title: Proinflammatory response of human epithelial cell to TNF, flagellin, wild type Salmonella

status: Public on Jul 31 2005

city: Atlanta

first: Hui

last: Zeng

state: GA

address: 1600 Clifton Rd. MS:G16

department: Influenza Branch

institute: Centers for disease control

summary:
T84 cells were stimulated with TNF, or flagellin, or wildtype Salmonella.  RNA were extracted from treated cells at 1, 2, 3, 4, 5, and 6 hour time points, labelled, and hybridized the arrays.
Keywords: Human

overall_design:
The objective of this study is to investigate the different proinflammatory response of human intestinal epithelial cells to three different treatments.
There are triplicates for each treatment. Data were analyzed according to publication guidline.

first: Andrew

last: Neish

first: Andam

last: Carlson

first: Yanwen

last: Guo


title: 2h dose response_AFB treatment

city: Palo Alto

first: Yingying

state: CA

country: USA

institute: Roche Palo Alto

summary:
RNA isolated from the 0, 10, 25, 50 and 100 micromolar AFB1 cultures at 120 min treatment was used for cDNA microarray experiments.  For each array hybridization experiment, RNAs from the treated sample and its corresponding time-matched control were co-hybridized to arrays and respectively quantified in different channels.  A dye swap strategy was used to eliminate the dye bias.
Keywords: dose response


status: Public on Jul 28 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Embryoid Bodies from Mouse R1 ES - 9 day
Keywords: other

overall_design: this experiment include 1 samples and 1 replicates


title: Neurogenic potential of human mesenchymal stem cells revisited

status: Public on Aug 10 2005

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

summary:
The possibility of generating neural cells from human bone marrow-derived mesenchymal stem cells by simple in vitro treatments is alluring both conceptually and practically. However, whether phenotypic modulations observed after chemical manipulation of such stem cells truly represent a genuine trans-lineage differentiation remains to be established. We have re-evaluated the effects of a frequently reported biochemical approach, based on treatment with butylated hydroxyanisole and dimethylsulphoxide, to bring about such phenotypic conversion by monitoring the morphological changes induced by the treatment in real time, by analysing the expression of phenotype-specific protein markers and by assessing the modulation of the cells’ transcriptome. Video time-lapse microscopy showed that conversion of mesenchymal stem cells to a neuron-like morphology could be reproduced in normal primary fibroblasts as well as mimicked by addition of drugs eliciting cytoskeletal collapse and disruption of focal adhesion contacts. Analysis of markers revealed that mesenchymal stem cells constitutively expressed multi-lineage traits, including several pertaining to the neural one. However, the applied “neural induction” protocol neither significantly modulated the expression of such markers, nor induced de novo translation of other neural specific proteins. Similarly, global expression profiling of over 21,000 genes demonstrated that gene transcription was poorly affected. Most strikingly, we found that the set of genes whose expression was altered by the inductive treatment did not match the set of genes found to be differentially expressed when comparing untreated mesenchymal stem cells and immature neural tissues. Conversely, by comparing these gene expression profiles with that obtained from comparisons between the same cells and an unrelated non-neural organ, such as liver, we found that the adopted “neural induction” protocol was no more effective in redirecting human mesenchymal stem cells toward a neural phenotype than toward an endodermal hepatic pathway.
Keywords: Differentiation analysis

overall_design: The reference samples, constituted by aRNA labelled with Cy3 derived from untreated hMSCs of 3 different donors, was compared to aRNA labelled with Cy5 obtained from hMSCs after 6 and 48 hours treatment or to aRNA labelled with Cy5 from human foetal brain (positive control) or adult liver (negative control).

first: Nicoletta

last: Bertani

first: Giorgia

last: Volpi

last: Sonego

first: Roberto

last: Perris


title: 50 uM AFB_time course

summary:
RNA isolated from the cultures treated with 0 and 50 micromolar AFB1 at 15, 30, 60, 90, 120 min was used for microarray experiments. For each array hybridization experiment, RNAs from the treated sample and its corresponding time-matched control were co-hybridized to arrays and respectively quantified in different channels.  A dye swap strategy was used to eliminate the dye bias.
Keywords: time-course


title: Genomic and Proteomic Characterization of Sessile and Planktonic Campylobacter jejuni NCTC 11168

status: Public on Jul 29 2005

first: John

middle: H

last: Nash

state: Ontario

address: 100 Sussex Drive

department: Institute for Biological Sciences

institute: National Research Council

summary:
In order to understand the cellular mechanisms that facilitate a surface-associated lifestyle, expression profiles were determined at the levels of transcription and translation for sessile and planktonic Campylobacter jejuni NCTC 11168 (obtained from American Type Culture Collection (ATCC 700819)). These investigations indicate that the immobilized bacteria undergo a shift in cellular priorities away from metabolic, motility and protein synthesis capabilities towards emphasis on iron uptake, oxidative stress defense and membrane transport.
Keywords: transcript profiling

overall_design: Growth in broth was achieved by transferring stock culture to MH broth in tissue culture flasks and incubated microaerobically. Growth on agar was achieved by transferring stock culture onto MH agar plates, spreading the culture to produce a lawn, and incubation microaerobically. Cell densities in both growth conditions increased steadily up to 12 hrs and maximum cell densities were achieved at 18 hrs following which cell death starts to occur. Thus based on the growth curve C. jejuni cells at 16 hrs of incubation were used in all studies.

first: Catherine

middle: D

last: Carrillo


title: MYC inactivation uncovers pluripotent differentiation and tumour dormancy in hepatocellular cancer

city: Stanford

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

summary:
Hepatocellular carcinoma is generally refractory to clinical treatment. Here, we report that inactivation of the MYC oncogene is sufficient to induce sustained regression of invasive liver cancers. MYC inactivation resulted en masse in tumour cells differentiating into hepatocytes and biliary cells forming bile duct structures, and this was associated with rapid loss of expression of the tumour marker alpha-fetoprotein, the increase in expression of liver cell markers cytokeratin 8 and carcinoembryonic antigen, and in some cells the liver stem cell marker cytokeratin 19. Using in vivo bioluminescence imaging we found that many of these tumour cells remained dormant as long as MYC remain inactivated; however, MYC reactivation immediately restored their neoplastic features. Using array comparative genomic hybridization we confirmed that these dormant liver cells and the restored tumour retained the identical molecular signature and hence were clonally derived from the tumour cells. Our results show how oncogene inactivation may reverse tumorigenesis in the most clinically difficult cancers. Oncogene inactivation uncovers the pluripotent capacity of tumours to differentiate into normal cellular lineages and tissue structures, while retaining their latent potential to become cancerous, and hence existing in a state of tumour dormancy.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

overall_design: Using regression correlation

first: Asa

last: Karlsson


title: Sulfur Starvation in Chlamydomonas

summary:
Responses of photosynthetic organisms to sulfur starvation include (i) increasing the capacity of the cell for transporting and/or assimilating exogenous sulfate, (ii) restructuring cellular features to conserve sulfur resources, and (iii) modulating metabolic processes and rates of cell growth and division. We used microarray analyses to obtain a genome-level view of changes in mRNA abundances in the green alga Chlamydomonas reinhardtii during sulfur starvation. The work confirms and extends upon previous findings showing that sulfur deprivation elicits changes in levels of transcripts for proteins that help scavenge sulfate and economize on the use of sulfur resources. Changes in levels of transcripts encoding members of the light-harvesting polypeptide family, such as LhcSR2, suggest restructuring of the photosynthetic apparatus during sulfur deprivation. There are also significant changes in levels of transcripts encoding enzymes involved in metabolic processes (e.g., carbon metabolism), intracellular proteolysis, and the amelioration of oxidative damage; a marked and sustained increase in mRNAs for a putative vanadium chloroperoxidase and a peroxiredoxin may help prolong survival of C. reinhardtii during sulfur deprivation. Furthermore, many of the sulfur stress-regulated transcripts (encoding polypeptides associated with sulfate uptake and assimilation, oxidative stress, and photosynthetic function) are not properly regulated in the sac1 mutant of C. reinhardtii, a strain that dies much more rapidly than parental cells during sulfur deprivation. Interestingly, sulfur stress elicits dramatic changes in levels of transcripts encoding putative chloroplast-localized chaperones in the sac1 mutant but not in the parental strain. These results suggest various strategies used by photosynthetic organisms during acclimation to nutrient-limited growth.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

overall_design: Computed

first: Zhaoduo

last: Zhang


title: Cisplatin-induced gene expression in DNA adenine methyltransferase (dam) and mismatch repair deficient E. coli

status: Public on Jul 27 2005

city: Cambridge

first: Jennifer

last: Robbins

state: MA

address: 77 Massachusetts Ave.

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary:
We used Affymetrix microarrays to determine the cisplatin-induced gene expression changes in E. coli deficient in dam and mismatch repair (dam, dam mutS, and mutS mutant strains).  E. coli deficient in dam are hypersensitive to cisplatin.  However introducing an additional mutation in mismatch repair (i.e., a mutation in mutS or mutL) abrogates this sensitivity and essentially restores wildtype levels of resistance.
Keywords: Drug-induced expression

overall_design: Overnight cultures were diluted 1000-fold and grown in Luria-Bertani (LB) medium until the cells reached exponential growth as determined by OD600.  The exponentially growing cells were resuspended in M9 minimal medium at a cell density of 2 X 108 cells/ml in a volume of 15 ml and treated with 150 uM cisplatin for 2 hours at 37°C. Following treatment cultures were resuspended in 15 ml LB and allowed to recover for 90 minutes at 37°C.  OD600 readings were taken after the recovery period, when RNA isolation began.  Total RNA was isolated from cells by extraction using the MasterPure RNA Purification Kit (Epicentre Technologies) according to the manufacture’s protocol.   The isolated total RNA was quantitated by absorption at 260 nm (typical yield from a 15 ml culture was 250-500 µg of total RNA), and the purity was determined by the ratio of absorption values at 260/280nm.  RNA quality was determined by formaldehyde agarose gel electrophoresis (1.2% agarose in FA Buffer pH 7.0 (20mM 3-[N-morpholino]propanesulfonic  acid, 5mM sodium acetate, 1mM ethylenadiaminetetraacetic acide (EDTA)) or by analysis on an Agilent 2100 Bioanalyzer.    All samples visualized by gel electrophoresis or by the bioanalyzer electropherogram showed clear distinct bands correlating to 16S and 23S ribosomal RNA, indicating that no detectable RNA degradation occurred and that RNA integrity was maintained throughout the RNA isolation procedure.

first: Zoran

last: Zdraveski

first: Martin

last: Marinus

last: Essigmann


title: K24-1/EGFP R5 RNA Timecourse

status: Public on Jul 26 2005

type:
Expression profiling by array
Genome variation profiling by array

summary:
The promoter upstream from eryAI (eryAp) was cloned in front of EGFP in pIJ8660.  This vector was integrated into the chromosome of K24-1, a clean host version of K41-135 (the overproducer strain obtained from Kosan Biosciences).  This strain was then grown in shake flask culture in R5 medium.  RNA was harvested up through three days. The 12 h RNA sample was used as the reference sample for all RNA hybridizations.  A genomic DNA vs. 12 h control was also done to determine initial relative transcript expression.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Amy

last: Lum


title: S. fradiae WT and KOS155-3C R5/No Glucose 02/09/03

summary:
RNA timecourse data for Streptomyces fradiae wildtype (ATCC19609) and overproducing strain KOS155-3C(RUS).  Strains were grown at 30 C in shake flask cultures in R5 medium with no glucose.  RNA samples were harvested over 5 days as tylosin was produced.  12 h RNA samples of each strain were used as the reference sample(green) within their respective timecourses.  The WT gDNA vs. 12 h RNA control displays relative gene expression at the beginning of the timecourse.  The 12 h RNA control compares initial RNA levels between the WT and overproducer.
Groups of assays that are related as part of a time series.
Keywords: time_series_design


title: Comparison of aortic and aortic valve endothelial cells in static and shear environments

status: Public on Jul 30 2005

first: Jonathan

middle: T

last: Butcher

address: 315 Ferst Dr.

department: Mechanical Engineering

institute: Georgia Institute of Technology

summary:
Porcine aortic and aortic valve endothelial cells were exposed to 20 dynes/cm2 steady laminar shear stress with static cultures serving as controls.  Total RNA was hybridized to Agilent Human 1 cDNA arrays and processed using the Agilent Feature Extraction Software
Keywords = aortic valve
Keywords = endothelial
Keywords = shear stress
Keywords: other

first: Robert

middle: M

last: Nerem


title: Entamoeba plus Caco2 cells

status: Public on Jul 22 2005

summary:
Entamoeba histolytica is a protozoan parasite which causes colitis and liver abscesses.  Using a genomic DNA microarray consisting of 1.6 - 2.0 kb genomic inserts we have generated a transcriptional profile of 1,971 unique parasite transcripts.  The arrays in this experiment set were used to (1) estimate relative transcript abundance for Entamoeba histolytica (HM-1:IMSS) trophozoites in mid-logarithmic growth and (2) to examine changes in the transcriptional profile of Entamoeba histolytica when the parasite interacts with colonic epithelial cells (Caco-2).  A time course was used such that RNA was isolated from ameba alone and ameba + Caco-2 cells at 3hrs, 6hrs and 9hrs corresponding to 10%, 50% and 90% cell monolayer destruction.  At least two biological experiments and three replicates were used for each time point.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

overall_design: User Defined

first: Ryan

last: Macfarlane


title: Stat6 dependent gene expression in lung and small intestine

city: San Francisco

first: David

last: Voehringer

address: 521, Parnassus Ave

department: Medicine, Infectious diseases

institute: HHMI

summary:
Gene expression in the lung and intestine of wild-type and stat6 deficient mice on BALB/c background infected with the helminth parasite Nippostrongylus brasiliensis was compared by competitive hybridization to spotted 70-mer oligonucleotide arrays.
Keywords: other

first: Richard

last: Locksley


title: RERG is a novel ras-related, estrogen-regulated and growth-inhibitory gene in breast cancer

status: Public on Jul 23 2005

summary:
Using microarray analysis, we identified a unique ras superfamily gene, termed RERG (ras-related and estrogen-regulated growth inhibitor), whose expression was decreased or lost in a significant percentage of primary human breast tumors that show a poor clinical prognosis. Importantly, high RERG expression correlated with expression of a set of genes that define a breast tumor subtype that is estrogen receptor-positive and associated with a slow rate of tumor cell proliferation and a favorable prognosis for these cancer patients. RERG mRNA expression was induced rapidly in MCF-7 cells stimulated by beta-estradiol and repressed by tamoxifen treatment. Like Ras, RERG protein exhibited intrinsic GDP/GTP binding and GTP hydrolysis activity. Unlike Ras proteins, RERG lacks a known recognition signal for COOH-terminal prenylation and was localized primarily in the cytoplasm. Expression of RERG protein in MCF-7 breast carcinoma cells resulted in a significant inhibition of both anchorage-dependent and anchorage-independent growth in vitro and inhibited tumor formation in nude mice. These features of RERG are strikingly different from most Ras superfamily GTP-binding pro-teins and suggest that the loss of RERG expression may contribute to breast tumorigenesis.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Charles

last: Perou


title: S. erythraea R5 Fall 2002 RNA Timecourse

summary:
Saccharopolyspora erythraea NRRL2338 (wildtype) and K41-135 (overproducer strain from Kosan Biosciences, KOVP) were grown in shake flask cultures in rich medium R5.  RNA samples were harvested for each strain over 5 days.  12 h samples taken for each strain were used as their respective reference ("time zero") samples.  The genomic DNA control compares NRRL2338 gDNA to NRRL2338 12 h RNA to show relative gene expression at the start of the timecourse.  The 12 h RNA control compares initial gene expression between the wildtype and overproducer strains.
Groups of assays that are related as part of a time series.
Keywords: time_series_design


title: Entamoeba heat shock experiments

summary:
Entamoeba histolytica is a protozoan parasite which causes colitis and liver abscesses.  A pilot microarray consisting of 360 unique parasite genes was constructed using identical methods to the larger array (1,971 unique genes).  The four arrays in this data set were used to ascertain whether the microarrays would be useful in detecting changes in transcript abundance by exposing parasites to heat shock (42 0C for 1 hr).  Approximately, 17% of the genes were regulated by at least two fold including many genes previously shown to be involved in heat shock response.  This data confirmed that the genomic DNA arrays were useful in detecting changes in transcript abundance.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set


title: Primary_breast_cancer

city: Redwood City

first: Jordan

last: Hiller

address: 1400 Seaport Blvd.

institute: PDL BioPharma

summary:
54 tumors of breast cancer; a random mix of histologies, stages, and grades.
Keywords: other

first: Laszlo

last: Radvanyi

first: Devender

last: Singh-Sandhu

first: Scott

last: Gallichan

first: Corey

last: Lovitt

first: Artur

last: Pedyczak

first: Kurt

last: Gish

first: Kevin

last: Kwok

first: Wedad

last: Hanna

first: Jane

last: Armes

first: Deon

last: Venter

first: Gustavo

last: Mallo

first: Jalil

last: Hakimi

first: Luciano

last: Ettore

first: Adrienne

last: Sum

first: Hong

first: Pamela

last: Dunn

first: Ray

last: Oomen

first: Neil

middle: L

last: Berinstein


title: mRNA decay data set

last: Stanford Microarray Database

summary:
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Yulei

last: Wang


title: Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways

summary:
The eubacterial species Streptomyces coelicolor proceeds through a complex growth cycle in which morphological differentiation/development is associated with a transition from primary to secondary metabolism and the production of antibiotics. We used DNA microarrays and mutational analysis to investigate the expression of individual genes and multigene antibiotic biosynthetic pathways during these events. We identified expression patterns in biosynthetic, regulatory, and ribosomal protein genes that were associated highly specifically with particular stages of development. A knowledge-based algorithm that correlates temporal changes in expression with chromosomal position identified groups of contiguous genes expressed at discrete stages of morphological development, inferred the boundaries of known antibiotic synthesis gene loci, and revealed novel physical clusters of coordinately regulated genes. Microarray analysis of RNA from cells mutated in genes regulating synthesis of the antibiotics actinorhodin (Act) and undecylprodigiosin (Red) identified proximate and distant sites that contain putative ABC transporter and two-component system genes expressed coordinately with genes of specific biosynthetic pathways and indicated the existence of two functionally and physically discrete regulons in the Red pathway.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

last: Huang


title: Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress

summary:
The Saccharomyces cerevisiae Yap1p transcription factor is required for the H2O2-dependent activation of many antioxidant genes including the TRX2 gene encoding thioredoxin 2. To identify factors that regulate Yap1p activity, we carried out a genetic screen for mutants that show elevated expression of a TRX2-HIS3 fusion in the absence of H2O2. Two independent mutants isolated in this screen carried mutations in the TRR1 gene encoding thioredoxin reductase. Northern blot and whole-genome expression analysis revealed that the basal expression of most Yap1p targets and many other H2O2-inducible genes is elevated in Deltatrr1 mutants in the absence of external stress. In Deltatrr1 mutants treated with H2O2, the Yap1p targets, as well as genes comprising a general environmental stress response and genes encoding protein-folding chaperones, are hyperinduced. However, despite the elevated expression of genes encoding antioxidant enzymes, Deltatrr1 mutants are extremely sensitive to H2O2. The results suggest that cells lacking thioredoxin reductase have diminished capacity to detoxify oxidants and/or to repair oxidative stress-induced damage and that the thioredoxin system is involved in the redox regulation of Yap1p transcriptional activity.
Groups of assays that are related as part of a time series.
Keywords: time_series_design

first: Audrey

last: Gasch

first: Vishy

last: Iyer


title: Global analysis of Caenorhabditis elegans operons

summary:
Caenorhabditis elegans and its relatives are unique among animals, possibly even among eukaryotes, in having operons.  In these regulated multigene transcription units, a polycistronic pre-mRNA is processed to monocistronic mRNAs by 3' end formation and trans-splicing utilizing a special snRNP, the SL2 snRNP, for downstream mRNAs1. Previously, the correlation between downstream location in an operon and SL2 trans-splicing has been strong, but anecdotal. Although only 28 operons have been reported previously, the complete sequence of the genome reveals numerous gene clusters.  To determine how many represent operons, we probed full-genome microarrays for SL2-containing mRNAs. We found significant enrichment for about 1200 genes including most of a group of several hundred genes represented by cDNAs that contain SL2 sequence. Analysis of their genomic arrangements indicates that >90% are downstream genes, falling in 790 distinct operons.  We conclude that the genome contains at least 1000 operons, 2- 8 genes in length, that contain ~15% of C. elegans genes. Most of the operons have not been reported previously, and numerous examples of co-transcription of genes encoding functionally related proteins are evident. Inspection of the operon list should reveal heretofore unknown functional relationships.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Chris

last: Link


title: Photoperiod induction of endodormancy in Vitis riparia axillary buds.

status: Public on Aug 05 2005

city: Brookings

first: Anne

middle: Y

last: Fennell

state: SD

address: 201 N. Campus Dr

department: Plant Science

institute: South Dakota State University

summary:
This study compares age matched V. riparia axillary buds at one time point during long photoperiod (paradormancy maintenance) and short photoperiod (endodormancy induced).
Keywords: endodormancy, photoperiod, paradormancy, grape, axillary bud

overall_design: Four independent replications of the long and short photoperiod treatment were compared.  Dye swaps were done for each photoperiod treatment (two replicates/dye).

first: David

last: Horvath

first: Kathy

last: Mathiason


title: Mtb Rv2869c mutant/WT +/- detergent

city: New York

first: Michael

last: Glickman

state: NY

institute: Sloan Kettering Institute for Cancer Research

summary:
The purpose of this experiment is to examine gene expression controlled by Rv2869c in the presence or absence of detergent (Tween 80) in the culture medium.
Keywords: parallel sample

overall_design: Wild type Mtb and the Rv2869c mutant were grown either with or without the detergent Tween 80 in the culture medium. Each hybridization is wild type versus mutant with three biologic replicates (+Tw) or Two biologic replicates (-Tw). Each array contains two spots for each gene. Each condition (+/-Tw) contains one dye swap (WTCy3).

middle: S

first: Hideki

last: Makinoshima


title: Downstream targets of let-60 Ras in Caenorhabditis elegans

summary:
In Caenorhabditis elegans, let-60 Ras controls many cellular processes, such as differentiation of vulval epithelial cells, function of chemosensory neurons, and meiotic progression in the germ line. Although much is known about the let-60 Ras signaling pathway, relatively little is understood about the target genes induced by let-60 Ras signaling that carry out terminal effector functions leading to morphological change. We have used DNA microarrays to identify 708 genes that change expression in response to activated let-60 Ras.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Beatrice

last: Romagnolo


title: muscle mRNA tagging

summary:
We present a global overview of muscle gene expression in C. elegans using a novel technique called mRNA-tagging, and have identified genes involved in contraction, muscle structure, and energy utilization.  Furthermore, we found that muscle-expressed genes are clustered in groups of 2-5 along the chromosomes, suggesting that expression from a chromatin domain can extend over several genes. These observations reveal a higher-order organization of the structure of the genome in which the order of genes along the chromosome is correlated with their expression in specific tissues.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Peter

last: Roy


title: Human blood expression for Huntington's disease versus control, Codelink

city: Charlestown

first: Dimitri

last: Krainc

address: Building 114, 16th St.

department: Neurology

institute: MassGeneral Institute for Neurodegeneration

summary:
Codelink Human Uniset I, II, and 20K expression levels for 12 symptomatic and 5 presymptomatic Huntington's disease patients versus 14 healthy controls.
Keywords: other


title: SW13_BRG1_3arrays

status: Public on Jul 21 2005

summary:
BRG1 response genes in SW13 cells
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Xin

last: Chen


title: Transcriptional analysis of doxorubicin-induced cardiotoxicity

city: Dallas

first: Wendy

last: Pan

state: TX

address: 5323 HarryHines Blvd

institute: UT Southwestern

summary:
Doxorubicin (Dox) is an effective chemotherapeutic agent against a broad range of tumors.  However, a threshold dose of doxorubicin causes an unacceptably high incidence of heart failure and limits its clinical utility.  We have established two models of doxorubicin cardiotoxicity in mice: 1) in an acute model, mice are treated with 15mg/kg of doxorubicin once; 2) in a chronic model, they receive 3mg/kg weekly for the first 12 of a total of 18 weeks.  Using echocardiography, we have monitored left ventricular function of the mouse hearts during treatment in chronic model and seen the expected development of dilated cardiomyopathy (DCM).  Treated mice showed histological abnormalities similar to those seen in patients with doxorubicin cardiomyopathy.  To investigate transcriptional regulation in these models, we used a microarray we generated with over 5000 independent cDNA clones from murine heart and skeletal muscle.  We have identified genes that respond to doxorubicin exposure in both model systems, and confirmed these results using real-time PCR.  In the acute model, a set of genes is regulated early and rapidly returns to baseline levels, consistent with the half-life of doxorubicin.  In the chronic model, which mimics the clinical situation much more closely, we identified dysregulated genes that implicate specific mechanisms of cardiac toxicity and may serve as biomarkers of doxorubicin induced dilated cardiomyopathy.
Keywords: time course

overall_design: In the chronic model of doxorubicin-induced cardiotoxicity, mice are injected with 3 mg/kg body weight of doxorubicin weekly for 12 weeks.  Treated and control mice were sacrificed and hearts harvested 1 day, 1, 3, 6, 12 and 18 weeks after the first injection.


title: Caenorhabditis elegans as an environmental monitor using DNA microarray analysis.

summary:
In order to assist in the identification of possible endocrine disrupting chemicals (EDC) in groundwater, we are developing Caenorhabolitis elegans as a high throughput bioassay system in which responses to EDC may be detected by gene expression using DNA microarray analysis. As a first step we examined gene expression patterns and vitellogenin responses of this organism to vertebrate steroids, in liquid culture. Western blotting showed the expected number and size of vitellogenin translation products after estrogen exposure. At 10(-9) M, vitellogenin decreased, but at 10(-7) and 10(-5), vitellogenin was increased. Testosterone (10(-5) M) increased the synthesis of vitellogenin, but progesterone-treated cultures (10(-5) M) had less vitellogenin. Using DNA microarray analysis, we examined the pattern of gene expression after progesterone (10(-5), 10(-7), and 10(-9) M), estrogen (10(-5) M), and testosterone (10(-9) M) exposure, with special attention to the traditional biomarker genes used in environmental studies [vitellogenin, cytochrome P450 (CYP), glutathione s-transferase (GST), metallothionein (MT), and heat shock proteins (HSP)]. GST and P450 genes were affected by estrogen (10(-5) M) and progesterone (10(-5) and 10(-7) M) treatments. For vitellogenin genes, estrogen treatment (10(-5) M) caused overexpression of the vit-2 and vit-6 genes (2.68 and 3.25 times, respectively). After progesterone treatment (10(-7) M), the vit-5 and vit-6 were down-regulated and vit-1 up-regulated (3.59-fold). Concentrations of testosterone and progesterone at 10(-9) M did not influence the expression of the vit, CYP, or GST genes. Although the analysis is incomplete, and low doses and combinations of EDC need to be tested, these preliminary results indicate C. elegans may be a useful laboratory and field model for screening EDC.
A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed.
Keywords: compound_treatment_design

first: Ian

last: Callard


title: Genome-wide SNP Microarray Mapping in Basal Cell Carcinomas Unveils Uniparental Disomy as a Key Somatic Event.

city: London

first: Muy-Teck

last: Teh

state: England

address: Blizard Building, 4, Newark Street,

department: Centre for Clinical & Diagnostic Oral Sciences

country: United Kingdom

institute: Queen Mary University of London

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Affymetrix 10K SNP mapping arrays were used to profile 14 basal cell carcinomas (BCCs) with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair.
Keywords: Genomic DNA on Affymetrix 10K SNP array

overall_design: 14 BCC/Blood pairs were used in this study to obtain genome-wide SNP profiles. By comparing tumour and blood DNA, LOH for each SNP could be obtained. Signal intensity for each SNP were used to deternime CNA.

first: M

first: Diana

last: Blaydon

first: Tracy

last: Chaplin

first: Nicola

middle: J

last: Foot

first: Spyros

last: Skoulakis

first: Manoj

last: Raghavan

first: Catherine

middle: A

last: Harwood

first: Charlotte

last: Proby

middle: P

last: Philpott

first: Bryan

last: Young

last: Kelsell


title: Genome-wide characterization of the Zap1p zinc-responsive regulon in yeast

last: Stanford Microarray Database

summary:
The Zap1p transcription factor senses cellular zinc status and increases expression of its target genes in response to zinc deficiency. Previously known Zap1p-regulated genes encode the Zrt1p, Zrt2p, and Zrt3p zinc transporter genes and Zap1p itself. To allow the characterization of additional genes in yeast important for zinc homeostasis, a systematic study of gene expression on the genome-wide scale was used to identify other Zap1p target genes. Using a combination of DNA microarrays and a computer-assisted analysis of shared motifs in the promoters of similarly regulated genes, we identified 46 genes that are potentially regulated by Zap1p. Zap1p-regulated expression of seven of these newly identified target genes was confirmed independently by using lacZ reporter fusions, suggesting that many of the remaining candidate genes are also Zap1p targets. Our studies demonstrate the efficacy of this combined approach to define the regulon of a specific eukaryotic transcription factor.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Audrey

last: Gasch


status: Public on Jul 20 2005

summary:
The von Hippel-Lindau (VHL) tumor suppressor functions as a ubiquitin ligase that mediates proteolytic inactivation of hydroxylated a subunits of hypoxia-inducible factor (HIF). Although studies of VHL defective renal carcinoma cells suggest the existence of other VHL tumor suppressor pathways, dysregulation of the HIF transcriptional cascade has extensive effects that make it difficult to distinguish whether, and to what extent, observed abnormalities in these cells represent effects on pathways that are distinct from HIF. Here, we report on a genetic analysis of HIF dependent and independent effects of VHL inactivation by studying gene expression patterns in C. elegans. We show tight conservation of the HIF-1/VHL-1/EGL-9 hydroxylase pathway. However, persisting differential gene expression in hif-1 versus hif-1; vhl-1 double mutant worms clearly distinguished HIF-1 independent effects of VHL-1 inactivation. Genomic clustering, predicted functional similarities, and a common pattern of dysregulation in both vhl-1 worms and a set of mutants (dpy-18, let-268, gon-1, mig-17 and unc-6), with different defects in extracellular matrix formation, suggest that dysregulation of these genes reflects a discrete HIF-1 independent function of VHL-1 that is connected with extracellular matrix function.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Bishop T, Lau KW, Epstein AC, Kim SK, Jiang M, O'rourke D, Pugh CW, Gleadle JM, Taylor MS, Hodgkin J, Ratcliffe PJ, Genetic Analysis of Pathways Regulated by the von Hippel-Lindau Tumor Suppressor in Caenorhabditis elegans., Bishop T, et al. (2004) PLoS Biol 2(10):e289, 2004-10-01, http://biology.plosjournals.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0020289
Keywords: Logical Set

first: Andrew

last: Epstein

first: Tammie

last: Bishop


title: LongSAGE analysis significantly improves genome annotation

city: Neuherberg

first: Matthias

last: Wahl

address: Ingolstaedter Landstrasse 1

department: Institute of Developmental Genetics

country: Germany

institute: GSF - National Research Center for Environment and Health

summary:
Owing to its increased tag length, LongSAGE tags are expected to be more reliable in direct assignment to genome sequences. Therefore, we evaluated the use of LongSAGE data in genome annotation by using our LongSAGE dataset of 202 015 tags (consisting of 41 718 unique tags), experimentally generated from mouse embryonic tail libraries. RESULTS: A fraction of LongSAGE tags could not be unambiguously assigned to its gene, due to the presence of widely conserved sequences downstream of particular CATG anchor sites. The presence of alternative forms of transcripts was confirmed in 45% of all detected genes. Surprisingly, a large fraction of LongSAGE tags with hits to the genome (66%) could not be assigned to any gene annotated in EnsEMBL. Among such cases, 2098 LongSAGE tags fell into a region containing a putative gene predicted by GenScan, providing experimental evidence for the presence of real genes, while 9112 genes were found out to be left out or wrongly annotated by the EnsEMBL pipeline. CONCLUSIONS: LongSAGE transcriptome data can significantly improve the genome annotation by identifying novel genes and alternative transcripts, even in the case of thus far best-characterized organisms like the mouse.
Keywords: other


title: 15.5dpc Ureteric tree cells Vs rest

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

summary:
Triplicate pairwise comparsion of FACS sorted GFP+ve Vs GFP-ve cells from the kidneys of the HoxB7-GFP transgenic mice on compugen 22K mouse arrays. HoxB7-GFP mice express GFP in the ureteric tree and its derivatives while the metanephric mesenchyme, interstitium, developing vasculature etc do not.
Keywords: repeat sample

first: Sean

last: Grimmond


title: 10.5dpc Metanephric mesenchyme Vs 13.5dpc fetal kidney

summary:
Direct comparison of dissected 10.5dpc metanephric mesenchyme Vs 13.5dpc fetal kidneys
Keywords: repeat sample


title: MtIFS1-expressing alfalfa

city: Ardmore

first: Bettina

last: Deavours

state: OK

institute: Samuel Roberts Noble Foundation

summary:
We used an M. truncatula 16K oligonucleotide array to profile gene expression in the leaves of transgenic alfalfa plants expressing Medicago truncatula isoflavone synthase 1 (MtIFS1).  RNA purified from leaves of MtIFS1-expressing lines C22 and B20 and vector control line VC11 was used to generate Cy5-labeled cDNA.  RNA purified from a second vector control line, VB2, was used to generate Cy3-labeled reference cDNA.  Three independently propagated cuttings of each line were used and a total of nine hybridizations were performed.  Our results indicated that MtIFS1-expression does not significantly alter global gene expression in the leaves.
Keywords = Medicago
Keywords = isoflavone synthase
Keywords = alfalfa
Keywords: other

middle: E

first: Richard

last: Dixon


title: 10.5dpc Metanephric mesenchyme Vs 11.5dpc metanephroi

summary:
Direct comparison of dissected 10.5dpc metanephric mesenchyme Vs 11.5dpc metanephroi
Keywords: repeat sample


summary:
10.5dpc Metanephric Mesenchyme V Intermediate Mesoderm
Keywords: repeat sample


title: Expression profiling soybean response to P. syringae reveals rapid HR-specific down regulation of photosynthesis genes

city: Urbana

first: min

last: li

state: IL

address: Rm230 1101 W peabody Dr

institute: University of Illinois at Urbana-Champaign

summary:
Transcript profiling during susceptible (S) and HR-associated resistance (R) responses was determined in soybean (Glycine max). Pseudomonas syringae pv. glycinea carrying or lacking the avirulence gene avrB, was infiltrated into cultivar Williams 82. Leaf RNA was sampled at 2, 8, and 24 hours post inoculation (hpi). Significant changes in transcript abundance were observed for 3,897 genes during the experiment at p = 0.000005. Many of the genes showed a similar direction of increase or decrease abundance in both the S and R responses, but the R response generally showed a significantly greater degree of differential expression. More than 25% of these responsive genes had not been previously reported as being associated with pathogen interactions, as 704 had no functional annotation and 378 had no homolog in NCBI databases. The highest number of transcriptional changes was noted at 8 hpi including the down regulation of 94 chloroplast-associated genes specific to the R response. Photosynthetic measurements were consistent with an R-specific reduction in photosystem II operating efficiency (FPSII) that was apparent at 8 hpi for the R response with little effect in the S or control treatments. Imaging analyses suggest that the decreased FPSII was a result of physical damage to PSII reaction centers.
Keywords = compatible
Keywords = disease
Keywords = genomic
Keywords = hypersensitive response
Keywords = incompatible
Keywords = plant
Keywords: susceptible vs resistant

overall_design: loop design, 10 samples, 14 comparision, 2-4 technical repeats including dye swaps, 2 biological repeats

first: Jijun

last: Zou

first: Sandra

last: Rodriguez-Zas

first: Mihai

last: Aldea

first: Min

last: Li

first: Jin

last: Zhu

first: Delkin

middle: O

last: Gonzalez

first: Lila

last: Vodkin

first: Evan

last: DeLucia

first: Steve

last: Clough


title: Tachyzoite to bradyzoite differentiation

status: Public on Aug 13 2005

last: Stanford Microarray Database

summary:
Developmental switching in Toxoplasma gondii, from the virulent tachyzoite to the relatively quiescent bradyzoite stage, is responsible for disease propagation and reactivation. We have generated tachyzoite to bradyzoite differentiation (Tbd-) mutants in T. gondii and used these in combination with a cDNA microarray to identify developmental pathways in bradyzoite formation. Four independently generated Tbd- mutants were analysed and had defects in bradyzoite development in response to multiple bradyzoite-inducing conditions, a stable phenotype after in vivo passages and a markedly reduced brain cyst burden in a murine model of chronic infection. Transcriptional profiles of mutant and wild-type parasites, growing under bradyzoite conditions, revealed a hierarchy of developmentally regulated genes, including many bradyzoite-induced genes whose transcripts were reduced in all mutants. A set of non-developmentally regulated genes whose transcripts were less abundant in Tbd- mutants were also identified. These may represent genes that mediate downstream effects and/or whose expression is dependent on the same transcription factors as the bradyzoite-induced set. Using these data, we have generated a model of transcription regulation during bradyzoite development in T. gondii. Our approach shows the utility of this system as a model to study developmental biology in single-celled eukaryotes including protozoa and fungi.
Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
Keywords: Logical Set

first: Upinder

last: Singh


title: Gestational Diabetes Induces Placental Genes for Chronic Stress and Inflammatory Pathways

status: Public on Jul 18 2005

city: Paris

first: Sylvie

last: Hauguel-de Mouzon

address: 24 rue de Chaligny

department: Hopital Saint Antoine

country: France

institute: Universite Paris6

summary:
A physiological state of insulin resistance is required to preferentially direct maternal nutrients toward the feto-placental unit, allowing adequate growth of the fetus. When women develop gestational diabetes mellitus (GDM), insulin resistance is more severe and disrupts the intrauterine milieu, resulting in accelerated fetal development with increased risk of macrosomia. As a natural interface between mother and fetus, the placenta is the obligatory target of such environmental changes. However, the molecular basis for the imbalance that leads to fetal, neonatal, and adult metabolic compromises is not well understood. We report that GDM elicits major changes in the expression profile of placental genes with a prominent increase in markers and mediators of inflammation. Within the 435 transcripts reproducibly modified, genes for stress-activated and inflammatory responses represented the largest functional cluster (18.5% of regulated genes). Upregulation of interleukins, leptin, and tumor necrosis factor-{alpha} receptors and their downstream molecular adaptors indicated an activation of pathways recruiting stress-activated protein/c-Jun NH2-terminal kinases. Transcriptional activation of extracellular matrix components and angiogenic activators pointed to a major structural reorganization of the placenta. Thus, placental transcriptome emerges as a primary target of the altered environment of diabetic pregnancy. The genes identified provide the basis to elucidate links between inflammatory pathways and GDM-associated insulin resistance.
Keywords: other

overall_design: To characterize gene targets that determine altered placental functions, the global pattern of gene expression was analyzed in placenta from matched control subjects and GDM pregnancies. Of 22,823 gene sequences surveyed, 8,627 ± 172 were present in control subjects and 9,378 ± 165 in GDM, representing placental transcriptome. The consecutive screening filters that we applied allowed us to narrow these numbers to 2,682 genes eligible for analysis. The average fold change value was then calculated for all pairwise comparisons, resulting in the final selection of 435 genes significantly modified in GDM.


title: Human myometrial adaptation to pregnancy

first: Khurram

last: Rehman

address: 5323 Harry Hines Blvd

department: Obstetrics and Gynecology

institute: UT Southwestern Medical Center

summary:
The human uterus undergoes profound physiological tissue remodelling during pregnancy. In the myometrium, altered gene expression must underlie these extensive molecular and structural changes. The purpose of this study was to compare expression profiles of pregnant and non-pregnant myometrium, in order to identify genes that participate in this process. mRNA from 14 non-pregnant and four pregnant human myometrial samples were analysed using a human UniGEM V microarray with 7075 cDNA elements. A total of 602 transcripts from the microarray were up-regulated >=2.0-fold in pregnant myometrium, with 37 transcripts up-regulated >=4.0-fold. In contrast, eight transcripts were down-regulated >=2.0-fold in pregnancy. To ensure accurate representation of differential gene expression, Northern blot analyses using total RNA from 16 samples of non-pregnant and pregnant myometrium were used to examine mRNA levels for four of the genes that were differentially expressed by microarray analysis, namely plasminogen activator inhibitor type 1 (PAI-1), milk fat globule-EGF factor 8 protein (MFGE8), secreted frizzled-related protein 4 (sFRP4) and estrogen receptor {alpha} (ER{alpha}). On the microarray these transcripts were up-regulated 7.5-fold for PAI-1 and 4.9-fold for MFGE8 in pregnant myometrium, and down-regulated 3.7-fold for sFRP4 and 2.9-fold for ER{alpha} in pregnancy. Northern blot analyses confirmed these changes. Our findings suggest that microarray technology is a useful tool for examining global changes in gene expression that occur as the myometrium differentiates from non-pregnant to pregnant status. Defining these changes provides new insight into the structural and functional adaptations of human myometrium during pregnancy.
Keywords: other

overall_design: RNA isolated from a total of 14 samples of non-pregnant myometrium and four samples of pregnant myometrium was analysed using a genomic expression microarray (GEM).


title: Synthesis vs. Abundance, Bradyzoite Development

status: Public on Jul 16 2005

summary:
Parasites grown as either tachyzoites or bradyzoites for 40 hours were pulsed with 2,4-dithiouracil (DTU) for 1 hour.  Following the pulse, mRNA was extracted and either used directly in microarray experiments (Abundance Arrays) or biotinylated and purified to select DTU labeled RNAs that were then used in microarray experiments (Synthesis Arrays).  Two independent tachyzoite and bradyzoite preparations were made and duplicate microarrays were performed for each sample.
A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions.
Keywords: development_or_differentiation_design

first: Michael

last: Cleary


title: Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data

summary:
Pulse chase measurements using thiouracil (DTU) labeling via UPRT and chasing with uracil  Data from tachyzoites is labeled "DTU Pulse Chase".  Two independent pulse chase experiments were performed in tachyzoites, pulse chase 1 and 2.  Duplicate arrays at each timepoint were performed for pulse chase 2 (2 a and b).  Data from bradyzoites are labeled "DTU Bradyzoite Pulse Chase".  Two independent pulse chase experiments were performed in bradyzoites and a single set of arrays were performed for each experiment.  Just one chase timepoint was used in the bradyzoite experiments, the 2 hour chase.
An RNA stablity experiment design type examines stability and/or decay of RNA transcripts.
Keywords: RNA_stability_design


title: Gene expression profile of keloid tissue

city: Kyoto

first: Motoko

last: Naitoh

state: Kyoto

address: Shyogoin-Kawahara cho 53

department: Molecular and Cellular Biology

country: Japan

institute: Institute for Frontier Medical Science, Kyoto University

summary:
Comparison of keloid to normal tissue
Keywords: examination of keloid tissue

overall_design: One sample for each type of tissue examined

first: Hiroshi

last: Kubota


title: Mouse hypoxia

institute: Stanford Microarray Database (SMD)

summary:
Vascular disruption following bony injury results in a hypoxic gradient within the wound microenvironment. Nevertheless, the effects of low oxygen tension on osteogenic precursors remain to be fully elucidated. In the present study, we investigated in vitro osteoblast and mesenchymal stem cell differentiation following exposure to 21% O(2) (ambient oxygen), 2% O(2) (hypoxia), and <0.02% O(2) (anoxia). Hypoxia had little effect on osteogenic differentiation. In contrast, short-term anoxic treatment of primary osteoblasts and mesenchymal precursors inhibited in vitro bone nodule formation and extracellular calcium deposition. Cell viability assays revealed that this effect was not caused by immediate or delayed cell death. Microarray profiling implicated down-regulation of the key osteogenic transcription factor Runx2 as a potential mechanism for the anoxic inhibition of differentiation. Subsequent analysis revealed not only a short-term differential regulation of Runx2 and its targets by anoxia and hypoxia, but a long-term inhibition of Runx2 transcriptional and protein levels after only 12-24 h of anoxic insult. Furthermore, we present evidence that Runx2 inhibition may, at least in part, be because of anoxic repression of BMP2, and that restoring Runx2 levels during anoxia by pretreatment with recombinant BMP2 rescued the anoxic inhibition of differentiation. Taken together, our findings indicate that brief exposure to anoxia (but not 2% hypoxia) down-regulated BMP2 and Runx2 expression, thus inhibiting critical steps in the osteogenic differentiation of pluripotent mesenchymal precursors and committed osteoblasts.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

first: Ali

last: Salim


title: Fundulus heteroclitus exposed to Cr(III)

status: Public on Jul 15 2005

city: Ocean Springs

first: Jonathan

last: Roling

state: MS

address: 703 East Beach Dr

department: Department of Coastal Sciences

institute: University of Southern Mississippi

summary:
Cr(III) is the dominant toxicant at some Superfund sites within the United States and therefore we are interested in its effects.  Cr(III)’s mechanisms are not well studied or understood because of its low bioavailability.  We have attempted to characterize the effects of Cr(III) on gene expression in the liver of adult male Fundulus heteroclitus.  The NOEC and LOEC were determined at 32 and 64mg/L, respectively, by measuring growth after exposing juveniles for 30 days.  Secondary exposures were performed with adult males at 32mg/L, livers excised, and RNA extracted.  Microarrays were probed with cDNA from untreated or Cr(III)-exposed adult fish and gene expression was quantified.  Cr(III) at 32mg/L altered the expression of 5 genes, including GSTalpha, GSTtheta, and ALDH4.  Ultimately, we anticipate using this gene expression information to determine whether chromium is available at potentially adverse concentrations in contaminated sites.
Keywords: dose response

platform_organism:
Fundulus heteroclitus
Pseudopleuronectes americanus

overall_design:
Four fish were untreated.  Four fish were exposed to 32mg/L (0.62mM) Cr(III) for 7 days with media renewals every 48 hours.

Mummichogs were housed at 25C in a 14/10 light/dark cycle at 18‰ salinity.  Adult mummichogs were exposed to Cr(III) at 0 or 32mg/L (0.62mM) (NOEC) individually in 4 L tanks for 7 days.  At the conclusion of the exposures, livers were excised and placed in TRI-Reagent® for RNA isolation (Sigma Chemical Co, St. Louis, MO), and stored at -80C.

first: William

last: Baldwin


title: Midlog Yeast Nucleosome Positioning

status: Public on Jul 14 2005

city: Worcester

first: Oliver

last: Rando

address: 364 Plantation St.

institute: UMass Medical School

type: Genome binding/occupancy profiling by genome tiling array

summary:
To measure nucleosome positions on a genomic scale, we developed a high-throughput DNA microarray method to identify nucleosomal and linker DNA sequences based on susceptibility of linker DNA to micrococcal nuclease. Nucleosomal DNA was isolated and labeled with Cy3 fluorescent dye (green), and mixed with Cy5-labeled total genomic DNA (red). This mixture was hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest.
Keywords = nucleosome
Keywords = yeast
Keywords = tiling microrray
Keywords: repeat sample


title: Aldosterone-responsive genes in kidney cortical collecting duct cell line, mpkCCDc14

city: Belmont

first: Ting Ting

last: Zhang

address: 115 Millman st

department: Mclean Hospital

institute: Harvard University

summary:
Aldosterone is arguably the single most important hormone implicated in the control of blood pressure and extracellular fluid volume in mammals. It acts primarily by increasing the rate of transepithelial sodium transport in the kidney tubules. Several monogenetic defects resulting in hypertension have now been attributed to abnormalities in sodium handling within the aldosterone-sensitive distal nephron, where the epithelial sodium channel, ENaC, constitutes the rate-limiting step of sodium transport. To date, the transcription-dependent aldosterone-signaling pathway between receptor and membrane transport effectors, remains incompletely understood. The broad aim of our study is to explore these intracellular signaling pathways that are critical to the functioning of sodium channels. Microarray analysis in an aldosterone-responsive kidney cortical collecting duct cell line (mpkCCDc14), allowed us to identify many potential aldosterone-regulated transcripts. The present study describes the identification, and possible physiological relevance of various aldosterone-regulated transcripts. The results of this study promise to extend our understanding of the molecular basis of aldosterone-regulated sodium transport in kidney epithelia, and provide approaches for regulating this process in disease states such as congestive heart failure and hypertension.
Keywords: hormone effect

overall_design: mpkCCD Cells were treated with 10-6M aldosterin or ethanol for 1 or 6 hrs.  Total RNAs were then isolated and cDNA was made and purified and recovered. The Cy3 or Cy5 was then coupled with cDNA from control or drug-treated cells, respectively. The labeled cDNA was hybridized with microarray slides.  4 arrays for each experimental conditions.

first: David

last: Pearce


title: Regional organization of gene expression in Streptomyces coelicolor

status: Public on Jul 12 2005

city: Stanford

address: 300 Pasteur Drive

summary:
Based on the chromosomal locations of genes inferred from sequence analysis to be essential for the viability of Streptomyces coelicolor, Bentley et al. (Bentley et al., 2002) have suggested that a 4.9 Mb central region of the linear S. coelicolor chromosome encodes core functions expressed during vegetative growth of this species, while 1.5 Mb and 2.3 Mb  chromosomal DNA segments lateral to this core encode auxiliary functions proposed to be required under other growth conditions.  To examine this hypothesis and experimentally identify genes expressed during vegetative growth of S. coelicolor cultures, we used DNA microarrays to measure globally the abundance of S. coelicolor transcripts in cells growing in liquid medium.  We found that, overall, genes corresponding to the 4.9 Mb core region of the S. coelicolor M145 chromosome were more highly expressed under non-limiting growth conditions than genes in the 1.5 Mb left and 2.3 Mb right chromosome arms, supporting the notion of the core versus auxiliary organization of genes on the chromosome.  To examine how this chromosomal distribution of transcripts changes under other growth conditions, we also measured gene expression changes during stationary phase and several stress conditions.  During stationary phase, the composition of S. coelicolor transcripts appears to shift from large quantities of growth-related transcripts encoded in the core region to those of less characterized genes, which may be essential for differentiation and other physiological responses, encoded throughout the chromosome.  After temperature and osmotic upshifts, we found that S. coelicolor transiently induces a set of several hundred genes located throughout the chromosome, which may function in response mechanisms common to the two stress conditions.
Keywords: all_pairs

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

first: N

last: Karoonuthaisiri


title: Neisseria gonorrhoeae FA1090 transcriptional response to iron availability

status: Public on Jul 11 2005

city: Oklahoma City

first: Thomas

middle: Francis

last: Ducey

address: 975 NE 10th Street, BRC 366

department: Microbiology and Immunology

institute: University of Oklahoma Health Sciences Center

summary:
4 pan-Neisseria arrays examining the gonococcal response to iron availability. Dual channel (Cy3/Cy5) arrays, using random nonamers for cDNA generation.

Arrays scanned with ScanArray ExpressHT microarray scanner.  Data analyzed using ArrayVision 7.0 and compiled in GeneSpring.
Keywords: other

first: Matthew

middle: B

last: Carson

first: Joshua

last: Orvis

first: Alain

last: Stintzi

middle: W

last: Dyer


title: Global transcriptome analysis of mouse uterus during embryo implantation by SAGE

status: Public on Jul 13 2005

city: Shantou

first: Zeng-Ming

last: Yang

address: 263 Daxue Road

department: Biology

country: China

institute: Shantou University

summary:
The aim of this study was to examine differential gene expression profile in mouse uterus on day 5 of pregnancy between implantation sites and inter-implantation sites. There are 104,520 tags sequenced and acquired, 51,306 for non-implantation site, and 53,214 for implantation site.
Keywords: Implantation, Uterus, Differential gene expression,

overall_design: Implantation sites and inter-implantation sites were isolated from the mouse uteri on day 5 of pregnancy from at least 20 mice.  Implantation sites were identified by tail-vein injection of 0.1 ml of 1% Chicago blue 5 min before sample collection. SAGE analysis was used to examine differential gene expression in mouse uterus during embryo implantation.

first: Zeng

first: Xing

last: Ma

first: Hua

last: Ni

first: Shi

last: Hu

first: Zhen

last: Tian

first: Yue

middle: C

last: Zhao

first: Ji

last: Liu

first: Ping

last: Wan


title: Transcriptional effect of aft1 and aft2 mutation in iron depleted conditions

first: Pierre-Louis

last: Blaiseau

address: 2 Place Jussieu

institute: Institute Jacques Monod

summary:
The paralogous transcription factors Aft1p and Aft2p activate the expression of genes involved in iron metabolism under iron depleted conditions. Both are able to bind to the same DNA consensus sequence in vitro. We used DNA microarrays and loss of function mutant strains to better understand the respective roles of Aft1p and Aft2p in the regulation of gene expression
Keywords: other

first: Maïté

last: Courel

first: Jean-Michel

last: Camadro


title: Juvenile and adult calvarial bone analysis

status: Public on Jul 09 2005

first: Oliver

last: Aalami

address: 257 Campus Dr.

institute: Stanford University

summary:
Differential transcriptional expression profiles of juvenile and adult calvarial bone.
Aalami OO, et al. (2005) Plast Reconstr Surg 115(7):1986-94
Keywords: Logical Set

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

first: O


title: Transdetermination study

status: Public on Jul 08 2005

city: Berlin

first: Ansgar

last: Klebes

address: Chausseestr. 117

institute: Humboldt University Berlin

summary:
Drosophila imaginal disc cells can switch fates by transdetermining from one determined state to another. We analyzed the expression profiles of cells induced by ectopic Wingless expression to transdetermine from leg to wing by dissecting transdetermined cells and hybridizing probes generated by linear RNA amplification to DNA microarrays. Changes in expression levels implicated a number of genes: lamina ancestor, CG12534 (a gene orthologous to mouse augmenter of liver regeneration), Notch pathway members, and the Polycomb and trithorax groups of chromatin regulators. Functional tests revealed that transdetermination was significantly affected in mutants for lama and seven different PcG and trxG genes. These results validate our methods for expression profiling as a way to analyze developmental programs, and show that modifications to chromatin structure are key to changes in cell fate. Our findings are likely to be relevant to the mechanisms that lead to disease when homologs of Wingless are expressed at abnormal levels and to the manifestation of pluripotency of stem cells.
Keywords: cell type comparison, response to genetic alteration (Wingless over-expression) or mechanical injury (regeneration)

overall_design:
Seeking to identify genes expressed in TD cells, we overexpressed Wg just after the molt to the third instar, and 3 days later isolated leg discs prior to pupariation. Probes generated from mRNA by linear amplification were applied to DNA microarrays. In order to distill the genes involved in transdetermination from the expression profiles of more than 14,000 genes of transdetermining (TD) cells, we generated nine different types of samples for control and comparative purposes: (1) wild-type wing (W); (2) leg (L) discs of 3rd instar larvae; (3-6) dorsal and ventral cells from both wild-type and Wg-expressing discs (D(wt), V(wt), D(wg) and V(wg)); (7) intact Wg-induced 1st leg discs; (8) micro-dissected TD cells from these discs (TD); and (9) 3/4 fragments of 2nd leg discs that were cultivated to obtain a population of regenerating cells (Sustar and Schubiger, 2005). Last, we prepared a ‘reference sample’ of wild-type leg discs by pooling amplified RNA of 1st, 2nd and 3rd leg discs of third instar male and female wildtype larvae. DNA arrays were hybridized to pairs of probes that had been generated from the same larva or, when this was impractical, to the common reference sample.
Strong overexpression of Wg produces ectopic growth in 1st leg discs. Previously, we have shown that this response to Wg overexpression is region specific (Maves and Schubiger, 1998; Sustar and Schubiger, 2005). Cells in the ventral part of the disc (VWg cells) produce only structures characteristic of this region – ‘fate map structures’. Cells in the dorsal part respond in two ways. Dorsal cells in the ‘weak point’ (TD cells) transdetermine to wing; dorsal cells surrounding the transdetermined region (DWg cells) regenerate a new posterior compartment. These two dorsal populations can be distinguished in the disc with the use of a reporter transgene that expresses GFP under the control of the vg boundary enhancer (vgBE) (Kim et al., 1996; Williams et al., 1991). Leg-to- wing transdetermination depends upon vg expression driven by the vgBE and expression of the vgBE-GFP reporter clearly marks transdetermining leg cells (Maves and Schubiger, 1998).
The 9 categories of experiments are:
category #1: prothoracic leg disc vs. reference (4 independent replicates, 1 dye-swap);
category #2: wing vs leg imaginal discs (9 independent replicates, 4 dye-swaps);
category #3: wg-induced 1st leg disc vs. reference (6 independent replicates, 3 dye-swaps);
category #4: TD cells vs. D(wg) cells (3 independent replicates, 1 dye-swap);
category #5: TD cells vs. V(wg) cells (5 independent replicates, 2 dye-swaps);
category #6: D(wg) cells vs V(wg) cells (3 independent replicates, 2 dye-swaps);
category #7: TD cells vs. D(wt) cells (2 independent replicates, 2 dye-swaps);
category #8: D(wt) cells vs V(wt) cells (3 independent replicates, 1 dye-swap);
category #9:regenerating discs vs reference (4 independent replicates, 2 dye-swaps);

first: Anne

last: Sustar

first: Katherina

last: Kechris

first: Hao

last: Li

first: Gerold

last: Schubiger

first: Thomas

last: Kornberg


title: Continuous GH treatment of old rat liver

status: Public on Jul 19 2005

city: Stockholm

first: Amilcar

last: Flores

country: Sweden

institute: Karolinska Institute

summary:
Effect of continuous GH treatment on old rat liver.  Male rats, 2-year-old, were treated with vehicle or human GH (0.34 microgram/gram body weight) for 3 weeks.
Keywords: response of old rat liver to growth hormone

overall_design: Comparison of treated and untreated rats.  Individual RNA were used for 4 microarray hybridization. Dye swapped.


title: CpG island methylation

status: Public on Jul 03 2005

city: Basel

first: Michael

last: Weber

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

type: Methylation profiling by genome tiling array

summary:
We compare the methylation status of CpG island clones by MeDIP in SW48 colon cancer cells relative to normal colon mucosa and WI38 primary fibroblasts.
Keywords: ordered

first: Jonathan

last: Davies

first: David

last: Wittig

last: Haase

first: Wan

last: Lam

first: Dirk

last: Schubeler


title: Gene expression in the Gli3Xt/Xt Vs wildtype developing limb

status: Public on Jul 01 2005

first: Sean

last: Grimmond

state: QLD

address: IMB, Uni of Qld

institute: Institute of Molecular Bioscience

summary:
We used microarray technology to investigate the transcriptional consequences of loss of Gli3
from the anterior mesenchyme of the developing mouse limb bud at both E11.5 and E12.5.
Comparisons were made between RNA derived from the anterior margin of Gli3Xt/Xt limb buds
and that derived from wild type littermates
Keywords: genetic modification

overall_design: The experiment contains a series of pairwise comparisons between staged mutant Gli3(Xt/Xt) and WT anterior portions of limb bud at 11.5dpc and 12.5dpc. Forelimbs and hindlimbs were studied independently given the developmental delay between limb buds.

first: Edwina

last: McGlinn

first: Kelly

last: Lammerts van Bueren

first: Salvatore

last: Fiorenza

first: Rong

last: Mo

first: Alisa

last: Po

first: Alistair

middle: R

last: Forrest

first: Marcelo

last: Soares

first: Maria

last: de Fatima Bonaldo

first: Chi-Chung

last: Hui

first: Brandon

last: Wainwright

first: Carol

last: Wicking


title: UPRT Transgenic cells, Human Arrays

last: Stanford Microarray Database

department: Stanford University, School of Medicine

summary:
UPRT Transgenic and wildtype control cells of both HeLa and U373MG tissue culture lines were grown in the presence of 2mM 2,4-dithiouracil for either 6 hours (HeLa) or 8 hours (U373MG) and total RNA, not thiouracil-purified, from both transgenic and wildtype samples was compared on microarrays.
An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
Keywords: all_pairs

overall_design: Computed

first: Michael

last: Cleary


first: Darrin

last: Taylor

institute: Institute for Molecular Bioscience, Uni of Qld

summary:
Direct comparison of dissected pools of 11.5dpc metanephroi V 13.5dpc fetal kidneys.
Keywords: repeat sample


title: microRNA expression during early zebrafish development

status: Public on Jul 04 2005

city: Cambridge

first: Eric

middle: A.

last: Miska

address: Tennis Court Rd

department: Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry We

institute: University of Cambridge

summary:
Values from samples in this series should be normalised prior to any comparison. Control probes used for normalisation are pre-3, pre-4 and pre-5.
Keywords = miRNA
Keywords = microRNA
Keywords = zebrafish
Keywords = Danio rerio
Keywords = development
Keywords: ordered

first: Erno

last: Wienholds

first: Wigard

last: Kloosterman

first: Ezequiel

last: Alvarez-Saavedra

first: Eugene

last: Berezikov

first: Ewart

last: de Bruijn

first: Niels

last: Tolstrup

first: R

middle: H

last: Horvitz

first: Sakari

last: Kauppinen

first: Ronald

last: Plasterk


title: Identification of Hundreds of Conserved and Non-conserved Human MicroRNAs

status: Public on Jun 19 2005

city: Rehovot

first: Omer

last: Barad

address: Plaut 10, Science Park

country: Israel

institute: Rosetta Genomics Ltd.

summary:
Determining the expression of known and computationally predicted microRNAs by microRNA microarray in several tissues (placenta, testis, thymus, brain and prostate)
Keywords: parallel sample

overall_design: microRNAs expression profile

first: Isaac

last: Bentwich

first: Amir

last: Avniel

first: Yael

last: Karov

first: Ranit

last: Aharonov

first: Shlomit

last: Gilad

first: Adi

last: Barzilai

first: Paz

last: Einat

first: Uri

last: Einav

first: Eti

last: Meiri

first: Eilon

last: Sharon

last: Spector

first: Zvi


title: Identification of PM-localized proteins

status: Public on Jun 21 2005

city: Madison

first: Michael

last: Sussman

state: WI

address: 425 Henry Mall

department: Biotechnology Center

institute: University of Wisconsin

summary:
In order to assess the quality of alleged PM identifications from Arabidopsis, PM-enriched fractions were compared to PM-depleted fractions using 18O isotopic labeling and mass spectrometry. The two samples submitted are biological replicates.
Keywords: Protein Localization via MS

overall_design: Two biological replicates were analyzed in order to assess sample complexity.  PM-derived vesicles were digested in 18O water and compared to PM-depleted fractions digested in 16O (natural abundance) water.  Relative ion intensities were then used to calculate a heavy/lite ratio with proteins showing enrichment in the upper phase having a ratio greater than 1 or 0 on a log2 scale.

first: Clark

last: Nelson

first: Adrian

middle: D

last: Hegeman

first: Amy

last: Harms


title: Basal gene expression in dam, dam mutS, and mutS mutant E. coli strains

first: Jennifer

last: Robbins

address: 77 Massachusetts Ave.

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary:
We determined the global gene expression profiles of wildtype, dam, dam mutS, and mutS mutant E. coli strains.
Keywords: Basal gene expression comparison

overall_design: Overnight cultures were diluted 1000-fold with fresh LB medium and cultured further.  Log phase cultures were diluted to a cell density of 2 X 108 cells/ml in M9 salts and incubated at 37°C for two hours, after which they were resuspended in LB broth for 90 minutes.  This treatment served as a mock treatment for cultures incubated with a chemical (cisplatin) in a parallel study (Robbins et al., unpublished results). Total RNA was isolated from cells by extraction using the MasterPure RNA Purification Kit (Epicentre Technologies) followed by DNAse digestion according to the manufacturer’s protocol.  The isolated total RNA was quantitated by absorption at 260 nm (typical yield from a 15 ml culture was 250-500 µg of total RNA), and the purity was determined by the ratio of absorption values at 260/280nm.  RNA quality was determined by formaldehyde agarose gel electrophoresis (1.2% agarose in FA Buffer pH 7.0 (20 mM 3-[N-morpholino]propanesulfonic acid, 5 mM sodium acetate, 1 mM ethylenadiaminetetraacetic acide (EDTA))) or by analysis on an Agilent 2100 Bioanalyzer.  All samples visualized by gel electrophoresis or by the bioanalyzer electropherogram showed clear distinct bands correlating to 16S and 23S ribosomal RNA, indicating that no detectable RNA degradation occurred and that RNA integrity was maintained throughout the RNA isolation procedure. mRNA was enriched from total RNA as described in the Affymetrix GeneChip Expression Analysis Technical Manual for GeneChip E. coli Sense Genome Arrays.

first: Zoran

last: Zdraveski

first: Martin

last: Marinus

first: John

last: Essigmann


title: Epigenomic profiles

city: Vancouver

first: Jon

last: Davies

state: BC

address: 675 W 10th Ave

institute: BC Cancer Research Centre

summary:
Chromosomal methylation profiles of normal and transformed cell lines
Keywords: parallel sample

last: Weber

first: Jonathan

first: David

last: Wittig

first: Edward

last: Oakeley

last: Haase

first: Wan

middle: L

last: Lam

first: Dirk

last: Schübeler


title: Substance P receptor-dependent genes and TFs

status: Public on Jun 17 2005

first: Ricardo

last: Saban

summary:
Tachykinins (TKs) are a family of peptides involved in the peripheral and central regulation of urinary functions through the stimulation of neurokinin (NK) NK1, NK2 and NK3 receptors. Recent evidence indicates that NK1 receptors are required in antigen-induced cystitis. Therefore, determining the regulatory network downstream NK1 receptor activation is a key step toward understanding the role of TKs in inflammation.

For this purpose, we used a Transcriptional Regulatory Network Analysis (TRNA) to identify biologically relevant transcriptional regulatory elements (TRE) that underline the NK1-dependent gene expression in bladder responses to inflammation.  Gene expression analysis was obtained using the urinary bladder isolated from WT and NK1-R-/- mice that were stimulated with intravesical instillation of saline or antigen challenge (in sensitized mice) in order to promote cystitis.  Based on cDNA array results, we selected a cluster of genes that was dependent on NK1 receptors for their up-regulation in response to inflammation.  Next, we used PAINT database to retrieve upstream promoter sequences for those NK1-R-dependent genes and to identify TREs on those promoters.  Finally, TREs were enriched statistically by selecting only those that were significantly expressed and a regulatory network downstream of NK1 receptor activation was determined.

This work indicates an overriding participation of NK1 receptors in bladder inflammation, provides a working model for the involvement of transcription regulators such as AP1, NF-kB, and Nkx-2.5, and evokes testable hypotheses regarding the regulatory network downstream of NK1 receptor activation.
Keywords: URINARY BLADDER INFLAMMATION

overall_design: All mice in this study were sensitized with 1 µg DNP4-human serum albumin (HSA) in 1 mg alum on days 0, 7, 14, and 21, intraperitoneally (i.p.).  In normal mice, this protocol induces sustained levels of IgE antibodies up to 56 days post-sensitization (20).  One week after the last sensitization, cystitis was induced. Briefly, sensitized WT and NK1R-/- mice were anesthetized (ketamine 40 mg/kg and xylazine 2.5 mg/kg, i.p.), then transurethrally catheterized (24 Ga.; 3/4 in; Angiocath, Becton Dickson, Sandy, Utah), and the urine was drained by applying slight digital pressure to the lower abdomen.  The urinary bladders were instilled with 200 µl of pyrogen-free saline or DNP4-OVA (1 µg/ml).  One, four, and twenty-four hours after instillation, mice were sacrificed with pentobarbital (100 mg/kg, i.p.) and bladders were removed rapidly. Gene expression was determined using Clontech 1.2 K arrays and genes specifically regulated in the WT were compared with those upregulated in NK1 KO. We have employed a bioinformatics approach to hypothesize functionally relevant transcriptional regulatory elements (TREs) of NK1R-dependent and -independent genes. We used the Promoter Analysis and Interaction Network Toolset (PAINT) available online at http://www.dbi.tju.edu/dbi/tools/paint (58). PAINT is a suite of bioinformatics and computational tools that integrate functional genomics information, as is the case of our microarray-based gene expression data, with genomic sequence and TRE data to derive hypotheses on the TREs relevant to the biological function under study. The TRE hypotheses are generated from statistical enrichment analysis and are defined as those TREs that are significantly enriched such as NK1R-dependent and –independent genes over random occurrence in the gene groups (58). The random occurrence is relative to a ‘reference’: all the genes on the microarray. Employing the microarray accounts for any ‘bias’ present in the genes on the microarray relative to entire genome and guards from incorrectly concluding that certain TREs are relevant to the current experiment.

first: Rajanikanth

last: Vadigepalli

first: Marcia


title: leaf_greenhouse

status: Public on Jun 15 2005

city: Leuven

first: Bert

last: Coemans

address: Kasteelpark Arenberg 13

department: department of biosystems - division of crop biotechnics

country: Belgium

institute: Katholieke Universiteit Leuven

summary: SuperSAGE was applied in the non-model organism banana (Musa acuminata)

overall_design: one leaf sample was analysed, no replicates were included

first: Hideo

last: Matsumura

first: Ryohei

last: Terauchi

first: Serge

last: Remy

first: Rony

last: Swennen

first: László

last: Sági


title: Radiation-induced changes in gene expression in the silkworm revealed by serial analysis of gene expression

status: Public on Jun 20 2005

city: Shanghai

first: Huang

last: Jianhua

institute: Shanghai Institute of Plant Physiology ang Ecology

summary: These results provide valuable information for understanding the mechanisms of radiation-induced changes in gene expression.

first: Jianhua

last: Huang

first: Xuexia

last: Miao

first: Weirong

last: Jin

first: Pierre

last: Cobble

first: Yong

last: Zhang

first: Wenbin

last: Liu

first: Yan

last: Shen

first: Guoping

last: Zhao


title: Affymetrix 100K SNP array data-

status: Public on Jul 02 2005

city: Boston

first: William

middle: R.

last: Sellers

address: 44 Binney Street

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
allele call files from analysis of NCI60 cell line DNA on 100K SNP arrays.
Keywords = NCI60, SNP array, cancer cell line
Keywords: other

first: Levi

last: Garraway

first: Hans

last: Widlund

first: Mark

last: Rubin

first: Gad

last: Getz

first: Aaron

last: Berger

first: Sridhar

last: Ramaswamy

first: Rameen

last: Beroukhim

first: Danny

last: Milner

first: Scott

last: Granter

first: Jinyan

last: Du

first: Charles

last: Lee

first: Stephan

middle: N

last: Wagner

first: Cheng

last: Li

first: Todd

last: Golub

first: David

last: Rimm

first: Matthew

last: Meyerson

last: Fisher


title: miRNA expression in zebrafish tissues

status: Public on Jul 05 2005

first: Eric

last: Miska

summary:
comparison of miRNA expression in zebrafish tissues
Keywords = miRNA
Keywords = microRNA
Keywords = zebrafish
Keywords = Danio rerio
Keywords = development
Keywords: other

first: Erno

last: Wienholds

first: Wigard

last: Kloosterman

first: Ezequiel

last: Alvarez-Saavedra

first: Eugene

last: Berezikov

first: Ewart

last: de Bruijn

first: Niels

last: Tolstrup

first: H

last: Horvitz

first: Sakari

last: Kauppinen

first: Ronald

last: Plasterk


title: Mecp2_null_versus_wt

status: Public on Jun 14 2005

first: Ulrike

last: Nuber

address: Ihnestrasse 73

institute: Max Planck Institute for molecular Genetics

summary:
This study aimed to identify target genes of MECP2 in the mouse brain. Genes differentially expressed in Mecp2 null and wt brain were found.
Keywords: Total brain tissue comparison

overall_design: This was a dye-swap experiment. RNA was isolated from total brain tissue of a 74 day old Mecp2-/y (Mecp2 null) animal with late symptoms (gait ataxia, hind limb clasping, breathing irregularities, uneven teeth, small stature) and a wild-type male littermate. Sample1 (wt) was labeled with Cy3 and sample2 (Mecp2 null) was labeled with Cy5 in the first co-hybridization experiment. In the dye swap experiment, sample1 (wt) was labeled with Cy5 and sample2 (Mecp2 null) was labeled with Cy3.


title: Comparison of polyribosomal to total transcript profiles

status: Public on Jun 06 2005

city: Tucson

middle: William

last: Galbraith

state: AZ

address: 303 Forbes Building

department: Plant Sciences and Bio5 Institute

institute: University of Arizona

summary:
Total and polyribosomal RNA was extracted from rosette leaves of 5-6-week-old wild-type and transgenic Arabidopsis plants (ecotype Col-0). After linear amplification using a modified Eberwine procedure, Cy3- or Cy5-labeled cDNA targets were produced from sense-strand RNA through reverse transcription
Keywords: repeat sample


title: Macrodissection versus Microdissection of Rectal Carcinoma: Minor Influence of Stroma to Tumor Gene Profiles

status: Public on Jun 07 2005

city: Leiden

first: Elza

last: de Bruin

country: Netherlands

institute: Leiden University Medical Center

summary:
Background: The molecular determinants of carcinogenesis, tumor progression and patient prognosis can be deduced from simultaneous comparison of thousands of genes by microarray analysis. However, the presence of stroma cells in surgically excised carcinoma tissues might obscure the tumor cell-specific gene expression profiles of these samples. To circumvent this complication, laser microdissection can be performed to separate tumor epithelium from the surrounding stroma and healthy tissue. In this report, we compared RNAs isolated from macrodissected, of which only surrounding healthy tissue had been removed, and microdissected rectal carcinoma samples by microarray analysis in order to determine the most reliable approach to detect the expression of tumor cell-derived genes by microarray analysis.
Results: As microdissection yielded low tissue and RNA quantities, extra rounds of mRNA amplification were necessary to obtain sufficient RNA for microarray experiments. These second rounds of amplification influenced the gene expression profiles. Moreover, the presence of stroma cells in macrodissected samples had a minor contribution to the tumor cell gene expression profiles, which can be explained by the observation that more RNA is extracted from tumor epithelial cells than from stroma.
Conclusion: These data demonstrate that the more convenient procedure of macrodissection can be adequately used and yields reliable data regarding the identification of tumor cell-specific gene expression profiles.
Keywords: macrodissection, microdissection, RNA amplification, stroma, rectal carcinoma

overall_design: Fresh frozen rectal carcinoma samples were obtained from 14 different rectal carcinoma patients. All 14 rectal carcinoma samples are macrodissected or microdissected for tumor epithelium. Six macrodissected samples were in addition amplified a second round and of four samples the stroma was microdissected as well. Six samples were replicated, of which one sample was an amplification duplicate experiment and the other five samples were labelling replicates.

first: Simone

last: van de Pas

first: Esther

last: Lips

last: van Eijk

first: Minke

last: van der Zee

first: Marcel

last: Lombaerts

first: Tom

last: van Wezel

first: Corrie

last: Marijnen

first: Han

last: van Krieken

first: Jan

last: Medema

first: Cornelis

last: van de Velde

first: Paul

last: Eilers

first: Lucy

last: Peltenburg


title: Hypoxia response

status: Public on Jun 25 2005

first: Min

last: Jiang

state: CA

institute: Stanford University

summary:
The goal of the study was to identify hypoxia-induced gene expression changes in C. elegans and to determine which of these responses to hypoxia were regulated by hif-1. Towards these aims, we analyzed mRNA expression patterns in synchronized populations of wild-type worms that were cultured in standard lab conditions (normoxia) or in hypoxia.  We also assayed mRNA from two mutant strains:  (i) animals carrying the strong loss-of-function mutation in hif-1 and (ii) C. elegans that carry a deletion in vhl-1 and express the HIF-1 protein at constitutively high levels.
In the microarray experiments, 3 strains were assayed:  wild type N2, hif-1 (ia04), and vhl-1 (ok161).  Worms were incubated for 4 hours in 21% oxygen or 0.1% oxygen at 210C.  Animals were quickly harvested in ice cold M9 buffer, and poly (A) RNA was isolated using established procedures.  No more than 3 minutes elapsed between the removal of plates from the hypoxic chamber and the addition of Trizol. RNA was isolated from three independent experiments for each experimental condition (3 genotypes; normoxia vs hypoxia).  mRNAs were hybridized to whole-genome microarrays which contained probes for 17,817 predicted genes (94% of the genome).
Ch1 in the array represents the data for the worms growed under hypoxia; and Ch2 in the array reprents the data for the worms growed under normoxia.
Keywords: Biological Replicates

overall_design: Set of arrays that are part of repeated experiments

first: C

last: Shen


title: Comparison of IS5 Deletion mutant to E.coli Motile and NonMotile Isolates

status: Public on Jun 02 2005

city: Saint Paul

first: Betsy

last: Martinez-Vaz

state: MN

address: 1479 Gortner Ave

department: Biochemistry , Molecular Biology and Biophysics

institute: University of Minnesota

summary:
These series of experiments compares the expression profile of the motility variants of E.coli MG1655 ( Motile and NonMotile isolates) to an isogenic E.coli MG1655 strain in which the IS5 upstream of flhDC has been deleted.

The expression profiles of genes in the E.coli MG1655 motile isolate and E.coli MG1655 Non_Motile isolate also compared.
Keywords: parallel sample

middle: M

first: Yang

last: Xie

first: Wei

last: Pan

first: Arkady

last: Khodursky


title: Detecting novel low-abundant transcripts in Drosophila

status: Public on Jun 03 2005

city: Evanston

first: San Ming

last: Wang

address: 1001 University Place

department: Center for Functional Genomics

institute: ENH Research Institute, Northwestern University

summary:
Increasing evidence suggests that low-abundant transcripts may play fundamental roles in biological processes. In an attempt to estimate the prevalence of low-abundant transcripts in eukaryotic genomes, we performed a transcriptome analysis in Drosophila using the SAGE technique. We collected 244,313 SAGE tags from transcripts expressed in Drosophila embryonic, larval, pupae, adult, and testicular tissue.
From these SAGE tags, we identified 40,823 unique SAGE tags. Our analysis showed that 55% of the 40,823 unique SAGE tags are novel without matches in currently known Drosophila transcripts, and most of the novel SAGE tags have low copy numbers. Further analysis indicated that these novel SAGE tags represent novel low-abundant transcripts expressed from loci outside of currently annotated exons including the intergenic and intronic regions, and antisense of the currently annotated exons in the Drosophila genome. Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies.
Keywords: other

first: Sanggyu

last: Lee

first: Jingyue

last: Bao

first: Guolin

last: Zhou

first: Joshua

last: Shapiro

first: Jinhua

last: Xu

first: Run Zhang

last: Shi

first: Xuemei

last: Lu

first: Terry

last: Clark

first: Deborah

last: Johnson

first: Yeong

last: Kim

first: Claudia

last: Wing

first: Charles

last: Tseng

last: Lin

last: Sun

first: Jun

first: Huanming

last: Yang

first: Jian

last: Du

first: Chung-I

last: Wu

first: Xiuqing

last: Zhang


title: Tiling Array HSF immunopurification

status: Public on May 30 2005

first: Steve

last: Russell

address: Downing Street

department: Department of Genetics

summary:
Mapping of in vivo Heat Shock Factor binding sites in drosophila embryos with genomic tiling arrays
Keywords: repeat sample

first: Steven

first: Robert

middle: A

last: White

first: Ian

last: Birch-Machin

first: Shan

last: Gao

first: David

last: Huen

first: Richard

last: McGirr


status: Public on Jun 01 2005

city: Mountain View

first: Mark

last: Fielden

address: 325 East Middlefield Road

institute: Iconix Biosciences

summary:
Development of a Large-Scale Chemogenomics Database to Improve Drug Candidate Selection and to Understand Mechanisms of Chemical Toxicity and Action
These data support the publication titled "Development of a Large-Scale Chemogenomics Database to Improve Drug Candidate Selection and to Understand Mechanisms of Chemical Toxicity and Action"
Copyright (c) 2005 by Iconix Pharmaceuticals, Inc.

Guidelines for commercial use:
http://www.iconixbiosciences.com/guidelineCommUse.pdf
Keywords: other

first: Brigitte

last: Ganter

first: Stuart

last: Tugendreich

first: Cecelia

middle: I

last: Pearson

first: Eser

last: Ayanoglu

first: Susanne

last: Baumhueter

first: Keith

last: Bostian

first: Lindsay

last: Brady

first: Leslie

middle: J

last: Browne

first: John

middle: T

last: Calvin

first: Gwo-Jen

last: Day

first: Naiomi

last: Breckenridge

first: Shane

last: Dunlea

first: Barrett

middle: P

last: Eynon

first: Mike

last: Furness

first: Joe

last: Ferng

first: Susan

middle: Y

last: Fujimoto

first: Li

last: Gong

first: Christopher

last: Hu

first: Radha

last: Idury

first: Michael

middle: S

last: Judo

first: Kyle

last: Kolaja

first: May

last: Lee

last: McSorley

first: James

last: Minor

first: Ramesh

middle: V

last: Nair

first: Georges

last: Natsoulis

first: Peter

last: Nguyen

first: Simone

last: Nicholson

first: Hang

last: Pham

first: Alan

last: Roter

first: Dongxu

first: Siqi

last: Tan

first: Silke

last: Thode

first: Alexander

last: Tolley

first: Antoaneta

last: Vladimirova

first: Zhiming

last: Zhou


title: IS5mapping isolates A and B

first: Betsy

last: Martinez-Vaz

summary:
These series contains the controls and the experimental arrays used to map IS5 elements in the E.coli isolates in group A and B. Group A isolates were later named "Motile" isolates, and Group B named "NonMotile.
Keywords: parallel sample

first: Yang

last: Xie

first: Wei

last: Pan

first: Arkady

middle: B

last: Khodursky


title: Gastric Cancer Study GC_126

status: Public on May 25 2005

city: San Francisco

first: Xin

last: Chen

institute: UCSF

summary:
126 gastric tissues (90 tumor, 14 lymphnode and 22 normal) assayed using 44K human arrays against common reference (CRG). Published by Leung et al, PNAS, 2002 (PubMed ID 12456890) and Chen et al, MBC, 2003.
A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc.
Series_overall_design: Using regression correlation
Keywords: other


title: Big bluestem/RAMP experiment

city: Fargo

first: Steve

last: Travers

state: ND

address: 218 Stevens Hall

department: Biological Sciences

institute: North Dakota State University

summary:
On September 13, 2003, leaf tissue was collected from Andropogon gerardii growing in field plots under two precipitation variability treatments:ambient and altered (50% longer interval). cDNA was synthesized, labelled alternately with Cy3 and Cy5 and cross-hybridized to a maize microarray developed in the Schnable lab at Iowa State.
Keywords: repeat sample

first: Steven

middle: E

first: Jianfa

last: Bai

first: Scot

last: Hulbert

first: Jan

last: Leach

first: Pat

last: Schnable

middle: K

last: Knapp

first: Philip

last: Fay

first: Melinda

last: Smith

first: Karen

last: Garrett


title: HaCaT +GLI1/2 24/72h

city: Salzburg

first: Veronika

last: Sander

address: Hellbrunnerstrasse 34

department: Molecular Biology

country: Austria

institute: University of Salzburg

summary:
hybridisation of mRNA from HaCaT keratinocytes expressing GLI1 or GLI2 in an tet-inducible manner for 24h or 72h on Incyte clone set

Detailed information about the protocols we used for array production, hybridisation and analysation and the biological background of our experiments can be found in our publications:

PMID: 15140221, 14691458, 12165851

Keywords = GLI1/2 target genes
Keywords: time-course

first: Thomas

last: Eichberger

first: Gerhard

last: Regl

first: Fritz

last: Aberger

first: Anna-Maria

last: Frischauf


title: Transcriptome effects of silencing a MAPK (SIPK) in tobacco

status: Public on May 19 2005

city: Rockville

first: Li

last: Zheng

state: MD

address: 9712 Medical Center Dr.

institute: The Institute for Genomic Research

summary:
Wildtype and SIPK -silenced (RNAi) tobacco cell suspension cultures were grown in MS medium at 25 C in the dark. Cell suspension cultures were transferred to fresh growth medium 3 days prior to pooling each genotype and dividing the pool into 3 x 10ml volumes per genotype. A 30 minute pre-incubation was used with xanthine (for abiotic controls and treatments), but no pre-treatment was used for the biotic stressors. For each treatment and abiotic/biotic controls, the cells were harvested by vacuum filtration at the appropriate time points (controls sampled at 0 hrs) and frozen in N2(l) for RNA extraction. In order to discern the effect of silencing SIPK on the transciptome in defence response, biological replicates of WT and SIPK-Ri were randomly paired on 3 slides per treatment or control group.
Series_weblink: http://www.tigr.org/tdb/potato
Keywords = potato, Biotic stress
Keywords: ordered

first: Brian

last: Ellis


title: Drosophila melanogaster technical error assessment using larvae and adults,

status: Public on May 12 2005

first: Scott

last: Rifkin

state: MA

address: 16 Divinity Ave

department: OEB

institute: Harvard University

summary:
Assessment of technical error in a dual-channel, two timepoint experiment using White lab Drosophila melanogaster microarrays
Keywords: repeat sample


title: mouse ventilator-induced lung injury

status: Public on May 10 2005

city: Pittsburgh

first: Tamas

last: Dolinay

state: PA

department: Pulmonary, Allergy and Critical Care

institute: Univerisity of Pittsburgh Medical Center

summary:
Isolated perfused and ventilated BALB/c mouse lung model
3 conditions
c-10cmH2O pressure ventilation 3h, LPS-10cmH2O pressure ventilation 3h in the presence of E. coli LPS in the perfusion buffer (3mg/kg),
ov-overventilation with 25cmH2O pressure 3h
Keywords: parallel sample

first: Naftali

last: Kaminski

first: Hong

last: Kim

first: Paul

last: Reynolds

first: Doerte

last: Karp

first: Stefan

last: Uhlig

first: Augustine

last: Choi


title: Identification of targets of Ultrabithorax

status: Public on May 17 2005

city: Hyderabad

first: L S

last: Shashidhara

state: AP

address: Uppal Road

country: India

institute: Centre for Cellular and Molecular Biology

summary:
The identity of every segment in the fruitfly Drosophila melanogaster is determined by the action of one or more homeotic selector genes. These genes encode proteins containing DNA-binding domains and function by regulating downstream target genes. The structure and function of homeotic genes are highly conserved across a wide range of animals including human. Although much information is available on the molecular and biochemical nature of homeotic genes, comparatively little is known regarding the mechanism/s that are used to generate segmental diversity. This series of experiments were carried out to determine targets of the homeotic gene Ultrabithorax.
Keywords: other

first: Prasad

last: Mohit

first: M

last: Madhavi

first: Gururaj

last: Sirdesai

first: L


title: Hepatic changes after 17 alpha Ethinylestradiol treatment (1D) of male rats

status: Public on May 04 2005

city: Stockholm

first: Amilcar

last: Flores

institute: Karolinska Institute

summary:
Male  rat treated with 17-alpha-Ethinylestradiol for 24 hours. Hepatic gene expression changes in comparison with control, excepient treated rats.
Keywords: repeat sample


title: GH effects on primary hepatocytes from male rats

summary:
Effects of bGH treatment of primary hepatocytes cultured on matrigel
Keywords: repeat sample