title: Induction of dnTCF-4 in Ls174T CRC cells

status: Public on Sep 10 2005

summary:
The transactivation of TCF target genes induced by Wnt pathway mutations constitutes the primary transforming event in colorectal cancer (CRC). We show that disruption of beta-catenin/TCF-4 activity in CRC cells induces a rapid G1 arrest and blocks a genetic program that is physiologically active in the proliferative compartment of colon crypts. Coincidently, an intestinal differentiation program is induced. The TCF-4 target gene c-MYC plays a central role in this switch by direct repression of the p21(CIP1/WAF1) promoter. Following disruption of beta-catenin/TCF-4 activity, the decreased expression of c-MYC releases p21(CIP1/WAF1) transcription, which in turn mediates G1 arrest and differentiation. Thus, the beta-catenin/TCF-4 complex constitutes the master switch that controls proliferation versus differentiation in healthy and malignant intestinal epithelial cells.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Cornelis

last: Verweij


title: Characteristic genome rearrangements in experimental evolution

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

country: USA

institute: Stanford Microarray Database (SMD)

summary:
Genome rearrangements, especially amplifications and deletions, have regularly been observed as responses to sustained application of the same strong selective pressure in microbial populations growing in continuous culture. We studied eight strains of budding yeast (Saccharomyces cerevisiae) isolated after 100–500 generations of growth in glucose-limited chemostats. Changes in DNA copy number were assessed at single-gene resolution by using DNA microarray-based comparative genomic hybridization. Six of these evolved strains were aneuploid as the result of gross chromosomal rearrangements. Most of the aneuploid regions were the result of translocations, including three instances of a shared breakpoint on chromosome 14 immediately adjacent to CIT1, which encodes the citrate synthase that performs a key regulated step in the tricarboxylic acid cycle. Three strains had amplifications in a region of chromosome 4 that includes the high-affinity hexose transporters; one of these also had the aforementioned chromosome 14 break. Three strains had extensive overlapping deletions of the right arm of chromosome 15. Further analysis showed that each of these genome rearrangements was bounded by transposon-related sequences at the breakpoints. The observation of repeated, independent, but nevertheless very similar, chromosomal rearrangements in response to persistent selection of growing cells parallels the genome rearrangements that characteristically accompany tumor progression.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Maitreya

last: Dunham


title: Mouse response to H. pylory

status: Public on Sep 09 2005

summary:
Helicobacter pylori infects the stomachs of half of all humans. It has a relatively benign relationship with most hosts, but produces severe pathology, including gastric cancer, in others. Identifying the relative contributions of host, microbial and environmental factors to the outcome of infection has been challenging. Here, we describe one approach for identifying microbial genes that affect the magnitude of host responses to infection. Single colony purified H. pylori isolates were obtained from 25 cases and 71 controls in a Swedish case-control study of gastric cancer. Strains were first phenotyped based on their ability to produce adhesins that recognize two classes of human gastric epithelial receptors. Thirteen binding strains and two non-binding controls were then subjected to whole genome genotyping using H. pylori DNA microarrays. A cohort of 'variable' genes was identified based on a microarray-determined call of 'absent' in at least one member of the strain panel. Each strain was subsequently introduced into two types of germ-free transgenic mice, each programmed to express a different host factor postulated to pose increased risk for development of severe pathology. Expression of biomarkers of host defense was quantitated 4 weeks after inoculation and magnitude of the response correlated with bacterial genotype. The proportion of genes encoding HsdS homologs (specificity subunit of hetero-oligomeric type I restriction-modification systems) was significantly higher in the pool of 18 variable genes whose presence directly correlated with a robust host response than their proportion in the remaining 352 members of the variable gene pool. This suggests that the functions of these HsdS homologs may include control of expression of microbial determinants that affect the extent of gastric responses to this potentially virulent pathogen.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Nina

last: Salama


title: Yeast HSF1 vs hsf1-ba1

status: Public on Sep 27 2005

city: Kanazawa

first: Hiroshi

last: Sakurai

state: Ishikawa

address: 5-11-80 Kodatsuno

department: School of Health Sciences

country: Japan

institute: Kanazawa University

summary:
Upon heat shock, Hsf1 protein is extensively phosphorylated, however, this modification is inhibited by an hsf1-bal mutation. To get genome-wide effect of the hyperphosphorylation on Hsf1-regulated transcription, the heat-induced gene expression profiles in HSF1 and hsf1-bal cells were compared.
Keywords: stress response

overall_design: Total RNA was isolated from HSF1 wild type and hsf1-ba1 cells grown at 39oC for 15 min. Probe cDNA was primed by oligo(dT) and was synthesized in the presence of 33P-dCTP. Hybridization was carried out using one GF100 GeneFilter filter set for GSM37978 and GSM76015 and other filter set for GSM76014 and GSM76016. Value higher than 30 in HSF1 wild type cells is confident. Fold changes should be calculated from GSM37978 and GSM76015 and from GSM76014 and GSM76016.


title: Cordycepin time course: Identification of unstable transcripts

summary:
mRNA degradation provides a powerful means for controlling gene expression during growth, development, and many physiological transitions in plants and other systems. Rates of decay help define the steady state levels to which transcripts accumulate in the cytoplasm and determine the speed with which these levels change in response to the appropriate signals.  When fast responses are to be achieved, rapid decay of mRNAs is necessary. Accordingly, genes with unstable transcripts often encode proteins that play important regulatory roles. Although detailed studies have been carried out on individual genes with unstable transcripts, there is limited knowledge regarding their nature and associations from a genomic perspective, or the physiological significance of rapid mRNA turnover in intact organisms. To address these problems, we have applied cDNA microarray analysis to identify and characterize genes with unstable transcripts in Arabidopsis thaliana (AtGUTs). Our studies showed that at least 1% of the 11,521 clones represented on Arabidopsis Functional Genomics Consortium microarrays correspond to transcripts that are rapidly degraded, with estimated half-lives of less than 60 min. AtGUTs encode proteins that are predicted to participate in a broad range of cellular processes, with transcriptional functions being over-represented relative to the whole Arabidopsis genome annotation. Analysis of public microarray expression data for these genes argues that mRNA instability is of high significance during plant responses to mechanical stimulation and is associated with specific genes controlled by the circadian clock.
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design:
Biological Replicate
Computed

first: Rodrigo

last: Gutierrez


title: Mast Cell Activation

summary:
BACKGROUND: In asthma and other allergic disorders, the activation of mast cells by IgE and antigen induces the cells to release histamine and other mediators of inflammation, as well as to produce certain cytokines and chemokines. To search for new mast cell products, we used complementary DNA microarrays to analyze gene expression in human umbilical cord blood-derived mast cells stimulated via the high-affinity IgE receptor (FcϵRI). : One to two hours after FcϵRI-dependent stimulation, more than 2,400 genes (about half of which are of unknown function) exhibited 2-200 fold changes in expression. The transcriptional program included changes in the expression of IL-11 and at least 30 other cytokines and chemokines. Human mast cells secreted 130-529 pg of IL-11/106 cells by 6 h after stimulation with anti-IgE. CONCLUSION: Our initial analysis of the transcriptional program induced in in vitro-derived human mast cells stimulated via the FcϵRI has identified many products that heretofore have not been associated with this cell type, but which may significantly influence mast cell function in IgE-associated host responses. We also have demonstrated that mast cells stimulated via the FcϵRI can secrete IL-11. Based on the previously reported biological effects of IL-11, our results suggest that production of IL-11 may represent one link between IgE-dependent mast cell activation in subjects with allergic asthma and the development of a spectrum of structural changes in the airways of these individuals; such changes, collectively termed "airway remodeling," can constitute an important long term consequence of asthma.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Max

last: Diehn


title: Transcriptome profiling of dark grown photoreceptor mutants of Arabidopsis.

status: Public on Sep 04 2005

city: Capital Federal

first: Maria

middle: Agustina

last: Mazzella

state: Buenos AIres

address: Vuelta de Obligado 2490

country: Argentina

institute: INGEBI

summary:
Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment.
Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses

overall_design: We analysed the transcriptome in dark grown seedlings of the WT, and photoreceptor mutants (ofur genotypes). We used the doble phytochrome mutant phyAphyB, the double cryptochrome mutant cry1cry2 and the quadruple mutant. All seedlings have the same treatment (3d grown in complete darkness). They do not have replicates.

middle: A

middle: V

last: Arana

first: Roberto

last: Staneloni

first: Susana

last: Perelman

middle: J

last: Rodriguez batiller

first: Jorge

last: Muschietti

first: Pablo

middle: D

last: Cerdan

first: Kunhua

last: Chen

first: Rodolfo

last: Sanchez

first: Tong

last: Zhu

first: Joanne

last: Chory

last: Casal


title: RNA Abundance  in E. coli

last: Stanford Microarray Database

summary:
Steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Jon

last: Bernstein


title: mRNA decay in E. coli

summary:
Half-lives of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

overall_design: User Defined


title: A Compendium of Microarrays for Normal Human Cell Cultures

status: Public on Sep 01 2005

city: Boston

first: Adam

middle: Mark

last: Papallo

state: MA

address: 100 Morrissey Blvd.

department: Department of Physics

institute: University of Massachusetts Boston

summary:
We have used DNA microarrays from multiple commercial  from GE Healthcare (formerly Amersham Biosciences) to measure the large-scale gene expression profiles for 61 normal human cell cultures of epithelial, endothelial, and muscle cells provided by Biowhittaker/Cambrex.  This compendium of baseline gene expression patterns for pure cell cultures provides an essential database for understanding the cellular mechanisms for the maintenance of stable cell types and for studying the transformation pathways from undifferentiated stem cells to terminally differentiated cell types.
Keywords: cell type comparison

overall_design: There are 61 samples.  Certain cell types have replicates.  These replicates are denoted by a number annexed to the end of the sample title/name.


title: wnt in human embryonic carcinoma cells

status: Public on Sep 08 2005

summary:
Background Wnt signaling is implicated in many developmental decisions, including stem cell control, as well as in cancer. There are relatively few target genes known of the Wnt pathway. Results We have identified target genes of Wnt signaling using microarray technology and human embryonal carcinoma cells stimulated with active Wnt protein. The ~50 genes upregulated early after Wnt addition include the previously known Wnt targets Cyclin D1, MYC, ID2 and beta TRCP. The newly identified targets, which include MSX1, MSX2, Nucleophosmin, Follistatin, TLE/Groucho, Ubc4/5E2, CBP/P300, Frizzled and REST/NRSF, have important implications for understanding the roles of Wnts in development and cancer. The protein synthesis inhibitor cycloheximide blocks induction by Wnt, consistent with a requirement for newly synthesized beta - catenin protein prior to target gene activation. The promoters of nearly all the target genes we identified have putative TCF binding sites; and we show that the TCF binding site is required for induction of Follistatin. Several of the target genes have a cooperative response to a combination of Wnt and BMP. Conclusion Wnt signaling activates genes that promote stem cell fate and inhibit cellular differentiation; and regulates a remarkable number of genes involved in its own signaling system.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Jonathan

last: Pollack


title: Gene expression in trout hepatocellular carcinoma

status: Public on Sep 06 2005

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary:
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide and its occurrence is associated with a number of environmental factors including ingestion of the dietary contaminant aflatoxin B1 (AFB1).  While etiology of the disease is relatively well defined, the molecular mechanisms of tumorigenesis are poorly understood.  In this study, we examined, for the first time, gene expression of AFB1-induced HCC by microarray in the rainbow trout (Oncorhynchus mykiss) tumor model.  Carcinogenesis was initiated in trout embryos with 50 ppb AFB1 and 13 months later control livers, tumors and tumor-adjacent liver tissues were isolated from juvenile fish.  Global gene expression was determined in histologically confirmed HCCs compared to non-cancerous adjacent tissue and sham-initiated control liver utilizing a rainbow trout oligonucleotide array containing approximately 1500 genes of known or probable relevance to toxicology, comparative immunology, carcinogenesis and stress physiology.  We observed distinct gene regulation patterns in HCC compared to non-cancerous tissue including upregulation of genes important for cell cycle control, transcription, cytoskeletal formation and the acute phase response and down regulation of genes involved in drug metabolism, lipid metabolism and retinol metabolism.  These gene classes have previously been observed to be important in the regulation of HCC in human and rodent models.  Overall, these findings contribute to a better understanding of the mechanism of AFB1-induced hepatocarcinogenesis in the trout model and identify conserved genes important for carcinogenesis in species separated evolutionarily by more than 400 million years.
Keywords: other

first: Lena

last: Gerwick

first: Jerry

last: Hendricks

first: Caprice

last: Rosato

first: Graham

last: Corley-Smith

first: Scott

last: Givan

first: George

last: Bailey

first: Christopher

last: Bayne

first: David

last: Williams


title: Single-nucleosome mapping of histone modifications in S. cerevisiae

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
We have used a high-resolution tiled microarray, with single-nucleosome resolution, to investigate the in vivo occurrence of combinations of 12 histone modifications on thousands of nucleosomes in actively growing S. cerevisiae. We found that histone modifications do not occur independently; there are roughly two groups of co-occurring modifications.  We find no evidence for a deterministic code of many discrete states, but instead see blended, continuous patterns that distinguish nucleosomes at one location (promoter nucleosomes, for example) from those at another location (over the 3’ ends of coding regions, for example). These results are consistent with the idea of a simple, redundant histone code, in which multiple modifications share the same role.
Keywords: ChIP-chip

overall_design: In mid-log phase S. cerevisiae, we performed ChIP-chip on 12 different histone modifications and compared their enrichment levels within the genome based on nucleosome position data in series GSE2563.  Each TLAD-amplified ChIP sample was labeled with Cy5 and hybridized against Cy3-labeled, TLAD-amplified input on oligonucleotide tiling arrays.  At least 3 biological/technical replicates were performed per epitope, with  more than one technical replicate for some of the biological replicates, for a total of 64 arrays.

first: Chih Long

last: Liu

first: Tommy

last: Kaplan

first: Minkyu

last: Kim

first: Stephen

last: Buratowski

first: Stuart

middle: L

last: Schreiber

first: Nir

last: Friedman


title: Role of antigenic drive in pathogenesis of MALT lymphoma

status: Public on Aug 31 2005

last: Stanford Microarray Database

summary:
In order to assess the effect that eradication therapy and re-infection have on colonization densities and histopathology of BALB/c mice, 35 mice were divided into four groups (A-D): 12 mice were infected for the duration of the experiment (23 months, primarily infected group B), 8 mice were infected together with group B, but also received a two week triple therapy at 18 months post infection (TT treated group C) and 9 additional mice were infected and treated along with group C and subsequently re-infected one month after the start of triple therapy (re-infected group D). The final group of 6 mice received no treatment or infection (control group A). All mice were sacrificed at 23 months post initial infection; their stomachs were removed and subjected to histopathological and gene expression analysis. The reference for all arrays used in this study consisted of pooled cDNA extracted from stomachs of five age-matched uninfected control animals.
Keywords: all pairs

overall_design: An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

first: Anne

last: Mueller


title: Gene expression patterns accompanying a dietary shift in Drosophila

city: Tucson

first: Therese

middle: Ann

last: Markow

state: AZ

address: 310 Biosciences West

department: EEB

institute: University of Arizona

summary:
The data in this series forms the basis for the analysis presented in the above named paper.  In this study, we used cDNA microarrays to ask if changes in gene expression are observed in response to a dietary shift in Drosophila melanogaster, a dietary generalist.

Methods: Flies used in this study were derived from a multifemale collection at Iraklion, Crete, Greece, in August 2002 and reared in the laboratory for several generations. Three replicates were performed. At the start of each replicate, we collected 300 newly eclosed adults, separated them by sex, and stored them at low density in shell vials with standard cornmeal media for 3 days. Sexually mature males and females were placed together and allowed to mate. Mated females were allowed to oviposit overnight in chambers containing cornmeal medium filled Petri dishes (http://flyfood.arl.arizona.edu/cornmeal.php3).  Hatching first instar larvae were reared for 36 hours on cornmeal medium in Petri dishes and then transferred to one of two conditions: 1) a control Petri dish consisting of cornmeal medium, or 2) an experimental Petri dish containing pure mashed banana. After 24 hours, larvae were plucked from these dishes, washed, transferred to microcentrifuge tubes in groups of 20, and flash frozen in liquid nitrogen. All samples were stored at -80C until RNA extraction. RNA was extracted from each tube using a Qiagen RNeasy kit (Qiagen, Inc., standard protocol).
We used cDNA microarrays printed by the Genetic Analysis and Technology Core Custom Microarray Facility at the University of Arizona to assess expression levels.
Printing material was amplified from BDGP Unigene library v1.0 containing 6K ESTs.  Products were purified using Millipore Multiscreen filtration plates and re-suspended in 50%DMSO solution. Each product was printed in triplicate on Corning GAPSII aminosilane slides using a Virtek Chipwriter PRO microarray spotter.
Between 10-15 micrograms of RNA were used for each reaction. RNA was reverse transcribed and labeled with one of two fluorescent dyes, Cy3 or Cy5 (details of protocol at http://gatc.arl.arizona.edu/Services/Microarray/aminoallyllabelling.html). Hybridization was completed on a Genomic Solutions Gentac automated hybridization station. Labeled material was allowed to hybridize to the array for 16 hours at 60°C.  Wash conditions were: 1) low stringency wash twice at 50°C for 40seconds (1X SSC/ 0.2% SDS), 2) medium stringency wash twice at 42°C for 40 seconds ( 0.1X SSC/ 0.2% SDS), 3) high stringency wash twice at 42°C for 40 seconds (0.1X SSC). Hybridized arrays were scanned using the Applied Precision ArrayworxE slide scanner. We performed three independent hybridizations and three dye flips for a total of six arrays (2 treatments x 2 dyes x 3 replications = 12 samples, for 6 arrays). Each replicate consisted of an independent biological sample isolated on separate days.

Identification of series:

There are 18 series in this experiment.  The second number in each series record represents the slide number (there were six slides used in this experiment). The third number in each series record represents the set on a given slide. For instance, for series record 331_2_1, these data correspond to slide 2, set 1.  Each slide has 3 series numbers assoicated with it, representing set 1,2, or 3 on the slide.  Each slide was paired with another in a "dye flip" experiment; thus, slides 2 and 3 were paired, slides 25 and 28 were paired, and slides 29 and 30 were paired.
Keywords = dietary shifts
Keywords = ecological genomics
Keywords: repeat sample

first: Laura

last: Carsten

first: Tom

last: Watts


title: Schizosaccharomyces pombe clr4 expression

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary:
Expression profiling in clr4 null cells versus wild-type cells.
Keywords: Expression

overall_design: Agilent 44K in situ 60mer DNA microarray was used to probe expression of transcripts up-regulated in clr4 null cells versus wild-type cells.

first: Hugh

middle: P

last: Cam

first: Tomoyasu

last: Sugiyama

first: EeSin

last: Chen

first: Xi

first: Peter

middle: C

last: FitzGerald

middle: I


title: Mouse R1 ES cell SAGE library

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Mouse R1 ES cell SAGE library
Keywords: other

overall_design: this experiment include 1 samples and 1 replicates


title: Drosophila melanogaster mutation accumulation lines

city: Cambridge

first: Scott

last: Rifkin

address: 16 Divinity Ave

department: OEB

institute: Harvard University

summary:
Experiment to estimate mutatational variance of gene expression in Drosophila melanogaster at two times in development using 12 mutation accumulation lines.
Keywords = evolution
Keywords = quantitative genetics
Keywords = Drosophila
Keywords = mutation
Keywords: other

overall_design: Each of 12 lines measured 8 times in each of two stages.  For each stage, the design has two hexagons with 6 interior connections (=hybridizations) (all except opposite nodes).  Each line in one hexagon is connected to one line in the other hexagon and that line's opposite.  Each line is also connected to itself twice in the other stage.  Dyes are balanced.

first: David

last: Houle

first: Junhyong

first: Kevin

last: White


title: Populus homeobox gene ARK1 overexpression

city: Davis

first: Andrew

last: Groover

address: 1100 West Chiles Rd

department: Institute of Forest Genetics

institute: USDA Forest Service

summary:
The Populus homeobox gene ARBORKNOX1 was overexpressed behind the cauliflower mosaic virus 35S promoter in clone INRA 717 P. alba X P. tremula.  The experiment here compares gene expression in defoliated stems of two independently transformed clones (mutants) versus wild type controls.
Keywords: mutant versus wildtype

overall_design: Experimental design has two biological replications of both mutant and wild type plants, and two technical replications within each biological replication.

middle: T

first: Stephen

last: DiFazio

first: Gayle

last: Dupper

first: Joeseph

middle: R

last: Fontana

first: Shawn

last: Mansfield

first: Ryan

last: Miller

first: Yvonne

last: Wang


title: Breast Cancer aCGH

last: Stanford Microarray Database

type:
Expression profiling by array
Genome variation profiling by array

summary:
Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH) analysis of DNA copy number variation in a series of primary human breast tumors. We have profiled DNA copy number alteration across 6,691 mapped human genes, in 44 predominantly advanced, primary breast tumors and 10 breast cancer cell lines. While the overall patterns of DNA amplification and deletion corroborate previous cytogenetic studies, the high-resolution (gene-by-gene) mapping of amplicon boundaries and the quantitative analysis of amplicon shape provide significant improvement in the localization of candidate oncogenes. Parallel microarray measurements of mRNA levels reveal the remarkable degree to which variation in gene copy number contributes to variation in gene expression in tumor cells. Specifically, we find that 62% of highly amplified genes show moderately or highly elevated expression, that DNA copy number influences gene expression across a wide range of DNA copy number alterations (deletion, low-, mid- and high-level amplification), that on average, a 2-fold change in DNA copy number is associated with a corresponding 1.5-fold change in mRNA levels, and that overall, at least 12% of all the variation in gene expression among the breast tumors is directly attributable to underlying variation in gene copy number. These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set, arrayCGH

first: Charles

last: Perou

first: Jonathan

last: Pollack


title: Relation of Gene Expression Phenotype to Immunoglobulin Mutation Genotype in B Cell Chronic Lymphocytic Leukemia

status: Public on Aug 27 2005

summary:
The most common human leukemia is B cell chronic lymphocytic leukemia (CLL), a malignancy of mature B cells with a characteristic clinical presentation but a variable clinical course. The rearranged immunoglobulin (Ig) genes of CLL cells may be either germ-line in sequence or somatically mutated. Lack of Ig mutations defined a distinctly worse prognostic group of CLL patients raising the possibility that CLL comprises two distinct diseases. Using genomic-scale gene expression profiling, we show that CLL is characterized by a common gene expression "signature," irrespective of Ig mutational status, suggesting that CLL cases share a common mechanism of transformation and/or cell of origin. Nonetheless, the expression of hundreds of other genes correlated with the Ig mutational status, including many genes that are modulated in expression during mitogenic B cell receptor signaling. These genes were used to build a CLL subtype predictor that may help in the clinical classification of patients with this disease.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Ash

last: Alizadeh


title: The Campylobacter jejuni stringent response controls specific stress survival and virulence-associated phenotypes

summary:
Campylobacter jejuni is a highly prevalent food-borne pathogen that causes diarrhoeal disease in humans. A natural zoonotic, it must overcome significant stresses both in vivo and during transmission despite the absence of several traditional stress response genes. Its ability to interact with and invade human intestinal epithelial cells closely correlates with virulence. A C. jejuni microarray-based screen revealed that several known virulence genes and several uncharacterized genes, including spoT, were rapidly upregulated during infection of human epithelial cells. spoT and its homologue relA have been shown in other bacteria to regulate the stringent response, an important stress response that to date had not been demonstrated for C. jejuni. We have found that C. jejuni mounts a stringent response that is regulated by spoT. Detailed analyses of a C. jejuni delta spoT mutant revealed that the stringent response is required for several specific stress, transmission and antibiotic resistance-related phenotypes. These include stationary phase survival, growth and survival under low CO2/high O2 conditions, and rifampicin resistance. A secondary suppressor strain that specifically rescues the low CO2 growth defect of the delta spoT mutant was also isolated. The stringent response additionally proved to be required for the virulence-related phenotypes of adherence, invasion, and intracellular survival in two human epithelial cell culture models of infection; spoT is the first C. jejuni gene shown to participate in longer term survival in epithelial cells. Comparing wt to the delta spoT mutant also revealed a strong correlation between gene expression profiles and phenotype differences observed. Together, these data demonstrate a critical role for the C. jejuni stringent response in multiple aspects of C. jejuni biology and pathogenesis.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Erin

last: Gaynor


title: Small RNA identification in Arabidopsis thaliana using modified MPSS

status: Public on Sep 02 2005

city: St. Louis

first: Blake

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary:
Small RNAs play important regulatory roles in most eukaryotes but only a small proportion of these molecules have been identified. We sequenced more than two million small RNAs from seedlings and the inflorescence of the model plant Arabidopsis thaliana. Known and new miRNAs were among the most abundant of the non-redundant set of more than 75,000 sequences, whereas more than half represented lower abundance small-interfering RNAs (siRNAs) that match repetitive sequences, intergenic regions, and genes. Individual or clusters of highly-regulated small RNAs were readily observed. Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs.
Keywords: small RNA identification , modified MPSS

overall_design: Small RNAs identified in seedlings and inflorescence tissues.


title: Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays

summary:
Somatic cell mutants can be informative in the analysis of a wide variety of cellular processes. The use of map- based positional cloning strategies in somatic cell hybrids to analyze genes responsible for recessive mutant phenotypes is often tedious, however, and remains a major obstacle in somatic cell genetics. To fulfill the need for more efficient gene mapping in somatic cell mutants, we have developed a new DNA microarray comparative genomic hybridization (array-CGH) method that can rapidly and efficiently map the physical location of genes complementing somatic cell mutants to a small candidate genomic region. Here we report experiments that establish the validity and efficacy of the methodology.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 2

status: Public on Aug 26 2005

summary:
Time course of batch growth.  Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose,  with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour.  The experimental (channel 2) samples were grown in batch for the indicated time.
Groups of assays that are related as part of a time series.
FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 6 h; name: 34357_Elapsed Time; Measurement: time(absolute) 10.5 h; name: 34365_Elapsed Time; Measurement: time(absolute) 8 h; name: 34358_Elapsed Time; Measurement: time(absolute) 9 h; name: 34359_Elapsed Time; Measurement: time(absolute) 11 h; name: 34368_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 34360_Elapsed Time; Measurement: time(absolute) 10 h; name: 34362_Elapsed Time
Keywords: time_series_design

first: Matt

last: Brauer


title: Homeostatic Adjustment and Metabolic Remodeling in Glucose-limited Yeast Cultures Time Course 1

summary:
Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time.  The "Low-D chemostat vs. High-D chemostat" hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours.
Groups of assays that are related as part of a time series.
FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 0 h; name: 45181_Elapsed Time; Measurement: time(absolute) 8.5 h; name: 38150_Elapsed Time; Measurement: time(absolute) 8.75 h; name: 38151_Elapsed Time; Measurement: time(absolute) 9 h; name: 38152_Elapsed Time; Measurement: time(absolute) 9.25 h; name: 38153_Elapsed Time; Measurement: time(absolute) 7.25 h; name: 38145_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 38154_Elapsed Time; Measurement: time(absolute) 7.5 h; name: 38146_Elapsed Time; Measurement: time(absolute) 9.75 h; name: 38155_Elapsed Time; Measurement: time(absolute) 7.75 h; name: 38147_Elapsed Time; Measurement: time(absolute) 10 h; name: 38156_Elapsed Time; Measurement: time(absolute) 8 h; name: 38148_Elapsed Time; Measurement: time(absolute) 8.25 h; name: 38149_Elapsed Time
FactorCategory: Growth Condition; name: Growth Condition; Growth Condition: chemostat dilution control; name: 45181_Growth Condition; Growth Condition: batch; name: 38150_Growth Condition; Growth Condition: batch; name: 38151_Growth Condition; Growth Condition: batch; name: 38152_Growth Condition; Growth Condition: batch; name: 38153_Growth Condition; Growth Condition: batch; name: 38145_Growth Condition; Growth Condition: batch; name: 38154_Growth Condition; Growth Condition: batch; name: 38146_Growth Condition; Growth Condition: batch; name: 38155_Growth Condition; Growth Condition: batch; name: 38147_Growth Condition; Growth Condition: batch; name: 38156_Growth Condition; Growth Condition: batch; name: 38148_Growth Condition; Growth Condition: batch; name: 38149_Growth Condition
Keywords: time_series_design


title: Distinction between serous tumors of low malignant potential and serous carcinomas

summary:
OBJECTIVES: The molecular pathogenesis of ovarian serous tumors of low malignant potential (S-LMP) is not well understood, although the collective data suggest that they arise through molecular mechanisms distinct from those leading to conventional serous carcinomas (S-Ca). To further examine the molecular differences between these two diseases, we studied the gene expression pattern of ovarian S-LMP and S-Ca using high-density spotted cDNA and tissue microarrays. METHODS: Total RNA from 23 ovarian S-LMP and S-Ca was analyzed on 43,200 spot cDNA microarrays and the differential expression of proteins encoded by differentially expressed genes was validated using tissue microarrays.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Keywords: clinical_history_design

last: Van De Rijn


title: Cj1223c Mutant vs. Overexpressed, Time Course

summary:
The Cj1223c gene was cloned downstream of a strong promoter into the replicating plasmid pRY108, and was highly expressed in the wild type Campylobacter jejuni 81-176 strain (overexpressed).  The Cj1223c gene was knocked out by allelic replacement in the 81-176 strain background (mutant).  This mutant also carried an empty pRY108 vector.  The Cj1223c overexpressing strain and the mutant were grown overnight in liquid broth, supplemented with kanamycin.  The following morning, both cultures were diluted back to O.D.600=0.100, and allowed to continue to grow, shaking.  At various time intervals (2, 6, 10, and 24 hours), samples of each culture were removed, combined with 1/10 stop solution, and the bacteria pelleted for RNA preparation.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Joanna

last: Mackichan


title: Host and non-host pathogens elicit different jasmonate/ethylene responses in Arabidopsis

summary:
Arabidopsis does not support the growth and asexual reproduction of the barley pathogen, Blumeria graminis f. sp. hordei Bgh). A majority of germlings fail to penetrate the epidermal cell wall and papillae. To gain additional insight into this interaction, we determined whether the salicylic acid (SA) or jasmonate (JA)/ethylene (ET) defence pathways played a role in blocking barley powdery mildew infections. Only the eds1 mutant and NahG transgenics supported a modest increase in penetration success by the barley powdery mildew. We also compared the global gene expression patterns of Arabidopsis inoculated with the non-host barley powdery mildew to those inoculated with a virulent, host powdery mildew, Erysiphe cichoracearum. Genes repressed by inoculations with non-host and host powdery mildews relative to non-inoculated control plants accounted for two-thirds of the differentially expressed genes. A majority of these genes encoded components of photosynthesis and general metabolism. Consistent with this observation, Arabidopsis growth was inhibited following inoculation with Bgh, suggesting a shift in resource allocation from growth to defence. A number of defence-associated genes were induced during both interactions. These genes likely are components of basal defence responses, which do not effectively block host powdery mildew infections. In addition, genes encoding defensins, anti-microbial peptides whose expression is under the control of the JA/ET signalling pathway, were induced exclusively by non-host pathogens. Ectopic activation of JA/ET signalling protected Arabidopsis against two biotrophic host pathogens. Taken together, these data suggest that biotrophic host pathogens must either suppress or fail to elicit the JA/ET signal transduction pathway.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Laurent

last: Zimmerli


title: MATT mapping of Transposon insertions sites of strain G27 GPS-cat library

summary:
Genomic DNA from pools of H. pylori strain G27 Clones as indicated (pools of 300 (300p) or insertions in specific mapped genes) were amplifed using the MATT method to label DNA adjacent to the site of transposon insertion with the primer pairs indicated. The left side of the transposon was labeled in the Cy3 channel (Primer S) and the right side of the transposon was labeled in the Cy5 channel (Primer N).
Keywords: reference_design

first: Nina

last: Salama


title: Comparison of Rostral, Middle, and Caudal E13.5 murine neocortex

city: Oxford

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

summary:
Rostral, Middle, and Caudal thirds of E13.5 murine neocortex are compared
Keywords: Tissue comparison

overall_design: Three pools of rostral (R1-3), three pools of middle (M1-3), and three pools of caudal (C1-3) E13.5 MF1 neocortex were collected from 4 embryos. All possible 18 comparisons were carried out.

middle: N

first: F

last: Livesey

first: James

last: Smith


title: Comparison of gene expression in Peg1 wild type and null murine telencephalons

first: Stephen

summary:
single E12.5 Peg1 mutant cortices were directely compared to single E12.5 wild type cortices.
Keywords: mutant analysis

overall_design: Six mutant cortices (M1,3,4,5,6,7) were compared to three wild type cortices (WT2,8,9). As Mest is an imprinted gene that is only expressed from the paternal allele, mutants were generated by crossing males carrying a LacZ-targeted allele in which exons 3-8 were removed to wild-type females, as described (Lefebvre, L., Viville, S., Barton, S. C., Ishino, F., Keverne, E. B. and Surani, M. A. (1998). Abnormal maternal behaviour and growth retardation associated with loss of the imprinted gene Mest. Nat Genet 20, 163-9.)

first: Azim

last: Surani

first: Frederick


title: Comparison of gene expression in FGFR1 heterozygous and null E12.5 murine telencephalons

summary:
We analysed changes in gene expression in the dorsal telencephalon of forebrain-specific FGFR1 mutant mice.
Keywords: mutant analysis

overall_design: Gene expression was compared between the dorsal telencephalons of single E12.5 embryos of two genotypes: FGFR1 heterozygous (HET1,3,8) and homozygous mutants (HOM2,4,7) that were both heterozygous for the FoxG1 transcription factor, as Cre recombinase expression is driven off the endogenous FoxG1 locus in these animals (Hebert, J. M., Lin, M., Partanen, J., Rossant, J. and McConnell, S. K. (2003b). FGF signaling through FGFR1 is required for olfactory bulb morphogenesis. Development 130, 1101-11. & Hebert, J. M. and McConnell, S. K. (2000). Targeting of cre to the Foxg1 (BF-1) locus mediates loxP recombination in the telencephalon and other developing head structures. Dev Biol 222, 296-306.

first: Grace

last: Nisbet

first: Jean

middle: M

last: Hebert

first: Susan

middle: K

last: McConnell

first: Steve


title: Comparison of Rostral and Caudal murine neocortex at E11.5

summary:
Rostral and caudal thirds of E11.5 neocortex are compared in both inbred (C57) and oubred (MF1) mice.
Keywords: Tissue comparison

overall_design: Two different strains of mice, one inbred (C57Bl\6), the other outbred (MF1), were used to control for strain-dependent variations in patterns of gene expression (Pavlidis and Noble, 2001; Sandberg et al., 2000). For each strain at each timepoint, three sets of pooled rostral and caudal tissue were collected from single litters. Gene expression screens were carried out within single litters to match embryos by developmental age as closely as possible. Individual pools contained material from the left and right cortices of at least two embryos, to correct for variation among dissections. Given the limited amount of RNA available when using such a screening strategy, the corresponding cDNA was amplified using the SMART system to generate enough material for synthesising array probes (Matz et al., 1999), as used successfully for our previous studies (Livesey et al., 2000; Livesey et al., 2004).


title: Barley single feature polymorphisms and drought stress gene expression

status: Public on Aug 25 2005

city: Riverside

first: xinping

last: cui

address: Department of Statistics, University of California, Riverside

department: Statistics

institute: University of California,Riverside

summary:
Detection of single feature polymorphisms comparing five barley genotypes. Gene expression under unstressed and drought stressed conditions.

Tissue from five entire five day old seedlings from drought stress or unstressed growth conditions was used for RNA extraction. For Barke, Morex and Stepoe the two types of RNA were pooled.  For Oregon Wolfe Barley Dominant and Recessive (OWBs), the two types of RNA were handled separately. Targets from three biological replicates of each genotype-treatment were generated and transcript levels were determined using Affymetrix Barley1 GeneChip arrays. Probe set, followed by single probe, comparisons between genotypes allows the identification of single feature polymorphisms in comparisons between genotypes. For the OWBs, comparisons between stressed and unstressed conditions defines stress-regulated genes.
Keywords: repeat

overall_design: Three genotypes, three replicates each.  Two additional genotypes, two sets of three replicates each.

first: Timothy

last: Close

first: Xinping

last: Cui


title: Yeast Membrane Bound Polysome

status: Public on Aug 24 2005

last: Stanford Microarray Database

summary:
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
mRNA species bound to membrane-associated polysomes were separated from other mRNAs by sedimentation equilibrium or sedimentation velocity. The distribution of individual transcripts in the 'membrane-bound' and 'cytosolic' fractions was quantitated for thousands of genes by hybridization to DNA microarrays. Transcripts known to encode secreted or membrane proteins were enriched in the membrane-bound fractions, whereas those known to encode cytoplasmic proteins were enriched in the fractions containing mRNAs associated with free and cytoplasmic ribosomes. On this basis, we identified over 275 human genes and 285 yeast genes that are likely to encode previously unrecognized secreted or membrane proteins.
Keywords: Logical Set

overall_design: Computed

first: Max

last: Diehn


title: Comparison of Rostral and Caudal murine neocortex at E13.5

summary:
Rostral and caudal thirds of E13.5 neocortex are compared in both inbred (C57) and oubred (MF1) mice.
Keywords: Tissue comparison


title: Host cell gene expression late during cytomegalovirus infection

summary:
Human fibroblast monolayers plated at a density of 3 x 104 cells/cm2 in 850 cm2 roller bottles were infected at confluency (day 5 post-seeding) with purified virions of human cytomegalovirus (CMV) strain AD169varATCC (AD) or the AD169 US27/US28 deletion mutant virus RV101 (RV) at a multiplicity of infection of 10. After virus adsorption for 1h at 37C with 5% CO2, the inoculum was removed and the cells were washed twice with culture medium prior to the addition of fresh medium. At 50, 72 and 98 hpi, infected monolayers were harvested, snap-frozen and stored at -80:C until the time course was completed. Uninfected confluent HF cultures were used as reference. mRNA was extracted using the FastTrack. 2.0 mRNA Isolation Kit (Invitrogen, Carlsbad, CA). Only RNA preparations reaching OD260/280 ratio values of 2.0 were used. Labeled cDNA populations were synthesized from 2 microg of mRNA per sample by reverse transcription and simultaneous incorporation of Cy3- (reference sample, green) or Cy5- (infected samples, red) dUTP using an oligo-dT20 primer and the Superscript II Reverse Transcriptase. Reference and sample cDNA populations were mixed and applied on the arrays. Hybridizations were performed at 650C for 16 to 18 h in a custom slide chamber with humidity maintained by a small reservoir of 3x SSC. The arrays were then washed, scanned with a Gene Pix 4000A Scanner, gridded and flagged with Gene Pix Pro 4.0 software before submission to the SMD.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Laura

last: Hertel


title: Anatomical compartments of the human eye

status: Public on Aug 23 2005

summary:
We used DNA microarrays representing ~30,000 human genes to analyze gene expression in the cornea, lens, iris, ciliary body, retina, and optic nerve.  Eight whole globes (G1-G8) were harvested from autopsy donors (age range=30-85 years-old) within 24 hours of death, and the tissues were immediately stored at 4◦ C in RNAlater (Ambion).  Four of the globes were from female donors (G3, G6-8) and four were from male donors (G1, 2, 4, 5).  Globes 4 and 5 were harvested as a set from a single donor, as were globes 6 and 7.  No ophthalmologic clinical records were available for any of the globes at the time of harvest.  Seven of the globes (G1-G7) were dissected into the following components: cornea, lens, iris, ciliary body, retina, and optic nerve, while only retinal tissue was available from G8.  The maculas and the peripheral retinal tissues were further dissected from several of the retinal samples.  The macula was defined as the visible xanthophyll-containing tissue temporal to the optic nerve, which encompassed an approximate area of 4 mm2.  For comparison purposes, three post-mortem brain specimens were analyzed.  Only those tissues that yielded adequate amounts of RNA were processed on the arrays.
An organism part comparison experiment design type compares tissues, regions, organs within or between organisms.
Differential gene expression in anatomical compartments of the human eye. Diehn et al. Genome Biology 2005, 6:R74
Keywords: organism_part_comparison_design

first: Jennifer

last: Junkermeier


title: Pombe_44k_ChIP-on-chip

first: Shiv

last: Grewal

summary:
ChIP-on-chip analyses of heterochromatin and RNAi components in fission yeast.
Keywords: ChIP-on-chip

overall_design: ChIP-on-chip analyses using custom Agilent 44K  in situ 60mer DNA microarray that tiles the entire Schizosaccharomyces pombe genome every 300 bp alternately on both strands were used to interrogate heterochromatin and RNAi components in fission yeast genome.

first: Hugh

last: Cam

first: Tomoyasu

last: Sugiyama

first: EeSin

last: Chen

first: Xi

first: Peter

last: FitzGerald


title: Effect of small RNA RyhB on global iron use in Escherichia coli

city: Sherbrooke

first: Eric

last: Masse

state: Quebec

address: 3001 12e Avenue

department: Biochemistry

institute: Universite de Sherbrooke

summary:
RyhB is a non-coding RNA regulated by the Fur repressor.  It has previously been shown to cause the rapid degradation of a number of mRNAs that encode proteins that utilize iron.  Here we examine the effect of ectopic RyhB production on global gene expression by microarray analysis.  Many of the previously identified targets were found, as well as other mRNAs encoding iron-binding proteins, bringing the total number of regulated operons to at least 18, encoding 56 genes.   The two major operons involved in Fe-S cluster assembly showed different behavior; the isc operon appears to be a direct target of RyhB action, while the suf operon does not.  This is consistent with previous findings suggesting that the suf genes but not the isc genes are important for Fe-S cluster synthesis under iron-limiting conditions, presumably for essential iron-binding proteins.  In addition, we observed repression of Fur-regulated genes upon RyhB expression, interpreted as due to intracellular iron-sparing resulting from reduced synthesis of iron-binding proteins.  Our results demonstrate the broad effects of a single non-coding RNA on iron homeostasis.
Keywords: RNA degradation, iron stavation, RyhB small RNA, iron-using proteins

overall_design:
Derivatives of MG1655 carrying either pBAD-ryhB or the control vector pNM12 were used in all experiments.
The strains used contain the (delta)ara714 allele to prevent catabolism of arabinose and the (delta)ryhB::cat allele to restrict RyhB expression to the inducible pBAD-ryhB vector.
Overnight bacterial cultures were incubated in LB media with ampicillin at a final concentration of 50 ug/mL at 37oC and diluted 1000-fold into 50 mL of fresh LB-ampicillin media at 37oC with agitation.  To induce RyhB expression, cultures carrying the pBAD-ryhB construct were grown to an O.D.600 of 0.5 and arabinose was added to the culture at a final concentration of 0.1%.  In some experiments, 50 uM FeSO4 was added to the new culture after dilution from overnight culture. Total RNA was extracted from cells at the indicated time using the hot phenol procedure.

last: Massé

first: Carin

last: Vanderpool

last: Gottesman


title: Breast Tumor Clinical Implications

summary:
The purpose of this study was to explore the possibility of classifying breast carcinomas based upon variations in gene expression patterns derived from cDNA microarrays, and to correlate tumor characteristics to clinical outcome. A total of 85 cDNA microarray experiments representing tumor and normal breast tissues from 78 individuals were analyzed by hierarchical-clustering. As reported previously, we identified a basal epithelial-like group, an ERBB2-overexpressing group and a normal breast-like group based on variations in gene expression. A novel finding was that the previously characterized lluminal epithelial/ER-positiven group could be divided into at least two subgroups, each with a distinctive expression profile. These subtypes proved to be reasonably robust by clustering using two different gene sets; first, a set of 456 cDNA clones previously selected to reflect the lintrinsicn properties of the tumors and, second, a gene set identified that highly correlated with patient outcome. Survival analyses on the sub-cohort of 51 patients with locally advanced breast cancer uniformly treated in a prospective study showed significantly different outcomes for the patients   belonging to the various groups, including a poor prognosis for the basal-like subtype and a significant difference in outcome for the two estrogen receptor-positive groups.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Charles

last: Perou


title: Spotting and validation of a Genome wide oligonucleotide chip with duplicate measurement of each gene

status: Public on Aug 19 2005

city: Odense

first: Mads

last: Thomassen

address: Soender Boulevard 9

department: Clinical Genetics (KKA)

country: Denmark

institute: Odense University Hospital

summary:
High reproducibility of DNA microarray data relies on precise and uniform manufacturing of a microarray experiment. It is often stated that data from spotted microarray chips are subjected to a high degree of technical variation during the experimental procedure influencing the extraction of meaningful biological information. We have developed a spotted genome wide microarray chip with oligonucleotides printed in duplicate in order to minimise undesirable biases, thereby optimizing detection of true differential expression. The study design consisted of an assessment of the microarray chip performance using self hybridisation with the MessageAmp and Fairplay labeling kits. Statistical methods have been used to asses the experimental variation. Three main findings revealed the applicability of the system. The linear range of the chips was three orders of magnitude, the minimum detectable fold change for differential expression was below 1.3, and the coefficient of variation for differential expression was 13 % for MessageAmp and 15 % for Fairplay. Substantial reduction of variance was attained with duplicate spotting. Furthermore, relative quantitation was more reproducible than absolute quantitation. A method called Intraclass Correlation Coeffcient (ICC) was introduced to assess the agreement between the two kits. By bootstrapping the results, we found that MessageAmp was significantly more reproducible than Fairplay. An analysis of variance (ANOVA) demonstrated no significant day to day variation. The results showed reproducible performance of our in-house made oligonucleotide chip and that it can be used to detect differential expression even when only a small amount of biological material is available.
Keywords: Two colour, self-hybridisation experiments

overall_design: Each of the two labeling kits FairPlay and MessageAmp was used in self-hybridisation experiments to test 11 chips. 11 different cDNA/ aRNA synthesis reactions were performed for each kit. 5 on day 1, 3 on day 2, and 3 on day 3. An aliquot of these reactions were used for Cy5 coupling while Cy3 were coupled to a pool of the 11 reactions (MessageAmp) and a pool of 11 new separate reactions (FairPlay). The reactions were performed on three different days and all the chips were from the same print batch.

first: Vibe

last: Skov

first: Freyja

last: Eiriksdottir

first: Qihua

last: Tan

first: Kirsten

last: Jochumsen

first: Niels

last: Fritzner

first: Jesper

last: Dahlgaard

first: Klaus

last: Brusgaard

first: Torben

last: Kruse


title: The SUCAST catalogue

city: Campinas

first: Renato

last: Vicentini

state: SP

address: Cidade Universitaria "Zeferino Vaz"

department: Centro de Biologia Molecular e Engenharia Genetica - CBMEG

country: Brazil

institute: Universidade Estadual de Campinas - UNICAMP

summary:
A collection of 237,000 expressed sequence tags generated by the Sugarcane EST sequencing project (SUCEST) was analyzed in search of signal transduction components. The SUCAST (Sugarcane Signal Transduction) Catalogue contains over 3500 components, with around 2900 involved in several aspects of cell signaling and transcription. Sequence comparisons and conserved protein domain analysis revealed 477 receptors, 510 protein kinases, 107 protein phosphatases, a large number of small GTPases, G-proteins, members of the calcium and inositol metabolism, and other signal transduction-related proteins. Over 600 transcription factors were also indexed. Moreover, 437 genes with no matches in the public databases and 111 genes of unknown function were catalogued. Several of the SUCEST cDNA libraries were derived from plants submitted to abiotic stresses or infected with endophytic nitrogen fixing bacteria and stress and pathogen response-related genes were also annotated. The abundance of transcripts among six different sugarcane tissues (flowers, roots, leaves, lateral buds, 1st and 4th internodes) was evaluated using microarrays and expression profile clustering. We identified 216 genes that are significantly more abundant in one of the tissues analyzed. A subset of the data was validated by real-time PCR. Additionally, genes with similar expression levels among different tissues were identified. The characterization of these elements and their promoters can aid in the development of tools for the genetic manipulation of this plant species and other economically important grasses.
Keywords: other

first: F

middle: S

last: Papini-Terzi

last: Rocha

first: R

middle: Z

last: Vencio

first: K

last: Oliveira

first: J

last: Felix

first: C

first: A

last: Simoes

first: E

last: Ulian

first: S

last: diMauro

last: daSilva

first: M

last: Menossi

first: G

last: Souza


title: H. pylori strain comparisons

status: Public on Aug 16 2005

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

institute: Stanford Microarray Database (SMD)

summary:
Helicobacter pylori enhances the risk for ulcer disease and gastric cancer, yet only a minority of H. pylori-colonized individuals develop disease. We examined the ability of two H. pylori isolates to induce differential host responses in vivo or in vitro, and then used an H. pylori whole genome microarray to identify bacterial determinants related to pathogenesis. Gastric ulcer strain B128 induced more severe gastritis, proliferation, and apoptosis in gerbil mucosa than did duodenal ulcer strain G1.1, and gastric ulceration and atrophy occurred only in B128+ gerbils. In vitro, gerbil-passaged B128 derivatives significantly increased IL-8 secretion and apoptosis compared with G1.1 strains. DNA hybridization to the microarray identified several strain-specific differences in gene composition including a large deletion of the cag pathogenicity island in strain G1.1. Partial and complete disruption of the cag island in strain B128 attenuated induction of IL-8 in vitro and significantly decreased gastric inflammation in vivo. These results indicate that the ability of H. pylori to regulate epithelial cell responses related to inflammation depends on the presence of an intact cag pathogenicity island. Use of an H pylori whole genome microarray is an effective method to identify differences in gene content between H. pylori strains that induce distinct pathological outcomes in a rodent model of H. pylori infection.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Nina

last: Salama


title: Macrophage response to lipopolysaccharide

city: San Diego

first: Timothy

last: Ravasi

address: 9500 Gilman Drive

department: Department of Bioengineering

institute: University of California-San Diego

summary:
Temporal analysis of bone marrow derived macrophages after 10 ug/ml lipopolysaccharide stimulation. C57BL6, C3H/ARC, BalbC and C3H/HeJ mouse strains analyzed.
Keywords: time course

overall_design:
Each time point stimulated with 10ug/ml LPS from Salmonella minnesota for the time indicated.
The RNA from each BMM stimulated time point was labeled with Cy3 and compared with a common reference (total RNA from C57BL6/J 17.5 embryo) labeled with Cy5.

first: Christine

middle: A

last: Wells

first: Geoff

last: Faulkner

first: Piero

last: Carninci

first: Yashushi

last: Okazaki

first: Yoshihide

last: Hayashizaki

first: Matthew

last: Sweet

first: Brandon

last: Wainwright

first: David

last: Hume


title: H. pilory diversity in human

summary:
Isolates of the gastric pathogen Helicobacter pylori harvested from different individuals are highly polymorphic. Strain variation also has been observed within a single host. To more fully ascertain the extent of H. pylori genetic diversity within the ecological niche of its natural host, we harvested additional isolates of the sequenced H. pylori strain J99 from its human source patient after a 6-year interval. Randomly amplified polymorphic DNA PCR and DNA sequencing of four unlinked loci indicated that these isolates were closely related to the original strain. In contrast, microarray analysis revealed differences in genetic content among all of the isolates that were not detected by randomly amplified polymorphic DNA PCR or sequence analysis. Several ORFs from loci scattered throughout the chromosome in the archival strain did not hybridize with DNA from the recent strains, including multiple ORFs within the J99 plasticity zone. In addition, DNA from the recent isolates hybridized with probes for ORFs specific for the other fully sequenced H. pylori strain 26695, including a putative traG homolog. Among the additional J99 isolates, patterns of genetic diversity were distinct both when compared with each other and to the original prototype isolate. These results indicate that within an apparently homogeneous population, as determined by macroscale comparison and nucleotide sequence analysis, remarkable genetic differences exist among single-colony isolates of H. pylori. Direct evidence that H. pylori has the capacity to lose and possibly acquire exogenous DNA is consistent with a model of continuous microevolution within its cognate host.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Vibrio cholerae in human vomitus vs. human stool

status: Public on Aug 17 2005

first: Regina

last: LaRocque

address: 55 Fruit Street

department: Division of Infectious Diseases

institute: Massachusetts General Hospital

summary:
Understanding gene expression by bacteria during the actual course of human infection may provide important insights into microbial pathogenesis. In this study, we evaluated the transcriptional profile of Vibrio cholerae, the causative agent of cholera, in clinical specimens from cholera patients. We collected samples of human stool and vomitus that were positive by dark-field microscopy for abundant vibrios and used a microarray to compare gene expression in organisms recovered directly from the early and late stages of human infection. Our results reveal that V. cholerae gene expression within the human host environment differs from patterns defined in in vitro models of pathogenesis. tcpA, the major subunit of the essential V. cholerae colonization factor, was significantly more highly expressed in early compared with late infection; however, the genes encoding cholera toxin were not highly expressed in either phase of human infection. Furthermore, expression of the virulence regulators, toxRS and tcpPH, was uncoupled. Interestingly, the pattern of gene expression indicates that the human upper intestine may be a uniquely suitable environment for the transfer of genetic elements that are important in the evolution of pathogenic strains of V. cholerae. These findings provide a more detailed assessment of the transcriptome of V. cholerae in the human host than previous studies of organisms in stool alone and have implications for cholera control and the design of improved vaccines.
Keywords: comparative gene expression analysis

overall_design: The V. cholerae microarray consists of 3,890 full-length PCR products representing the annotated open reading frames from the initial release of the V. cholerae N16961 genome. Each labeling and hybridization was performed in duplicate. Genomic DNA was used as a universal internal control for the quality of the microarray and to allow for the comparison of results across multiple experiments. Data were normalized using locally-weighted regression (Lowess) to obtain the relative abundance of each transcript as an intensity ratio with respect to that of genomic DNA. High correlation coefficients were observed between technical replicates (Pearson’s correlation coefficient (r) > 0.80) and between results of separate clinical specimens of vomitus (r > 0.77) and of stool (r > 0.80). Hence, the results from the two clinical vomitus specimens and the five clinical stool specimens were pooled. Fold changes for the relative expression of a given gene between the two clinical specimens were calculated by dividing the normalized median intensity ratios with respect to genomic DNA.

first: Jason

middle: B

last: Harris

first: Michelle

last: Dziejman

first: Xiaoman

last: Li

first: Edward

last: Ryan

first: Firdausi

last: Qadri

first: John

middle: J

last: Mekalanos

first: Stephen

last: Calderwood


title: Transcription profiles of che and flgM mutants of Typhimurium 14028 at 3h on agar plates

city: Austin

first: Rasika

last: Harshey

state: TX

department: Section of Molecular Genetics and Microbiology

institute: Institute of Cellular and Molecular Biology

summary:
Transcription profiles of Typhimurium 14028 wt versus 14028 cheA, cheB, cheZ, flgM and flgM/cheY mutants at 3h on agar plates
Keywords: other

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

platform_organism:
Salmonella
Salmonella enterica

first: Tim

middle: Q

last: Wang

first: Steffen

last: Porwollik

first: Michael

last: McClelland

first: Jonathan

middle: G

last: Frye


title: Exploring the scope of TOR/PKA co-regulation in MDN

first: Ted

last: Powers

address: One Shields Ave

department: Molecular and Cellular Biology

institute: UC Davis

summary:
To identify genes co-regulated by TOR and PKA during growth in MDN
Keywords: Media, Wild type and mutant strains, and dose response

overall_design: BCY1, bcy1 deletion, TPK, and tpk1-3 deletion strains were grown in MDN with and without rapamycin treatment.  Different combinations of these samples were examined.


title: 14028 cheY mutant time course expression on plate

summary:
time course of transcriptional profile of Typhimurium 14028 wt versus 14028 cheY mutant on agar plate
Keywords: time-course


title: Identification of new target genes of TOR during growth in MDN

summary:
To identify novel targets of TOR when prototrophic strain S288c is grown in MDN media.
Keywords: Media and dose response

overall_design: Arrays compare growth in MDN with and without addition of rapamycin.  For comparison, growth in YPD versus MDN as well as SCD versus MDN were examined as well.


status: Public on Aug 20 2005

last: Stanford Microarray Database

department: Stanford University, School of Medicine

summary:
These are the 94 microarray experiments that are published in the paper: John Wang and Stuart K. Kim. Global analysis of dauer gene expression in Caenorhabditis elegans, Development 2003 130: 1621-1634. There are 94 individual microarray experiments divided into 3 broad experiments. The first experiment is a time course of dauer exit; each time course is labeled as "Dauer MTC#". The second experiment is a time course of L1 development after starvation arrest; each time couse is labeled "L1 MTC#". The final experiment is a comparison of pure dauers (0 hours) versus 12 hours after dauer exit and are labeled "Dauer Adjust". Every time course was repeated 4 times (#N)however for the dauer 4 and 7 hour time points there are only 3 replicates. For instance, all the time points labeled as "Dauer MTC#1" are from the same starting pool of dauer worms that were aliquoted into 10 fractions and analyzed at the time indicated. Every sample is compared to a common reference RNA that is used throughout all the hybridizations. In some cases there is a "-2" after the hour designation; this means the first hybridization failed for some technical reason and thus the second hybridization (same RNA) is reported.
Groups of assays that are related as part of a time series.
Keywords: time_series_design


title: Coffee leaf miner infestation in coffee plants

status: Public on Aug 15 2005

first: Jorge

middle: Maurício Costa

last: Mondego

address: Cidade Universitária Zeferino Vaz s/n

department: Genetics and Evolution

institute: UNICAMP

summary:
Coffee leaf miner is an important plague in coffee crops. Using subtracted cDNA libraries and nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of coffee plants from an hybrid progeny (C. arabica x C. racemosa), containg resistant (R) and susceptible plants (S) to the infestation of coffee leaf miner. Leaf discs were collected from non-infested plants (R control - RC; S control - SC), infested plants after moth oviposition (R oviposition - Ro; S oviposition - So) and infested after larvar eclosion (R eclosion - Re; S eclosion - Se).
Isolation and characterization of Coffea genes induced during coffee leaf miner (Leucoptera coffeella) infestation. Plant Science 169(2):351-360
Keywords: ordered

first: Oliveiro

last: Guerreiro-Filho

first: Mário Henrique

last: Bengtson

first: Rodrigo

middle: D

last: Drummond

first: Juliana

last: Felix

first: Melina

last: Duarte

first: Daniel

last: Ramiro

first: Miriam

last: Maluf

first: Mari

last: Sogayar

first: Marcelo

last: Menossi


title: RNase G complementation of rne null mutation identifies functional interrelationships with RNase E

status: Public on Aug 13 2005

summary:
The Escherichia coli endoribonucleases RNase E (Rne) and RNase G (Rng) have sequence similarity and broadly similar sequence specificity. Whereas the absence of Rne normally is lethal, we show here that E. coli bacteria that lack the rne gene can be made viable by overexpression of Rng. Rng-complemented cells accumulated precursors of 5S ribosomal RNA (rRNA) and the RNA component of RNase P (i.e. M1 RNA), indicating that normal processing of these Rne-cleaved RNAs was not restored by RNase G; additionally, neither 5S rRNA nor M1 RNA was generated from precursors by RNase G cleavage in vitro. Using DNA microarrays containing 4405 Escherichia coli open reading frames (ORFs), we identified mRNAs whose steady-state level was affected by Rne, Rng or the N-terminal catalytic domain of RNase E. Most transcript species affected by RNase E deficiency were also elevated in an rne deletion mutant complemented by Rng. However, approximately 100 mRNAs that accumulated in Rne-deficient cells were decreased by rng-complemention, thus identifying targets whose processing or degradation may be the basis for RNase E essentiality. Remarkably prominent in this group were mRNAs implicated in energy-generating pathways or in the synthesis or degradation of macromolecules.
Set of arrays that are part of repeated experiments
Keywords: Biological Replicate

overall_design: Biological Replicate

first: Jon

last: Bernstein


title: Aft2 in yeast iron regulation

summary:
Iron homeostasis in the yeast Saccharomyces cerevisiae is regulated at the transcriptional level by Aft1p, which activates the expression of its target genes in response to low-iron conditions. The yeast genome contains a paralog of AFT1, which has been designated AFT2. To establish whether AFT1 and AFT2 have overlapping functions, a mutant containing a double aft1aft2 deletion was generated. Growth assays established that the single aft2 strain exhibited no iron-dependent phenotype. However, the double-mutant aft1aft2 strain was more sensitive to low-iron growth conditions than the single-mutant aft1 strain. A mutant allele of AFT2 (AFT2-1up), or overexpression of the wild-type AFT2 gene, led to partial complementation of the respiratory- deficient phenotype of the aft1 strain. The AFT2-1up allele also increased the uptake of 59Fe in an aft1 strain. DNA microarrays were used to identify genes regulated by AFT2. Some of the AFT2-regulated genes are known to be regulated by Aft1p; however, AFT2-1up-dependent activation was independent of Aft1p. The kinetics of induction of two genes activated by the AFT2-1up allele are consistent with Aft2p acting as a direct transcriptional factor. Truncated forms of Aft1p and Aft2p bound to a DNA duplex containing the Aft1p binding site in vitro. The wild-type allele of AFT2 activated transcription in response to growth under low-iron conditions. Together, these data suggest that yeast has a second regulatory pathway for the iron regulon, with AFT1 and AFT2 playing partially redundant roles.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Esha

last: Ray


title: Mouse Exons

city: Toronto

first: Mark

last: Robinson

institute: University of Toronto

type: Expression profiling by genome tiling array

summary:
Exon tiling array encompassing 837,251 probes across the mouse genome.  12 tissue pools.
Keywords: Agilent

overall_design:
Composition of the 12 mRNA pools analyzed (mRNA per array hybridization):

1-   Heart (2 microgram), Skeletal muscle (2 microgram)
2-   Liver (2 microgram)
3-   Whole brain (1.5 microgram), Cerebellum (0.48 microgram), Olfactory bulb (0.15 microgram)
4-   Colon (0.96 microgram), Intestine (1.04 microgram)
5-   Testis (3 microgram), Epididymis (0.4 microgram)
6-   Femur (0.9 microgram), Knee (0.4 microgram), Calvaria (0.06 microgram), Teeth+mandible (1.3 microgram), Teeth (0.4 microgram)
7-   15 day Embryo (1.3 microgram), 12.5 day Embryo (12.5 microgram), 9.5 day Embryo (0.3 microgram), 14.5 day Embryo head (0.25 microgram), ES cells (0.24 microgram)
8-   Digit (1.3 microgram), Tongue (0.6 microgram), Trachea (0.15 microgram)
9-   Pancreas (1 microgram), Mammary gland (0.9 microgram), Adrenal gland (0.25 microgram), Prostate gland (0.25 microgram)
10-   Salivary gland (1.26 microgram), Lymph node (0.74 microgram)
11-   12.5 day Placenta (1.15 microgram), 9.5 day Placenta (0.5 microgram), 15 day Placenta (0.35 microgram)
12-   Lung (1 microgram), Kidney (1 microgram), Adipose (1 microgram), Bladder (0.05 microgram)

Labeling and hybridization:

mRNA pools were reverse-transcribed with random nonamer primers (1 microgram/reaction) and T18VN (0.25 microgram/reaction) to synthesize cDNA.  The reaction contained a 1:1 mixture of 5-(3-aminoallyl) thymidine 5'-triphosphate (Sigma, St. Louis, MO) and thymidine triphosphate (TTP) in place of TTP.  cDNA products were bound to QIAquick PCR Purification columns (Qiagen, Germany) following the manufacturer's instructions, washed three times with 80% ethanol, and eluted with water.  Purified cDNA was reacted with N-hydroxy succinimide esters of Cy3 or Cy5 (Amersham Pharmacia Biotech, Piscataway, NJ) following the manufacturer's instructions.  Hydroxylamine-quenched Cy-labeled cDNAs were separated from free dye molecules using QIAquick columns.  Mixed labeled cDNAs were added to hybridization buffer containing 1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate (MES), pH 6.5, 33% formamide and 40 µg herring sperm DNA (Invitrogen, Carlsbad, California).  Hybridizations were carried out in a final volume of 0.5 ml injecting into an Agilent hybridization chamber at 42°C on a rotating platform in a hybridization oven (Robbins Scientific Corporation, Sunnyvale, California) for 16-24 h. Slides were then washed (rocking ~30 seconds in 6x SSPE, 0.005% sarcosine, then rocking ~30 seconds in 0.06x SSPE) and scanned with a 4000A microarray scanner (Axon Instruments, Union City, California).  Each array was hybridized with two samples simultaneously, each from a different pool.

Image processing and data normalization:

TIFF images were quantitated with GenePix (Axon Instruments).  Individual channels were spatially detrended (i.e overall correlations were removed between spot intensity and position on the slide) by subtracting from each spot's log intensity a weighted average of the log intensities of nearby spots.  Most weights were a product of two Gaussian functions, one of the difference in rows between the spots and one of the difference in columns, however 10% of the spots ("high expressors") were always assigned a weight of zero.  The widths of the row and column Gaussians were chosen to minimize the sum, across all spots, of the squared difference between the weighted average and the actual log intensity of the spots.  The "high expressors" spots were those with the largest difference between their log intensity and the median log intensity over a 7x7 window of neighboring spots.  After spatial detrending, we transformed the log intensities back into linear intensities and all single-channels were normalized to each other (in the linear domain), using channel-specific affine transforms.  That is, for each single channel, we normalized all the detrending intensities by adding an offset parameter (which was possibly negative) and then multiplying by a positive scale parameter.  The scale and offset parameters of each channel's transform were set so that the median intensities and the difference between the 75th and 25th percentile intensities were identical across channels.

first: Brendan

last: Frey

first: Wen

last: Zhang

first: Naveed

last: Mohammad

first: Quaid

last: Morris

first: Timothy

last: Hughes


title: Hyperinfectivity study

status: Public on Aug 11 2005

last: Stanford Microarray Database

summary:
Hyperinfectivity study.  A=patient A, B=patient B, C=patient C, stationary phase=stationary phase vibrio for comparison, and numbers represent technical replicates of the denoted sample.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Douglas

last: Merrell


title: Characterization of three reflux-induced esophageal tumor cell

city: Baltimore

first: Irene

last: Kim

address: 720 Rutland Avenue

department: Medicine

institute: Johns Hopkins University

summary:
Goal of the microarray study is to identify 2-fold or more differentially expressed genes common to all three "tumor vs. normal" dye-swap pairs.
Keywords: repeat sample

first: Anirban

last: Maitra


title: Identification of genes expressed in C. elegans touch receptor neurons

summary:
By culturing and isolating wild-type and mec-3 mutant cells from embryos and applying their amplified RNA to DNA microarrays, here we have identified genes that are known to be expressed in touch receptors, a previously uncloned gene (mec-17) that is needed for maintaining touch receptor differentiation, and more than 50 previously unknown mec-3-dependent genes.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Martin

last: Chalfie


title: Chitin sensor

summary:
Strains VCXB21 and VCXB21 pDel were added 0.6 mM chitobiose at early log phase. Samples isolated after 30 min. cDNA from VCXB21 was prepared from 2 ug RNA and labeled with Cy3. cDNA from VCXB21pDel was prepared from 2 ug RNA and labeled with Cy5.
A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out.
Keywords: genetic_modification_design

first: Karin

last: Meibom


title: Expression profiling in inflammatory bowel disease

city: Kiel

first: Robert

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

country: Germany

institute: University Clinic of Schleswig Holstein

summary:
The series was designed to identify new genes involved in the pathophysiology of inflammatory bowel disease (Crohn's disease and ulcerative colitis).
This series represents a group of 31 samples, subdivided into 3 groups: 1) Normal controls: 11 samples; 2) patients with Crohn's diseases: 10 samples; 3) patients with ulcerative colitis: 10 samples. Each sample originated from a different patient or normal control, in total n=31 individuals were examined.
Keywords = Inflammatory bowel disease
Keywords = Crohn's disease
Keywords = ulcerative colitis
Keywords = expression screening
Keywords = expression profiling
Keywords: other

first: Christine

last: Costello

first: Nancy

last: Mah

last: Häsler

first: Tim

last: Lu

first: Susanna

last: Nikolaus

first: Holger

last: Eickhoff

first: Hans

last: Lehrach

first: Stefan

last: Schreiber


title: Chitin oligosaccharide induction

summary:
Strain N16961 grown in M9 + 0.5 % lactate to OD 0.2. Culture was split and one part added 0.6 mM of indicated chitin oligosaccharide. Samples was isolated after 30 and 60 min. cDNA was prepared from 2 ug RNA and labeled with Cy3 (no induction) and Cy5 (induction with chitin oligosaccharide). Samples from at least two independent experiments and a total of four hybridizations for each chitin oligosaccharide and time.
A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients.
Keywords: growth_condition_design


title: mgrA acts as a repressor of the rlrA pathogenicity islet

summary:
Streptococcus pneumoniae normally resides in the human nasopharynx in a non-disease state.  In response to yet unknown triggers it can descend to the lower respiratory tract and/or invade the bloodstream.  Regulation and activation of virulence genes play essential roles in this process of disease development.  A putative transcriptional regulator in S. pneumoniae, MgrA, with homology to a virulence gene activator, mga, of Group A streptococcus (GAS) was previously identified as being required for development of pneumonia in a murine model.  In this work we confirm that mgrA is required for both nasopharyngeal carriage and pneumonia.  Transcriptional profiling by microarray technology through the growth course of a strain that bears a deletion of mgrA (AC1500) with that of a strain that over expresses Mgra (AC1481) is used to show that MgrA .  This is manifested phenotypically by a decrease in adherence to epithelial cells in tissue culture since rlrA pathogenicity islet contains genes mediating adherence.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Elizabeth

last: Joyce


title: Folic Acid study in HT-29 cells

city: Wageningen

first: Jaap

last: Keijer

address: Bornsesteeg 45

country: Netherlands

institute: RIKILT Institute of Food Safety

summary:
Low intracellular folate levels diminish the growth rate of HT-29 human colon cancer cells. This is accompanied by a metabolic shift from cytosolic glycolysis towards mitochondrial oxidative phosphorylation, as demonstrated by a lower lactate production and an increased mitochondrial oxygen consumption rate. To obtain insight in the molecular effects underlying these changes, the steady state gene expression profiles of HT-29 cells with different intracellular folate concentrations were compared. The gene expression profile of HT-29 cells with low intracellular folate levels (grown for 3 weeks in 10 ng/ml folic acid (PGA)) was clearly distinct from that of the other exposure conditions, which provide sufficient intracellular folate levels (100 ng/ml PGA, 10 ng/ml methyltetrahydrofolate (MTHF) or 100 ng/ml MTHF). Intracellular folate deficiency, contrary to expectation, did not lead to major changes in expression of genes involved in energy metabolism. This suggests that the shift towards mitochondrial oxidative phosphorylation is not mediated at the transcription level. Furthermore, only minor changes in the expression of folate metabolism related genes were observed. The changes that were observed were consistent with nucleotide salvage and in agreement with nucleotide need of the slow-growing folate-deficient HT-29 cells. The major observed effects were on cell cycle related gene expression, which was increased and interferon-responsive gene expression, which was reduced. The increase in cell cycle related gene expression seems compensatory to the reduced cell growth. Down-regulation of the interferon-response may be explained by decreased expression of signal transducer and activator of transcription 1 upon folate deficiency.
Keywords: dose response, folic acid, HT-29 cells, human

overall_design: In the present study, large-scale gene expression analysis was performed to reveal mechanistic details of the metabolic switch from aerobic glycolysis to mitochondrial OXPHOS upon folate deficiency in HT-29 human colon cancer cells and to provide new molecular insight into the folate deficient-induced inhibition of colon cancer cell growth. Therefore, as in our previous experiment, HT-29 human colon cancer cells were cultured for 3 weeks in different types and concentrations of folate; synthetic folic acid (pteroylglutamic acid, PGA ; 10 or 100 ng/ml) or natural folate (methyl-tetrahydrofolate, MTHF; 10 or 100 ng/ml) to obtain different intracellular levels of folate. Large scale oligo arrays with 10.296 human oligo probes of which about 300 oligo probes are involved in energy metabolism, were used to study folate induced gene expression changes in order to better understand the metabolic switch and the growth inhibitory effects upon folate deficiency in HT-29 human colon cancer cells.

first: Yvonne

last: Dommels

first: Marjolein

last: Reinders


title: Differentiation mutants in the protozoan parasite Toxoplasma gondii.

last: Stanford Microarray Database

summary:
Two forms of the protozoan parasite Toxoplasma gondii are associated with intermediate hosts such as humans: rapidly growing tachyzoites are responsible for acute illness, whereas slowly dividing encysted bradyzoites can remain latent within the tissues for the life of the host. In order to identify genetic factors associated with parasite differentiation, we have used a strong bradyzoite-specific promoter (identified by promoter trapping) to drive the expression of T. gondii hypoxanthine-xanthine-guanine phosphoribosyltransferase (HXGPRT) in stable transgenic parasites, providing a stage-specific positive/negative selectable marker. Insertional mutagenesis has been carried out on this parental line, followed by bradyzoite induction in vitro and selection in 6-thioxanthine to identify misregulation mutants. Two different mutants fail to induce the HXGPRT gene efficiently during bradyzoite differentiation. These mutants are also defective in other aspects of differentiation: they replicate well under bradyzoite growth conditions, lysing the host cell monolayer as effectively as tachyzoites. Expression of the major bradyzoite antigen BAG1 is reduced, and staining with Dolichos biflorus lectin shows reduced cyst wall formation. Microarray hybridizations show that these mutants behave more like tachyzoites at a global level, even under bradyzoite differentiation conditions.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: User Defined

first: Upinder

last: Singh


title: Crab shell attachment

summary:
Strain N16961 was incubated with crab shell in artificial seawater media for 24 hours. cDNA from 1 ug RNA was labeled with Cy3 (planktonic bacteria) and Cy5 (crab attached bacteria).
A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients.
Keywords: growth_condition_design


title: Unfolded Protein Response

summary:
To dissect the requirements of membrane protein degradation from the ER, we expressed the mouse major histocompatibility complex class I heavy chain H-2K(b) in yeast. Like other proteins degraded from the ER, unassembled H-2K(b) heavy chains are not transported to the Golgi but are degraded in a proteasome-dependent manner. The overexpression of H-2K(b) heavy chains induces the unfolded protein response (UPR). In yeast mutants unable to mount the UPR, H-2K(b) heavy chains are greatly stabilized. This defect in degradation is suppressed by the expression of the active form of Hac1p, the transcription factor that upregulates UPR-induced genes. These results indicate that induction of the UPR is required for the degradation of protein substrates from the ER.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Max

last: Diehn


title: LuxS signaling system and regulation of pneumococcal genes

status: Public on Aug 03 2005

summary:
We were interested in determining if the LuxS signaling system contributed to the regulation of pneumococcal genes.  To accomplish this, we compared the in vitro transcriptional profiles over time of S. pneumoniae D39, a serotype 2 strain of pneumococcus, with that of an isogenic deletion mutant, (delta)luxS, using a spotted S. pneumoniae- specific DNA microarray.  For in vitro time course experiments, broth cultures of D39 and (delta)luxS were grown to low density (optical densities between ~0.01- 0.02), the cells were collected by centrifugation, washed 1x with sterile PBS, back diluted to ~3x105CFU/ ml into fresh broth, and immediately incubated at 37oC in a 5% CO2 chamber for 45 minutes.  At this point, the first sample was collected.  Subsequently, growth was monitored for approximately 8 generations by measuring both the optical density (OD600) and determining viable counts every 30 to 45 minutes.  At these points samples were also harvested by centrifugation for RNA isolation and stored at -80oC until processing.   For microarray probe synthesis, experimental samples were generated using 0.5ug total bacterial RNA isolated from either D39 or (delta)luxS strains at the various time points throughout the growth curve. These RNAs were used as templates for reverse transcription, and the resulting cDNAs were labelled with Cy5. The reference sample for each time course was generated from the D39 time zero RNA.  Subsequent to reverse transcription, the resulting cDNAs were labelled with Cy3.  The probes were mixed in hybridization buffer, heated to 99oC for at least 2 minutes, centrifuged briefly, and applied to the microarray.  Hybridizations were carried out at 60oC for at least 24 hours.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Phages DT1 and 2972 gene expression study

status: Public on Aug 10 2005

city: Québec

first: Sylvain

last: Moineau

state: Québec

department: Biochemistry and microbiology

institute: Université Laval

summary:
This series represents the gene expression study of phages DT1 and 2972 during the whole process of infection. Gene expression was measured at nine time intervals (0, 2, 7, 12, 17, 22, 27, 32, 37 minutes) during phage infection.
Keywords: time-course

sample_organism:
Moineauvirus DT1
Brussowvirus bv2972

platform_organism:
Moineauvirus DT1
Brussowvirus bv2972

last: Duplessis

last: Russell

first: Dennis

last: Romero


title: Murine DN T-reg cells impart prolonged cardiac allograft survival

status: Public on Jul 29 2005

summary:
Recent studies have demonstrated that both mouse and human alpha beta TCR(+)CD3(+)NK1.1(-)CD4(-)CD8- double-negative regulatory T (DN Treg) cells can suppress Ag-specific immune responses mediated by CD8+ and CD4+ T cells. To identify molecules involved in DN Treg cell function, we generated a panel of murine DN Treg clones, which specifically kill activated syngeneic CD8+ T cells. Through serial cultivation of DN Treg clones, mutant clones arose that lost regulatory capacity in vitro and in vivo. Although all allogeneic cardiac grafts in animals preinfused with tolerant CD4/CD8 negative 12 DN Treg clones survived over 100 days, allograft survival is unchanged following infusion of mutant clones (19.5 +/- 11.1 days) compared with untreated controls (22.8 +/- 10.5 days; p < 0.001). Global gene expression differences between functional DN Treg cells and nonfunctional mutants were compared. We found 1099 differentially expressed genes (q < 0.025%), suggesting increased cell proliferation and survival, immune regulation, and chemotaxis, together with decreased expression of genes for Ag presentation, apoptosis, and protein phosphatases involved in signal transduction. Expression of 33 overexpressed and 24 underexpressed genes were confirmed using quantitative real-time PCR. Protein expression of several genes, including Fc epsilon RI gamma subunit and CXCR5, which are >50-fold higher, was also confirmed using FACS. These findings shed light on the mechanisms by which DN Treg cells down-regulate immune responses and prolong cardiac allograft survival.
Type 2 experiment where functional DN T-reg cells (CN4 or TN12) were cy-3 labeled and co-hybridized with non-functional mutant cell lines (CN4.8 or CN12.8).  Used 100 ug total-RNA each channel and no amplifaction.
A transcript identification design type characterizes the length and position of transcripts and allows identification of all forms of transcripts in the genome.
Keywords: transcript_identification_design

first: B

middle: P

last: Lee


title: Genomic comparisons of Salmonella enterica serovar Enteritidis isolates

status: Public on Aug 06 2005

city: Irvine

first: Michael

last: McClelland

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary:
Comparative genomic hybridization of a temporally and locally diverse set of S. enterica ssp I serovar Enteritidis isolates, and some closely related serovar Dublin and Gallinarum strains, to the sequenced Enteritidis PT4
Keywords: other

first: Steffen

last: Porwollik

first: Carlos

last: Santiviago

first: Pui

last: Cheng


title: Stomach parietal cells expression analysis

status: Public on Aug 05 2005

city: Los Angeles

first: Nils

middle: Werner Georg

last: Lambrecht

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

department: Physiology

institute: UCLA

summary:
Gene expression analysis of stomach parietal cells and mixed stomach epithelial cells
Keywords: other

overall_design: Each set of experiments (n = 3) contained one dye swap experiment