tag: Male, age 5 weeks


title: mouse brain antisense U74A


title: mating responsive genes 16

status: Public on Nov 03 2006

city: Athens

first: Paul

last: Mack

state: GA

address: 1057 Green St.

department: Genetics

country: USA

institute: University of Georgia

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "335.17UGA.CEL" and "6hrUGA17.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm

data_processing: RMA (Irizarry 2003), probe-based linear model (Chu et al 2002)

label: Biotin (Enzo RNA transcript Labeling Kit)

organism: Drosophila melanogaster

source_name: female lower reproductive tract

growth_protocol: 12 hr light/dark cycle 23C + or - 2C holding and culturing regimes

extract_protocol: TRIzol - chloroform

treatment_protocol: Females were all same aged (3 days old) and either mated or not. Mated females were dissected at the following timeepoints: 0, 3, 6, 24 hrs postmating. Unmated (control) females were dissected at times interspersed with dissections of mated females.

tag: Females from this sample were mated then dissected 6hrs postmating.


title: mating responsive genes 19

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "294.UGA18" and "24hrUGA18.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm

tag: Females from this sample were mated then dissected 24hrs postmating.


title: mating responsive genes 13

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "261.11uga.CEL" and "3hrUGA11.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm

tag: Females from this sample were mated then dissected 3hrs postmating.


title: mating responsive genes 20

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "336.19UGA.CEL" and "24hrUGA19.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: Case_10_2005031547


title: mating responsive genes 17

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "464.36.cel" and "6hrUGA36.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: mating responsive genes 11

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "466.40.cel" and "0hrUGA40.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm

tag: Females from this sample were mated then dissected immediately following mating.


title: mating responsive genes 14

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "460.12.cel" and "3hrUGA12.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: mating responsive genes 18

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "565.49uga.cel" and "6hrUGA49.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: mating responsive genes 9

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "463.21.cel" and "0hrUGA21.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: mating responsive genes 21

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "564.48" and "24hrUGA48.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: JKD6051 and JKD6052 genomic comparison

city: Heidelberg

first: Benjamin

middle: Peter

last: Howden

state: Victoria

address: Studley Rd

department: Infectious Diseases

country: Australia

institute: Austin Health

description:
Genomic DNA was extracted after growth in brain heart infusion broth
Two µg of genomic DNA from each isolate was digested with AluI then purified using the QIAquick PCR purification kit (Qiagen). Cy3 and Cy5 were directly incorporated during cDNA synthesis and the probe was hybridized to TIGR version2 Staphylococcus aureus arrays. Slide data was obtained using IMAGENE.

data_processing: The data was normalized and analyzed using freely available filters and plug-in applications for the BioArray Software Environment (BASE) (available at http://base.thep.lu.se). The data was subjected to a global median ratio and Lowess transformation. The fold ratio of the background-corrected mean signal intensities for each gene ID in the data set were calculated.

organism: Staphylococcus aureus

tag: hetero-vancomycin intermediate staphylococcus aureus (hVISA) strain related to the vancomycin susceotible strain JKD6052

tag: Vancomycin susceptible Staphylococcus aureus (VSSA) strain, precursor of JKD6051


title: JKD6021 and JKD6023 genomic comparison

tag: Vancomycin intermediate Staphylococcus aureus (VISA) strain, related to the vancomycin susceptible strain JKD6021

tag: Vancomycin susceptible Staphylococcus aureus (VSSA) strain, precursor of JKD6023


title: JKD6008 and JKD6009 genomic comparison

tag: Vancomycin intermediate Staphylococcus aureus (VISA) strain related to the vancomycin susceptible strain JKD6009

tag: Vancomycin susceptible Staphylococcus aureus (VSSA), precursor of JKD6008


title: JKD6000 and JKD6001 genomic comparison

tag: Vancomycin intermediate Staphylococcus aureus (VISA) strain related to vancomycin susceptible strain JKD6000

tag: Vancomycin susceptible staphylococcus aureus strain (VSSA), precursor of VISA strain JKD6001


title: mating responsive genes 10

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "465.39.cel" and "0hrUGA39.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: JKD6004 and JKD6005 genomic comparison

tag: hetero-vancomycin intermediate Staphylococcus (hVISA) strain, related to the vancomycin susceptible strain JKD6004

tag: Vancomycin susceotible staphylococcus aureus (VSSA) strain, precursor of the hVISA strain JKD6005


title: mating responsive genes 12

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "260.10uga.CEL" and "3hrUGA10.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: mating responsive genes 7

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "334.14UGA.CEL" and "0hrUGA14.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: mating responsive genes 4

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "295.UGA8C.cel" and "CtrlUGA8C.CEL" keywords: reproduction, reproductive tract, accessory gland proteins, sperm

tag: females of this sample were unmated controls


title: mating responsive genes 2

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "209.cont2-7.cel" and "CtrlUGA2-7.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm

tag: female lower reproductive tract = upper uterus, seminal receptacle, paired spermathecae, paired accessory glands.


title: Case_15_2004070119

description: Comparison between individual with Gastrointestinal stromal tumor (GIST) vs normal individual

tag: normal individual, Tissue

tag: Age


title: mating responsive genes 1

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "217.1C.cel" and "CtrlUGA1C.CEL".


title: mating responsive genes 8

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "457.20.cel" and "0hrUGA20.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: mating responsive genes 15

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "292.UGA15.CEL" and "3hrUGA15.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 6

city: Seattle

first: Yasuhiro

last: Oda

state: WA

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

department: Department of Microbiology

institute: University of Washington

description: The software package lcDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Duplicate calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides for each (10 slides in total) were used to generate each data set.

data_processing: Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA).

organism: Rhodopseudomonas palustris

source_name: Comparative experiment (#1-2) of wild-type vs hupV mutant

tag: RNA from hupV mutant grown under N2-fixing conditions

tag: RNA from wild-type grown under N2-fixing conditions


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 5

source_name: Comparative experiment (#1-1) of wild-type vs hupV mutant


title: mating responsive genes 6

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "333.13UGA.CEL" and "0hrUGA13.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm

tag: Females from this sample were mated then dissected immediately following mating.


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 12

data_processing: Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA)

source_name: Comparative experiment (#1-2) of wild-type vs hupS mutant

tag: RNA from hupS mutant grown under N2-fixing conditions


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 10

source_name: Comparative experiment (#3-2) of wild-type vs hupV mutant


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris11

source_name: Comparative experiment (#1-1) of wild-type vs hupS mutant


title: mating responsive genes 5

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "297.UGA10C.cel" and "CtrlUGA10C.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 15

source_name: Comparative experiment (#2-1) of wild-type vs hupS mutant

tag: RNA from wild-type mutant grown under N2-fixing conditions


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 8

source_name: Comparative experiment (#2-2) of wild-type vs hupV mutant


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 9

source_name: Comparative experiment (#3-1) of wild-type vs hupV mutant


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 14


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 13


title: mating responsive genes 3

description: Three-day-old mated and unmated females were dissected to remove the lower reproductive tract (upper uterus, sperm-storage organs, and accessory glands). Mated females were dissected either immediately following mating (0 hr) or at 3, 6, or 24 hrs following the termination of mating. Tracts of 12-40 females of like category were pooled and total RNA extracted via a TRIzol-based protocol. Processing and labeling of transcript was performed by the Molecular Biology Core Facility at the Medical College of Georgia. Arrays from mated females at the different timepoints were compared to unmated females. This sample is also known as "218.3C.cel" or "CtrlUGA3C.CEL". keywords: reproduction, reproductive tract, accessory gland proteins, sperm


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 2

source_name: Calibration experiment (#1-2)

tag: Mixed RNA from wild-type and hupV mutant grown under nitrogen-fixing conditions


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 4

source_name: Calibration experiment (#2-2)


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 7

source_name: Comparative experiment (#2-1) of wild-type vs hupV mutant


title: 15caf1kr

city: Toulouse

first: Serguei

last: Sokol

address: 135 av de Rangueil

department: Lab. Biotech. and Bioprocess

country: France

institute: INSA

description: Yeast treated at caffeine (2mM) vs non treated. 15 min from the start of treatment.

data_processing: VALUE=log(CH2/CH1)-K, where CH1=max(10,CH1_SIG_MEDIAN-CH1_BKD_MEDIAN), same for CH2. K - is a normalization coefficient K=mean_over_all_spots(log(CH2/CH1))

tag: 'drug

value: caffeine', 'time:15 min', 'concentration:0mM'

value: caffeine', 'time:15 min', 'concentration:2mM'


title: 15caf2kr

description: Yeast treated at caffeine (20mM) vs non treated. 15 min from the start of treatment.

value: caffeine', 'time:15 min', 'concentration:20mM'


title: cr5_2_kr

description: Yeast treated at congo red (0.1mg/ml) vs non treated. 5 min from the start of treatment.

value: congo red', 'time:5 min', 'concentration:0mg/ml'

value: congo red', 'time:5 min', 'concentration:0.1mg/ml'


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 1

source_name: Calibration experiment (#1-1)


title: 90caf1kr

description: Yeast treated at caffeine (2mM) vs non treated. 90 min from the start of treatment.

value: caffeine', 'time:90 min', 'concentration:0mM'

value: caffeine', 'time:90 min', 'concentration:2mM'


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris3

source_name: Calibration experiment (#2-1)


title: cfw90_2_kg

description: Yeast treated at calcofluor white (0.1mg/ml) vs non treated. 90 min from the start of treatment.

data_processing: VALUE=log(CH1/CH2)-K, where CH1=max(10,CH1_SIG_MEDIAN-CH1_BKD_MEDIAN), same for CH2. K - is a normalization coefficient K=mean_over_all_spots(log(CH1/CH2))

value: calcofluor white', 'time:90 min', 'concentration:0.1mg/ml'

value: calcofluor white', 'time:90 min', 'concentration:0mg/ml'


title: cr90_2_kr

description: Yeast treated at congo red (0.1mg/ml) vs non treated. 90 min from the start of treatment.

value: congo red', 'time:90 min', 'concentration:0mg/ml'

value: congo red', 'time:90 min', 'concentration:0.1mg/ml'


title: cr5_1_kr

description: Yeast treated at congo red (0.02mg/ml) vs non treated. 5 min from the start of treatment.

value: congo red', 'time:5 min', 'concentration:0.02mg/ml'


title: 5caf2kr

description: Yeast treated at caffeine (20mM) vs non treated. 5 min from the start of treatment.

value: caffeine', 'time:5 min', 'concentration:0mM'

value: caffeine', 'time:5 min', 'concentration:20mM'


title: Regulation of uptake hydrogenase and effects of hydrogen utilization on gene expression in Rhodopseudomonas palustris 16

source_name: Comparative experiment (#3-2) of wild-type vs hupS mutant


title: 5caf1kr

description: Yeast treated at caffeine (2mM) vs non treated. 5 min from the start of treatment.

value: caffeine', 'time:5 min', 'concentration:2mM'


title: 90caf2kr

description: Yeast treated at caffeine (20mM) vs non treated. 90 min from the start of treatment.

value: caffeine', 'time:90 min', 'concentration:20mM'


title: cr90_1_kr

description: Yeast treated at congo red (0.02mg/ml) vs non treated. 90 min from the start of treatment.

value: congo red', 'time:90 min', 'concentration:0.02mg/ml'


title: cr15_1_kr

description: Yeast treated at congo red (0.02mg/ml) vs non treated. 15 min from the start of treatment.

value: congo red', 'time:15 min', 'concentration:0mg/ml'

value: congo red', 'time:15 min', 'concentration:0.02mg/ml'


title: cfw5_2_0704

description: Yeast treated at calcofluor white  (0.1mg/ml) vs non treated. 5 min from the start of treatment.

value: calcofluor white', 'time:5 min', 'concentration:0mg/ml'

value: calcofluor white', 'time:5 min', 'concentration:0.1mg/ml'


title: cfw5_1_0704

description: Yeast treated at calcofluor white  (0.02mg/ml) vs non treated. 5 min from the start of treatment.

value: calcofluor white', 'time:5 min', 'concentration:0.02mg/ml'


title: cfw90_1_0704

description: Yeast treated at calcofluor white  (0.02mg/ml) vs non treated. 90 min from the start of treatment.

value: calcofluor white', 'time:90 min', 'concentration:0.02mg/ml'


title: cr15_2_kr

description: Yeast treated at congo red (0.1mg/ml) vs non treated. 15 min from the start of treatment.

value: congo red', 'time:15 min', 'concentration:0.1mg/ml'


title: vcc1723  wt stationary phase

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Stationary phase, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50966.gif

hyb_protocol: not provided

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1010, 26880; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.17; Parameter Scan Time = 12:22:43; Parameter PMT Volts = 500; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 178234; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.13; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.17; Parameter Scan Time = 12:22:43; Parameter PMT Volts = 710; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 177460; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.25; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov

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

organism: Vibrio cholerae

source_name: wt mid log  in LB 37 C ( 2 ug RNA)

label_protocol: not provided

extract_protocol: not provided

tag: wt mid log  in LB 37 C ( 2 ug RNA)

source_name: wt 11h in LB 37C ( 2 ug RNA)

tag: wt 11h in LB 37C ( 2 ug RNA)


title: vcc 629  rpoS mutant versus wt

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50959.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2090, 26890; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.67; Parameter Scan Time = 11:16:11; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 178168; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.67; Parameter Scan Time = 11:16:11; Parameter PMT Volts = 660; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 177394; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.23; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov

source_name: wt 11h  in LB 37 C ( 2 ug RNA)

tag: wt 11h  in LB 37 C ( 2 ug RNA)

source_name: rpoS mutant 11h in LB 37C ( 2 ugRNA)

tag: rpoS mutant 11h in LB 37C ( 2 ugRNA)


title: vcc1504  hapR stationary

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52926.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 27070; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.31; Parameter Scan Time = 14:27:22; Parameter PMT Volts = 530; Parameter Scan Date = 2004-06-10; Parameter Pixel Size = 10; Parameter Laser on time = 181538; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.18; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.31; Parameter Scan Time = 14:27:22; Parameter PMT Volts = 670; Parameter Scan Date = 2004-06-10; Parameter Pixel Size = 10; Parameter Laser on time = 180729; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.27; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov

source_name: wt 11h in LB 37 C ( 2ug RNA)

tag: wt 11h in LB 37 C ( 2ug RNA)

source_name: hapR mutant 11h in LB 37 C ( 2ug RNA)

tag: hapR mutant 11h in LB 37 C ( 2ug RNA)


title: cfw15_2_0704

description: Yeast treated at calcofluor white  (0.1mg/ml) vs non treated. 15 min from the start of treatment.

value: calcofluor white', 'time:15 min', 'concentration:0.1mg/ml'


title: vcc632 rpoS mutant versus wt

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50958.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1590, 26400; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.95; Parameter Scan Time = 13:51:51; Parameter PMT Volts = 530; Parameter Scan Date = 2004-03-31; Parameter Pixel Size = 10; Parameter Laser on time = 177398; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.95; Parameter Scan Time = 13:51:51; Parameter PMT Volts = 640; Parameter Scan Date = 2004-03-31; Parameter Pixel Size = 10; Parameter Laser on time = 176624; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.29; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: vcc1505  hapR stationary

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52925.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 820, 27840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.18; Parameter Scan Time = 14:18:50; Parameter PMT Volts = 530; Parameter Scan Date = 2004-06-10; Parameter Pixel Size = 10; Parameter Laser on time = 181530; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.18; Parameter Scan Time = 14:18:50; Parameter PMT Volts = 670; Parameter Scan Date = 2004-06-10; Parameter Pixel Size = 10; Parameter Laser on time = 180721; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.27; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: cfw15_1_0704

description: Yeast treated at calcofluor white  (0.02mg/ml) vs non treated. 15 min from the start of treatment.

value: calcofluor white', 'time:15 min', 'concentration:0mg/ml'


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide16 (T21-C)

city: Brookings

first: Xiuqing

last: Wang

state: SD

address: NPB 252, SDSU

department: Department of Biology and Microbiology

institute: South Dakota State University

description: The goal of the study was to uncover the molecular mechanism of mucosal immunity development using avian infectious bronchitis virus (IBV) as a model system. To achieve this goal, we monitored the kinetics of local gene transcription profiles in trachea tissues after administration of animals with an attenuated IBV strain (IBV-Mass) using chicken 13K cDNA Microarray. More specifically, immune-related gene transcription profiles in trachea at 1, 3, 5, 8, 12 and 21 days after the primary immunization and at 1 and 2 days after a second immunization were characterized. There are total 9 groups including 8 time points for vaccinated groups and 1 pooled age-matched control group. RNAs from each group were used to compare with RNAs from other four groups as determined by the loop-design. Four different RNA samples at each time point were used for hybridization with the respective four other groups. The use of the loop-design allows the direct comparisons between the 9 groups, which would enhance the statistical power and lower the variation. This design is preferred over other methods when the goal of the study is to uncover the kinetics of gene transcription profiles.

hyb_protocol: Hybridization was performed based on the protocol provided by FHCRC (http://www.fhcrc.org/science/shared_resources/genomics/dna_array/spotted_arrays/chicken_array/HybridizationWashProtocol.pdf) with slight modifications. Briefly, nonfat milk was used in pre-hybridization to block non-specific binding sites. For hybridization, the mixture of 20X SSC (6.0µl), 2% SDS (2.4µl) and labeled cDNA samples (5µg for each) was applied to 13k array slide. The total volume was 60µl. Slide was incubated at 63°C for 4hrs followed by incubating at 55°C for 11hrs.

scan_protocol: After washing, slides were dried by quick spin and ready for scanning. Arrays were scanned using a GenePix 4000B Microarray Scanner (Molecular Device Corporation, Sunnyvale, CA) and image analysis was performed by using GenePixPro6.0.

data_processing: Data were collected using GenePixPro6.0 with the LOWESS normalization.

organism: Gallus gallus

label_protocol: Message RNA amplification was carried out  with MessageAmp aminoallyl Amplification Kit (Ambion, #1752). Then, amplified RNA was used for cDNA synthesis, which was subsequently labeled with Cy3 and Cy5 Monoreactive dye (Amersham, # PA23001 and # PA25001). Purification of the cDNA was performed with QIAquick PCR Purification Kit (QIAGEN, #28104). All procedures were performed by following the manufacturers’ instructions.

extract_protocol: Total RNA was extracted from the pooled samples of age-matched control and vaccinated chickens using RNeasy mini tissue kit from QIAGEN Inc. (Valencia, CA). Residue DNA was removed with RNase-free DNase (QIAGEN). The concentration of total RNA was determined using NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). The quality and quantity of selected RNA samples was examined by gel electrophoresis.

tag: Ti

value: RNA derived from chicken trachea tissues at day i (i=1,3,5,8,12,21,22,24) after the initial IBV-Mass inoculation; Ci:Control RNA derived from chicken trachea tissue at day i after inoculation with sterile distilled water.

tag: Note

value: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization. The pooled control RNA was used for hybridization.

source_name: C (pooled common conference)


title: vcc1491  wt stationary phase

description:
Simple annotation: Stationary phase, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50965.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 880, 27490; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.01; Parameter Scan Time = 11:53:30; Parameter PMT Volts = 520; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 178205; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.14; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.01; Parameter Scan Time = 11:53:30; Parameter PMT Volts = 690; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 177431; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.24; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: 15caf2kg

description: Yeast treated at caffeine  (20mM) vs non treated. 15 min from the start of treatment.

value: caffeine', 'time:15 min', 'concentration:20mM'


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide18 (T24-T3)


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide11 (T1-T8)

value: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization. We used pooled control RNA for hybridization.


title: 5caf1kg

description: Yeast treated at caffeine  (2mM) vs non treated. 5 min from the start of treatment.

value: caffeine', 'time:5 min', 'concentration:0mM'


title: 15caf1kg

description: Yeast treated at caffeine  (2mM) vs non treated. 15 min from the start of treatment.

value: caffeine', 'time:15 min', 'concentration:2mM'

value: caffeine', 'time:15 min', 'concentration:0mM'


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide14 (T8-T22)


title: cfw90_2_0704

description: Yeast treated at calcofluor white  (0.1mg/ml) vs non treated. 90 min from the start of treatment.

value: calcofluor white', 'time:90 min', 'concentration:0mg/ml'

value: calcofluor white', 'time:90 min', 'concentration:0.1mg/ml'


title: 5caf2kg

description: Yeast treated at caffeine  (20mM) vs non treated. 5 min from the start of treatment.

value: caffeine', 'time:5 min', 'concentration:20mM'


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide15 (T12-T24)


title: vcc1482  wt stationary phase

description:
Simple annotation: Stationary phase, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50964.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 27190; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 42.02; Parameter Scan Time = 14:22:28; Parameter PMT Volts = 510; Parameter Scan Date = 2004-03-31; Parameter Pixel Size = 10; Parameter Laser on time = 177429; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 42.02; Parameter Scan Time = 14:22:28; Parameter PMT Volts = 700; Parameter Scan Date = 2004-03-31; Parameter Pixel Size = 10; Parameter Laser on time = 176655; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.29; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide12 (T3-T12)


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide17 (T22-T1)


title: Gene Transcription Profile of Local Innate and Adaptive Immunity during Early Phase of IBV Infection Slide1 (C3-T3)

description: To understand the mechanistic basis of local innate and adaptive immunity against infectious bronchitis virus (IBV) at the molecular level, we examined the gene transcription profile of tracheal epithelial layers at 3 days after infection of chickens with an attenuated IBV-Massachusetts strain. For the DNA microarray experiment, total RNA was reverse transcribed and labeled with Cy3 and Cy5 fluorescent dyes and hybridized to the chicken 13K cDNA microarray (FHCRC, Seattle, WA) which contains 13,000 genes derived from both embryonic and adult chicken tissues including immune genes. The experiment was repeated four times using swapped Cy3 or Cy5 dye labeling.

extract_protocol: Total RNA was extracted from the samples of age-matched control and vaccinated chickens using RNeasy mini tissue kit from QIAGEN Inc. (Valencia, CA). Residue DNA was removed with RNase-free DNase (QIAGEN). The concentration of total RNA was determined using NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). The quality and quantity of selected RNA samples was examined by gel electrophoresis.

value: Control RNA derived from chicken trachea tissue 3 days after inoculation with sterile distilled water.

value: RNA derived from chicken trachea tissues 3 days after the initial IBV-Mass inoculation.


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide10 (C-T5)


title: vcc1500  rpoS mutant

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50609.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 680, 27430; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.20; Parameter Scan Time = 10:30:17; Parameter PMT Volts = 520; Parameter Scan Date = 2004-03-25; Parameter Pixel Size = 10; Parameter Laser on time = 176201; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.35; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.20; Parameter Scan Time = 10:30:17; Parameter PMT Volts = 680; Parameter Scan Date = 2004-03-25; Parameter Pixel Size = 10; Parameter Laser on time = 175432; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.26; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide13 (T5-T21)


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide09 (T24-C)


title: 90caf1kg

description: Yeast treated at caffeine  (2mM) vs non treated. 90 min from the start of treatment.

value: caffeine', 'time:90 min', 'concentration:2mM'

value: caffeine', 'time:90 min', 'concentration:0mM'


title: 90caf2kg

description: Yeast treated at caffeine  (20mM) vs non treated. 90 min from the start of treatment.

value: caffeine', 'time:90 min', 'concentration:20mM'


title: HapR 11hr 3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62126.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 27770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alex,,Nielsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.83; Parameter Scan Time = 12:43:46; Parameter PMT Volts = 480; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200468; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.06; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.83; Parameter Scan Time = 12:43:46; Parameter PMT Volts = 710; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200029; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.18; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen

source_name: HapR 11hr 1

tag: HapR 11hr 1


title: short term cultured GBM_ID GLI72U2_untreated control_rep2

city: Berlin

first: Wolf

middle: C

last: Mueller

address: Amrumer Str. 1

department: Neuropathology

institute: Charité Universitätsmedizin Berlin

description: short term cultured glioblastoma sample_ID GLI72U2_untreated control_replica 2

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cells were cultured in L-Glutamine free DMEM. Supplement with 1% L-Glutamine, heat inactivated 10%FBS, 1% Penicillin/Streptomycin. Grown in a 37° humidified atmosphere of 5% CO2/95%air.

extract_protocol: TRIzol extraction (Invitrogen Life Technologies) followed by clean-up using RNaesy Mini kit (Quiagen) according to manufacturers instructions.

treatment_protocol: sample was co-cultured with samples of the same short term cultured glioblastoma that was  5`aza-treated  but left untreated for 16h

tag: short term cultured glioblastoma_GLI72_passage 15


title: cr15_1_kg

description: Yeast treated at congo red  (0.02mg/ml) vs non treated. 15 min from the start of treatment.

value: congo red', 'time:15 min', 'concentration:0.02mg/ml'

value: congo red', 'time:15 min', 'concentration:0mg/ml'


title: cr5_1_kg

description: Yeast treated at congo red  (0.02mg/ml) vs non treated. 5 min from the start of treatment.

value: congo red', 'time:5 min', 'concentration:0.02mg/ml'

value: congo red', 'time:5 min', 'concentration:0mg/ml'


title: short term cultured GBM_ID GLI72U1_untreated control_rep1

description: short term cultured glioblastoma sample_ID GLI72U1_untreated control_replica 1


title: short term cultured GBM_ID GLI60U2_untreated control_rep2

description: short term cultured glioblastoma sample_ID GLI60U2_untreated control_replica 2

source_name: short term cultured GBM_ID GLI60U2_untreated control_rep1

tag: short term cultured glioblastoma_GLI60_passage 15


title: vcc1688  hapR stationary

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-06/52924.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1210, 27530; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.11; Parameter Scan Time = 14:13:05; Parameter PMT Volts = 520; Parameter Scan Date = 2004-06-10; Parameter Pixel Size = 10; Parameter Laser on time = 181525; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.19; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.11; Parameter Scan Time = 14:13:05; Parameter PMT Volts = 670; Parameter Scan Date = 2004-06-10; Parameter Pixel Size = 10; Parameter Laser on time = 180715; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.26; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: cr15_2_kg

description: Yeast treated at congo red  (0.1mg/ml) vs non treated. 15 min from the start of treatment.

value: congo red', 'time:15 min', 'concentration:0.1mg/ml'


title: vcc733 wt stationary phase

description:
Simple annotation: Stationary phase, wild-type
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50963.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1400, 26760; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.99; Parameter Scan Time = 13:45:45; Parameter PMT Volts = 510; Parameter Scan Date = 2004-03-31; Parameter Pixel Size = 10; Parameter Laser on time = 177392; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.99; Parameter Scan Time = 13:45:45; Parameter PMT Volts = 690; Parameter Scan Date = 2004-03-31; Parameter Pixel Size = 10; Parameter Laser on time = 176618; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.29; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide06 (T12-T21)

description: The goal of the study was to uncover the molecular mechanism of mucosal immunity development using avian infectious bronchitis virus (IBV) as a model system. To achieve this goal, we monitored the kinetics of local gene transcription profiles in trachea tissues after administration of animals with an attenuated IBV strain (IBV-Mass) using chicken 13K cDNA Microarray. More specifically, immune-related gene transcription profiles in trachea at 1, 3, 5, 8, 12 and 21 days after the primary immunization and at 1 and 2 days after a second immunization were characterized. There are total 9 groups including 8 time points for vaccinated groups and 1 pooled age-matched control group. RNAs from each group were used to compare with RNAs from other four groups as determined by the loop-design. Four different RNA samples at each time point were used for hybridization with the respective four other groups. The use of the loop-design allows the direct comparisons between the 9 groups, which would enhance the statistical power and lower the variation. This design is preferred over other methods when the goal of the study is to uncover the kinetics of gene transcription profiles.

value: RNA derived from chicken trachea tissues at day i (i=1,3,5,8,12,21,22,24) after the initial IBV-Mass inoculation; Ci:Control RNA derived from chicken trachea tissue at day i after inoculation with sterile distilled water.

value: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization. We used pooled control RNA for hybridization.


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide07 (T21-T22)

scan_protocol: After washing, slides were dried by quick spin and ready for scanning. Arrays were scanned using a GenePix 4000B Microarray Scanner (Molecular Device Corporation, Sunnyvale, CA) and image analysis was performed by using GenePixPro6.0

value: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization. We used pooled control RNA for hybridization


title: short term cultured GBM_ID GLI56U2_untreated control_rep2

description: short term cultured glioblastoma sample_ID GLI56U2_untreated control_replica 2

source_name: short term cultured GBM_ID GLI56U2_untreated control_rep1

tag: short term cultured glioblastoma_GLI56_passage 15


title: vcc1488  rpoS mutant

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-03/50607.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 27050; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.04; Parameter Scan Time = 10:18:20; Parameter PMT Volts = 520; Parameter Scan Date = 2004-03-25; Parameter Pixel Size = 10; Parameter Laser on time = 176187; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.33; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.04; Parameter Scan Time = 10:18:20; Parameter PMT Volts = 680; Parameter Scan Date = 2004-03-25; Parameter Pixel Size = 10; Parameter Laser on time = 175419; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.26; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: cr90_1_kg

description: Yeast treated at congo red  (0.1mg/ml) vs non treated. 90 min from the start of treatment.

value: congo red', 'time:90 min', 'concentration:0.02mg/ml'

value: congo red', 'time:90 min', 'concentration:0mg/ml'


title: short term cultured GBM_ID GLI60U1_untreated control_rep1

description: short term cultured glioblastoma sample_ID GLI60U1_untreated control_replica 1


title: short term cultured GBM_ID GLI56U1_untreated control_rep1

description: short term cultured glioblastoma sample_ID GLI56U1_untreated control_replica 1

tag: short term cultured GBM_ID GLI56_untreated control


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide08 (T22-T24)

value: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization. The pooled control RNA was used for hybridization.


title: cr5_2_kg

description: Yeast treated at congo red  (0.1mg/ml) vs non treated. 5 min from the start of treatment.

value: congo red', 'time:5 min', 'concentration:0.1mg/ml'


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide03(T3-T5)


title: vcc 1720  rpoS mutant versus wt

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50960.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1010, 27060; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nadia,,Dolganov Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.13; Parameter Scan Time = 12:08:44; Parameter PMT Volts = 510; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 178220; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.15; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 41.13; Parameter Scan Time = 12:08:44; Parameter PMT Volts = 700; Parameter Scan Date = 2004-04-08; Parameter Pixel Size = 10; Parameter Laser on time = 177446; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.24; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nadia,,Dolganov


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide05 (T8-T12)

hyb_protocol: Hybridization was performed based on the protocol provided by FHCRC (http://www.fhcrc.org/science/shared_resources/genomics/dna_array/spotted_arrays/chicken_array/HybridizationWashProtocol.pdf) with slight modifications. Briefly, nonfat milk was used in pre-hybridization to block non-specific binding sites. For hybridization, the mixture of 20X SSC (6.0µl), 2% SDS (2.4µl) and labeled cDNA samples (5µg for each) was applied to 13k array slide). The total volume was brought to 60µl. Slide was incubated at 63°C for 4hrs followed by incubating at 55°C for 11hrs.

value: RNA derived from chicken trachea tissues at day i (i=1,3,5,8,12,21,22,24) after the initial IBV-Mass inoculation; Ci:Control RNA derived from chicken trachea tissue at day i  after inoculation with sterile distilled water.

value: Chickens were re-inoculated with IBV-Mass at day 21 after the initial immunization.  We used pooled control RNA for hybridization (that is “C (pooled common conference)”in hybridization was a mix of C1+C3+C5+…+C24 ).


title: short term cultured GBM_ID GLI72T2_5`aza-dc_96h_rep2

description: short term cultured glioblastoma sample_ID GLI72_treated with 5`aza-dC for 96h_replica 2

treatment_protocol: 16h after seeding the cells were treated with 5umol 5`aza-dC for 96h.


title: HapR 11hr 2

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62125.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 27770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alex,,Nielsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.70; Parameter Scan Time = 12:35:25; Parameter PMT Volts = 480; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200460; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.04; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.70; Parameter Scan Time = 12:35:25; Parameter PMT Volts = 710; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200021; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.17; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide04 (T5-T8)


title: short term cultured GBM_ID GLI72T1_5`aza-dc_96h_rep1

description: short term cultured glioblastoma sample_ID GLI72_treated with 5`aza-dC for 96h_replica 1


title: short term cultured GBM_ID GLI60T2_5`aza-dc_96h_rep2

description: short term cultured glioblastoma sample_ID GLI60_treated with 5`aza-dC for 96h_replica 2


title: cfw15_1_kg

description: Yeast treated at calcofluor  (0.1mg/ml) vs non treated. 5 min from the start of treatment.

value: calcofluor white', 'time:15 min', 'concentration:0.02mg/ml'

value: calcofluor white', 'time:15 min', 'concentration:0mg/ml'


title: cfw15_2_kg

value: calcofluor white', 'time:15 min', 'concentration:0.1mg/ml'


title: Gene Transcription Profiles during Development of Mucosal Immunity Slide02 (T1-T3)


title: HapR 11hr 1

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62124.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 27770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alex,,Nielsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.65; Parameter Scan Time = 12:28:44; Parameter PMT Volts = 490; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200453; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.02; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.65; Parameter Scan Time = 12:28:44; Parameter PMT Volts = 710; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200015; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.18; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen


title: RpoS 11hr 3

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62122.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 27770; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alex,,Nielsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.38; Parameter Scan Time = 12:08:38; Parameter PMT Volts = 490; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200433; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.04; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.38; Parameter Scan Time = 12:08:38; Parameter PMT Volts = 690; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 199995; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.17; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen

source_name: RpoS 11hr 2

tag: RpoS 11hr 2


title: cr90_2_kg

value: congo red', 'time:90 min', 'concentration:0.1mg/ml'


title: short term cultured GBM_ID GLI60T1_5`aza-dc_96h_rep1

description: short term cultured glioblastoma sample_ID GLI60_treated with 5`aza-dC for 96h_replica 1


title: Gene Transcription Profile of Local Innate and Adaptive Immunity during Early Phase of IBV Infection Slide2 (C3-T3)

description: To understand the mechanistic basis of local innate and adaptive immunity against infectious bronchitis virus (IBV) at the molecular level, we examined the gene transcription profile of tracheal epithelial layers at 3 days after infection of chickens with an attenuated IBV-Massachusetts strain. For the DNA microarray experiment, total RNA was reverse transcribed and labeled with Cy3 and Cy5 fluorescent dyes and hybridized to the chicken 13K cDNA microarray (FHCRC, Seattle, WA) which contains 13,000 genes derived from both embryonic and adult chicken tissues including immune genes. The experiment was repeated four times using swapped Cy3 or Cy5 dye labeling.

value: Control RNA derived from chicken trachea tissue 3 days after inoculation with sterile distilled water.

value: RNA derived from chicken trachea tissues 3 days after the initial IBV-Mass inoculation.


title: RpoS 11hr 2

description:
Simple annotation: Mutant vs Wild-type, Mutant
Image: http://smd.stanford.edu/MicroArray/gifs/2005-06/62121.gif

scan_protocol: not provided Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 0, 27360; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Alex,,Nielsen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.27; Parameter Scan Time = 12:01:15; Parameter PMT Volts = 490; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 200426; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 2.01; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.27; Parameter Scan Time = 12:01:15; Parameter PMT Volts = 720; Parameter Scan Date = 2005-06-25; Parameter Pixel Size = 10; Parameter Laser on time = 199987; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [48444]; Parameter Laser Power = 1.17; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Alex,,Nielsen