title: Rapid tRNA decay can result from lack of non-essential modifications

status: Public on Oct 28 2005

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

institute: Best Institute

summary:
A microarray tiling approach was utilized to assay tRNA modifications by comparing hybridization affinity of tRNA-modification mutants to wild-type across all annotated yeast tRNAs.
Keywords: Assaying noncoding RNA modifications

overall_design: Complementary probes were tiled on average every 5 bases across all tRNAs as well as other noncoding RNAs including 50 bases of flanking genomic sequence.  Probes were normalized to a uniform melting temp of 55 degrees celsius and concatenated to 60 bases.

first: Andrei

last: Alexandrov

first: Irina

last: Chernyakov

first: Weifing

last: Gu

first: Shawna

last: Hiley

first: Timothy

last: Hughes

first: Elizabeth

last: Grayhack

first: Eric

last: Phizicky


title: Rats hypothalamus during heat acclimation without and together with superimposed hypohydration

status: Public on Oct 29 2005

city: Jerusalem

first: Michal

last: Horowitz

department: Physiology

country: Israel

institute: Hebrew University

summary:
We studied the global genomic response in the hypothalamus during heat acclimation, with and without combined hypohydration stress. Rats were acclimated for 2 days or for 30 days at 34°C. Hypohydration (10% decrease in body weight) was attained by water deprivation. Functional analyses demonstrated a bi-phasic acclimatory profile with a transient upregulation of genes encoding ion channels, transporters, and transmitter signaling upon 2 days acclimation, suggesting enhanced neuronal excitability at that acclimation phase. Following long acclimation most genes returned to their pre-acclimation expression levels. In both acclimation phases, genes encoding hormones and neuropeptides, linked with metabolic rate and food intake, were downregulated. The response to hypohydration was characterized by an upregulation of a large number of genes primarily associated with the regulation of ion channels and cell-volume and neuronal excitability. During 2 days acclimation, the response was transiently desensitized, recovering upon LTHA. The results suggest that hypohydration overrides the heat acclimatory status.
Keywords: other

overall_design: We analyzed 9 arrays for euhydrated and 9 arrays for hypohydrated rats.

first: Hagit

last: Schwimmer


title: Comparison of the microbial diversity of an uncontaminated and a 2,4,6-trinitrotoluene contaminated soil sample

status: Public on Oct 26 2005

city: Louvain-la-Neuve

first: Laurent

last: Eyers

address: Place Croix du Sud 2/19

department: Unit of bioengineering

country: Belgium

institute: Catholic University of Louvain

summary:
Microbial community analysis with DNA oligonucleotide microarrays targeting ribosomal RNA (rRNA) provides a highly parallel interrogation of nucleic acids isolated from environmental samples. High fidelity readout is essential for accurate interpretation of hybridisations. We describe the hybridisation of in vitro transcribed 16S rRNA from an uncontaminated and 2,4,6-trinitrotoluene contaminated soil to an oligonucleotide microarray containing group- and species-specific perfect match (PM) probes and their 2 corresponding mismatch (MM) probes. Thermal dissociation analysis was used to determine the specificity of each PM-MM probe set. Functional ANOVA often discriminated PM-MM probe sets when Td values (temperature at 50% probe-target dissociation) could not. Maximum discrimination for many PM and MM probes often occurred at temperatures greater than the Td. Comparison of signal intensities measured prior to dissociation analysis from hybridisations of the two soil samples revealed significant differences in domain-, group- and species-specific probes. Functional ANOVA showed significantly different dissociation curves for 11 PM probes when hybridisations from the two soil samples were compared, even though initial signal intensities for 3 of the 11 did not vary. This approach provides a highly parallel, multi-level analysis that incorporates MM probes and dissociation curves into high fidelity microarray analysis of complex environmental nucleic acid profiles.
Keywords: Microbial diversity, thermal dissociation analysis

overall_design:
Two samples (uncontaminated and 2,4,6-trinitrotoluene contaminated soil samples).
Each hybridisation experiment was done in triplicate.

first: James

middle: C

last: Smoot

first: Laura

middle: M

first: Céline

last: Bugli

first: Hidetoshi

last: Urakawa

first: Zack

last: McMurry

first: Slil

last: Siripong

first: Said

last: El Fantroussi

first: Philippe

last: Lambert

first: Spyros

middle: N

last: Agathos

first: Dave

middle: A

last: Stahl


title: Differential gene expression of ydgG mutant

status: Public on Nov 01 2005

city: Storrs

first: Thomas

middle: K

last: Wood

state: CT

address: 191 Auditorium Rd

department: Chemical Engineering

country: USA

institute: University of Connecticut

summary:
The E. coli Genechip antisense genome array was used to study the differential gene expression profile of E. coli K12 ydgG mutant compared to its isogenic wild type in a mature biofilm.
Keywords: E. coli K12 antisense chip

overall_design: Overnight cultures were diluted 100X into 1 L shake flasks containing 250 mL of LB + 0.2 % and 10 g of glass wool. The cells were shaken at 250 rpm and 37 C for 24 hours (final OD600=5 for the suspended cells), to form a biofilm on the glass wool, and RNA was isolated from the biofilm and Affymetrix protocol was used for preparing fragmented and labelled cDNA that was hybrizide to the chips.

first: Moshe

last: Herzberg

first: Ian

last: Kaye

first: Wolfgang

last: Peti


title: Effects of water restriction on gene expression in mouse renal medulla

status: Public on Oct 25 2005

city: Tucson

first: Kevin

last: Greer

state: AZ

department: Biomedical Engineering

institute: University of Arizona

summary:
In order to identify novel gene targets of vasopressin regulation in the renal medulla, we performed a cDNA microarray study on the inner medullary tissue of mice following a 48 hour water restriction protocol.
Keywords: Stress Response

overall_design: Three renal medulla of 3 water restricted (WR) mice and three control mice (C) were hybridized against each other such that each WR sample was hybridized against each C sample.

first: Heddwen

middle: L

last: Brooks

first: Matt

middle: R

last: McReynolds


city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
All the array experiments published in "Gene expression patterns in human liver cancers" by Chen X, et al.
Hepatocellular carcinoma (HCC) is a leading cause of death worldwide. Using cDNA microarrays to characterize patterns of gene expression in HCC, we found consistent differences between the expression patterns in HCC compared with those seen in nontumor liver tissues. The expression patterns in HCC were also readily distinguished from those associated with tumors metastatic to liver. The global gene expression patterns intrinsic to each tumor were sufficiently distinctive that multiple tumor nodules from the same patient could usually be recognized and distinguished from all the others in the large sample set on the basis of their gene expression patterns alone. The distinctive gene expression patterns are characteristic of the tumors and not the patient; the expression programs seen in clonally independent tumor nodules in the same patient were no more similar than those in tumors from different patients. Moreover, clonally related tumor masses that showed distinct expression profiles were also distinguished by genotypic differences. Some features of the gene expression patterns were associated with specific phenotypic and genotypic characteristics of the tumors, including growth rate, vascular invasion, and p53 overexpression.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Xin

last: Chen


title: Chromatin and siRNA pathways cooperate to maintain DNA methylation

city: Seattle

first: Robert

last: Tran

state: WA

address: 1100 Fairview Ave N; A1-111

institute: Fred Hutchinson cancer research center

type: Methylation profiling by genome tiling array

summary:
DNA methylation occurs at preferred sites in eukaryotes, although the basis for preference is not known. We use a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related RNA silencing component (AGO4) in methylating target loci. We find that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that corresponds to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants. Our results suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism. Thus, parallel pathways would be needed to maintain silencing of transposable elements.
Keywords: Methylation profiling using Msp I enzyme

overall_design: Methylation profiling of Arabidopsis mutant in CNG methylation pathways on Arabidopsis oligo and  random arrays.

first: Daniel

last: Zilberman

first: Cecilia

last: de Bustos

first: Renata

middle: F

last: Ditt

first: Jorja

middle: G

last: Henikoff

first: Anders

last: Lindroth

first: Jeffrey

last: Delrow

first: Tom

last: Boyle

first: Samson

last: Kwong

first: Terri

middle: D

last: Bryson

first: Steven

middle: E

last: Jacobsen


title: Molecular Conservation of Zebrafish and Human Liver Tumors.

city: Singapore

first: Siew Hong

last: Lam

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

summary:
Zebrafish has been advocated as a cancer model, but little is known about the molecular similarities between zebrafish and human tumors. Comparative analysis of microarray data from zebrafish liver tumors with those from four human tumor types revealed molecular conservation at various levels between fish and human tumors. This approach provides a useful strategy for identifying expression signature that is strongly associated with a disease phenotype.
Keywords: Diseased vs normal.

overall_design: We analyzed 10 arrays for zebrafish liver tumor tissue and 10 arrays for normal liver tissue.

first: Siew

middle: H

first: Yi

last: Wu

first: Lance

last: Miller

first: Jan

last: Spitsbergen

first: Zhang

last: Huiqing

first: Kunde

last: Govindarajan

first: Serene

last: Lee

first: Sinnakarupa

last: Mathavan

first: Vinsensius

middle: B

last: Vega

first: Donald

last: Buhler

first: Edison

middle: T

last: Liu

first: Zhiyuan

last: Gong


title: Chronic heat stress gene expression in mice liver

status: Public on Oct 24 2005

city: Columbia

first: Sachin

middle: S

last: Bhusari

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: Univ of Missouri

summary:
This study was done to know the transcritional changes occuring in mice liver in response to chronic heat stress at 34*c for a period of two weeks.
Keywords: Chronic heat stress response on liver gene expression.

overall_design: The microarray study was done in Reference design. We used a in-house Rat-specific oligonucleotide microarray containing 1400 liver specific genes. Heat stress (HS) group had 6 mice, while thermoneutral group had 7 mice. Each microarray hybridization was done in using a reference design in which experimental sample was hybridized against a mouse reference RNA. For each biological sample, two or three technical replicates hybridizations were done out of which one hybridization was in swap dye design to detect dye specific bias.

first: Leonard

last: Hearne

last: Spiers

first: William

last: Lamberson

first: Eric

last: Antoniou


title: Analyzing the role of transcription elongation factors Spt4-5 in splicing

city: Santa Cruz

first: Todd

last: Burckin

address: 1156 High Street

department: Molecular, Cell, & Developmental Biology

institute: University of California Santa Cruz

summary:
A set of 22 expts. aimed at identifying splicing events dependent upon on the Spt4-5 transcription elongation factors in yeast.  Four spt mutants and an mRNA capping mutant were analyzed four times each, including biological and technical (dye-swap) replicates.  Two wt vs wt expts. were also performed.
Keywords = transcription/spt5/spt4/splicing/DEDS
Keywords: other

first: Yuanyuan

last: Xiao

first: Jean Y

last: Yang

first: Lily

last: Shiue

first: Grant

last: Hartzog

first: Mark

last: Segal


title: Functional genomic analysis of three nitrogenase isozymes in the photosynthetic bacterium Rhodopseudomonas palustris

status: Public on Nov 10 2005

first: Yasuhiro

last: Oda

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

department: Department of Microbiology

institute: University of Washington

summary:
To address the question of how photosynthetic bacterium Rhodopseudomonas palustris differentially regulates gene expression of three nitrogenase isozymes (Mo, V, and Fe nitrogenases), we constructed Mo strain (Mo nitrogenase only strain), V strain (V nitrogenase only strain), and Fe strain (Fe nitrogenase only strain), and analyzed the whole genome transcriptome profiles of each mutant and wild-type cells grown under nitrogen-fixing conditions.
Keywords: Genetic modification

overall_design: RNA was isolated from various Rhodopseudomonas palustris strains that were grown to the mid-logarithmic phase of growth. Fluorescently labeled cDNA was prepared by direct incorporation of either Cy3-dCTP or Cy5-dCTP during a first-strand reverse transcription reaction. The hybridization mixtures containing the two labeled cDNA samples to be compared were applied to microarray slides that had been covered with Lifterslips (Erie Scientific Company, Portsmouth, NH). The slides were assembled with hybridization chambers (Corning, Corning, NY) and submerged in a 65ºC water bath. After 14-16 h of hybridization, the slides were washed and scanned with a ScanArray 4000XL scanner (PerkinElmer, Boston, MA). Images (Cy3 and Cy5) were captured as TIFF files and were analyzed with the image processing software ImaGene version 5.6 (BioDiscovery, Inc., El Segundo, CA). The software package lcDNA was used for data normalization and assessment of the statistical confidence intervals of gene expression. Duplicate calibration experiments and three comparative experiments using RNA from three separately grown cultures (three biological replicates) with duplicate slides for each (10 slides in total) were used to generate each data set.

first: Sudip

last: Samanta

first: Federico

last: Rey

first: Liyou

last: Wu

first: Xiudan

first: Tingfen

last: Yan

first: Jizhong

last: Zhou

first: Caroline

last: Harwood


title: Effect of in vitro transcription time on the fidelity of T7-based RNA linear amplification

status: Public on Nov 04 2005

last: Stanford Microarray Database

summary:
Zhao et al. Amplification Figure 1
This experiment was designed to evaluate the effect of in vitro transcription time on the fidelity, reproducibility, and yield of T7 based linear amplification. Duplicate reactions were performed at 37 degree for 2, 3, 4, 5, and 6 hours. Two additional 5-hour incubation reactions were stored at 4 degree overnight to determine the effect of low temperature incubation on amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with the G50 column cleanup step.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Hongjuan

last: Zhao


title: Cell division cycle in a human cancer cell line (HeLa)

status: Public on Oct 22 2005

summary:
This experiment set contains the complete set of raw data for Whitfield et al. (2002)Mol.Biol.Cell.  HeLa S3 cells were synchronized by three different methods (double thymidine block, thymidine-nocodazole block or mitotic shake-off)in five independent time courses.  mRNA from the first and second double thymidine block experiments were converted to cDNA by standard methods using an oligo-dT/random hexamer mix and hybridized to 24K arrays; mRNA from the third double thymidine and thymidine-nocodazole block experiments were converted to cDNA using olido-dT alone and hybridized to 43K arrays; total RNA from the mitotic shake-off experiment was first amplified using a modified eberwine protocol, aRNA converted to cDNA by reverse transcription with random hexamer and hybridized to 43K arrays.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Michael

last: Whitfield

first: Janos

last: Demeter


title: prp43 COLD SHIFT

status: Public on Oct 20 2005

first: Roland

middle: J

last: Nagel

address: Sinsheimer Labs

department: Biology

institute: UCSC

summary:
Cold senstive alleles of prp43, S249A and G429A were assayed for splicing and RNA processing defects.

Keywords: splicing, pre-mRNA processing

overall_design: RNA was isolated from cold senstive alleles of prp43, S249A and G429A after cold shift to 16C for 60 mins. Cy3/Cy5 labeled RNA's were hybridized to Yeast Splicing Chip v62 using WT RNA cold shifted to 16C for 60 mins as a reference. There are 4 hybes in the series which include reciprocal dye swap experiements for each cold sensitive allele.


title: Comparison of Transcript Profiles in Wild-type and o2 Maize Endosperm in Different Genetic Backgrounds

city: Ames

first: Hongwu

last: Jia

state: IA

address: 1407 Agronomy Hall

department: Agronomy

institute: Iowa State University

summary:
Mutations in the Opaque2 (O2) gene of maize (Zea Mays L.) improve the nutritional value of maize by reducing the level of zeins in the kernel. The phenotype of o2 grain is controlled by many modifier genes and is therefore strongly dependent on the genetic background. We sought to distinguish between two hypotheses to explain differences in phenotypic severity:  1. Differences in phenotypic severity are due to genotype specific differentially expressed genes and 2.  Differences in phenotypic severity are due to differences in the degree of differential expression of a set of differentially expressed genes.  Eight pairs of inbred lines and their o2 counterparts were characterized for phenotypes controlled by o2 (lysine content, kernel density, seed weight and shoot to root ratio of seedlings).  The inbred line B46 was identified as having severe o2 effects while the line M14 was identified as having minimal o2 effects.  Transcripts that were differentially expressed between the wild-type and o2 versions of these two lines were identified by microarray hybridization.  While genotype specific differentially expressed transcripts were identified, many transcripts were identified with reduced degree of differential expression in M14 relative to B46.   Thus, a combination of genotype specific transcripts and degree of differential expression of transcripts can explain differences in phenotypic severity in these two genetic backgrounds.  To identify the transcripts most likely to be differentially expressed in a given genetic background, we used RNA from eight genotype pools in microarray hybridization.  By averaging across genotypes in this way, genotype-specific changes are minimized.
Keywords: Genetic modification

overall_design: A triplicate dye-swap design was used for each comparison (B46/o2, M14/o2, and mixed w.t./mixed o2). For each single dye-swap experiment two slides were used. Three pairs of independent samples were used in each comparison.

first: Dan

last: Nettleton

first: Gricelda

last: Vazquez-Carrillo

first: Joan

last: Peterson

first: Paul

last: Scott


title: Drosophila adults 0.5% O2 6hr

status: Public on Oct 21 2005

city: Eugene

first: Eric

last: Johnson

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular biology

institute: University of Oregon

summary:
Identify genes with increased transcript abundance after low oxygen stress in Drosophila adults.
Keywords: hypoxic response

overall_design: There are 6 Oregon-R experiments comparing low oxygen exposed to normal oxygen.  Samples 1-4 have hypoxic RNA labeled with cy5, and samples 5&6 are dye-swaps with the hypoxic RNA labeled with cy3.  Samples 7&8 are Sb/Tm3 flies to control for background effects.

first: Guowen

last: Liu

first: Julianne

last: Roy


title: Diversity, Topographic Differentiation, and Positional Memory in Human Fibroblasts

status: Public on Nov 03 2005

summary:
A fundamental feature of the architecture and functional design of vertebrate animals is a stroma, composed of extracellular matrix and mesenchymal cells, which provides a structural scaffold and conduit for blood and lymphatic vessels, nerves, and leukocytes. Reciprocal interactions between mesenchymal and epithelial cells are known to play a critical role in orchestrating the development and morphogenesis of tissues and organs, but the roles played by specific stromal cells in controlling the design and function of tissues remain poorly understood. The principal cells of stromal tissue are called fibroblasts, a catch-all designation that belies their diversity. We characterized genome-wide patterns of gene expression in cultured fetal and adult human fibroblasts derived from skin at different anatomical sites. Fibroblasts from each site displayed distinct and characteristic transcriptional patterns, suggesting that fibroblasts at different locations in the body should be considered distinct differentiated cell types. Notablegroups of differentially expressed genes included some implicated in extracellular matrixsynthesis, lipid metabolism, and cell signaling pathways that control proliferation, cellmigration, and fate determination. Several genes implicated in genetic diseases werefound to be expressed in fibroblasts in an anatomic pattern that paralleled the phenotypicdefects. Finally, adult fibroblasts maintained key features of Hox gene expressionpatterns established during embryogenesis, suggesting that Hox genes may directtopographic differentiation and underlie the detailed positional memory in fibroblasts.
Keywords: Logical Set

overall_design: Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc


title: Detection of Differential Gene Expression in Brown Adipose Tissue of Hibernating Arctic Ground Squirrels

city: Fairbanks

first: Jun

state: AK

address: 311 Irving Building

department: Institute of Arctic Biology

institute: University of Alaska Fairbanks

summary:
Hibernation is an energy-saving strategy adopted by a wide range of mammals to survive highly seasonal or unpredictable environments. Arctic ground squirrels living in Alaska provide an extreme example, with 6-9 months long hibernation seasons when body temperature alternates between levels near 0 C during torpor and 37 C during arousal episodes. Heat production during hibernation is provided, in part, by non-shivering thermogenesis that occurs in large deposits of brown adipose tissue (BAT). BAT is active at tissue temperatures from 0 to 37 C during rewarming and continuously at near 0 C during torpor in subfreezing conditions.  Despite its crucial role in hibernation, the global gene expression patterns in BAT during hibernation compared to the non-hibernation season remain largely unknown. We report a large-scale study of differential gene expression in BAT between winter hibernating and summer active arctic ground squirrels using mouse microarrays. Selected differentially expressed genes identified on the arrays were validated by quantitative real-time PCR using ground squirrel specific primers. Our results show that the mRNA levels of the genes involved in nearly every step of the biochemical pathway leading to non-shivering thermogenesis are significantly increased in BAT during hibernation, whereas those of genes involved in protein biosynthesis are significantly decreased compared to the summer active animals in August. The differentially expressed genes also include those involved in adipose differentiation, substrate transport, and structure remodeling, which may enhance thermogenesis at low tissue temperatures in BAT.
Keywords: hibernating animals vs. summer active animals

overall_design: Four Wistar mouse arrays (MA07, MA08, MA10, MA11) each carrying 9,600 probes were used to screen the differentially expressed genes in brown adipose tissue (BAT) between 5 winter hibernating (BAT_torpor_1, BAT_torpor_2, BAT_torpor_3, BAT_torpor_4, BAT_torpor_5) and 3 summer active (BAT_summer_1, BAT_summer_2, BAT_summer_3) arctic ground squirrels. There are technical replicas (samples split from the same total RNA extraction) for BAT_summer_1 (a, b), BAT_summer_2 (a, b), and BAT_torpor_5 (a, b).

first: Adlai

last: Burman

first: Calen

last: Nichols

first: Linda

last: Alila

first: Louise

last: Showe

first: Bert

last: Boyer

first: Brian

last: Barnes

first: Thomas

last: Marr


title: Triiodothyronine Treatment: Effects on vastus lateralis skeletal muscle

status: Public on Oct 18 2005

last: Stanford Microarray Database

summary:
Healthy men received 75 5g/d of T3 for 14 days. Microbiopsies of vastus lateralis skeletal muscle were performed before and after the treatment. For microarray experiments, we used samples from five subjects. After amplification of total RNA (Wang et al. 2000a), fluorescently labeled cDNA was prepared from each experimental sample. For each subject, probes from basal and T3 treatment conditions labeled with cyanine (Cy) 3 or Cy5 dyes were hybridized to cDNA microarray. After a filtering procedure to eliminate bad-quality spots and background correction, log2 transformed data for each experiment were normalized and centered to the mean.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Karine

last: Clement


title: Comparison of H. pylori subclones

summary:
Helicobacter pylori has a very plastic genome, reflecting its high rate of recombination and point mutation. This plasticity promotes divergence of the population by the development of subclones and presumably enhances adaptation to host niches. We have investigated the genotypic and phenotypic characteristics of two such subclones isolated from one patient as well as the genetic evolution of these isolates during experimental infection. Whole-genome genotyping of the isolates using DNA microarrays revealed that they were more similar to each other than to a panel of other genotyped strains recovered from different hosts. Nonetheless, they still showed significant differences. The genomic evolution of both isolates during the infection of conventionally raised and germ-free mice was monitored over the course of 3 months. The Cag PAI-positive isolate was also surveyed after a 10 month colonization of conventionally raised transgenic animals (n = 9 mice). Microarray analysis of the Cag PAI and sequence analysis of the cagA, recA, and 16S rRNA genes disclosed no changes in recovered isolates. Together, these results reveal that the H. pylori population infecting one individual can undergo significant divergence, creating stable subclones with substantial genotypic and phenotypic differences.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Nina

last: Salama


title: Autoimmune family study

city: Nashville

first: Zheng

state: TN

institute: Vanderbilt University

summary:
Patients with autoimmune disorders exhibit highly reproducible gene expression profiles in their peripheral blood mononuclear cells. These signatures may result from chronic inflammation, other disease manifestations, or may reflect family resemblance. To test the latter hypothesis, we determined gene expression profiles in unaffected first-degree relatives of individuals with autoimmune disease. Gene expression profiles in unaffected first-degree relatives resembled the profiles found in individuals with autoimmune diseases. A high percentage of differentially expressed genes in unaffected first-degree relatives were previously identified as autoimmune signature genes. Examination of the linear regression relationship of gene transcript levels between parent-offspring pairs revealed that autoimmune signature genes display high levels of family resemblance. Taken together, these results support the hypothesis that these variations in gene transcript levels are associated with family resemblance rather than clinical manifestations of disease.
Keywords: Gene expression profiling

overall_design: Gene expression profiling of autoimmune families

last: Aune


title: Gene expression in miscellaneous human tissues and cell lines

summary:
Each tissue or cell line polyA+ RNA-labeled with Cy5 was hybridized against a common reference pool consisting of 11 different cell lines described elsewhere (Perou et al. 2000)
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Max

last: Diehn

first: Alexander

last: Pergamenschikov


title: MMRRC_B6_1wk

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
This series represents all data from brain, kidney and liver of 1 week old B6 litter mates
Keywords: other


title: MMRRC_B6_8wk

summary:
This series represents all data from brain, kidney and liver of 8 week old B6 litter mates
Keywords: other


title: LymphomaTransformation

summary:
Transformation of Follicular Lymphoma to Diffuse Large Cell Lymphoma:  Alternative Patterns with Increased or Decreased Expression of c-myc and its Regulated genes        The natural history of follicular lymphoma (FL) is frequently characterized by transformation to a more aggressive diffuse large B cell lymphoma (DLBCL). We compared the gene expression profiles between transformed DLBCL and their antecedent FL. No genes were observed to increase or decrease their expression in all the cases of histological transformation. However, two different gene expression profiles associated with the transformation process were defined, one in which c-myc and genes regulated by c-myc showed increased expression and one in which these same genes showed decreased expression. Further, there was a striking difference in gene expression profiles between transformed DLBCL and de novo DLBCL, since the gene expression profile of transformed DLBCL was more similar to their antecedent FL than to de novo DLBCL. The study demonstrates that transformation from FL to DLBCL can occur by alternative pathways and that transformed DLBCL and de novo DLBCL have very different gene expression profiles that may underlie the different clinical behaviors of these two types of morphologically similar lymphomas.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Ash

last: Alizadeh

first: Janos

last: Demeter


title: Arabidopsis stn7-stn8 double mutant vs WT

city: Chicago

first: christos

last: Noutsos

country: Germany

institute: University of Chicago

summary:
Comparison of the Arabidopsis stn7-stn8 double mutant invlolved in state transition vs WT
Keywords: other

first: A

last: Biehl

first: E

last: Richly

first: C

last: Dietzmann

first: J

last: Kurth

first: F

last: Salamini

first: D

last: Leister


title: Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae

status: Public on Oct 15 2005

summary:
In Saccharomyces cerevisiae, the Ca2+/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca2+ and Na+, and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca2+ (200 mM) or Na+ (0.8 M) to yeast. 163 genes exhibited increased expression that was reduced 50% or more by calcineurin inhibition. These calcineurin dependent genes function in signaling pathways, ion/small molecule transport, cell wall maintenance, vesicular transport, and include many open reading frames of heretofore-unknown function. Three distinct gene classes were defined: 28 genes displayed calcineurin-dependent induction in response to Ca2+ and Na+, 125 showed calcineurin-dependent expression following Ca2+ but not Na+ addition, and 10 were regulated by calcineurin in response to Na+ but not Ca2+. Analysis of crz1D cells established Crz1p as the major effecter of calcineurin-regulated gene expression in yeast. We identified the Crz1p binding site as 5-GNGGC(G/T)CA-3 by in vitro site selection. A similar sequence, 5-GAGGCTG-3, was identified as a common sequence motif in the upstream regions of calcineurin/Crz1p-dependent genes. This finding is consistent with direct regulation of these genes by Crz1p.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Hiroyuki

last: Yoshimoto


title: Arabidopsis stn8 mutant vs WT

summary:
Comparison of the Arabidopsis stn8 mutant invlolved in state transition vs WT
Keywords: other


title: HPEC senescent vs immortalized cells

last: Stanford Microarray Database

summary:
Cellular senescence forms a barrier that inhibits the acquisition of an immortal phenotype, a critical feature in tumorigenesis. The inactivation of multiple pathways that positively regulate senescence are required for immortalization. To identify these pathways in an unbiased manner, we performed DNA microarray analyses to assess the expression of 20,000 genes in human prostate epithelial cells (HPECs) passaged to senescence. These gene expression patterns were then compared with those of HPECs immortalized with the human Papillomavirus 16 E7 oncoprotein. Senescent cells display gene expression patterns that reflect their nonproliferative, differentiated phenotype and express secretory proteases and extracellular matrix components. A comparison of genes transcriptionally up-regulated in senescence to those in which expression is significantly down-regulated in immortalized HPECs identified three genes: the chemokine BRAK, DOC1, and a member of the insulin-like growth factor axis, IGFBP-3. Expression of these genes is found to be uniformly lost in human prostate cancer cell lines and xenografts, and previously, their inactivation was documented in tumor samples. Thus, these genes may function in novel pathways that regulate senescence and are inactivated during immortalization. These changes may be critical not only in allowing cells to bypass senescence in vitro but in the progression of prostate cancer in vivo.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Samuel

last: DePrimo


title: Gene expression pattern in Caco-2 cells following rotavirus infection

status: Public on Oct 13 2005

summary:
Rotaviruses are recognized as the leading cause of severe dehydrating diarrhea in infants and young children worldwide. Preventive and therapeutic strategies are urgently needed to fight this pathogen. In tissue culture and in vivo, rotavirus induces structural and functional alterations in the host cell. In order to better understand the molecular mechanisms involved in the events after rotavirus infection, we identified host cellular genes whose mRNA levels changed after infection. For this analysis, we used microarrays containing more than 38,000 human cDNAs to study the transcriptional response of the human intestinal cell line Caco-2 to rotavirus infection. We found that 508 genes were differentially regulated >2-fold at 16 h after rotavirus infection, and only one gene was similarly regulated at 1 h postinfection. Of these transcriptional changes, 73% corresponded to the upregulation of genes, with the majority of them occurring late, at 12 or more hours postinfection. Some of the regulated genes were classified according to known biological function and included genes encoding integral membrane proteins, interferon-regulated genes, transcriptional and translational regulators, and calcium metabolism-related genes. A new picture of global transcriptional regulation in the infected cell is presented and families of genes which may be involved in viral pathogenesis are discussed.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Dino

last: Feigelstock


title: Arabidopsis stn7 mutant vs WT

summary:
Comparison of the Arabidopsis stn7 mutant invlolved in state transition vs WT
Keywords: other


title: Transcript analysis of early nodulation events in Medicago truncatula

status: Public on Oct 14 2005

city: St Paul

first: Kathryn

last: VandenBosch

state: MN

address: Room 250 BioSci 6022 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

summary:
For transcript analysis of early nodulation events in Medicago truncatula we compared transcripts from inoculated and uninoculated roots corresponding to defined stages between 1 and 72 h post inoculation (hpi).
Keywords: time course

overall_design:
Time course of 6 time points consists of 36 microarrays.
Each time point experiment consists of three direct (reps1, 2, 3) and three dye-swapped (reps 4, 5, 6) technical replicates.

first: Dasharath

middle: P

last: Lohar

first: Natasha

last: Sharopova

first: Gabrielle

last: Endre


title: Rice indica genome tiling experiments

city: New Haven

first: Xing-Wang

last: Deng

address: 165 Prospect

department: MCD Biology

institute: Yale University

type: Expression profiling by genome tiling array

summary:
This experiment was designed to identify transcribed regions of indica rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of  838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogate the indica genome, respectively.
The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies.
Keywords: genome tiling experiments

first: Lei

last: Li

first: Xiangfeng

last: Wang

first: Viktor

last: Stolc

first: Xueyong

first: Dongfen

last: Zhang

first: Ning

last: Su

first: Waraporn

last: Tongprasit

first: Songgang

first: Zhukuan

last: Cheng

first: Jun

first: XingWang


title: MMRRC_B6_6m

first: Sridar

last: Chittur

summary:
This series represents all data from brain, kidney and liver of 6 month old B6 litter mates
Keywords: other


title: Helicobacter pylori bacterial populations

summary:
Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host?pathogen relationships.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Nina

last: Salama


title: Molecular characterisation of soft tissue tumours: a gene expression study

last: Stanford Microarray Database

summary:
Soft-tissue tumours are derived from mesenchymal cells such as fibroblasts, muscle cells, or adipocytes, but for many such tumours the histogenesis is controversial. We aimed to start molecular characterisation of these rare neoplasms and to do a genome-wide search for new diagnostic markers. We analysed gene-expression patterns of 41 soft-tissue tumours with spotted cDNA microarrays. After removal of errors introduced by use of different microarray batches, the expression patterns of 5520 genes that were well defined were used to separate tumours into discrete groups by hierarchical clustering and singular value decomposition. Synovial sarcomas, gastrointestinal stromal tumours, neural tumours, and a subset of the leiomyosarcomas, showed strikingly distinct gene-expression patterns. Other tumour categories--malignant fibrous histiocytoma, liposarcoma, and the remaining leiomyosarcomas--shared molecular profiles that were not predicted by histological features or immunohistochemistry. Strong expression of known genes, such as KIT in gastrointestinal stromal tumours, was noted within gene sets that distinguished the different sarcomas. However, many uncharacterised genes also contributed to the distinction between tumour types. These results suggest a new method for classification of soft-tissue tumours, which could improve on the method based on histological findings. Large numbers of uncharacterised genes contributed to distinctions between the tumours, and some of these could be useful markers for diagnosis, have prognostic significance, or prove possible targets for treatment.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

first: Matt

last: Van De Rijn


title: Time course analysis of genes regulated by E. coli sigma E (rpoE) after overexpression

city: San Francisco

first: Virgil

middle: Arthur

last: Rhodius

address: Genentech Hall, 600 16th Street

department: Microbiology and Immunology

institute: UCSF

summary:
DNA microarray analysis of genes regulated by the alternative sigma factor, sigma E (rpoE). Sigma E-dependent genes were initially identified by comparing a wild type (wt) E. coli K-12 strain that has a low level of sigma E, with a strain over-expressing sigma E (following induction of rpoE from an inducible promoter by IPTG). We monitored changes in gene expression in 4 separate time-courses after induction and used SAM (Statistical Analysis of Microarrays) to identify 75 significantly induced and 8 significantly repressed genes. Some of these genes are part of operons in which other gene members were clearly induced but were not marked as significant in our strict selection criteria. Therefore, to fully describe the sigma E regulon we expanded this set by using the statistics from SAM to analyze the reproducibility and significance of the expression ratios of all the genes adjacent to and in the same orientation as the highly significant genes. This gave 96 genes organized in 50 sigma E-dependent transcription units (TUs), of which 42 were induced and 8 were repressed. This study is detailed in Rhodius et al 2006 (PLoS Biol 4(1): e2)
Keywords: time course

overall_design: This series consists of 4 replicated time courses. Each time course consists of a comparison between wild type E.coli MG1655 that has a low level of sigma E, and an over-expressing sigma E strain following induction of rpoE from an inducible promoter by IPTG. Both strains were grown to mid log and then induced with IPTG and incubation resumed. Samples were removed for comparative microarray analysis immediately prior to induction, and at 2.5, 5, 10, 15, 20, 30 and 60 min after induction. To correct for changes in growth state, control and over-expressed samples were always compared from the same time point.

first: Wonchul

last: Suh

first: Gen

last: Nonaka

first: Joyce

last: West

first: Carol

last: Gross


title: Heme Deficient vs Wild Type in Low Iron

city: Salt Lake City

first: Robert

last: Crisp

state: UT

address: 30 North Medical Drive

department: Dep't of Pathology

institute: University of Utah

summary:
Heme Deficient or Wild Type (normal heme) for 6 hrs with iron chelation by BPS.
Keywords: Cell Type Comparison

overall_design:
Single Experiment with Probe Reversal
1.  GSM78518 (Cy3) vs GSM78519 (Cy5)
2.  GSM78520 (Cy3) vs GSM78521 (Cy5)

first: Jerry

last: Kaplan


title: Gene expression profile in juvenile Spo11 knockout testes

city: Bethesda

first: Rafael

middle: Dan

last: Camerini-Otero

state: MD

address: 5 Memorial Dr. Rm.205

department: GBB

institute: NIDDK

summary:
Spo11, a meiosis-specific protein, introduces double strand breaks on chromosomes and initiates meiotic recombination in a wide variety of organisms. Mouse null Spo11 spermatocytes fail to synapse chromosomes and to progress beyond zygotene stage of meiosis. We analyzed gene expression profiles in Spo11-/- adult and juvenile wild type testis to determine genes expressed in different stages of meiosis and spermatogenesis. These genes were characterized using Gene Ontology. To focus on genes involved in meiosis we performed comparative gene expression analysis of Spo11 -/- and wild type testes from 12 and 15 day mice. We found that the knockout of Spo11 gene causes dramatic changes in the level of expression of genes that participate in meiotic recombination (Hop2, Brca2, Mnd1, FancG) and in the meiotic checkpoint (cyclin B2, Cks2) at 15 day, but does not affect genes encoding protein components of the synaptonemal complex. Finally, we uncovered unknown genes that are affected by disruption of the Spo11gene and therefore, may be specifically involved in meiosis and spermatogenesis.
Keywords: repeat sample

overall_design: Microarray experiments were performed in quadruplicate with different mouse pairs from the same mouse litter. The chips were scanned using the GenePix 4000A scanner (Axon Instruments) and primary data were analyzed using the Genepix 3.0 software. Primary data were flagged using four default parameters set in the Genepix 3.0 program. For further analysis, the data were imported into Excel (Microsoft) and normalized by the Median Centering Method. We performed the statistical analysis using a modified t-test implemented in SAM software (Tusher et al., 2001). We defined differentially expressed genes at a 1% false discovery rate confidence level and a cutoff for differential expression equal to 1.5 for juvenile Spo11-/- microarray experiments

first: Natalya

last: Smirnova

first: Peter

last: Romanienko

first: Pavel

last: Khil

first: Daniel


title: Gene Expression Signature Shared in Autoimmune Diseases Not in Unaffected Family Members

first: Zheng

last: Liu

summary:
Even though autoimmune diseases are heterogeneous, believed to result from the interaction between genetic and environmental components, patients with these disorders exhibit reproducible patterns of gene expression in their peripheral blood mononuclear cells. A portion of this gene expression profile reflects family resemblance rather than the actual presence of an autoimmune disease.  Here we wanted to identify that portion of this gene expression pattern that is independent of family resemblance and determine if it is a product of disease duration, disease onset, or other factors.  By increasing the number of autoimmune samples in our analysis and employing supervised clustering algorithms, we identified 100 genes whose expression profiles are shared in individuals with various autoimmune diseases but are not shared by first-degree relatives of individuals with autoimmune disease or by controls.  Individuals with early disease (1 yr after onset) and established disease (10 yr after onset) exhibit a near identical expression pattern suggesting that this unique profile reflects disease onset rather than disease duration.
Keywords: gene expression signatures

overall_design:
supervised gene expression profiling were performed to a cohort sample pool: control individuals(8), unaffected family members of autoimmune diseases patients (8), and individuals with autoimmune diseases (54).
we try to identify a gene expression signatures that were exclusively associated with autoimmune diseases but not infulenced by genetic components

first: Aune

middle: M

last: Thomas


title: MMRRC_FVB_1wk

first: Sridar

last: Chittur

summary:
This series represents all data from brain, kidney and liver of 1 week old FVB litter mates
Keywords: other


title: Mutant Mouse Regional Resource Center (MMRRC) Research

summary:
This study is part of the Mutant Mouse Regional Resource Center Research. The series subsets represent the strain and age group for easy comparisons. Each subseries has data for three different tissues (brain, liver and kidney) and 2 sexes.
Keywords: other


title: H2A.Z marks the 5' end of genes

status: Public on Oct 07 2005

city: Worcester

first: Oliver

last: Rando

state: MA

address: 364 Plantation St.

institute: UMass Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
In S. cerevisiae, histone variant H2A.Z is deposited in euchromatin at the flanks of silent heterochromatin to prevent its ectopic spread.  The degree to which H2A.Z is found and functions elsewhere is unknown.  Here we show that H2A.Z nucleosomes are found at promoter regions of nearly all genes in euchromatin.  They generally occur as two positioned nucleosomes that flank a nucleosome-free region (NFR) that contains the transcription start site.  Astonishingly, enrichment at 5’ ends is independent of transcriptional state as it is observed not only at actively transcribed genes, but also at inactive loci.  Mutagenesis of a typical promoter revealed a 22 bp segment of DNA sufficient to program formation of a NFR flanked by two H2A.Z nucleosomes.  This segment contains a binding site of the Myb-related protein Reb1 and an adjacent dT:dA tract.  Efficient deposition of H2A.Z is further promoted by a specific pattern of histone H3 and H4 tail acetylation and the bromodomain protein Bdf1, a component of the Swr1 complex that deposits H2A.Z.  These data define DNA- and histone-based mechanisms by which dividing cells define the 5’ ends of genes and preserve their euchromatic state in the absence of transcription.
Keywords: ChIP-chip

overall_design: In mid-log phase S. cerevisiae, we performed ChIP-chip on Htz1 (the histone variant H2A.Z) and compared its 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. Five replicates (2 biological, 3 technical) were performed .

first: Ryan

last: Raisner

first: Paul

last: Hartley

first: Marc

last: Meneghini

first: Marie

middle: Z

last: Bao

first: Stuart

last: Schreiber

first: Hiten

last: Madhani


title: Molecular mechanism for switching of P.falciparum invasion pathways into human erythrocytes

status: Public on Oct 04 2005

city: Parkville

first: Ken

last: Simpson

state: Victoria

address: 1G Royal Parade

department: Genetics and Bioinformatics

country: Australia

institute: The Walter and Eliza Hall Institute

summary:
The malaria parasite, Plasmodium falciparum, exploits multiple ligand-receptor interactions, called invasion pathways, to invade the host erythrocyte. Strains of P.falciparum vary in their dependency on sialated red cell receptors for invasion. We show that switching from sialic acid-dependent to –independent invasion is reversible and depends on parasite ligand utilisation. Expression of P.falciparum reticulocyte-binding like homologue 4 (PfRh4) correlates with sialic acid-independent invasion and PfRh4 is essential for switching invasion pathways. Differential activation of PfRh4 represents a novel mechanism of invasion pathway control and provides P.falciparum with exquisite adaptability in the face of erythrocyte receptor polymorphisms and host immune responses.
Keywords: Plasmodium falciparum, erythrocyte invasion, invasion pathways, EBA175, Rh4

overall_design: Experiment contains no replication.  There are three genotypes: wildtype W2mef parasites, a cloned variant that can invade via a sialic acid independent pathway, and a parasite in which EBA175 has been knocked out and which also invades via a sialic acid independent pathway.

first: Janine

last: Stubbs

first: Tony

last: Triglia

first: David

last: Plouffe

first: Christopher

last: Tonkin

first: Manoj

last: Duraisingh

first: Alexander

last: Maier

first: Elizabeth

last: Winzeler

first: Alan

last: Cowman


title: MMRRC_129_1wk

first: Sridar

last: Chittur

summary:
This series represents all data from brain, kidney and liver of 1 week old (129sv strain) litter mates
Keywords: other


title: Comparison of Trypanosoma cruzi strains from patients with indeterminate and cardiac forms of Chagas disease

status: Public on Oct 08 2005

city: Ribeirao Preto

first: Ricardo

last: Vêncio

state: SP

address: Av. Bandeirantes, 3900

department: Computing and Mathematics Department

country: Brazil

institute: Universidade de São Paulo

summary:
Gene expression profiles in T. cruzi strains isolated from individuals presenting the indeterminate and cardiac forms of Chagas disease. Genetic markers differentially expressed may be of potential use in diagnostic/prognostic tests and could assist the understanding of pathogenesis of Chagas disease
Keywords: other

first: Cassio

last: Baptista

first: Bianca

last: Zingales


title: Ethanol treated vs paired control

city: Phildelphia

first: Rishi

last: Khan

state: PA

address: 1020 Locust Street Room 381

department: Pathology

institute: Thomas Jefferson University

summary:
6 ethanol treated animals with their paired controls
Keywords: repeat sample

sample_organism:
Rattus norvegicus
unidentified

overall_design: Reference Design with 6 biological repeats (6 treated, 6 control, 12 reference)

first: Maria

last: Covarrubias

first: James

last: Schwaber


title: Influence of exhaustive endurance exercise on gene expression in peripheral blood

city: Tuebingen

first: Janko

last: Dietzsch

address: Sand 14

department: ZBIT (Center for Bioinformatics Tuebingen)

institute: University Tuebingen

summary:
cDNA microarray screening for gene expression changes in peripheral blood of eight half-marathon runners before (time point 0), immediately (time point 1) after and 24 h (time point 2) after exercise
for details see publication: ...
Keywords: repeat sample

first: Derek

last: Zieker

first: Judith

last: Fliegner

first: Elvira

last: Fehrenbach

first: Hinnak

last: Northoff


status: Public on Oct 03 2005

city: Rockville

first: Li

last: Zheng

address: 9712 Medical Center Dr.

institute: The Institute for Genomic Research

summary:
Six different Solanaceae species, Potato (Solanum tubersosum), Tomato (Lycopersicum esculentum), Pepper (Capsicum annuum), Tobacco (Nicotiana tabaccum), Petunia and Nicotiana benthiamana were grown at 25C, 16h light and 8h darkness. Mature leaves were harvested after 4-6 weeks. RNA was isolated using Qiagen RNeasy. Tomato, pepper, petunia, tobacco and N. benthamiana samples were hybridized against potato samples.
Keywords: Solanaceae comparative gene expression profiling

sample_organism:
Capsicum annuum
Solanum lycopersicum
Nicotiana tabacum
Nicotiana benthamiana
Petunia x hybrida
Solanum tuberosum

first: Willem

last: Rensink


title: Variation in gene expression and aberrantly regulated chromosomal regions in cloned mice

city: Tokyo

first: Takashi

last: Kohda

address: 1-5-45 Yushima, Bunko-ku

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

summary:
DNA microarray analysis has been carried out to know the precise genome-wide gene expression profiles of somatic cloned mice derived from Sertoli or cumulus cells.   It demonstrated unexpectedly large epigenetic diversity in neonatal cloned mice, despite their normal appearance and genetic identity.  In three neonatal tissues of the cloned mice, a total of 9–40% of the examined genes exhibited more than two times higher or lower levels in donor cell-dependent or -independent manner compared to those in normal controls.  Relatively few (0.4–4%) of the genes exhibited up- or down-regulation in the same manner in both types of clones.  Cluster analysis of the variations in gene expression led to identification of several chromosomal regions in which gene expression was aberrantly controlled in the somatic clones.  These results provide a more complete understanding of how somatic clones differ from each other and from normal individuals produced by sexual reproduction and indicate the significant difficulties that exist for the application of somatic cloning in regenerative medicine.
Keywords: clone mouse

overall_design: Neonatal tissues of four Sertoli cell-derived clones, four cumulus cell-derived clones, and four normal controls (two males and two females) were analysed by DNA microarray.  Cloning by nuclear transfer was performed according to the method developed by Wakayama et al., with slight modifications.  Immature Sertoli and cumulus cells were collected from newborn male (0-8 days after birth) and mature female (2-3 months old) C57BL/6 x DBA/2 F1(BDF1) mice, respectively, and used as nuclear donor cells.  Cloned pups were obtained from the recipients at term (day 19.5) by caesarean section.  All control mice were genetically identical to the somatic cell clones, e.g., BDF1. The control neonates were produced by in vitro fertilization.

first: Kimiko

last: Inoue

first: Narumi

last: Ogonuki

first: Hiromi

last: Miki

first: Mie

last: Naruse

first: Tomoko

last: Kaneko-Ishino

first: Atsuo

last: Ogura

first: Fumitoshi

last: Ishino


city: Ann Arbor

first: Xiaoju

last: Wang

state: MI

address: 1500 E. Medical Center Drive

institute: University of Michigan

summary:
High-density phage epitope microarray from 31 samples were used for unsupervised analysis (GSM36153...GSM36183).

129 samples from prostate cancer patients and controls were screened on small focused epitope chips, which contained 180 phage elements. These data were used to train GA/KNN program (GSM36184...GSM36312).

128 samples from localized prostate cancer patients and controls were screened on small focused epitope chips. These independent data were used to validate the epitomic profile (GSM36313...GSM36375, GSM40203...GSM40213, GSM40216, GSM40218, GSM40219, GSM40222, GSM40225, GSM40227, GSM40229, GSM40233, GSM40237, GSM40246...GSM40294).

Three subgroups of samples were used as test sets to validate the specificity of epitomic profile (GSM36376...GSM36410, GSM40214, GSM40215, GSM40217, GSM40220, GSM40221, GSM40224, GSM40226, GSM40228, GSM40231, GSM40234...GSM40236, GSM40238...GSM40244).

Project----Identification of humoral signature for prostate cancer
diagnosis

We constructed a prostate cancer cDNA phage display library.
cDNAs were reverse-synthesized from mDNA pool isolated from prostate cancer tissues. Enzyme-digested cDNA fragments were then inserted into phage vector to make a whole prostate cancer phage expressed cDNA library. In order to select cancer specific phage epitope from this library, we performed several cycles of affinity enrichment. We used the bounded IgG pool
isolated from prostate cancer patient sera to select the tumor specific phage epitope clones. Once we had the enriched phage epitope library, we cultured the phage library on LB-agar dish for individual phage
colonies. About 2300 phage colonies from agar dish were picked up using
toothstick and cultured in 96-well microtiter plates. Each clone
was labeled as microtiter plate #, column #, row#, i.e. clone ID. These 2300 clones were then spotted on slides in single spot (no any duplicate), i.e. each spot (labeled by clone ID) represents a single phage clone.

The phage epitope microarrays were then screened using cancer or
control sera. We employed two color system. Cy5-anti human IgG was to detect human IgG. For green color, we used Cy3-labeled anti-phage capsid protein as internal reference to normalize the ammount difference of phage particles spotted on each spot. Thus the ratio of Cy5/Cy3 would count for the immune response in cancer or control sera.

Once we identified humoral signature in prostate cancer patients, we
could sequence the phage clone to characterize the nature of the genes
or proteins.
Keywords: autoantibody signatures


title: Cerebral cortical contusion in rat, 1 and 4 dpi

status: Public on Oct 01 2005

city: Stockholm

first: A G Christina

last: von Gertten

address: Nkklab R2:02, Karolinska hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary:
Traumatic brain injury (TBI) initiates a complex sequence of destructive and neuroprotective cellular responses. The initial mechanical injury is followed by an extended time period of secondary brain damage. Due to the complicated pathological picture a better understanding of the molecular events occurring during this secondary phase of injury is needed. This study was aimed at analysing gene expression patterns following cerebral cortical contusion in rat using high throughput microarray technology with the goal of identifying genes involved in an early and in a more delayed phase of trauma, as genomic responses behind secondary mechanisms likely are time-dependent.
Keywords: Traumatic brain injury, genomic response

overall_design: Cerebral cortical contusions by weight drop were made on male rats. Cortex from individual animals were analysed in comparative hybridisation with the corresponding uninjured side. Two time points were compared 1 dpi (n=3, ie 3 replicates) and 4 dpi (n=4, i.e 4 replicates).  Individual animals were analysed and total RNA from injured ipsilateral cortex and uninjured contralateral cortex were labelled with Cy5 and Cy3 dyes, then hybridised onto a 6240 cDNA probe microarray. Expression ratios were calculated using injured/ un-injured cortex. Dye swaps were used.

first: Christina

first: Amilcar

last: Flores Morales

first: Staffan

last: Holmin

first: Tiit

last: Mathiesen

first: Ann-Christin

last: Sandberg Nordqvist


title: H3K36me2 ChIP-chip

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: 203 Fordham Hall CB# 3280

institute: UNC-Chapel Hill

summary:
Set2p, which mediates histone H3 Lysine 36 dimethylation (H3K36me2) in Saccharomyces cerevisiae, has been shown to associate with RNA polymerase II (RNAP II) at individual loci.  Here, ChIP-chip experiments normalized to general nucleosome occupancy reveal that nucleosomes within open reading frames (ORFs) and downstream non-coding chromatin were highly dimethylated at H3K36, and that Set2p activity begins at a stereotypic distance from the initiation of transcription genome-wide. H3K36me2 is scarce in regions upstream of divergently transcribed genes, telomeres, silenced mating loci, and regions transcribed by RNA polymerase III, providing evidence that the enzymatic activity of Set2p is restricted to its association with RNAP II. The presence of H3K36me2 within ORFs correlated with the "on" or "off" state of transcription, but the degree of H3K36 dimethylation within ORFs did not correlate with transcription frequency. This provides evidence that H3K36me2 is established during the initial instances of gene transcription, with subsequent transcription having at most a maintenance role. Accordingly, newly activated genes acquire H3K36me2 in a manner that does not correlate with gene transcript levels. Finally, nucleosomes dimethylated at H3K36 appear to be refractory to loss from highly transcribed chromatin. Thus H3K36me2, which is highly conserved throughout eukaryotic evolution, provides a stable molecular mechanism for establishing chromatin context throughout the genome by distinguishing potential regulatory regions from transcribed chromatin.
Keywords: ChIP-chip

overall_design: Tweleve independent ChIP-chip experiments were  performed using H3K36me2 specific antibody. The data was normalized using eight independent H4-myc ChIP-chip experiments. A control experiment was done in a strain in which SET2 had been deleted. The input DNA was used as a reference in all experiments. Direct comparison of the normalize data was done by performing ChIP-chips where the H4-myc ChIP DNA was used as the reference.


title: Genomic Analysis of anti-HBV Activity by siRNA and Lamivudine in Stable HBV-producing Cell

city: Beijing

first: yong

last: guo

state: Beijing

address: Qinghuayuan

department: Medical Systems Biology Research Center

country: China

institute: Tsinghua University

summary:
We designed seven siRNAs based on the conserved HBV sequences and tested their effects on the expression of HBV genes following sorting of siRNA positive cells. Among these seven siRNAs, siRNA-1 and siRNA-7 were found to effectively suppress HBV gene expressions. We further addressed the global gene expression changes in stable HBV-producing cells induced by siRNA-1 and siRNA-7 using human genome-wide oligo microarrays. Data from the gene expression profilings indicated that siRNA-1 and siRNA-7 altered the expression of 54 and 499 genes, respectively, in HepG2.2.15 cells, which revealed the different siRNA had a varied pattern of gene expression profile and suggested complicated influence of siRNA on host cell. We further observed that eighteen of these genes were suppressed by both siRNA-1 and siRNA-7. Interestingly, seven of these genes were originally activated by HBV, which suggested these seven genes might be involved in the HBV-host cell interaction. Finally, we have compared the effects of siRNA and lamivudine on HBV and host cell, which revealed that siRNA is more effective in inhibiting the HBV expression at mRNA and protein level in vitro, and the gene expression profiling of HepG2.2.15 treated by lamivudine is totally different from siRNA¡¯s.
Keywords: other

overall_design:
siRNA vs. control
lamivudine vs. mock

first: Yong

last: Guo


title: Diversity of gene expression in adenocarcinoma of the lung.

status: Public on Sep 30 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
The global gene expression profiles for 67 human lung tumors representing 56 patients were examined by using 24,000-element cDNA microarrays. Subdivision of the tumors based on gene expression patterns faithfully recapitulated morphological classification of the tumors into squamous, large cell, small cell, and adenocarcinoma. The gene expression patterns made possible the subclassification of adenocarcinoma into subgroups that correlated with the degree of tumor differentiation as well as patient survival. Gene expression analysis thus promises to extend and refine standard pathologic analysis.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Mitchell

last: Garber


title: Populus homeobox gene ARK2 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 ARBORKNOX2 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.


title: Ras/cAMP signal transduction, perturbations

city: Bar Harbor

first: Gregory

last: Carter

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
Disruption of Ras/cAMP signaling by perturbation of pathway elements and controlled cAMP concentration. All cultures grown in SC medium.
Keywords: other

overall_design: to be completed by submitter

first: G

middle: W

first: S

last: Rupp

last: Fink

first: T

last: Galitski


title: Changes in Gene expression during the development and progression of mammary tumors in MMTV-Wnt-1 and MMTV-Neu TG mice

city: New York

first: Shixia

last: Huang

department: Cell Biology

institute: Memorial Sloan-Kettering Cancer Center

summary:
Gene expression profiling of samples from normal virgin mammary glands, hyperplastic mammary glands, mamary tumors, and lung metastases from MMTV-Wnt-1 transgenic (TG) mice, and mammary tumors and lung metastases from MMTV-Neu trangenic (TG) mice
Keywords: Array analysis, multi-step tumorigenesis, metastasis, MMTV-Wnt-1 trangenic mice, MMTV-Neu transgenic mice

overall_design:
1.  We compared expression prifiles among 5 normal virgin mammary glands, 7 hyperplastic mammary glands and 23 mammary tumors from MMTV-Wnt-1 transgenic  mice, and 12 mammary tumors from MMTV-Neu transgenic mice.

2.  We compared expression profiles between 23 mammary tumors and 10 lung metastases from MMTV-Wnt-1 transgenic mice and 12 mammary tumors and 5 lung metastases from MMTV-Neu transgenic mice.

The experiments for the above comparisons were performed in the same time frame using a single array print and the same batch of reference RNA.

first: Yi

last: Li

first: Yidong

last: Chen

first: Katrina

last: Podsypanina

first: Mario

last: Chamorro

first: Adam

last: Olshen

first: Kartiki

last: Desai

first: Anne

last: Tann

first: David

last: Petersen

first: Jeffrey

last: Green

first: Harold

last: Varmus


title: Toxicogenomic profiling of trout tumor promoters

status: Public on Sep 28 2005

city: Corvallis

first: Susan

middle: C.

last: Tilton

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary:
Indole-3-carbinol (I3C), from cruciferous vegetables, has been found to suppress or enhance tumors in several animal models.  We previously reported that dietary I3C promotes hepatocarcinogenesis in rainbow trout (Oncorhynchus mykiss) at concentrations that differentially activated estrogen receptor (ER) or aryl hydrocarbon receptor (AhR)-mediated responses based on individual protein biomarkers.  In this study, we evaluated the relative importance of these pathways as potential mechanisms for I3C on a global scale.  Hepatic gene expression profiles were examined in trout after dietary exposure to 500 and 1500 ppm I3C and 3,3,-diindolylmethane (DIM), a major in vivo component of I3C, and were compared to the transcriptional signatures of two model hepatic tumor promoters; 17beta-estradiol (E2), an ER agonist, and beta-naphthoflavone, an AhR agonist.  We demonstrate that I3C and DIM acted similar to E2 at the transcriptional level based on correlation analysis of expression profiles and clustering of gene responses.  Of the genes regulated by E2 (fold change >2.0 or <0.50), most genes were regulated similarly by DIM (87-92%) and I3C (71%) suggesting a common mechanism of action.  Of interest were upregulated genes associated with signaling pathways for cell growth and proliferation, vitellogenesis, and protein folding, stability and transport. Other genes down-regulated by E2, including those involved in acute-phase immune response, were also down-regulated by DIM and I3C.  Gene regulation was confirmed by qRT-PCR and western blot.  These data indicate I3C promotes hepatocarcinogenesis through estrogenic mechanisms in trout liver and suggest DIM may be an even more potent hepatic tumor promoter in this model.
Keywords: dose response

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Reference design with dye-swapping

middle: C

first: Scott

middle: A

last: Givan

first: Cliff

last: Pereira

first: George

last: Bailey

last: Williams


title: Microarray analysis reveals previously unknown changes in Toxoplasma gondii infected human cells

status: Public on Sep 23 2005

last: Stanford Microarray Database

summary:
Cells infected with the intracellular protozoan parasite Toxoplasma gondii undergo upregulation of pro-inflammatory cytokines, organelle redistribution, and protection from apoptosis. To examine the molecular basis of these and other changes, gene expression profiles of human foreskin fibroblasts infected with Toxoplasma were studied using human cDNA microarrays consisting of ~22,000 known genes and uncharacterized ESTs. Early during infection (1-2 h), <1% of all genes show a significant change in the abundance of their transcripts. Of the 63 known genes in this group, 27 encode proteins associated with the immune response. These genes are also upregulated by secreted, soluble factors from extracellular parasites indicating that the early response does not require parasite invasion. Later during infection, genes involved in numerous host cell processes, including glucose and mevalonate metabolism, are modulated. Many of these late genes are dependent on the direct presence of the parasite; i.e. secreted products from either the parasite or infected cells are insufficient to induce these changes. These results reveal several previously unknown effects on the host cell and lay the foundation for detailed analysis of their role in the host-pathogen interaction.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Ira

last: Blader


title: Genomic alterations in primary hyperaldosteronism

status: Public on Oct 11 2005

city: Paris

first: Guillaume

last: Assié

country: France

institute: Inserm Institut Cochin

summary:
Transcriptome comparison of an aldosterone producing adenoma transcriptome and its adjacent zona glomerulosa.
Both tissues are from the same individual, are differentiated for aldosterone production, but the adjacent zona glomerulosa produces no aldosterone by negative feedback.
Keywords = aldosterone producing adenoma transcriptome
Keywords: parallel sample

first: Colette

last: Auzan

first: Jean Marie

last: Gasc

first: Erno

last: Baviera

first: André

last: Balaton

first: Xavier

last: Jeunemaitre

first: Jean Marc

last: Elalouf

first: Pierre Francois

last: Plouin

first: Pierre

last: Corvol

first: Eric

last: Clauser


title: Transcriptional profiling of HHV-6 infeceted T cells

status: Public on Sep 22 2005

first: Tomoiku

last: Takaku

address: 6-7-1, Nishishinjuku, Shinjuku

department: First Department of internal Medicine

institute: Tokyo Medical University

summary:
The immune response to viral infection represents complex network of dynamic gene and protein interactions. We present here the dynamic gene network of host immune response during human herpesvirus type 6 (HHV-6) infection in a adult T cell leukemia (ATL) cell line. Using a pathway-focused oligonucleotide DNA microarray, we found a possible association between chemokines genes regulating Th1/Th2 balance and genes regulating T-cell proliferation during HHV-6B infection.
Keywords: Time course experiment

overall_design: This study aimed to determine genes regulating immune response during viral infection using an in vitro model system. We utilized a CD4+ T cell line which shows an efficient propagation of HHV-6B, as a model of acute infection of HHV-6B as well as that of persistent infection We explored a pathway-focused oligonucleotide DNA microarray that contains genes closely related with inflammatory responses.

first: Junko

last: Ohyashiki

first: Kazuma


title: Genomic Profiling of Mixer and Sox17beta Targets During Xenopus Endoderm Development

first: Julie

last: Baker

department: Genetics

institute: Stanford University

summary:
The transcription factors Mixer and Sox17beta have well characterized roles in endoderm specification during Xenopus embryogenesis.  In order to more thoroughly understand the mechanisms by which these endodermal regulators act, we expressed Mixer and Sox17beta in naïve ectodermal tissue and, using oligonucleotide-based microarrays, compared their genomic transcriptional profile to that of unaffected tissue.  Using this novel approach, we identified 71 transcripts that are upregulated by Mixer or Sox17beta, 63 of which have previously uncharacterized roles in endoderm development.   Furthermore, an in situ hybridization screen using antisense probes for several of these clones identified six targets of Mixer and/or Sox17beta that are expressed in the endoderm during gastrula stages, providing new and regional markers of the endoderm.  Our results contribute further insight into the functions of Mixer and Sox17beta and bring us closer to understanding at the molecular level the pathways that regulate endoderm development.
Keywords: comparative genomic response to cell type specification

overall_design: Three samples (uninjected control, Mixer injected, Sox17beta injected), two replicates each.

first: Kari

last: Dickinson

first: Jeff

last: Leonard


title: 2,4-dibencilaminoquinazoline induced apoptosis in three human cancer cell lines

status: Public on Sep 21 2005

city: Pamplona

first: Raquel

last: Malumbres

state: Navarra

address: Avenida Pio XII 55

department: Hemato-Oncology

country: Spain

institute: University of Navarra/ Clínica Universidad de Navarra

summary:
In the search of new symmetrical derivatives with anticancer activity, we have looked for novel compounds able to induce a selective proapoptotic mechanism in cancer cells.
The potential antitumoral activity of several quinazoline derivatives was evaluated in vitro examining their cytotoxic effects against human breast (HTB26), colon (HT29) and bladder (T24) cancer cell lines. Non-tumoral human cell lines were used to test the selectivity of the cytotoxic compounds against cancer cells. Several compounds showed selectivity for cancer cell lines; among them, 2,4-dibencilaminoquinazoline was chosen as the best candidate and its mechanism of action was studied in more detail. This compound was tested for its ability to induce caspase-3 activation and nuclear chromatin degradation in the three cancer cell lines. A time dependent evaluation of apoptosis was performed in the three cancer cell lines, including an expression microarray study at the points of caspase activation and chromatin degradation. 2,4-dibencilaminoquinazoline treatment produces few changes in the expression of genes as evaluated by using microarrays and RT-PCR assays.
In conclusion, 2,4-di-p-bromofenilaminoquinazoline is a promising anticancer drug showing cytostatic and apoptotic effects mainly in a transcription independent manner.
Keywords: Apoptosis induction, time course

overall_design:
12 slides were hybridized, 6 of them being dye-swap replicates of the other 6. In each slide, a treated sample and an untreated sample (negative control) were hybridized.
In summary, 2 slides were used for each time point and each cell line, one of them being a dye-swap of the other.

first: Elena

last: Cubedo

first: Lucía

last: Cordeu

first: Eva

last: Bandrés

first: Amaia

last: Rebollo

first: Jesús

last: García-Foncillas


title: K14Cre; Brca2F/F; p53F/F tumor analysis

city: Amsterdam

first: Daoud

last: Sie

address: Plesmanlaan 161

country: Netherlands

institute: Dutch Cancer Institute

type: Genome variation profiling by genome tiling array

summary:
K14Cre; Brca2F/F; p53F/F tumor analysis
Keywords: Comparative Genomic Hybridization, aCGH

overall_design: Four arrays in a double dye-swap setup of spleen vs tumor tissue.

first: Henne

last: Holstege


title: Nla18/DK1622

status: Public on Sep 20 2005

first: Mitchell

last: Singer

address: 1 Shields Ave

department: Microbiology

institute: The University of California, Davis

summary:
NtrC-like activators regulate transcription of a wide variety of adaptive genes in bacteria.  Previously we demonstrated that a mutation in the NtrC-like activator gene nla18 severely inhibits M. xanthus fruiting body development and vegetative growth.  In this study, we found that inactivation of nla18 has dramatic effects on gene expression patterns during development and vegetative growth.  Gene expression in nla18 cells is altered in the early stages of fruiting body development. In addition, nla18 cells are defective for two of the earliest events in development, production of the intracellular starvation signal ppGpp and production of A-signal.  Taken together, these results indicate that the developmental program in nla18 cells goes awry very early.  Inactivation nla18 also causes a dramatic decrease in the vegetative growth rate of M. xanthus cells.  When the vegetative gene expression profiles of nla18 cells were compared to their wild type counterparts using DNA microarrays, we found that more than 700 genes have altered expression patterns.  Furthermore, inactivation of nla18 seems to have a profound effect on expression of genes that code for putative membrane and membrane-associated proteins.  This idea is supported by our finding that the profiles of membrane proteins isolated from nla18 cells during vegetative growth are noticeably different from the profiles of wild type M. xanthus cells.  These results demonstrate that Nla18 is an important regulator of gene expression during both vegetative growth and fruiting body development.
Keywords: vegetative analysis

overall_design: 5 biological replicates, normalized ratios to Cy3


title: Differential protein expression by Porphyromonas gingivalis in response to secreted epithelial cell components

status: Public on Sep 17 2005

city: Seattle

first: Murray

last: Hackett

state: WA

address: HSB H330 1959 NE Pacific Street

department: Chemical Engineering

institute: University of Washington

summary:
The human oral pathogen Porphyromonas gingivalis colonizes the gingival crevice and invades gingival epithelial cells. Multidimensional capillary high-performance liquid chromatography coupled with tandem mass spectrometry and two-dimensional gel electrophoresis were used to analyze the proteome of P. gingivalis as it adapts to a set of experimental conditions designed to reflect important features of an epithelial cell environment. 1014 proteins (46% of the total theoretical proteome) were identified in four independent analyses; 479 of these proteins showed evidence of differential expression after exposure of P. gingivalis to either conditioned epithelial cell growth medium or control conditions: i.e., they were only detected under one set of conditions. Moreover, 276 genes annotated as hypothetical were found to encode expressed proteins. Among the proteins up-regulated in the presence of epithelial cell components were a homolog of the internalin proteins of Listeria monocytogenes and subunits of the ATP-dependent Clp protease complex. Insertional inactivation of clpP, encoding the Clp proteolytic subunit, resulted in approximately a 50% reduction in invasion of P. gingivalis. These results suggest that adaptation to an epithelial cell environment induces a major shift in the expressed proteome of the organism. Furthermore, ClpP, that is up-regulated in this environment, is required for optimal invasive activity of P. gingivalis.
Keywords: proteome analysis of P. gingivalis

overall_design: P. gingivalis exposed to control keratinocyte growth medium or conditioned keratinocyte growth medium

first: Yi

last: Zhang

first: T

last: Wang

first: W

last: Chen

first: O

last: Yilmaz

first: Y

last: Park

first: Il-Young

last: Jung

first: M

first: R

last: Lamont


title: CFTR dependent response

city: Boston

first: Nina

last: Reiniger

address: 181 Longwood Ave

department: Medicine

institute: Brigham & Women's Hospital, Channing Laboratory

summary:
Wild-type and dF508 CFTR mutant human bronchial epithelial cells were uninfected or infected for 3 hours at an MOI of 30-50 with P.aeruginosa strain PAO1. Each cell line was tested in 4 replicates.  Each replicate consists of 4 data sets: 2 sets of duplicate spots on 2 arrays. The two arrays in each replicate were dye-swapped  pairs where the opposite dye was used for each sample in the second array. I have called replicates "Rep1, Rep2..." etc. I have indicated duplicates from the same slide as eg."Slide1A and Slide1B" I have refered to the two arrays used in each replicate as "Slide1" and "Slide 2".
Keywords: other

first: Jeffrey

middle: K

last: Ichikawa

first: Gerald

last: Pier


title: Differential Expression of Novel Potential Regulators in Hematopoietic Stem Cells.

last: Stanford Microarray Database

summary:
Pairwise comparisons of purified mouse LT-HSC, ST-HSC and MPP.
The hematopoietic system is an invaluable model both for understanding basic developmental biology and for developing clinically relevant cell therapies. Using highly purified cells and rigorous microarray analysis we have compared the expression pattern of three of the most primitive hematopoietic subpopulations in adult mouse bone marrow: long-term hematopoietic stem cells (HSC), short-term HSC, and multipotent progenitors. All three populations are capable of differentiating into a spectrum of mature blood cells, but differ in their self-renewal and proliferative capacity. We identified numerous novel potential regulators of HSC self-renewal and proliferation that were differentially expressed between these closely related cell populations. Many of the differentially expressed transcripts fit into pathways and protein complexes not previously identified in HSC, providing evidence for new HSC regulatory units. Extending these observations to the protein level, we demonstrate expression of several of the corresponding proteins, which provide novel surface markers for HSC. We discuss the implications of our findings for HSC biology. In particular, our data suggest that cell-cell and cell-matrix interactions are major regulators of long-term HSC, and that HSC themselves play important roles in regulating their immediate microenvironment.
An experiment design type where the label orientations are reversed. exact synonym:flip dye, dye flip
Keywords: dye_swap_design

first: Susan

last: Prohaska


title: Transcriptional profiling of EBV gene in nasal NK/T lymphoma and chronic active EBV infection

first: Junko

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

summary:
Nasal T/NK lymphoma is a unique subtype of non-Hodgkin lymphoma (NHL) that is aggressive and incurable closely associated with Epstein-Barr virus (EBV)3. The clonal expansion of EB infected T- or NK cell is also seen in patients with chronic active EBV (CAEBV) infection, suggesting that two diseases might partly share a similar mechanism by which EBV affect host cellular genes. In order to understand the pathogenesis of EBV-associated T/NK lymphoproliferative disorders (LPD) and design new therapies, we employed a novel EBV DNA microarray to compare patterns of EBV expression in SNK/T cells established from EBV-associated T/NK LPD.
Keywords: parallel sample

overall_design: Comparison of EBV lgene expression among EBV infectyed cells.For a dual color analysis of EBV gene expression, the cDNA obtained from EBV-negative cells was labeled with Cy3 as a reference, and cDNA obtained from EBV-positive cells was labeled with Cy5.  The EBV gene expression was then compared among various types of EBV infected cells.

first: Yu


title: Anti-IFN antibody 16 array set

summary:
Timecourse experiment (0hr, 2hr,6hr and 21hr) where RNA was extracted from non-rested PBMCs which were exposed to 4 different conditions- nothing (mock), interferon (IFN)gamma, IFN gamma and a non-specific antibody and IFN gamma with purified patient antibody. The purified patient antibody is demonstrated to have a specific anti-interferon gamma effect over time, with the expression profile in the arrays with IFN gamma plus patient antibody most closely resembling the mock arrays.
A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied.
Keywords: disease_state_design

overall_design: Using regression correlation

first: Cheryl

last: Hemingway


title: Use of array CGH in the diagnosis of patients with mental retardation

status: Public on Sep 16 2005

city: Nijmegen

first: Joris

middle: Andre

last: Veltman

address: Geert Grooteplein 10

department: Human Genetics

institute: Radboud University Nijmegen Medical Centre

summary:
This series represent the data set belonging to the publication by de Vries et al. Diagnostic genome profiling in mental retardation. American Journal of Human Genetics, vol 77: 606-616 (2005). In this study 100 patients with unexplained mental retardation were analyzed for DNA copy-number changes using a tiling-resolution genomewide microarray containing 32,447 BACs.
Keywords: CGH

overall_design: See de Vries et al. Diagnostic genome profiling in mental retardation. American Journal of Human Genetics, vol 77: 606-616 (2005). In brief, each patient was hybridized in duplicate with label swap onto the tiling resolution BAC arrays. DNA from 72 parents was hybridized once to the same array in order to distinguish between disease-causing alterations and normal copy number variations. De novo alterations were validated by FISH and MLPA.

first: Bert

last: de Vries

first: Rolph

last: Pfundt

first: Leisink

last: Martijn

first: David

last: Koolen

first: Lisenka

middle: E

last: Vissers

first: Irene

last: Janssen

first: Simon

last: van Reijmersdal

first: Willy

last: Nillesen

first: Erik

last: Huys

first: Nicole

last: de Leeuw

first: Dominique

last: Smeets

last: Sistermans

first: Ton

last: Feuth

first: Conny

last: van Ravenswaaij-Arts

first: Ad

last: Geurts van Kessel

first: Eric

middle: F

last: Schoenmakers

first: Han

middle: G

last: Brunner


title: c-Myc responsive genes

city: Rockville

first: Alexandra

middle: Geraldine

last: Dace

address: 9600 Gudelsky Drive

department: University of Maryland Biotechnology Institute

institute: University of Maryland

summary:
Samples are from clones of Erythroleukemia cells C19 (parental) and c-Myc overexpressing cells Cl56 induced for 5days with Hexamethyl-bis acetamide(differentiation triggering agent) were pooled and reverse-transcribed and hybridized. Comparison of both transcriptomes give access to c-Myc responsive genes involved in differentiation.
Keywords: other

first: Shoshana

last: Segal

first: Cathryn

last: Stevens

first: Nilton

middle: D

last: Medina

first: James

middle: B

last: Ames

last: York


title: Genes modulated by DNA demethylation in UM1 cells

first: Takanori

last: Tsuji

address: 77 AVenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary:
Ornithine decarboxylase antizyme 1 mediates DNA demethylation. Using a human oral cancer cell line, UM1, genes induiced by DNA demethylation were screened. To verify the methylation status of those induced genes, the gene expression profile was compared with that of 5-Aza-2’-deoxycytidine treated sample.
Keywords: DNA demthylation, ornithine decarboxylase antizyme 1, 5-Aza-2’-deoxycytidine

overall_design: Preparation of samples, hybridization process and data analysis were performed according to the manufacture's protocol (BD Biosciences). To verify the genes induced by ornithine decarboxylase antizyme via DNA demethylation, 5-Aza-2’-deoxycytidine treatment was carried out as a parallel experiment.

first: Guo-fu

last: Hu


title: BW25113 glucose to acetate transition

status: Public on Sep 14 2005

city: Los Angeles

first: Katy

last: Kao

address: 420 Westwood Plaza/5805 Boelter Hall

institute: University of California, Los Angeles

summary:
In bacterial adaptation to the dynamic environment, metabolic genes are typically thought to be the executors, whereas global transcription regulators are regarded as the decision makers. Although the feedback from metabolic consequence is believed to be important, much less is understood. This work demonstrates that the gluconeogenic genes in Escherichia coli, ppsA, sfcA, and maeB, provide a feedback loop to the global regulator, CRP, in carbon source transition. Disruption of one of the gluconeogenic pathways has no phenotype in balanced growth, but causes a significant delay in the diauxic transition from glucose to acetate. To investigate the underlying mechanism, we measured the transcriptome profiles during the transition using DNA microarray, and Network Component Analysis was employed to obtain the transcription factor activities.  Results showed that one of the global regulators, CRP, was insufficiently activated during the transition in the ppsA deletion mutant. Indeed, addition of cAMP partially rescued the delay in transition.  These results suggest that the gluconeogenic flux to phosphoenolpyruvate is important for full activation of adenylate cyclase through phosphorylated enzyme IIAglu of the phosphotransferase system. Reduction of this flux causes insufficient activation of CRP and a global metabolic deficiency, which exemplifies a significant feedback interaction from metabolism to the global regulatory system.
Keywords: Time course

overall_design: Cells were grown up in M9 glucose media until mid log phase, then harvested and transitioned into M9 acetate media.  Samples were taken immediately prior to transition to acetate (reference sample) and at 5, 15, 30, 60, 120, 180, 240, 300, and 360 minutes after transition.


title: Copy number aberrations in mouse breast tumors reveal loci and genes important in tumorigenic RTK signaling

status: Public on Sep 13 2005

city: San Francisco

first: Graeme

last: Hodgson

department: Neurological Surgery

institute: UCSF

summary:
Receptor tyrosine kinase (RTK) signaling plays a key role in the development of breast cancer. Defining the genes and pathways in the RTK signaling network that are important regulators of tumorigenesis in vivo will unveil potential candidates for targeted therapeutics. To this end, we utilized microarray comparative genomic hybridization (array CGH) to identify and compare copy number aberrations in 5 mouse models of breast cancer induced by wild-type and mutated forms of oncogenic ErbB2 or the polyomavirus middle T antigen (PyMT). We observed distinct genomic alterations amongst the various models including recurrent chromosome 11 amplifications and chromosome 4 deletions, respectively syntenic with human 17q21-25 and 1p35-36. Expression of oncogenic Erbb2 (NeuNT) under control of the endogenous ErbB2 promoter results in frequent (85%) amplification at the Erbb2 locus with striking structural similarity to the human amplicon, resulting in overexpression of at least 2 of the genes, ErbB2 and Grb7. Chromosome 11 amplicons distal to Erbb2 arise in a model (DB) over expressing a mutant variant of PyMT (Y315/322F) unable to activate PI3K. These amplicons are not observed in DB hyperplasias or in tumors over expressing wild type PyMT, and result in over expression of Grb2 and Itgb4. Distal chromosome 4 deletions occur in a significantly higher proportion of Erbb2 than PyMT tumors and encompass 14-3-3 sigma (Sfn), which is expressed at low or undetectable levels in the majority of TM tumors. Our studies highlight loci and genes important in the regulation of tumorigenic RTK signaling in mammary epithelial cells in vivo.
Keywords: Comparative Genomic Hybridization

overall_design: 110 mouse breast tumor genomic DNA samples were labeled with cy3 and co-hybridized with normal, strain matched mouse spleen genomic DNA labeled with cy5 to DNA microarrays in the presence of excess mouse cot-1 DNA. Results presented are those of a single hybridization.

first: John

first: Tiffany

last: Malek

first: Sophia

last: Bornstein

first: Sujatmi

last: Hariono

first: David

last: Ginzinger

first: William

middle: J

last: Muller

first: Joe

last: Gray


title: A comparison of gene expression signatures from breast tumors and breast tissue derived cell lines

last: Stanford Microarray Database

institute: Stanford Microarray Database (SMD)

summary:
Cell lines derived from human tumors have historically served as the primary experimental model system for exploration of tumor cell biology and pharmacology. Cell line studies, however, must be interpreted in the context of artifacts introduced by selection and establishment of cell lines in vitro. This complication has led to difficulty in the extrapolation of biology observed in cell lines to tumor biology in vivo. Modern genomic analysis tool like DNA microarrays and gene expression profiling now provide a platform for the systematic characterization and classification of both cell lines and tumor samples. Studies using clinical samples have begun to identify classes of tumors that appear both biologically and clinically unique as inferred from their distinctive patterns of expressed genes. In this review, we explore the relationships between patterns of gene expression in breast tumor derived cell lines to those from clinical tumor specimens. This analysis demonstrates that cell lines and tumor samples have distinctive gene expression patterns in common and underscores the need for careful assessment of the appropriateness of any given cell line as a model for a given tumor subtype.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Computed

first: Charles

last: Perou