title: EV49+50, Histone 3 Lysine 4 methylation in wild-type Arabidopsis thaliana seedlings

summary:
The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype.  This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3.  In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis
These data were normalized and subjected to hypothesis testing. Error rate was controlled only by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

Wild-type seedlings, 9 days old.
This is the normalized result of the paired dye swap samples EV49 and EV50.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using false discovery rate (FDR) controlling methods. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K4 methylation compared to mean values found in euchromatic regions are flagged in the column. No family-wise error rate method were used to analyze this sample.
Keywords: other


title: VC133+137, DNA methylation in ddm1 seedling Arabidopsis thaliana plants

status: Public on Jun 12 2004

city: Austin

first: Matthew

middle: Wayne

last: Vaughn

state: TX

address: 10100 Burnet Rd

department: Texas Advanced Computing Center

country: USA

institute: University of Texas at Austin

type: Methylation profiling by genome tiling array

summary:
This series is a technical replicate of VC133+135.
The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thanliana genotype.
McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb. The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment.
In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3. Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
ddm1 seedlings, 9 days old.
Below is the normalized result of the paired dye swap samples VC133 and VC137.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using both family-wise error rate (FWER) and false discovery rate (FDR) controlling methods. The step-down multiple comparisons procedure of Holm (1979) was used to control the FWER below alpha = 0.01, while the step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the last two columns.
Keywords: other

first: Zachary

middle: B

last: Lippman

first: Anne-Valerie

last: Gendrel

first: Mik

last: Black

middle: W


title: DNA methylation in wild-type bolting Arabidopsis thaliana plants

summary:
The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thanliana genotype.
McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment.
In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3. Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
This is the normalized result of the paired dye swap samples VC121 and VC127.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms.
These samples were not subjected to hypothesis testing. Therefore, P-values are reported as -1 and no features are flagged as significantly methylated.
Keywords: other


title: PDGF stimulation kinetics

status: Public on Jun 23 2004

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary:
Subconfluent AG01518 fibroblasts were starved for 16 hours in the presence of 0.1% BSA, and then stimulated for 1, 4, 10 or 24 hours with PDGF-BB (10 ng/ml in starvation medium), or left untreated for the same periods of time. Total RNA was isolated using the RNeasy kit (Qiagen). The RNA quality was checked by formaldehyde agarose gel electrophoresis (RNeasy protocol, Qiagen). Total RNA (40 mg) from cells treated for a given period of time with PDGF or starvation medium alone were labelled in reverse transcription reactions (Superscript II kit, Invitrogen) with dCTP-Cy5 and dCTP-Cy3, respectively (Amersham). In every second replicate experiment the fluorescent deoxynucleotides were swapped. Purified cDNA probes labelled with Cy3 and Cy5 were mixed per pair, and hybridized to cDNA microarray chips (hver1.2.1) from the Sanger Institute/LICR/CRUK Consortium (see http://www.sanger.ac.uk/Projects/Microarrays/
for details and hybridization protocols). For each time point, we performed at least four independent hybridizations, and used at least two different batches of RNA. Chips were scanned in a Perkin Elmer/GSI Lumonics ScanArray 4000 scanner and spot intensities were measured using the QuantArray software (histogram method with background subtraction). Normalization and statistical analysis of the quadruplicate data sets were performed using GeneSpring 5.0 analysis software (Silicon Genetics). A Lowess non-linear normalization was applied and the median of the ratio distribution for each array was set to 1. Regulated spots were selected based on the average ratio values above 1.750 for up-regulated genes and below 0.571 for down-regulated genes. In addition, we considered only genes that were significantly regulated (t-test, p<0.05) based on replicate hybridizations (global error model, GeneSpring). For all features selected using this protocol, the signal was significantly above the background, indicating that the expression of these genes was detectable. Finally, Hver1.2.1 microarrays contain replicate spots (1 to 6) corresponding to the same gene. Genes represented by spots that were not regulated in a similar manner were discarded. We show the average ratio of one representative spot for each regulated gene, with standard error calculated from multiple hybridizations and with the annotation provided by the microarray facility (Hver1.2.1_NCBI33).
Keywords: time-course

first: Carl-Henrik

last: Heldin


title: breast cancer / tamoxifen monotherapy (whole tissue tumor biopsies)

status: Public on Jun 07 2004

city: Carlsbad

first: Xiao-Jun

last: Ma

state: CA

address: 2715 Loker Ave. W.

institute: AviaraDx, Inc.

summary:
dataset of 60 patients with ER-positive primary breast cancer and treated with tamoxifen monotherapy for 5 years. Data were generated from whole tissue sections of breast cancers.
Sample_keyword: breast cancer, tamoxifen, recurrence
Keywords: other


title: Histone 3 Lysine 4 methylation in ddm1 Arabidopsis thaliana seedlings

type: Genome binding/occupancy profiling by genome tiling array

summary:
The purpose of the chromatin immunoprecipitation/microarray (ChIP/chip) experiment is to determine which regions of a genome are enriched for a particular histone modification in a single Arabidopsis thanliana genotype.
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-9 (H3mK9) or dimethyl histone-H3 lysine-4 (H3mK4) is performed on a selected genotype.  This purified DNA from each immunoprecipiation (mH3K9, mH3K4, no antibody control) is used for random amplification to increase the quantity of DNA for microarray hybridization.
The amplified DNA from each experimental sample is then labeled with Cy5 and hybridized against total input DNA from the corresponding genotype, labeled in Cy3.  In a single hybridization, the total input DNA serves as a baseline and is compared to the immunoprecipitated samples. Ratios of normalized signal intensities were calculated to identify enrichment of a particular sequence after immunoprecipitation, in comparison to the total input DNA. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis
These data were normalized and subjected to hypothesis testing. Error rate was controlled only by Benjamini and Hochberg's step-up procedure for limiting the False Discovery Rate.

Ddm1 seedlings, 9 days old
This is the normalized result of the paired dye swap samples EV55 and EV56.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using false discovery rate (FDR) controlling methods. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found after hypothesis-testing with a controlled error rate to be significantly enriched or depleted for H3K4 methylation compared to mean values found in euchromatic regions are flagged in the column. No family-wise error rate method were used to analyze this sample.
Keywords: other


title: EV33+34 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings

type: Expression profiling by genome tiling array

summary:
The two samples in this series are complementary hybridizations in a dye-swap analysis.
Below is the normalized result of the paired dye swap samples EV33 and EV34.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using a false discovery rate (FDR) controlling method. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the column.
Standard errors and P-values are not available.
Keywords: other


title: VC109+111 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings

summary:
Biological replicate of EV33+34.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
Below is the normalized result of the paired dye swap samples VC109 and VC110.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using a false discovery rate (FDR) controlling method. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the column.
Standard errors and P-values are not available.
Keywords: other


title: Steroids Effect on HUVEC Response to LPS or Cytokines

status: Public on Jun 19 2004

city: San Antonio

first: Phillip

last: Bowman

address: 3400 Rawley E. Chambers Ave

institute: Institute of Surgical Research

summary:
Pooled first passage cryopreserved, human umbilical vein endothelial cells (HUVEC) were obtained from Cascade Biologics (Portland, OR), thawed, and cultured according to the supplier’s recommendations in Medium 200. After thawing, cells were seeded onto 0.2% gelatin coated tissue culture plates and cultivated under 95% air, 5% CO2 at 37 oC.
Confluent cells were cultured in steroids-depleted medium for 96 hrs before the addition of 17β-estradiol (17βE) or hydrocortisone (H) to 1 µM for 5 hrs. For Lipopolysaccharide (LPS) or cytokine mix (CM)-treatments, cells or pretreated with vehicle (0.1% ethanol), 1µM 17βE, or H for 1 hr were exposed to 100 ng/ml LPS or a mixture of proinflammatory cytokines (CM, 500 U/ml IL-1b, 2500 U/ml TNF-α, and 1250 U/ml IFN-γ) for 4 hours. All treatments were done in quadruplicates. At the end of treatment, total cellular RNA was isolated.
Keywords: parallel sample

middle: D

first: Baiteng

last: Zhao

first: James

middle: A

last: Bynum


title: Dog heart and high fat diet

status: Public on Jun 06 2004

city: Toulouse

first: Rouet

last: Philippe

state: FRANCE

address: 37 Allées Jules Guesde

country: France

institute: Louis Bugnard

summary:
Time course series of High fat diet
Keywords: time-course

first: Pierre

last: Philip-Couderc


title: HCT116-Clone2 cells 24 hours after XR treatment at 4 Gy

status: Public on Jun 04 2004

city: Ottawa

first: Felix

middle: M.

last: Mesak

state: ON

address: 503 Smyth Rd. 3rd Floor

department: Centre for Cancer Therapeutics

country: Canada

institute: Ottawa Regional Cancer Centre

summary:
cDNA microarray study of X-radiation (XR) resistant HCT116-Clone2 cells 24 hours after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords = X-radiation (XR)
Keywords = XR resistant
Keywords = colorectal cancer cells
Keywords = HCT116
Keywords: repeat sample

middle: M

first: Cheng

middle: E

last: Ng

first: Wei

middle: L

last: Tan


title: EV39+40 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings

summary:
Technical replicate of EV33+34.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
Below is the normalized result of the paired dye swap samples EV39 and EV40.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using a false discovery rate (FDR) controlling method. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the column.
Standard errors and P-values are not available.
Keywords: other


title: HCT116-Clone2 cells 6 hours after XR treatment at 4 Gy

summary:
cDNA microarray study of X-radiation (XR) resistant HCT116-Clone2 cells 6 hours after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords = X-radiation (XR)
Keywords = XR resistant
Keywords = colorectal cancer cells
Keywords = HCT116
Keywords: repeat sample


title: VC110+112 mRNA levels in Wild-type versus ddm1 bolting Arabidopsis thaliana plants

summary:
Biological replicate of EV23+24.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
Below is the normalized result of the paired dye swap samples VC110 and VC112.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using a false discovery rate (FDR) controlling method. The step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the column.
Standard errors and P-values are not available.
Keywords: other


title: Unirradiated HCT116-Clone2 cells

summary:
cDNA microarray study of unirradiated X-radiation (XR) resistant HCT116-Clone2 cells versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords: repeat sample


title: uranyl nitrate exposure

status: Public on Jun 10 2004

city: Montpellier

first: Magali

last: Taulan

institute: INSERM

summary:
SAGE analysis in kidney obtained from control mice or after acute or chronic exposure to uranyl nitrate (UN).
Keywords: other


title: CEA_SGF:E00002#REtsAF-Bcl2_ZVAD

status: Public on Jun 01 2004

city: Versailles

first: Nelly

last: Godefroy

address: 45 Avenue des Etats Unis

department: Laboratoire de Genetique et de Biologie Cellulaire

institute: Universite de Versailles

summary:
p53 can induce apoptosis through multiple mechanisms including transactivation, transrepression or protein interactions but the determinism of the choice between them is poorly understood. In order to know the role of caspases in this choice, effect of caspase inhibition by ZVAD on p53 target genes transcription is tested by DNA chip analysis.
Keywords: repeat sample


title: vGPCR and lytic KSHV time course in TIME cells

status: Public on May 18 2004

city: San Francisco

first: Don

last: Ganem

institute: University of California, San Francisco

summary:
TIME cells either expressing KSHV-RTA or KSHV-vGPCR alone, or TIME cells infected with KSHV and lytically reactivated with RTA for 6, 12, or 20 hours.
Keywords = KSHV
Keywords = host shutoff
Keywords = vGPCR
Keywords: other


title: VC134+136, DNA methylation in wild-type seedling Arabidopsis thaliana plants

first: Matthew

last: Vaughn

summary:
The purpose of the McrBC methylation microarray* assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thanliana genotype.
McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between* 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment.
In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3.* Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray.* Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
wild-type seedlings, 9 days old.
Below is the normalized result of the paired dye swap samples VC134 and VC136.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using both family-wise error rate (FWER) and false discovery rate (FDR) controlling methods. The step-down multiple comparisons procedure of Holm (1979) was used to control the FWER below alpha = 0.01, while the step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the last two columns.
Keywords: other


title: LPS-induced and E. coli-induced gene expression in wildtype and MyD88-/- mouse macrophages

status: Public on May 16 2004

city: Malmö

first: Harry

last: Björkbacka

address: CRC 91:12, UMAS entrance 72

department: Dept. of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

summary:
Comparison of gene expression in wildtype and MyD88-/- C57BL/6J mouse macrophages treated with 10 ng/mL LPS for 2 hours versus media treated control macrophages, and, wildtype and MyD88-/- C57BL/6J mouse macrophages treated with live E. coli bacteria (log phase; 1 bact per 1 macrophage) for 2 hours versus media treated control macrophages. Cells from 4 mice of each geneotype were used and each individual provided its own control. Hybridizations of treated and control samples from each mouse were dye swap replicated. Wildtype macrophages treated with LPS vs control (GSM22617-GSM22623,GSM22625), MyD88-/- macrophages treated with LPS vs control (GSM22626-GSM22632), wldtype macrophages treated with E. coli vs control (GSM22633-GSM22640, and MyD88-/- macrophages treated with E. coli vs control (GSM22641-GSM22648).
Keywords: other

last: Bjorkbacka


title: Embryonic stem cell study

city: Menlo Park

first: Gregory

last: Fisk

address: 230 Constitution Dr.

institute: Geron Corp.

summary:
Cell culture:
H9 hESCs were grown using feeder-free conditions for 7 days after passage then either RNA was harvested or embryoid bodies were prepared, cultured in suspension for 4 days, plated on gelatin-coated plates, and cultured for an additional 9 days in embryoid body medium. Detailed protocols for feeder-free culture and embryoid body formation are available at www.geron.com/scprotocols.pdf

RNA preparation:
Cells were then harvested in situ by overlaying with RLT lysis buffer (Qiagen, Valencia, CA). RNA was prepared using RNeasy Midi kits as described by the manufacture (Qiagen). To remove contaminants, RNA was precipitated by adding an equal volume of LiCl Precipitation Solution (Ambion, Austin, TX), washed with 70% ethanol and resuspended in water.

Probe preparation:
Probes were prepared from 20ug of total RNA by direct incorporation of Cy3 or Cy5 dCTP (Amersham Biosciences, Piscataway, NJ) into oligo dT primed first strand cDNA using SuperscriptIII reverse transcriptase (Invitrogen), as described by the dye manufacturer. RNA was removed by alkaline hydrolysis, then neurtralized probes were purified using Qiaquick columns as described by the manufacturer (Qiagen).

Hybridization/Washing:
Purified probes were dried and resuspended MWG Hybridization Buffer C (MWG Biotech) with the addition of 20 ug of sheared salmon sperm DNA. Slides were hybridized overnight at 42°. After the coverslips were removed, the slides were rinsed in 2X SSC + 0.1% SDS, washed in 2X SSC + 0.1% SDS for 5 min, 1X SSC for 5 min, 0.2X SSC for 5 min and 0.1X SSC for 5 min. Slides were then dried by centrifugation.

Scanning:
Arrays were scanned using a GenePix 4000A microarray scanner (Axon Insturments, Fremont, CA) with 100% scan power and PMT voltage set to minimize saturated pixels and approximately equalize signal intensities in the two channels. Image processing and data extraction were performed using GenePix Pro 3.0.6 (Axon Instruments).

Data Analysis:
Average background signal from negative control spots was subtracted from Cy3 and Cy5 signal intensities. In cases where background was larger than signal, signal was set to 1. Log ratios were calculated for each spot and log ratios from replicate spots were averaged. Data was normalized using the “Lowess” method, and analyzed for differential expression. Differentially expressed genes were defined as those with log transformed expression ratios more than 1.5 SD from the mean. This lower threshold was chosen since comparison of the microarray dat to qRT-PCR on the samples used for the microarray experiment indicated that the data was compressed. For example, TDGF1 was up-regulated 100-fold in uES versus EB by qRT-PCR, but only ~5-fold by microarray analysis in the same sample. Normalization and identification of differentially expressed genes was performed using the MIDAS package (Saeed et al. (2003) Biotechniques 34(2):374-8).
Keywords: other

first: Ralph

last: Brandenberger

first: Henry

last: Wei

first: Sally

last: Zhang

first: Shirley

last: Lei

first: Jaji

last: Murage

middle: J

first: Yan

last: Li

first: Chunhui

last: Xu

first: Rixun

last: Fang

first: Karl

last: Guegler

first: Mahendra

middle: S

last: Rao

first: Ramumkar

last: Mandalam

first: Jane

last: Lebkowski

first: Lawrence

last: Stanton


title: Pept2 (Slc15a2) KO mice kidneys with WT:WT controls

status: Public on May 27 2004

city: Munich - Neuherberg

first: Johannes

last: Beckers

state: Bavaria

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: GSF - National Research Center

summary:
Comparison of kidneys of 4 different Pept2 KO individuals (GSE1585), pool of them and kidneys of WT individuals versus another WT individual (GSE1586).
Keywords = Pept2
Keywords = Slc15a2
Keywords = kidney
Keywords = KO
Keywords = WT
Keywords = pool
Keywords = pooling
Keywords = normal variatons
Keywords = C57BL/6
Keywords = 129Sv
Keywords: other

first: Alexei

last: Drobyshev

first: Isabelle

last: Frey


title: Effect of bovine viral diarrhoea virus infection in Madin-Darby bovine kidney cells

status: Public on May 31 2004

city: Ames

first: John

middle: D.

last: Neill

state: IA

address: 2300 Dayton Ave.

institute: National Animal Disease Center

summary:
Analysis of gene expression induced in Madin-Darby bovine kidney cells (MDBK)  infected with  Bovine viral diarrhoea virus BVDV2 strain 1373.
Keywords: other

first: Julia

middle: F

last: Ridpath


title: psad1_vs_WT

status: Public on May 11 2004

city: Chicago

first: christos

last: Noutsos

institute: University of Chicago

summary:
Series of 6 repetitions of hybridization of treatment (psad1) and control (WT) each. Comparison of the Arabidopsis psad1 mutant lacking Photosystem I protein PSI-D1 versus WT. A. Ihnatowicz et al., Plant J 37 (2004), pp. 839-852
Keywords: repeat sample

first: A

last: Biehl

first: E

last: Richly

first: C

last: Dietzmann

first: J

last: Kurth

first: F

last: Salamini

first: D

last: Leister


title: Pig peri-implantation embryo development transcriptional profiling

status: Public on May 13 2004

first: Christopher

middle: K

last: Tuggle

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
A novel porcine cDNA microarray, containing PCR products selected for embryonic expression, was used for transcriptional profiling during conceptus development. Total RNA from quadruplicate samples of small spherical (1-5mm), large spherical (6-11mm), tubular (13-45mm), and filamentous (>100mm) was extracted, amplified, and converted to 32P labeled target and hybridized to membranes.  Porcine peri-implantation embryo development order is from small spherical to large spherical, then to Tubular, then to filamentous. All this morphological transmission is within two days (day 10 to day 12). In this study, we investigated the gene expression changes by a specifically selected porcine embryo gene array. A number of genes were found to be differentially expressed during those developmental stages and confirmed by quantitative PCR.
Keywords = Gene expression
Keywords = porcine conceptus
Keywords = cDNA microarray
Keywords = peri-implantation
Keywords = transcriptional profiling
Keywords: time-course

first: S

middle: H

last: Lee

last: Zhao

middle: C

last: Recknor

last: Nettleton

last: Kang

first: B

first: W

last: Hwang


title: DNA methylation in ddm1 seedling Arabidopsis thaliana plants

first: Matthew

last: Vaughn

summary:
The purpose of the McrBC methylation microarray assay is to determine which regions of a genome are methylated versus those that are unmethylated in a single Arabidopsis thaliana genotype.
McrBC is a methylation-sensitive enzyme that restricts DNA only at purine-Cmethyl half sites when separated between 50bp and 3kb. A designated amount of DNA from a particular genotype is sheared to a size range of 1kb-10kb using nebulization. We restrict half of the nebulized DNA with McrBC, and the methylated fraction is then removed from the unmethylated fraction through gel purification of DNA fragments greater than 1kb.* The remaining nebulized DNA is subjected to the same gel purification scheme, but with no McrBC treatment.
In a single hybridization, the untreated sample is labeled with Cy5 and the McrBC-treated sample with Cy3. Thus, after labeling and microarray hybridization, the ratio of normalized Cy5 to normalized Cy3 represents the relative methylation at the sequence represented by the spot on the microarray. Dye swap analysis is carried out to take account of experimental variation by repeating the hybridization with identical samples labeled with Cy3 and Cy5, respectively.
ddm1 seedlings, 9 days old.
The two samples in this series are complementary hybridizations in a dye-swap analysis.
This is the normalized result of the paired dye swap samples VC131 and VC135.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms. The style of hypothesis test proposed by Black and Doerge (2002) was applied to each of the features represented on each array, with rejection of the null hypothesis indicating a significant change in fluorescence intensity.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using both family-wise error rate (FWER) and false discovery rate (FDR) controlling methods. The step-down multiple comparisons procedure of Holm (1979) was used to control the FWER below alpha = 0.01, while the step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the last two columns.
Keywords: other

first: Zachary

last: Lippman

first: Anne-Valerie

last: Gendrel

first: Mik

last: Black


title: EV23+24 mRNA levels in Wild-type versus ddm1/+ backcross bolting Arabidopsis thaliana plants

summary:
The two samples in this series are complementary hybridizations in a dye-swap analysis.
Below is the normalized result of the paired dye swap samples EV23 and EV24.
The ANOVA model of Kerr, Martin and Churchill (2000) was used to analyze the data from the dye-swap experiments, with terms included to account for gene, dye-by-gene, treatment-by-gene, and random error terms.
To account for the number of hypothesis tests being made, and thus provide some level of error rate control, significance was assessed using both family-wise error rate (FWER) and false discovery rate (FDR) controlling methods. The step-down multiple comparisons procedure of Holm (1979) was used to control the FWER below alpha = 0.01, while the step-up procedure of Benjamini and Hochberg (1995) was used to control the FDR below alpha = 0.01. For the purposes of this experiment, the hypotheses were assumed to be independent.
Features found to be significantly enriched for DNA methylation after hypothesis-testing with a controlled error rate are flagged in the last two columns.
Keywords: other


title: HCT116-Clone2 cells 10 min after XR treatment at 4 Gy

first: Felix

last: Mesak

summary:
cDNA microarray study of X-radiation (XR) resistant HCT116-Clone2 cells 10 minutes after XR treatment at 4Gy versus unirradiated HCT116-Clone10 cells. HCT116-Clone10 cells have similar XR response with parental HCT116 cells.
Keywords = X-radiation (XR)
Keywords = XR resistant
Keywords = colorectal cancer cells
Keywords = HCT116
Keywords: repeat sample

first: Cheng

last: Ng

first: Wei

last: Tan


title: SARB48_hydrogen_peroxide_2mM_DNA

status: Public on May 10 2004

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary:
Gene content of Salmonella enterica sv Paratyphi C SARB48 5h after treatment with 2mM hydrogen peroxide
Keywords: parallel sample

sample_organism: Salmonella enterica subsp. enterica serovar Paratyphi C

first: Jonathan

middle: G

last: Frye

first: Felisa

last: Blackmer

first: Pui

last: Cheng

first: Steffen

last: Porwollik


title: TY2_Chloramphenicol_300ug/ml_RNA

summary:
Gene expression of Salmonella enterica sv Typhi TY2 after 30min exposure of log cells to 300ug/ml Chloramphenicol
Keywords: parallel sample

sample_organism: Salmonella enterica subsp. enterica serovar Typhi


title: TY2_Rifampicin_125ug/ml_DNA

summary:
Gene content of Salmonella enterica sv Typhi TY2 after 30min treatment of log phase cells with 125ug/ml Rifampicin
Keywords: parallel sample


title: TY2_hydrogen_peroxide_2mM_DNA

summary:
Gene content of Salmonella enterica sv Typhi TY2 3h after treatment with 2mM hydrogen peroxide
Keywords: parallel sample


title: CT18_Rifampicin_125ug/ml_DNA

summary:
Gene content of Salmonella enterica sv Typhi CT18 30min after treatment with 125ug/ml Rifampicin
Keywords: parallel sample


title: TAQ100F2_mitomycinC_2ug/ml_DNA

summary:
Gene content in Salmonella enterica sv Typhimurium TAQ100F2 (Ames strain, cured of Fels phages and Fels2 reintroduced) 3h after exposure to 2mM hydrogen peroxide
Keywords: parallel sample

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: TAQ100F2_hydrogen_peroxide_2mM_RNA

summary:
Gene expression of Salmonella enterica sv Typhimurium TAQ100F2 (Ames strain cured of Fels prohages and subsequent reintroduction of Fels2) 30min after exposure to 2mM hydrogen peroxide
Keywords: parallel sample


title: S.enterica_log_vs_overnight_DNA

summary:
Gene content comparison of Salmonella enterica sv Typhimurium LT2, sv Typhi CT18 and sv Typhi TY2 cultures grown to log phase versus cultures grown overnight
Keywords: parallel sample


title: Effect of potassium-depleted diet on kidney

status: Public on May 30 2004

city: Paris

first: Alain

last: Doucet

institute: Institut des Cordeliers

summary:
Libraries obtained from microdissected kidney outer medullary collecting duct from C57Bl6/J mice control or after 3 days potassium-depleted diet.
Keywords: other

first: Lydie

last: Cheval

first: Jean-Marc

last: Verbavatz

first: Patrick

last: Bruneval

first: Jean-Paul

last: Duong Van Huyen

last: Elalouf


title: TA100_hydrogen_peroxide_2mM_DNA

summary:
Gene content in Salmonella enterica sv Typhimurium TA100 (Ames strain) after exposure to 2mM hydrogen peroxide
Keywords: time-course


title: TAQ100F2_hydrogen_peroxide_2mM_DNA

summary:
Gene content in Salmonella enterica sv Typhimurium TAQ100F2 (Ames strain, cured of Fels phages, and Fels2 reintroduced) after exposure to 2mM hydrogen peroxide
Keywords: time-course


title: TA100_hydrogen_peroxide_2mM_RNA

summary:
Gene expression in Salmonella enterica sv Typhimurium TA100 after exposure to 2mM hydrogen peroxide
Keywords: parallel sample


title: CT18_MitomycinC_2ug/ml_DNA

summary:
Gene content in Salmonella enterica sv Typhi CT18 3h after treatment with 2ug/ml Mitomycin C
Keywords: repeat sample


title: LT2_mitomycinC_2ug/ml_DNA

type:
Expression profiling by array
Genome variation profiling by array

summary:
Gene content in Salmonella enterica sv Typhimurium LT2 3h after treatment with 2ug/ml mitomycin C
Keywords: repeat sample


title: DT104_hydrogen_peroxide_2mM_DNA

summary:
Gene content in Salmonella enterica sv Typhimurium DT104 after treatment with 2mM hydrogen peroxide
Keywords: time-course


title: 14028s_hydrogen_peroxide_2mM_DNA

summary:
Gene content in Salmonella enterica sv Typhimurium 14028s after treatment with 2mM hydrogen peroxide
Keywords: time-course


title: SL1344_heat_shock_42C_RNA

summary:
Gene expression in Salmonella enterica sv Typhimurium SL1344 after heat shock to 42C
Keywords: time-course

first: Emily

last: Proctor


title: SL1344_heat_shock_37C_RNA

summary:
Gene expression in Salmonella enterica sv Typhimurium SL1344 after heat shock to 37C
Keywords: time-course


title: SL1344_hydrogen_peroxide_2mM_DNA

summary:
Gene content in Salmonella enterica sv Typhimurium SL1344 post treatment with 2mM hydrogen peroxide
Keywords: parallel sample


title: LT2_MitomycinC_2ug/ml_RNA

summary:
Gene expression of Salmonella enterica sv Typhimurium LT2 post treatment with 2ug/ml mitomycin C.
Keywords: time-course


title: 14028s:rpoH_heat_shock_37C_RNA

summary:
Gene expression in Salmonella enterica sv Typhimurium 14028s rpoH mutant strain IB314 after heat shock to 37C
Keywords: time-course


status: Public on May 08 2004

city: Epalinges

first: Pascale

last: Anderle

country: Switzerland

institute: ISREC

summary:
Genomic profile of transporters and ion channels in differentiated or undifferentiated Caco-2 cells grown for 5 days, 1 week, 2 weeks or 3 weeks in flasks or filters
Keywords: ordered


title: LT2_hydrogen_peroxide_2mM_DNA

summary:
Gene content Salmonella enterica sv Typhimurium LT2 post treatment with 2mM hydrogen peroxide
Keywords: time-course


title: 14028s_hydrogen_peroxide_2mM_RNA

summary:
Gene expression in Salmonella enterica sv Typhimurium 14028s post treatment with 2mM hydrogen peroxide
Keywords: time-course


title: Simulated Microgravity Inhibits Differentiation and Alters Gene Expression Profiles of 2T3 Pre-osteoblasts

status: Public on May 07 2004

city: Atlanta

first: Hanjoong

last: Jo

state: GA

department: Biomedical Engineering

institute: Emory University

summary:
Exposure to microgravity causes bone loss in humans, and the underlying mechanism is believed to be at least partially due to a decrease in bone formation by osteoblasts.  Here, we examined the hypothesis that microgravity changes osteoblast gene expression profiles, resulting in bone loss.  For this study, we developed an in vitro system that simulates microgravity using the Random Positioning Machine (RPM) to study the effects of microgravity on 2T3 pre-osteoblast cells grown in gas-permeable culture disks.  Exposure of 2T3 cells to simulated microgravity using RPM for up to 9 days significantly inhibited alkaline phosphatase activity, recapitulating an expected bone loss response, without altering cell proliferation and shape.  Next, we carried out a DNA microarray analysis to determine the gene expression profile of 2T3 cells exposed to 3 days of simulated microgravity.  Among 10,000 genes examined with the microarray, 88 were downregulated while 52 were upregulated significantly by simulated microgravity by more than two-fold in comparison to the static 1g condition.  By using real-time PCR assays, we verified the microarray data using some of the expected genes.  For example, we confirmed that microgravity induced downregulation of alkaline phosphatase, runt related transcription factor 2 (runx2), osteomodulin, and parathyroid hormone 1 receptor, while confirming upregulation of cathepsin K mRNAs.  In addition to the changes of the expected genes, the microarray data identified many more genes.  The identification of these gravisensitive genes provide an useful insight in generating further hypotheses regarding their roles not only in microgravity-induced bone loss, but also in general population of patients with similar pathologic conditions such as osteoporosis.
Keywords: other

first: Steven

last: Pardo

first: Mamta

last: Patel

first: Michelle

last: Sykes

first: Manu

middle: O

last: Platt

first: Nolan

last: Boyd

first: George

middle: P

last: Sorescu

first: Min

last: Xu

first: Jack

last: van Loon

first: May

last: Wang


title: LT2_hydrogen_peroxide_2mM_RNA

first: Michael

last: McClelland

summary:
Gene expression Salmonella enterica sv Typhimurium LT2 post treatment with 2mM hydrogen peroxide
Keywords: time-course

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

first: Felisa

last: Blackmer

first: Jonathan

last: Frye

first: Pui

last: Cheng

first: Steffen

last: Porwollik

first: Feilsa


title: Genomic comparisons of Salmonella enterica sspI strains

summary:
Comparative genomic analysis of the most important S. enterica sspI clinical isolates and respective strains from the SARB collection
Keywords: other

sample_organism: Salmonella enterica subsp. enterica serovar Gallinarum

sample_organism: Salmonella enterica subsp. enterica serovar Infantis

sample_organism: Salmonella enterica subsp. enterica serovar Muenchen

sample_organism: Salmonella enterica subsp. enterica serovar Thompson

sample_organism: Salmonella enterica subsp. enterica serovar Heidelberg

sample_organism: Salmonella enterica subsp. enterica serovar Oranienburg

sample_organism: Salmonella enterica subsp. enterica serovar Senftenberg

sample_organism: Salmonella enterica subsp. enterica serovar Typhisuis

sample_organism: Salmonella enterica subsp. enterica serovar Abortusovis

sample_organism: Salmonella enterica subsp. enterica serovar Paratyphi A

sample_organism: Salmonella enterica subsp. enterica serovar Agona

sample_organism: Salmonella enterica subsp. enterica serovar Muenster

sample_organism: Salmonella enterica subsp. enterica serovar Saintpaul

sample_organism: Salmonella enterica subsp. enterica serovar Dublin

sample_organism: Salmonella enterica subsp. enterica serovar Newport

sample_organism: Salmonella enterica subsp. enterica serovar Montevideo

sample_organism: Salmonella enterica subsp. enterica serovar Choleraesuis

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

sample_organism: Salmonella enterica subsp. enterica serovar Paratyphi B var. L(+) tartrate +

sample_organism: Salmonella enterica subsp. enterica serovar Emek

first: E

first: Carmen

last: Choy

first: Emily

last: Proctor

middle: Fidelma


title: TAQ100F1_hydrogen_peroxide_2mM_DNA

summary:
Gene content in Salmonella enterica sv Typhimurium TAQ100F1 (Ames strain, cured of Fels phages, and Fels1 reintroduced) 3h after exposure to 2mM hydrogen peroxide
Keywords: parallel sample

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: The effect of Ras on the signalling networks in senescence

status: Public on May 04 2004

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

summary:
Activated Ha-ras was introduced to HMF3A cells. HMF3A cells are conditionally immortalised human mammary fibroblasts. They undergo co-ordinated senescence upon inactivation of LT antigen, when cultured at 39C. The introduction of Ras did not prevent this but affected the molecular profile.
Keywords = Senescence
Keywords = fibroblast
Keywords = Ras
Keywords = immortalization
Keywords = transformation
Keywords: ordered

first: Mike

last: O'Hare

first: Parmjit

last: Jat


title: Operon array expression profile agamous

status: Public on May 02 2004

city: Pasadena

first: Frank

last: Wellmer

address: 1200 E. California Blvd.

department: Biology 156-29

institute: California Institute of Technology

summary:
Comparison of gene expression profiles of wild-type and agamous inflorescences.
This series contains the data for four replicate experiments performed with four sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy3	mutant-Cy5
Set 2:  	wild type-Cy5	mutant-Cy3
Set 3:	wild type-Cy3	mutant-Cy5
Set 4:	wild type-Cy5	mutant-Cy3
Keywords: repeat sample


title: Aquaporin-1 Knockout vs Wild type Mice

status: Public on May 05 2004

city: Tucson

first: Heddwen

last: Brooks

state: AZ

address: 1501 N Campbell Ave

department: Physiology

institute: University of Arizona

summary:
This experiment compared aRNA derived from the kidney inner medula of three mice lacking a functional aquaporin-1 gene to three wild type mice. Each sample was hybridized 4 times, against 4 of the other 5 samples, using an interwoven loop experimental design.
Keywords: repeat sample


title: Operon array expression profile apetala2

summary:
Comparison of gene expression profiles of wild-type and apetala2 inflorescences.
This series contains the data for four replicate experiments performed with four sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy3	mutant-Cy5
Set 2:  	wild type-Cy5	mutant-Cy3
Set 3:	wild type-Cy3	mutant-Cy5
Set 4:	wild type-Cy5	mutant-Cy3
Keywords: repeat sample


title: Operon array expression profile pistillata

summary:
Comparison of gene expression profiles of wild-type and pistillata inflorescences.
This series contains the data for four replicate experiments performed with four sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy3	mutant-Cy5
Set 2:  	wild type-Cy5	mutant-Cy3
Set 3:	wild type-Cy3	mutant-Cy5
Set 4:	wild type-Cy5	mutant-Cy3
Keywords: repeat sample


title: Operon array expression profile apetala1

summary:
Comparison of gene expression profiles of wild-type and apetala1 inflorescences.
This series contains the data for four replicate experiments performed with four sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy3	mutant-Cy5
Set 2:  	wild type-Cy5	mutant-Cy3
Set 3:	wild type-Cy3	mutant-Cy5
Set 4:	wild type-Cy5	mutant-Cy3
Keywords: repeat sample


title: cDNA array expression profile apetala3

summary:
Comparison of gene expression profiles of wild-type and apetala3 inflorescences.
This series contains the data for three replicate experiments performed with three sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy5		mutant-Cy3
Set 2:  	wild type-Cy3		mutant-Cy5
Set 3:	wild type-Cy5		mutant-Cy3
Keywords: repeat sample


title: Operon array expression profile apetala3

summary:
Comparison of gene expression profiles of wild-type and apetala3 inflorescences.
This series contains the data for four replicate experiments performed with four sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy3	mutant-Cy5
Set 2:  	wild type-Cy5	mutant-Cy3
Set 3:	wild type-Cy3	mutant-Cy5
Set 4:	wild type-Cy5	mutant-Cy3
Keywords: repeat sample


title: cDNA array expression profile apetala2

summary:
Comparison of gene expression profiles of wild-type and apetala2 inflorescences.
This series contains the data for three replicate experiments performed with three sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy5		mutant-Cy3
Set 2:  	wild type-Cy3		mutant-Cy5
Set 3:	wild type-Cy5		mutant-Cy3
Keywords: repeat sample


title: U2AF associated RNA

status: Public on May 01 2004

city: Kansas City

first: Marco

last: Blanchette

state: MO

institute: Stowers Institute for Medical Research

summary:
Genome wide identification of the RNAs associated with the Drosophila large U2AF subunit
Keywords: repeat sample

first: Emmanuel

last: Labourier

first: Donald

last: Rio


title: cDNA array expression profile agamous

summary:
Comparison of gene expression profiles of wild-type and agamous inflorescences.
This series contains the data for three replicate experiments performed with three sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy5		mutant-Cy3
Set 2:  	wild type-Cy3		mutant-Cy5
Set 3:	wild type-Cy5		mutant-Cy3
Keywords: repeat sample


title: cDNA array expression profile apetala1

summary:
Comparison of gene expression profiles of wild-type and apetala1 inflorescences.
This series contains the data for three replicate experiments performed with three sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy5		mutant-Cy3
Set 2:  	wild type-Cy3		mutant-Cy5
Set 3:	wild type-Cy5		mutant-Cy3
Keywords: repeat sample


title: Adipose tissue of gonadectomized mice injected with dihydrotestosterone

status: Public on Apr 24 2004

city: Ste-Foy

first: Carl

last: Bolduc

state: Québec

address: 2705 Boul. Laurier

department: Anatomy and physiology

institute: Molecular Endocrinology and Oncology Research Center, Laval University Medical Center (CHUL)

summary:
Comparison of retroperitoneal adipose tissue of intact male mice and gonadectomized C57BL6 male mice. Gonadectomized mice were untreated or injected with dihydrotestosterone (DHT) and sacrificed 3 or 24 hours after injection.
Keywords: other

first: Marianne

last: Larose

first: Nicolas

last: Lafond

first: Mayumi

last: Yoshioka

first: Marc-André

last: Rodrigue

first: Jean

last: Morissette

first: Claude

last: Labrie

first: Vincent

last: Raymond

first: Fernand

first: Jonny

last: St-Amand


title: Effect of feeding and females on male salivary glands

status: Public on Apr 21 2004

city: Stillwater

first: Richard

middle: C.

last: Essenberg

state: OK

address: 246 NRC

department: Department of Biochemistry and Molecular Biology

institute: Oklahoma State University

summary:
A differential display experiment was done to compare genes expressed in salivary glands from unfed males, males fed in the presence of females and males fed in the absence of females. Possible differential bands were excised, cloned and sequenced.  A macroarray study was done on these clones as probes.  RNA from the salivary glands of ticks from the three conditions was labelled and hybridized.  Two sets of primers were used in the differential display, and these same two were used in the labelling, so there are two platforms, corresponding to what primer pair was used.  Two independent RNA isolations were done,  Experiment 1 used one, 2 and 3 the other.  Experiment 2 used exposure to X-ray film, while 1 and 3 used a phosphorimager plate.  Two exposures of the X-ray film were found to give acceptable results, 1 and 5 min.  These were averaged in the analysis.
Keywords = salivary_gland
Keywords = feeding
Keywords = male
Keywords = female
Keywords: other

first: Felix

last: Anyomi

first: John

middle: R

last: Sauer


title: Control and Il31 tx NHEK cells compared via SuperArray cDNA panel Chemokines and Receptors

status: Public on Apr 14 2004

city: Seattle

first: Cosette

last: LeCiel

state: WA

institute: ZymoGenetics

summary:
Gene Expression Array Analysis using NHEK control vs Il31 tx RNA
Keywords: time-course


title: HSP27 3A vs WT

status: Public on Apr 09 2004

city: Reno

first: Kimberly

last: Baker

state: NV

address: 1664 North Virginia St.

department: Cell and Molecular Biology

institute: University of Nevada School of Medicine

summary:
human bronchial smooth muscle cells were infected with adenoviral constructs containing either the phosphorylation mutant form of HSP27 (HSP27-3A) or the wild type form (HSP27-WT) at 40 MOI for 4 days.  All sets were stimulated with a cytokine mixture containing 10 ng/ml IL-1beta, TNF-alfa, and gamma-IFN for 20 hours prior to harvest.  This series represents 4 separate preparations of cells and RNA, with each set being subjected to a dye flip and hybridized to 2 different slides.
Keywords: parallel sample

first: Cherie

middle: A

last: Singer

first: William

middle: T

last: Gerthoffer


title: Adenovirus vs Mock Infection

summary:
human bronchial smooth muscle cells were either infected with empty adenoviral type 5 vector at 40 MOI for 4 days, or Mock infected.  Each sample set was then stimulated with a mixture of 10ng/mL IL-1beta, TNF-alfa, and gamma-IFN for 20 hours prior to RNA harvest.  RNA samples were split, and the series consists of 3 slides, 2 of which are dye flipped.
Keywords: parallel sample


title: Effect of cigarette smoke on normal human bronchial epithelial cells, and S9 toxicity

status: Public on Apr 06 2004

city: Oklahoma City

first: Stewart

middle: Alan

last: Shields

address: 825 NE 13th St

department: Arthritis/Immunology

institute: Oklahoma Medical Research Foundation

summary:
Temporal analysis of the effect of cigarette smoke on normal human bronchial epithelial cells (NHBE), and S9 toxicity.
Keywords: other

first: Ellen

middle: D

last: Jorgensen

first: Igor

last: Dozmorov

first: Mark

middle: B

last: Frank

first: Michael

last: Centola

first: Anthony

last: Albino


title: Cytokine Stimulated Vs Unstimulated

summary:
human bronchial smooth muscle cells were growth arrested.  One group was stimulated with 10ng/mL of IL-1beta, TNF-alfa, and gamma IFN for 20 hours.  For every cDNA sample, 2 dyeflipped slides were hybridized (these have the same date in the titles).  All cy3 (channel 2) measurements were normalized to the dye coupling control before a ratio of the values was taken.
Keywords: parallel sample

middle: J


title: Tubular carcinoma and adenoma

city: Seoul

first: Inchul

last: Lee

address: 388-1 Poongnap-Dong, Songpa-Gu

department: Pathology

country: South Korea

institute: University of Ulsan College of Medicine

summary:
AIM: To analyze the expression profiles of premalignant and/or preclinical lesions of gastric cancers. METHODS: We analyzed the expression profiles of normal gastric pit, tubular adenoma and carcinoma in situ using microdissected cells from routine gastric biopsies. For the DNA microarray analysis of formalin-fixed samples, we developed a simple and reproducible RNA extraction and linear amplification procedure applying two polymerase-binding sites. The amplification procedure took only 8 h and yielded comparable DNA microarray data between formalin-fixed tissues and unfixed controls. RESULTS: In comparison with normal pit, adenoma/carcinoma showed 504 up-regulated and 29 down-regulated genes at the expected false significance rate 0.15%. The differential expression between adenoma and carcinoma in situ was subtle: 50 and 22 genes were up-, and down-regulated in carcinomas at the expected false significance rate of 0.61%, respectively. Differentially expressed genes were grouped according to patterns of the sequential changes for the 'tendency analysis' in the gastric mucosa-adenoma-carcinoma sequence. CONCLUSION: Groups of genes are shown to reflect the sequential expression changes in the early carcinogenic steps of stomach cancer. It is suggested that molecular carcinogenic pathways could be analyzed using routinely processed biopsies.
Keywords: other


title: IL-10-conditioned dendritic cells elicit innate inflammatory gene products in response to danger signals

status: Public on Apr 15 2004

city: Oxford

first: Steve

last: Cobbold

state: Oxfordshire

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

summary:
IL-10-Conditioned Dendritic Cells, Decommissioned for Recruitment of Adaptive Immunity, Elicit Innate Inflammatory Gene Products in Response to Danger Signals

Dendritic cells (DCs) are the professional APCs of the immune system, enabling T cells to perceive and respond appropriately to potentially dangerous microbes, while also being able to maintain T cell tolerance toward self. In part, such tolerance can be determined by IL-10 released from certain types of regulatory T cells. IL-10 has previously been shown to render DCs unable to activate T cells and it has been assumed that this process represents a general block in maturation. Using serial analysis of gene expression, we show that IL-10 pretreatment of murine bone marrow-derived DCs alone causes significant changes in gene expression. Furthermore, these cells retain the ability to respond to Toll-like receptor agonists, but in a manner skewed toward the selective induction of mediators known to enhance local inflammation and innate immunity, among which we highlight a novel CXCR2 ligand, DC inflammatory protein-1. These data suggest that, while the presence of a protolerogenic and purportedly anti-inflammatory agent such as IL-10 precludes DCs from acquiring their potential as initiators of adaptive immunity, their ability to act as initiators of innate immunity in response to Toll-like receptor signaling is enhanced.
Keywords: other

first: K

last: Nolan

first: V

last: Strong

first: D

last: Soler

first: P

last: Fairchild

first: S

first: R

last: Croxton

first: J

last: Gonzalo

first: A

last: Rubio

first: H

last: Wells

first: M

last: Waldmann

first: Diana

last: Zelenika

first: Elizabeth

last: Adams

first: Susan

last: Humm

first: Luis

last: Graca

first: Sara

last: Thompson

first: Chun-Yen

last: Lin

last: Frewin

first: Sian

last: Cartland

first: Stephen

last: Yates

first: Alison

last: Paterson


title: 24 weeks of HFD

status: Public on Mar 30 2004

city: Toulouse

first: Rouet

last: Philippe

address: 37 Allées Jules Guesde

institute: Louis Bugnard

summary:
Heart from dog at 24 weeks of HFD
Keywords: repeat sample

first: Pierre

last: Philip-Couderc


title: 15 weeks of HFD

summary:
Heart from dog at 15 weeks of HFD
Keywords: repeat sample


title: cDNA array expression profile pistillata

first: Frank

last: Wellmer

summary:
Comparison of gene expression profiles of wild-type and pistillata inflorescences.
This series contains the data for three replicate experiments performed with three sets of biologically independent samples.
Cy3 and Cy5 dyes were used as follows:
Set 1:	wild type-Cy5		mutant-Cy3
Set 2:  	wild type-Cy3		mutant-Cy5
Set 3:	wild type-Cy5		mutant-Cy3
Keywords: repeat sample


title: time course following a low light to high light shift

status: Public on Apr 01 2004

city: Berkeley

first: Heidi

middle: Kristine

last: Ledford

address: 111 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

summary:
Time course following a low light to high light shift. Strains used are wild type (CC-125) and npq1 lor1. Results in "VALUE" column are the log2 of Cy3/Cy5 ratios following normalization in SNOMAD.
Keywords: time-course


title: 10 weeks of HFD

summary:
Heart from dog at 10 weeks of HFD
Keywords: repeat sample


title: TK6 and WTK1 LCLs plus NO

city: Bethesda

first: Ana

middle: I

last: Robles

state: MD

address: 37 Convent Dr 37/3060D

institute: National Cancer Institute/NIH

summary:
Cell lines. TK6 and WTK1 are EBV-immortalized human lymphoblastoid cell lines that have been derived from the same donor. TK6 cells bear wild-type TP53 tumor suppressor, while WTK1 cells bear a mutant TP53 containing a C-to-T transition in exon 7, resulting in a change of Met to Ile at codon 237, and coding for a functionally inactive protein. Cells were maintained in exponentially growing suspension culture at 37ºC in a humidified, 5% CO2 atmosphere in RPMI medium1640 supplemented with 10% heat-inactivated calf serum, 100 units/ml penicillin, 100 mg/ml streptomycin, and 2 mM L-glutamine.  Stock cells were subcultured and maintained at a density not greater than 1.5 x 106 cells per ml in 150-mm dishes throughout experiments.

NO treatment. Cells at a density of 4 x 105 cells per ml in 100 ml of custom RPMI 1640 medium without calcium nitrate (GIBCO) and calf serum were exposed to pure NO gas (Matheson, Gloucester, MA) by diffusion through Silastic tubing (0.025 in. ID, 0.047 in OD, Dow Corning, Midland, MI) delivery system.  NO diffuses through this permeable membrane at a constant rate, and was delivered through 30 cm-long tubing into the medium of well-stirred cell suspensions for 2 h.  Cells similarly exposed to argon gas served as negative controls.  Total dose (and rate) of NO delivered under these conditions was 390 mmol (533 nM/s), calculated from nitrite plus nitrate content of the medium as determined by automated analysis using the Griess reagent [N-(1-napthy)-ethylenediamine and sulfanilic acid].  At the end of treatment, cells were collected by centrifugation, washed once, resuspended in fresh culture medium containing 10% heat inactivated calf serum, and incubated at 37 ºC. At the indicated times, cells were washed in cold phosphate-buffered saline, harvested and stored at -80 ºC for RNA extraction.

cDNA microarray hybridization and analysis. Cells were lysed with Trizol reagent (INVITROGEN, Carlsbad, CA), and total RNA was extracted according to the manufacturer's instructions at 0, 6, 12, and 24h after NO treatment.  Fluorescently-labeled cDNA probes were generated using 40 µg of total RNA by a single round of reverse transcription in the presence of aminoallyl-dUTP (SIGMA, St. Louis, MO), followed by a coupling reaction to Cy3 or Cy5 monofunctional NHS-ester (Amersham Pharmacia, Piscataway, NJ). Complex probes (containing untreated (time 0) Cy3-labeled cDNA and NO or argon-treated Cy5-labeled cDNA) were denatured and hybridized to glass slides featuring 9, 180 cDNA clones based on the Hs Unigene build #131 platform (GPL 257), and printed by the NCI Microarray Facility, Advanced Technology Center, Gaithersburg, MD. Upon overnight incubation at 42 ºC, the slides were washed successively in 1 X SSC/ 0.1% SDS, 1 X SSC and 0.2 X SSC for 2 min each, then rinsed in 0.5 X SSC and spin-dried. The two fluorescent intensities were measured simultaneously using a GenePix 4000A scanner, and the acquired image was processed with GenePix Pro 3.0 software (Axon Instruments, Union City, CA).
Keywords: time-course


title: adventitious root development P. contorta

city: Raleigh

first: Debbie

middle: Ross

last: Craig

state: NC

address: 840 Main Campus Drive

department: Forestry

institute: North Carolina State University

summary:
After four weeks the primary roots were cut off from the seedlings. The hypocotyl cuttings were treated in Hoagland nutrient solution at pH 5.8 containing 1.23 mM indole-3-butyric acid(IBA) for six hours then transferred to Hoagland nutrient solution lacking IBA. The hypocotyls were harvested at the following time points: day o,3,6,9,12 and 33.
Keywords: time-course

first: Monika

last: Brinker

first: Leonel

last: van Zyl

first: Wenbin

last: Liu

first: Deborah

first: Ron

last: Sederoff

first: David

last: Clapham

last: von Arnold


title: 9 weeks HFD

summary:
Heart dog at 9 weeks of HFD
Keywords: repeat sample


title: Gene expression in mouse ovary and testis

status: Public on Mar 27 2004

first: Rafael

middle: Dan

last: Camerini-Otero

address: 5 Memorial Dr. Rm.205

department: GBB

institute: NIDDK

summary:
To investigate the genomic distribution of genes with sex- biased expression patterns in mice we analyzed the chromosomal distribution of genes preferentially expressed in sexually dimorphic tissues such as testis and ovary.
Keywords: repeat sample

first: Natalya

last: Smirnova

first: Pavel

last: Khil

first: Peter

last: Romanienko

first: Daniel


title: GcrA depletion study (Caulobacter vibrioides)

status: Public on Mar 23 2004

city: Stanford

last: Brende

address: 279 Campus Dr

department: Developmental Biology

institute: Stanford University

summary:
Supporting data for:  Holtzendorff et. al., "Oscillating global regulators."
Keywords = gcrA
Keywords = global regulator
Keywords: repeat sample

first: Julia

last: Holtzendorff

first: Dean

last: Hung

first: Ann

last: Reisenauer

first: Patrick

middle: H

last: Viollier

first: Harley

last: McAdams

first: Lucy

last: Shapiro


title: HBC-3 matrigel differentiation

status: Public on Apr 29 2004

city: New York

first: Leslie

last: Rogler

state: NY

address: 1300 Morris Park Ave

department: Liver Research Center/ Department of Medicine

institute: Albert Einstein College of Medicine

summary:
This series represents in vitro bile ductular differentiation of HBC-3 cells, A, B and C denote the 3 biological repeats
Keywords = HBC-3 cells
Keywords = murine hepatoblast cells
Keywords = matrigel
Keywords: time-course

first: Tammy

last: Ader

first: Raquel

last: Norel

first: Charles


status: Public on Mar 20 2004

city: El Paso

first: William

last: Baldwin

state: TX

address: 500 W. University Ave.

department: Biological Sciences

institute: Unversity of Texas at El Paso

summary:
Alterations in gene expression in FVB/NJ mouse liver following 4-nonylphenol (4-NP) treatment for 32 weeks. Mice were treated with 45 mg/kg/day 4-NP for 32 weeks, livers excised and differential gene expression determined. Samples 1 and 2 are controls and samples 3 and 4 are mice treated with 4-NP.

Arrays were visualized from the K-screen, and analyzed and quantified with a phosphoimager (Molecular Imager FX, Bio-Rad, Hercules, CA) and the ResGen PathwaysTM Universal Microarray Analysis SoftwareTM (Research Genetics, Carlsbad, CA).  Local background was subtracted automatically from the individual spot intensities, and spot intensities were normalized to the mean intensity of all spots on the array.  This is called datapoint normalization on the ResGen Pathways Microarray Analysis SoftwareTM.  Normalized gene intensities on the arrays probed with 4-NP treated mouse livers and untreated mouse liver cDNA were compared, and fold differences were calculated.
Keywords: ordered

middle: S

first: Laura

middle: M

last: Chapman

first: Ricardo

last: Acevedo


title: Rb knockout retinal explant comparison

status: Public on Mar 16 2004

city: Memphis

first: Michael

last: Dyer

state: TN

address: 332 N Lauderdale

institute: St Jude

summary:
knockout and wildtype sample pair
Keywords = rod
Keywords = retina
Keywords = mouse
Keywords = Rb
Keywords: other


title: EP300 knock-out image segmentation

city: Cambridge

first: Ahmed

middle: Ashour

last: Ahmed

address: Robinson Way

department: Oncology, University of Cambridge

institute: Cancer Research UK Cambridge Research Institute

summary:
This study examines the effect of four different image segmentation methods on the precision of the data.
Keywords: other

first: James

last: Brenton


title: Fol expression data

status: Public on Mar 22 2004

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

summary:
Fusarium oxysporum f.sp. lycopersici expression during nutrient starvation. 6 repeats of each nitrogen and carbon starvation.

Data cited in:
Molecular Plant Pathology
Volume 6, Issue 4, Page 459-470, Jul 2005

Keywords: parallel sample


title: Detection of genes in different carbohydrates isolated by NSH using single channel slide based hybrdizations

status: Public on Mar 14 2004

first: Patricia

last: Ayoubi-Canaan

address: 246 Noble Research Center

department: Biochemistry and Molecular Biology

institute: Oklahoma State University

summary:
Isolation of genes from Aspergillus nidulans grown in different complex carbohydrates by NSH and the NSH method was evaluated by using single channel non competitive slide based hybridizations
Keywords = NSH
Keywords = subtraction
Keywords = aspergillus
Keywords = polysaccharide
Keywords = exopolygalacturonase
Keywords: repeat sample

first: Anamika

last: Ray

first: Sunita

last: Macwana

last: Ayoubi

first: Leo

last: Hall

first: Rolf

last: Prade

first: Andrew

last: Mort


title: Control heart group

first: Rouet

last: Philippe

state: FRANCE

summary:
5 heart control dogs
Keywords: repeat sample

first: Pierre

last: Philip-Couderc


title: PDGF-induced genes regulated by the PI3K and MEK/ERK signaling pathways

status: Public on Mar 13 2004

city: Boston

first: Geoffrey

last: Cooper

state: MA

address: 5 Cummington St

department: Biology

institute: Boston University

summary:
Human T98G glioblastoma cells were stimulated with platelet-derived growth factor (PDGF) and analyzed by DNA microarrays, which identified 74 immediate-early gene transcripts. Cells were then treated with inhibitors to identify subsets of genes that are targets of the phosphatidylinositol 3-kinase (PI3K) and MEK/ERK signaling pathways. Four groups of PDGF-induced genes were defined: independent of PI3K and MEK/ERK signaling, dependent on PI3K signaling, dependent on MEK/ERK signaling, and dependent on both pathways.  Cells were grown in Minimal Essential Medium (Invitrogen) supplemented with fetal calf serum (10%). For growth factor/inhibitor treatments, cells were incubated in serum-free medium for 72 h, and either left unstimulated, or stimulated for 30 min with human PDGF-BB (50 ng/ml) (Sigma). U0126 (Cell Signaling Technology) and LY294002 (BioMol) were added 60 min prior to PDGF addition.
Keywords: other

first: John

middle: W

last: Tullai

middle: E

last: Schaffer

first: Steven

last: Mullenbrock

first: Simon

last: Kasif


title: Eye development in mouse and rat

status: Public on Mar 11 2004

city: Louisville

first: Thomas

last: Knudsen

state: KY

address: 501 S Preston St

department: Birth Defects Center

institute: University of Louisville

summary:
In this series the ocular primordium was microdissected from normal CD-1 (outbred) mouse embryos harvested days 8-10 post-coitus, corresponding to human development during the 3rd-4th weeks post-fertilization. The precise embryological age was ascertained by counting somite pairs to an accuracy of +/- 2 pairs per litter. Samples were pooled as follows: optic pit pooled from 48-50 embryos (6 litters) on 8 d.p.c. (4-8 somite pairs), optic vesicle pooled from 36-40 embryos (5 litters) on 9 d.p.c. (16-20 somite pairs), and optic cip pooled from 27-30 embryos (3 litters) on 10 d.p.c. (28-32 somite pairs). The common reference for this series was RNA collected from embryonic headfold microdissected on 8 d.p.c. RNA samples were collected from CD-1 rat embryos at equivalent somite stages for the headfold, optic vesicle, and opic cup.

Keywords = embryo
Keywords = eye development
Keywords = mouse
Keywords = rat
Keywords: time-course

sample_organism:
Mus musculus
Rattus norvegicus

first: Kimberly

middle: R

last: Nemeth

first: Amar

middle: V

last: Singh

first: Jeffrey

last: Charlap


title: MeHg intervention with PK11195

summary:
In this time course pregnant CD-1 (outbred) dams were exposed to MeHg as monomethylmercuric chloride intraperitoneally on 9 d.p.c. The test dose of 5.0 mg/kg MeHg was selected as a dose with an estimated 20% increased risk for encephalopathy in term fetuses, with no evidence of maternal toxicosis. Exposed embryos were co-treated with PK11195, a nontoxic ligand of the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) that effectively suppresses developmental toxicity induced with MeHg. The anticipated remediation with 5.0 mg/kg and 4.0 mg/kg PK11195 is <10% malformations. Sampling intervals ranged from 3.0h to 6.0h post-exposure. All measurements were on RNA from the embryonic forebrain (prosencephalon).
Keywords = time series
Keywords = mercury
Keywords = PK11195
Keywords = embryo
Keywords = Fetal Minamata Disease
Keywords: time-course


title: Universal Microarray System (UMAS) to investigate yeast response to galactose

status: Public on Mar 12 2004

city: New Haven

first: Kevin

last: McConnell

state: CT

address: 2 Church Street South, Suite 401

institute: Agilix Corporation

summary:
We describe a transcriptional analysis platform consisting of a universal micro-array system (UMAS) combined with an enzymatic manipulation step that is capable of generating expression profiles from any organism without requiring a priori species-specific sequence information. The transcriptome is converted to cDNA and processed with restriction endonucleases to generate low-complexity pools (80–120) of equal length DNA fragments. The resulting material is amplified and detected with
the UMAS system, comprising all possible 4,096 (4^6) DNA hexamers. Ligation to the arrays yields thousands of 14-mer sequence tags. The compendium of signals from all pools in the array-of-universal arrays comprises a full-transcriptome expression profile. The technology was validated by analysis of the galactose response of Saccharomyces cerevisiae, and the resulting profiles showed excellent agreement with the literature and real-time PCR assays.
Keywords: other

first: Matthew

last: Roth

first: Li

last: Feng

first: Paul

first: Cesar

last: Guerra

first: Jason

middle: P

last: Affourtit

last: Piper

first: Lorri

last: Guccione

first: Jayashree

last: Hariharan

first: Maura

last: Ford

first: Stephen

last: Powell

first: Harish

last: Krishnaswamy

first: Jennifer

last: Lane

first: Lisa

first: Gino

last: Intrieri

first: Jane

last: Merkel

first: Clotilde

last: Perbost

first: Anthony

last: Valerio

first: Brenda

last: Zolla

first: Carol

last: Graham

first: Jonathan

last: Hnath

first: Chris

last: Michaelson

first: Rixin

last: Wang

first: Baoge

last: Ying

first: Conrad

last: Halling

first: Craig

last: Parman

first: Debasish

last: Raha

first: Brent

last: Orr

first: Barbara

last: Jedrzkiewicz

first: Ji

last: Liao

first: Anton

last: Tevelev

first: Martin

last: Mattessich

first: David

last: Kranz

first: Michelle

last: Lacey

first: Joesph

middle: C

last: Kaufman

first: Junhyong

last: Kim

first: Darin

last: Latimer

last: Lizardi


title: Oxygen sensing in embryo culture

first: Thomas

last: Knudsen

summary:
This series compares the effects that two pharmacologically distinct ligands at the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) has on gene expression in early mouse embryos cultured under different oxygen levels. Mouse embryos averaging 16-18 somite pairs were explanted on 9 d.p.c. and grown in culture under optimal oxygenation (21% oxygen, hyperbaric with respect to arterial blood = 80-100 mmHg). Most embryos (>90%) develop normally in over a 24h culture period. When embryos receive suboptimal oxygenation for 2.0h (5% oxygen, similar to venous blood = 38-40 mmHg) a high percentage of them (>60%) go on to develop abnormally or else fail. These hypoxic embryos are remediated with 5 uM PK11195 to ~25% malformation rate. Cultured embryos were exposed to different oxygen levels (5% or 21%) in the presence of the Bzrp ligands PK11195 (Bzrp antagonist) versus Ro5-4864 (Bzrp agonist). The sampling time was guided by p53 protein induction with hypoxia, and remediation with PK11195, at 4.0h of culture and exposures. Thus all measurements were on RNA from the prosencephalon collected 2.0h after start of the test period on 9 d.p.c.
Keywords = peripheral benzodiazepine receptor
Keywords = oxygen sensing
Keywords = Bzrp ligands
Keywords = PK11195
Keywords = Ro5-4864
Keywords = embryo
Keywords = p53 protein induction
Keywords: ordered

first: Kimberly

last: Nemeth

first: Amar

last: Singh

first: Jeffrey

last: Charlap


title: MeHg-induced encephalopathy

summary:
In this dose series pregnant CD-1 (outbred) dams were exposed to methylmercury (MeHg) as monomethylmercuric chloride injected intraperitoneally on 9 d.p.c. Test doses were 10.0 mg/kg and below. This regimen induces symptoms of Fetal Minimata Disease (FMD) in term fetuses. Risks with respect to FMD for the various test doses were 10.0 mg/kg (40% risk), 5.0 mg/kg (20% risk), 2.5 mg/kg (NOAEL), and 1.25 mg/kg (subNOAEL). All measurements were on RNA from the embryonic forebrain (prosencephalon and surrounding tissue) at 3.0h post-treatment.
Keywords = dose series
Keywords = mercury
Keywords = embryo
Keywords = Fetal Minamata Disease
Keywords: dose response

overall_design: Test doses were 10.0 mg/kg (40% risk), 5.0 mg/kg (20% risk), 2.5 mg/kg (NOAEL), and 1.25 mg/kg (subNOAEL).


title: 5.0 mg/kg MeHg exposure

summary:
In this time course pregnant CD-1 (outbred) dams were exposed to MeHg as monomethylmercuric chloride intraperitoneally on 9 d.p.c. The test dose of 5.0 mg/kg MeHg was selected as a dose with an estimated 20% increased risk for encephalopathy in term fetuses, with no evidence of maternal toxicosis. Sampling intervals ranged from 1.5h to 24.0h post-exposure. All measurements were on RNA from the embryonic forebrain (prosencephalon) using contemporous control embryos as a reference.
Keywords = time series
Keywords = mercury
Keywords = embryo
Keywords = Fetal Minamata Disease
Keywords: time-course


title: 2CdA intervention with PK11195

summary:
In this time course pregnant CD-1 (outbred) dams were exposed to the 2-chloro analogue of 2'-deoxyadenosine (a metabolic toxin) on 8 d.p.c. The test dose of 2.5 mg/kg 2CdA was modeled for a 5% increased risk of microphthalmia in term fetuses. Exposed embryos were co-treated with PK11195, a nontoxic ligand of the mitochondrial peripheral-type benzodiazepine receptor (Bzrp) that effectively blocks p53 protein induction and developmental toxicity induced with 2CdA. Sampling intervals were anchored to the conditional biomarker (p53 protein induction) expressed in 2CdA-treated embryos between 3.0- and 4.5h post-exposure. Since p53 protein induction has been defined as a critical event in 2CdA-induced microphthalmia, these sampling intervals represent times before (3.0h), during (4.5h), and after (6.0h) this critical event. No p53 induction is observed in embryos co-treated with 2CdA and PK11195. All measurements were on RNA from the embryonic headfold.
Keywords = time series
Keywords = 2-chloro-2'-deoxyadenosine
Keywords = PK11195
Keywords = embryo
Keywords = p53 protein induction
Keywords = microphthalmia
Keywords: time-course


title: Comparison of Bzrp ligands

summary:
This series compares the effects that two pharmacologically distinct ligands at the mitochondrial peripheral-type benzodiazepine receptor (Bzrp). PK11195 (4.0 mg/kg, a presumed antagonist) has no observable adverse effects in pregnant mice on either 8 days post-coitus (d.p.c.) or 9 d.p.c. Furthermore, PK11195 is shown to rescue mouse fetuses from microphthalmia or microphthalmia-microcephaly induced with 2CdA or MeHg, respectively; effects of PK11195 on EtOH-induced craniofacial malformations are not yet unkown. Ro5-4864 (4.0 mg/kg, a presumed agonist) is weakly teratogenic on 8 d.p.c. (effects on 9 d.p.c. unknown) and this Bzrp ligand does not rescue fetuses from malformations induced with either 2CdA or MeHg; effects of Ro5-4864 on EtOH-induced craniofacial malformations is unknown for either sensitive (C57BL/6J) or insensitive (C57BL/6N) strains. The 4.0 mg/kg dose of Bzrp ligands is consistent with pharmacological activity in several studies. Pregnant mice were exposed to these agents on 8 d.p.c. (2CdA, EtOH) or 9 d.p.c. (MeHg). The test dose of 2.5 mg/kg 2CdA was modeled for a 5% increased risk of microphthalmia in term fetuses. Full remediation with PK11195 anticipated. The test dose of 5.0  mg/kg MeHg gives an estimated 20% increased risk of microphthalmia-microcephaly (encephalopathy) in term fetuses. Partial remediation with PK11195 is anticipated to <10% malformations. Again the effects of PK11195 on EtOH teratogenicity is not yet known. The sampling time was chosen as the time of p53 protein induction (3.0h to 4.5h post-treatment). Whereas co-treatment with PK11195 suppresses embryonic p53 protein induction Ro5-4864 does not block this reaction. All measurements were on RNA from the embryonic headfold (8 d.p.c.) or prosencephalon (9 d.p.c.).
Keywords = peripheral benzodiazepine receptor
Keywords = Bzrp ligands
Keywords = PK11195
Keywords = Ro5-4864
Keywords = embryo
Keywords = p53 protein induction
Keywords: ordered


title: aerobic knock-out

status: Public on Mar 10 2004

city: La Jolla

first: Jinseong

last: Cheong

state: CA

institute: University of California at San Diego

summary:
Six different knock-out strains' expression data under aerobic condition
Keywords: parallel sample

first: Markus

last: Covert

first: Eric

last: Knight

first: Jennie

middle: L

last: Reed

last: Herrgard

first: Bernhard

middle: O

last: Palsson


title: Human lupus and normal CD4 T cells response to anti-CD3 treatment

status: Public on Mar 05 2004

city: Chicago

first: Luting

last: Xu

state: IL

address: 303 E. Chicago Ave.

department: Rheumatology Division

institute: Northwestern University Feinberg School of Medicine

summary:
cDNA microarray profiling reveals differential gene expression patterns under anergy- and AICD-inducing conditions.
Keywords: time-course

first: Li

last: Zhang

first: Yajun

last: Yi

first: Hee-Kap

last: Kang

first: Syamal

middle: K

last: Datta


title: Effect of LPS and LPS-binding protein treatment for 2 hours on RAW 264.4 cells

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

institute: California Institute of Technology

summary:
All samples were gathered from mouse RAW 264.7 cells (macrophages). Control total RNA was extracted from untreated RAW 264.7 cells cultured for 2 hours. Test total RNA was extracted from lipopolysaccharide (100ng/ml) and lipopolysaccharide-binding protein (100pM) treated RAW 264.4 cells cultured for 2 hours. Experiment design included three control vs test arrays and three dye swap arrays.
Keywords: other

first: Yun Anna

last: Cao

first: Mi Sook

last: Chang

first: Sun Young

last: Lee

first: Meghdad

last: Rahdar

first: Robert

last: Hsueh


title: Effect of LPS and LPS-binding protein treatment for 48 hours on RAW 264.4 cells

summary:
All samples were gathered from mouse RAW 264.7 cells (macrophages). Control total RNA was extracted from untreated RAW 264.7 cells cultured for 48 hours. Test total RNA was extracted from lipopolysaccharide (100ng/ml) and lipopolysaccharide-binding protein (100pM) treated RAW 264.4 cells cultured for 48 hours. Experiment design included three control vs test arrays and three dye swap arrays.
Keywords: other


title: ABA or GA calli treatment

city: Tsukuba

first: Junshi

last: Yazaki

state: Ibaraki

address: 2-1-2 Kan-nondai

department: Molecular Genetics

country: Japan

institute: National Institute of Agrobiological Sciences

summary:
The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing either ABA or GA (Gibberellin) plant hormones and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer.
Keywords: other

first: Zenpei

last: Shimatani

first: Akiko

last: Hashimoto

first: Yuko

last: Nagata

first: Fumiko

last: Fujii

first: Kanako

last: Shimbo

first: Shoshi

last: Kikuchi


title: Identification and distinct regulation of yeast TATA-box containing genes

city: University Park

first: Frank

last: Pugh

state: PA

address: 452 North Frear Laboratory

institute: The Pennsylvania State University

summary:
Despite being one of the first eukaryotic transcriptional regulatory elements identified, the sequence of a native TATA box and its significance remain elusive. Applying criteria associated with TATA boxes we queried several Saccharomyces genomes and arrived at the consensus TATA(A/T)A(A/T)(A/G).  Approximately 20% of yeast genes contain a TATA box.  Strikingly, TATA box-containing genes are associated with responses to stress, are highly regulated, and preferentially utilize SAGA rather than TFIID when compared to TATA-less promoters.  Transcriptional regulation in yeast appears to be mechanistically bipolar, possibly reflecting a need to balance inducible stress-related responses with constitutive housekeeping functions.
A strain containing amino terminal HA-tagged TBP and its parental untagged counterpart BY4741 (Resgen) were grown at 23?C in CSM to OD600 = 0.8-1.0. Cultures were shifted to 37?C for 5 minutes (to mimic heat treatments used elsewhere (Huisinga and Pugh, 2004)), then crosslinked at 23?C with 1% formaldehyde. ChIP was performed as described previously (Strahl-Bolsinger et al., 1997) with the some modification.  Following cell disruption with glass beads, the chromatin was partially purified by centrifugation (Kurdistani and Grunstein, 2003).  HA-TBP was immunopurified with 12CA5 antibody.  After elution and reversal of the crosslinks, samples were subjected to non-specific amplification, labeling, and array hybridization as described (Bohlander et al., 1992; Chitikila et al., 2002).  The amplification procedure was modified as follows.  Following 15 round B amplification cycles, DNA was purified via QIAquick PCR Purification kit.  Ten cycles were used in round C.  Intergenic microarrays were generated by PCR amplification of entire intergenic regions of all yeast genes, then spotted onto glass slides.  Spot intensities were filtered to remove any signal that was less then one standard deviation above local background.  Three replicates were performed and their log2 ratios (enriched/input) were averaged.
Keywords = Chromatin Immunoprecipitation
Keywords = genome-wide binding
Keywords: other

first: Andrew

middle: D

last: Basehoar

first: Sara

middle: J

last: Zanton

first: B Franklin


title: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 ...

status: Public on Mar 03 2004

city: Guelph

first: John

last: Nash

state: ON

address: 110 Stone Road West

department: Laboratory for Foodborne Zoonoses

institute: Public Health Agency of Canada

summary:
We examined two variants of the genome-sequenced strain, Campylobacter jejuni NCTC11168, which show marked differences in their virulence properties including colonization of poultry, invasion of Caco-2 cells, and motility. Transcript profiles obtained from whole genome DNA microarrays and proteome analyses demonstrated that these differences are reflected in late flagellar structural components and in virulence factors including those involved in flagellar glycosylation, and cytolethal distending toxin production. We identified putative s28 and s54 promoters for many of the affected genes, and found that greater differences in expression were observed for s28-controlled genes. Inactivation of the gene encoding s28, fliA, resulted in an unexpected increase in transcripts with s54 promoters, as well as decreased transcription of s28-regulated genes. This was unlike the transcription profile observed for the attenuated C. jejuni variant, suggesting that the reduced virulence of this organism was not entirely due to impaired function of s28. However, inactivation of flhA, an important component of the flagellar export apparatus, resulted in expression patterns similar to that of the attenuated variant. These findings indicate that the flagellar regulatory system plays an important role in campylobacter pathogenesis and that flhA is a key element involved in the coordinate regulation of late flagellar genes and of virulence factors in C. jejuni. Furthermore, we provide a model for flagellar regulation, which forms a foundation for the study of the unique regulatory networks in this important human pathogen.
Keywords: parallel sample

first: Catherine

last: Carrillo

first: Eduardo

last: Taboada

first: Patricia

last: Lanthier

last: Kelly

first: Peter

last: Lau

first: Rachel

last: Verhulp

first: Oksana

last: Mykytczuk

first: Jonathan

last: Sy

first: Wendy

middle: A

last: Findlay

first: Kingsley

last: Amoako

first: Susantha

last: Gomis

first: Philip

last: Willson

last: Austin

first: Andy

last: Potter

first: Lorne

last: Babiuk

first: Brenda

last: Allan

first: Christine

last: Szymanski

middle: N


title: anaerobic knock-out

first: Jinseong

last: Cheong

summary:
Six different knock-out strains' expression data under anaerobic condition
Keywords: parallel sample

first: Markus

last: Covert

first: Eric

last: Knight

first: Jennie

last: Reed

last: Herrgard

first: Bernhard

last: Palsson


title: Zucker diabetic fatty (ZDF)/Zucker lean control (ZLC) comparisons

status: Public on Mar 01 2004

city: Seoul

first: MyeongHo

last: Jung

address: 5 Nokbun-dong, Eunpyung-gu

department: Biomedical Sciences

institute: National Institute of Health

summary:
Gene expression profiles in tissues of Zucker diabetic fatty (ZDF) rats compared with age matched Zucker lean control (ZLC) rats.
Keywords: other

first: YoungHo

last: Suh


title: Strain differences in copper sulfate

city: Saint Louis

first: Justin

last: Fay

state: MO

address: 4566 Scott Ave, Box 8232

department: Genetics

institute: Washington University

summary:
Each strain was grown overnight then diluted in fresh rich media. After three hours strains were again rediluted into either rich media or rich media supplemented with copper sulfate. After another three hours cultures were sampled, cells lysed and flash frozen using liquid nitrogen. RNA was extrated using hot phenol-chloroform, reverse transcripbed using amino-allyle dUTP and labelled with either Cy3 or Cy5 flourescent dye. Each hybridization is of a single sample compared to a reference pool contructed from all the strains with the same treatment. Labelled probe were hybridized to DNA microarrays spotted with 6144 70 bp oligonucleotides obtained from Qiagen-Operon. After an overnight hybridization, microarrays were scanned using a GenePix 4000A scanner and spot intensities extracted using GenePix 4.0 software. Bad spots were flagged based on the image.
Keywords: other

first: Heather

last: McCullough

first: Paul

last: Sniegowski

first: Michael

middle: B

last: Eisen


title: Effect of LPS and LPS-binding protein treatment for 4 hours on RAW 264.4 cells

first: Sangdun

last: Choi

summary:
All samples were gathered from mouse RAW 264.7 cells (macrophages). Control total RNA was extracted from untreated RAW 264.7 cells cultured for 4 hours. Test total RNA was extracted from lipopolysaccharide (100ng/ml) and lipopolysaccharide-binding protein (100pM) treated RAW 264.4 cells cultured for 4 hours. Experiment design included three control vs test arrays and three dye swap arrays.
Keywords: other

first: Yun Anna

last: Cao

first: Mi Sook

last: Chang

first: Sun Young

last: Lee

first: Meghdad

last: Rahdar

first: Robert

last: Hsueh


title: Muscle - atypical diabetes protein expression

first: Donald

middle: B.

last: Thomason

address: 894 Union Ave

department: Physiology

institute: The University of Tennessee Health Science Center

summary:
Skeletal muscle biopsies from atypical diabetics at presentation and remission. Protein expression determined with antibody arrays
Keywords: other

first: Aidar

last: Gosmanov

first: Guillermo

last: Umpierrez


title: HMF3A_with_3Dwt

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

summary:
HMF3A cells, created from adult human mammary fibroblasts by immortalisation with a thermolabile SV40 large T antigen and the catalytic sub-unit of human telomerase, undergo co-ordinated induction of cellular senescence upon inactivation of T antigen. HMF3A cells cease proliferating by 4 days at 39°C. We directly compared the gene expression profiles of cells at 33.5°C and after shift up to 39.5°C for 7 days (10 arrays, 3 biological replicates). To eliminate genes that change in response to the temperature shift, we compared the profiles of HMF3Dwt cells at 33°C and those shifted up to 39°C for 7 days (4 arrays, 2 biological replicates). Since HMF3Dwt cells were immortalised with wild type U19 LT antigen, they proliferate at both temperatures.
To break up the list of genes obtained with the 7 day shift, we performed several further comparisons on the arrays. HMF3A cells at 33°C were compared to the primary donor fibroblasts (HMF3 passage 8, 4 arrays), HMF3A cells shifted to 39°C for 2 days (4 arrays, 2 biological repeats), HMF3A cells shifted to 39°C for 7 days and then shifted back to 33°C for 3 days (8 arrays, 4 biological repeats) or 7 days (4 arrays, 2 biological repeats). As a comparison to the irreversible process of senescence, we sought to identify genes that changed upon reversible growth arrest, quiescence. Thus changes that occurred when the cells were grown to confluency and starved were also determined (2 biological replicate, 6 arrays).
Keywords = Rb
Keywords = fibroblast
Keywords = immortalization
Keywords = LT antigen
Keywords = p53
Keywords = quiescence
Keywords = senescence
Keywords: ordered

first: Louise

last: Mansfield

first: Alan

last: Mackay

first: Silvia

last: Benvenuti

first: Mike

last: O'Hare

first: Parmjit

last: Jat


title: GSEp53_v_Con

summary:
HMF3A cells, created from adult human mammary fibroblasts by immortalisation with a thermolabile SV40 large T antigen and the catalytic sub-unit of human telomerase, undergo co-ordinated induction of cellular senescence upon inactivation of T antigen. Given the importance of p53, we sought to determine what gene changes were affected if its activation was inhibited. To do this we used the Genetic Suppressor Element (GSE)56 which inhibits the transcriptional activity of p53 (Ossovskaya, 1996). The presence of the GSEp53 delayed the arrest of the HMF3A cells when LT was inactivated. However the cells did arrest. We thus examined the array profiles for 3A-GSEp53 cells after 2 and 7 days of LT inactivation (against 3A-GSEp53 cells at 33°C) and compared these to the profiles for 3A-puro cells.
Keywords = p53
Keywords = LT antigen
Keywords = fibroblast
Keywords = senescence
Keywords = Rb
Keywords: other


title: HMF3A_RNAi

summary:
HMF3A cells, created from adult human mammary fibroblasts by immortalisation with a thermolabile SV40 large T antigen and the catalytic sub-unit of human telomerase, undergo co-ordinated induction of cellular senescence upon inactivation of T antigen.
The pSUPER-retro vector system (Brummelkamp, 2002) was used to selectively target genes for mRNA degradation in an attempt to determine if they had a role, in the changes to the transcriptome upon LT inactivation. The genes chosen for targeting were BTG2, NR4A3, DUSP1, PHLDA1 and STACb.
Keywords = LT antigen
Keywords = senescence
Keywords = fibroblast
Keywords = BTG2
Keywords = DUSP1
Keywords = MKP-1
Keywords = NR4A3
Keywords = STAC
Keywords = PHLDA1
Keywords = RNAi
Keywords: other