title: Nutrient-dependent regulation of gene expression in Saccharomyces cerevisiae

status: Public on May 25 2010

city: Göteborg

first: Goutham

last: Vemuri

address: Kemivagen 10

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary:
Fatty acid synthesis is closely linked to nutrient availability and cellular energetic status. The committed step in fatty acid synthesis is the acetyl CoA carboxylase. Eukaryotes have two genes encoding acetyl CoA carboxylases, one encoding a cytosolic enzyme and another coding for a mitochondrial enzyme. They catalyze the synthesis of malonyl CoA in the cytosol and the mitochondria, respectively. While cytosolic malonyl CoA is the precursor for fatty acid synthesis, mitochondrial malonyl CoA controls the transfer of fatty acyl group into the mitochondria by inhibiting carnitine/palmitoyl transferase activity and thus, regulates β-oxidation. In Saccharomyces cerevisiae, β-oxidation is restricted to the peroxisomes, raising the question of the function of the mitochondrial isoform (HFA1). In this study, we replaced the cytosolic Acc1 with Hfa1 expressed in the cytosol by removing the mitochondrial leader peptide, under control of the HFA1 promoter. We studied fatty acid synthesis and transcription profiles in this strain during starvation for carbon or nitrogen, using glucose or ethanol as the carbon source. Under all the conditions studied, the key sensor of energetic status, Snf1, was activated, indicating active inhibition of fatty acid synthesis. The pool size of fatty acids was smaller when Acc1 was replaced with truncated Hfa1 for fatty acid synthesis. Yet, the transcription profiles were similar in both the cases. These results point towards the conclusion that Hfa1 is either catalytically less efficient or it is more sensitive to inhibition by Snf1.
Gene expression from a strain of Saccharomyces cerevisiae where cytosolic fatty acid synthesis occurs by mitochondrial acetyl CoA carboxylase (without its mitochondrial leader peptide) is compared with that in a reference strain while growing in chemostats on carbon or nitrogen starvation using glucose or ethanol as the carbon source.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design:
There are two strains (reference or mutant), two carbon sources (glucose or ethanol) and two limitations (carbon or nitrogen), resulting in 8 comparisons. Each array was performed in duplicate, resulting in 16 CEL files.
Growth was limited by either carbon or nitrogen. When carbon was the limited nutrient, we tested growth on either glucose or ethanol (both using ammonium sulfate as the nitrogen source). When ammonium sulfate was limiting, we used either glucose or ethanol as the carbon source.


title: Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity (1 of 2)

status: Public on Feb 11 2011

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

country: USA

institute: NIH

summary:
BACKGROUND: In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but also poised for activation. However, the responsiveness of genes to perturbations has never been studied systematically. To distinguish gene responses to specific factors from responsiveness in general, it is necessary to analyze gene expression profiles of cells responding to a large variety of disturbances, and such databases did not exist before.

RESULTS: We estimated the responsiveness of all genes in mouse ES cells using our recently published database on expression change after controlled induction of 53 transcription factors (TFs) and other genes. Responsive genes (N = 4746), which were readily upregulated or downregulated depending on the kind of perturbation, mostly have regulatory functions and a propensity to become tissue-specific upon differentiation. Tissue-specific expression was evaluated on the basis of published (GNF) and our new data for 15 organs and tissues. Non-responsive genes (N = 9562), which did not change their expression much following any perturbation, were enriched in housekeeping functions. We found that TF-responsiveness in ES cells is the best predictor known for tissue-specificity in gene expression. Among genes with CpG islands, high responsiveness is associated with H3K27me3 chromatin marks, and low responsiveness is associated with H3K36me3 chromatin, stronger tri-methylation of H3K4, binding of E2F1, and GABP binding motifs in promoters.

CONCLUSIONS: We thus propose the responsiveness of expression to perturbations as a new way to define the dynamic status of genes, which brings new insights into mechanisms of regulation of gene expression and tissue specificity.

overall_design: Total RNA was isolated by TRIzol (Invitrogen) after 2 days. Cy3-CTP labeled sample targets were prepared with total RNA by Low RNA Input Fluorescent Linear  Amplification Kit (Agilent). Cy5-CTP labeled reference target was produced from mixture of Stratagene Universal Mouse Reference RNA and MC1 cells RNA. Most samples were collected in 2 replications taken from different animals, except bone and fat, which had only one replication.

first: Alexei

middle: A

last: Sharov

first: Akira

last: Nishiyama

first: Yulan

last: Piao

first: Lina

last: Correa-Cerro

first: Tomokazu

last: Amano

first: Marshall

last: Thomas

first: Samir

last: Mehta

middle: S


title: Skeletal muscle biopsies before and after hyperinsulinemic-euglycemic clamp

status: Public on Jun 04 2010

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

summary:
6 lean humans were submitted to a 3 hours hyperinsulinemic-euglycemic clamp. Skeletal muscle biopsies were taken before and after the clamp.
Set of arrays that are part of repeated experiments

overall_design:
Biological Replicate
Computed

first: Karine

last: Clement


title: Transcriptome analysis of Streptococcus mutans biofilms in response to starch and sucrose.

status: Public on May 15 2010

city: Rochester

first: Marlise

middle: I

last: Klein

state: NY

address: 601 Elmwood Ave.

department: Dentistry - Center for Oral Biology

institute: University of Rochester

summary: Transcriptional profiling to investigate the response of Streptococcus mutans biofilms to starch and sucrose at distinct stages of biofilm development.

overall_design: RNA was extracted and purified from four replicate samples of each biofilm sample of interest and labeled with Cy3. For each replicate, labeled RNA was hybridized to slides along with Cy5-labeled reference RNA, extracted from S. mutans UA159 cells grown to mid-log.

first: Hyun

last: Koo

first: Jose

last: Lemos


title: The Leukemia-associated Mllt10/Af10- Dot1l, dedicated b-catenin coactivators essential for intestinal homeostasis

status: Public on Apr 20 2010

city: London

first: Vivian

last: Li

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

summary:
Background: Wnt signaling maintains the undifferentiated state of intestinal crypt progenitor cells by inducing the formation of nuclear TCF4/beta-catenin complexes. In colorectal cancer, activating mutations in Wnt pathway components cause inappropriate activation of TCF4/beta-catenin-driven transcription. Despite the passage of a decade after the discovery of TCF4 and beta-catenin as the molecular effectors of the Wnt signal, few transcriptional activators essential and unique to the regulation of this transcription program have been found.

Methodology/Principal Findings: Using proteomics, we identified the leukemia-associated Mllt10/Af10 and the methyltransferase Dot1l, as Tcf4/beta-catenin interactors in mouse small intestinal crypts. Mllt10/Af10-Dot1l, essential for transcription elongation, are recruited to Wnt target genes in a beta-catenin -dependent manner, resulting in H3K79 methylation over their coding regions in vivo in proliferative crypts of mouse small intestine, in colorectal cancer and Wnt-inducible HEK293T cells. Depletion of MLLT10/AF10 in colorectal cancer and Wnt-inducible HEK293T cells followed by expression array analysis identifies MLLT10/AF10 and DOT1L as essential activators dedicated to Wnt target gene regulation. In contrast, previously published b-catenin coactivators p300 and beta-catenin displayed a more pleiotropic target gene expression profile controlling Wnt and other pathways. tcf4, mllt10/af10 and dot1l are co-expressed in Wnt-driven tissues in zebrafish and essential for Wnt-reporter activity. Intestinal differentiation defects in apc-mutant zebrafish can be rescued by depletion of Mllt10 and Dot1l, establishing these genes as activators downstream of Apc in Wnt target gene activation in vivo. Morpholino-depletion of mllt10/af10-dot1l in zebrafish results in defects in intestinal homeostasis and a significant reduction in the in vivo expression of direct Wnt target genes and in the number of proliferative intestinal epithelial cells.

Conclusions/Significance: We conclude that Mllt10/Af10-Dot1l are essential, dedicated activators of Wnt-dependent transcription, critical for maintenance of intestinal proliferation and homeostasis. The methyltransferase Dot1l may present an attractive candidate for drug targeting in colorectal cancer.

overall_design: 6 samples for Ls174T cells: si-b-catenin against si-control and dyeswap of it, si-control, si-MLLT10, si-BRG1 and si-P300 are hybridized against common reference RNA; 6 samples of HEK293T cells: Wnt3A or control medium (CM) induction for 9 hours, si-MLLT10, si-DOT1L, si-BRG1 and si-P300 upon 9 hour Wnt3A induction are all hybridized against common reference RNA

first: Tokameh

last: Mahmoudi

first: Sylvia

middle: F

last: Boj

first: Pantelis

last: Hatzis

first: Nadia

last: Taouatas

first: Robert

middle: G

last: Vries

first: Hans

last: Teunissen

first: Harry

last: Begthel

first: Jeroen

last: Korving

first: Shabaz

last: Mohammed

first: Albert

middle: J

last: Heck

last: Clevers


title: Genome-wide analysis of the effects of Power Training and Hormone Replacement Therapy on muscle properties

status: Public on Apr 22 2010

city: Jyväskylä

first: Eija

last: Pöllänen

address: PO Box 35/Viveca

department: Department of Health Sciences

country: Finland

institute: University of Jyväskylä

summary:
Muscle mass and strength reduce during ageing with a steeper decline in women around the age of 50, which suggests that the menopausal transition is one of the mechanisms for age-induced neuromuscular deteriorations. At the moment, there is no clear explanation for the decline in muscle properties although both physical exercise and maintaining near premenopausal estrogen levels by hormonal replacement have been helpful in their preservation. However, the molecular consequences of both treatments in skeletal muscle are mostly unknown. The goal of this genome-wide study was to investigate the transcriptional networks through which power training (PT) comprising of jumping activities and estrogen containing hormone replacement therapy (HRT) may aid in the prevention of functional limitation ensued from insufficient muscle mass and physical performance after menopause.
We used m. vastus lateralis samples obtained from postmenopausal women participating in a yearlong randomized double-blinded placebo-controlled trial with PT and HRT interventions. Muscle samples were available from eight PT, ten HRT and nine control women. Women in the PT group participated in a progressive PT program comprising mostly of jumping exercises for lower limbs with additional resistance exercises for the upper body. HRT intervention was double-blinded. All participants used either estradiol/noretisterone acetate preparation or placebo. Using statistical threshold p-value <0.05 and |fold change| >1.2 we identified 665 genes being differentially expressed among the studied 50-57-yr-old postmenopausal women. We used the hierarchical clustering method with extensive enrichment analysis in order to reveal enrichment of known GO or KEGG functional categories among co-regulated gene-clusters. In the enrichment analysis false discovery rate was set to be less than 15%. Transcription of “response to contraction”-, “insulin signaling”- and “adipocytokine signaling”-genes were upregulated by PT. Both PT and HRT were similarly effective on transcriptional regulation of glycolytic energy metabolism and calcium signaling. The HRT specifically affected “mitochondrion”-genes. In addition, we identified functional categories, such as “muscle development”, which were changed during the trial in all study groups. Our study revealed transcriptional changes in several functional categories in thigh muscle tissue of early postmenopausal women. The results emphasize that during the first years of the postmenopausal period, muscle properties are under transcriptional modulation, which both PT and HRT partially counteract leading to preservation of muscle mass and performance. More specifically, our findings indicate that PT and HRT may function through improving energy metabolism, improving the response to contraction, preserving functionality of mitochondria and reducing reorganization of muscle tissue. Therefore these treatments are recommended for preservation of adequate muscle mass and function.

overall_design: 54 samples, which formed 3 study groups with 2 timepoints, i.e., 8 power training subjects, 10 hormone replacement subjects and 9 controls. 6 control subjects had replicated samples resulting in a total of 60 hybridizations.

first: Vidal

last: Fey

first: Vuokko

last: Kovanen

first: Sarianna

last: Sipilä


title: Genome wide rhythmic transcription under light/dark cycles in Ostreococcus tauri

city: Rennes

first: annabelle

last: monnier

address: 2 avenue du Professeur Léon Bernard

institute: UMR 6061 Génétique et Développement

summary:
Genome wide rhythmic transcription under light/dark cycles is associated with sequential transcription of specific biological processes genes in Ostreococcus tauri.
Transcriptional profiling of Ostreococcus tauri under light/dark cycles. In order to identify genes with a diurnal rhythm, cells entrained under 12:12  light/dark  cycles were sampled every 3 hours for 27 hours with two overlapping time points at Time 9 (Light ON at Time 9; Light OFF at Time 21)   in 3 independent experiments.

overall_design: Two-conditions experiment, test situation (kinetic point) vs. Pool of each samples. Biological triplicates: 3 independant kinetics, 9 points per kinetics, Technical triplicates per array.

first: François-Yves

last: Bouget

first: Annabelle

last: Monnier


title: Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult

status: Public on Apr 14 2010

city: Bethesda

first: Biswajit

last: Das

address: 18 Library Drive, Building 18T, Room 106

department: Laboratory of Gene Regulation and Development

institute: National Institutes of Health/National Institute of Child Health and Human Development

summary: To adapt to its changing dietary environment, the digestive tract is extensively remodeled from the embryo to the adult during vertebrate development. Xenopus laevis metamorphosis is an excellent model system for studying mammalian gastrointestinal development and is used to determine the genes and signaling programs essential for intestinal development and maturation. The metamorphosing intestine can be divided into four distinct developmental time points and these were analyzed with X. laevis microarrays. Due to the high level of conservation in developmental signaling programs and homology to mammalian genes, annotations and bioinformatics analysis were based on human orthologs. Clustering of the expression patterns revealed co-expressed genes involved in essential cell processes such as apoptosis and proliferation. The two largest clusters of genes have expression peaks and troughs at the climax of metamorphosis respectively. Novel conserved gene ontology categories regulated during this period include transcriptional activity, signal transduction, and metabolic processes.  Interestingly, the induced genes associated with metamorphic climax correlated with the gene expression peaks observed around birth in the mouse intestine. Thus both mouse and amphibian, share similarities at the molecular levels for intestinal maturation and remodeling, which appears to be under the influence of increasing levels of circulating thyroid hormone. Moreover, our genome-wide analysis of the intestine during development identified larval/embryo- and adult-specific genes. Detailed analysis revealed 17 larval specific genes that may represent molecular markers for human colonic cancers, while many adult specific genes are associated with dietary enzymes. This global developmental expression study provides the first detailed molecular description of intestinal remodeling and maturation during postembryonic development, which should help improve our understanding of intestinal organogenesis and human diseases. This study significantly contributes towards our understanding of the dynamics of molecular regulation during development and tissue renewal, which is important for future basic and clinical research and for medicinal applications.

overall_design: Time series experiment through natural metamorphosis of intestine in Xenopus laevis. Biological replicates: 3 replicates for each stage of major change during amphibian metamorphosis (except in the climax where 2 bioogical replicates were used). Universal reference design was used instead of dye-swap design for 2-color hybridizations.

first: Rachel

last: Heimeier

first: Daniel

middle: R

last: Buchholz

first: Maria

last: Fiorentino

first: Yun-Bo

last: Shi


title: Differential genome-wide gene expression profiling of bovine largest and second largest follicles

status: Public on Mar 31 2010

city: Tsukuba

first: KENGO

last: HAYASHI

country: Japan

institute: National Institute of Agrobiological Sciences

summary:
We tried to classify largest (F1) and second largest follicles (F2) by global gene expression profiles and to identify differentially expressed genes between the follicular groups using combination of microarray and quantitative real-time PCR (QPCR) analysis. F1 (10.7 ± 0.7 mm) and F2 (7.8 ± 0.2 mm) were collected for microarray and QPCR analysis. Global gene expression profiles of each follicle were analyzed by hierarchical cluster analysis and expression profiles of representative 16 genes were confirmed by QPCR analysis.
Hierarchical cluster analysis classified the follicles into two clusters by microarray expression profiles. The cluster A was composed of only F2 and was characterized by highly expression of 31 genes including IGFBP5, whereas the cluster B contained only F1 and was predominately expressed 45 genes including CYP19, FSHR and INHA. The QPCR analysis confirmed AMH, CYP19, FSHR, GPX3, PGF, PLA2G1B, SCD and TRB2 were greater in F1 than F2, while CCL2, GADD45A, IGFBP5, PLAUR, SELP, SPP1, TIMP1 and TSP2 were greater in F2 than F1. Expression of stage-specific genes in follicles may be closely associated with its growth or atresia. Several genes identified in this study will provide intriguing candidates for the determinant of follicular growth.

overall_design: Global gene expression of three largest follicles and two second largest follicles were analyzed

first: Kengo

last: Hayashi

first: Koichi

last: Ushizawa

first: Misa

last: Hosoe

first: Toru

last: Takahashi


title: Identification of miR-489 or miR-504 target genes in head and neck cancer

status: Public on Jan 05 2010

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

summary: We recently identified a subset of down-regulated miRNAs such as miR-489 and miR-504 in HNSCC. Cell growth inhibitions occurred in miR-489 and miR-504 transfectants compared with the controls, suggesting that both miRNAs function as tumor suppressors. The aims of our expression studies were identification of these miRNAs target genes.

overall_design: miR-489 transfected cancer cells vs control cells, miR-504 transfected cancer cells vs control cells


status: Public on Jan 06 2010

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary:
The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.

Study of chromatin accessibility and expression using exon arrays.

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

overall_design:
University of Washington Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSTUDY%2FEDACC.1631

first: John

last: Stamatoyannopoulos


title: Gene expression C. elegans age-1 mutants with neuron- or intestine-restricted age-1 activity

status: Public on Dec 31 2009

first: Catherine

last: Wolkow

address: 251 Bayview Blvd

institute: NIA IRP, NIH

summary:
The goal of this experiment was to identify transcripts regulated non-autonomously by age-1 activity in neurons or intestine.  Comparisons of gene expression were made between age-1(mg44) null adults and CY251 (age-1(mg44); bvIs2) and CY262 (age-1(mg44); bvIs1); all were relative to wildtype (N2).  The integrated transgenes, bvIs2 and bvIs1, carry the age-1 cDNA expressed from the neuronal ric-19 promoter (bvIs2) or intestinal ges-1 promoter (bvIs1).
Transcripts upregulated in age-1(mg44) adults compared to wildtype (>=1.5 fold; p<0.05) or downregulated (<0.6 fold; p<0.05) were considered to be age-1 target genes.  Rescue in CY251 or CY262 was determined by change in the transgenic background versus age-1(mg44) (all relative to N2 wildtype).  Non-autonomous rescue of a target gene was usually determined by transcript levels that were at least 50% rescued compared to wildtype.

overall_design: Biological replicates: 2 age-1(mg44), 3 CY251 and 3 CY262

first: Wendy

middle: B

last: Iser

first: Mark

last: Wilson

first: Shailaja

middle: K

last: Rao

first: Kevin

last: Becker


title: GSK-3β inhibition promotes engraftment of ex vivo expanded hematopoietic stem cells

status: Public on Mar 26 2010

city: Randwick

first: Kap-Hyoun

last: Ko

state: NSW

address: High Street

department: Cord and Marrow Transplant Facility

country: Australia

institute: Sydney Children's Hospital

summary: Glycogen synthase kinase-3β (GSK-3β) has been recently identified as an important regulator of stem cell function. In vitro studies show that GSK-3β inhibition delays proliferation of human haematopoietic progenitor cells while increasing numbers of late dividing multipotent progenitors. Gene expression analysis revealed that GSK-3β inhibition modulates the expression of a subset of genes that are transcriptional targets for cytokines. GSK-3β inhibition antagonised down-regulation of genes encoding cyclin dependent kinase inhibitor p57 and a member of the growth arrest and DNA damage 45 family, GADD45B as well as up-regulation of cyclin D1 by cytokines, providing a possible mechanism for the BIO-induced delay in cell cycle progression.  Surprisingly, inhibition of GSK-3β earlier shown to prevent β-catenin degradation and promote the nuclear accumulation of β-catenin was not sufficient to activate its transcriptional targets in haematopoietic stem cells. GSK-3β inhibition up-regulated the expression of a several positive regulators of stem cell function suppressed during cytokine-induced proliferation. The data supports a clinical role for GSK-3β inhibition to improve engraftment efficiency of ex vivo expanded stem cells.

overall_design: Total RNA was isolated from three groups following expansion of CD34+ cells in cytokikes and then treatment with BIO, as described below.

first: Kap-hyoun

first: Tiffany

last: Holmes

first: Patricia

last: Palladinetti

first: Emma

last: Song

first: Robert

last: Nordon

first: Tracey

last: O’Brien

first: Alla

last: Dolnikov


title: Dendritic Cells

status: Public on Jan 01 2010

city: Giessen

first: Jochen

last: Wilhelm

address: Gaffkystrasse 10

department: ECCPS Microarray Unit

country: Germany

institute: Uniklinikum Giessen

summary: Dendritic cells (DC) play a crucial role in initiating, shaping and controlling the immune response. They are the most important antigen presenting cells in the immune system. DC can be divided in immature and mature DC. DCs reside in an immature state in most tissues or they circulate in the blood, where they recognize and phagocytose pathogens and other antigens. Direct contact with many pathogens leads to the maturation of DCs. The property to stimulate T cells is reserved for mature DC (O`Doherty, U. 1994). This functional maturation results in an up-regulation of the surface molecule MHC class II, adhesion molecules (CD54 and CD58) and co-stimulatory receptors (CD80 and CD86) as well as decreased antigen uptake capacity (CD206). (Banchereau, J. and Steinman, R.M. 1998).     Immunosuppressive drugs have revolutionized organ transplantation and improved the therapeutic management of autoimmune diseases. These drugs interfere on lymphocytes but they also act at the earliest stage of immune response. They are targeting key functions of dendritic cells (Hackstein H. and Thomson A.W., 2004 review). Sanglifehrin A (SFA) is a new immunosuppressive drug. It is a representative of a class of macrolides produced by the actinomycetes strain Streptomyces A92-308110 that bind to cyclophilin A (CypA), the binding protein of cyclosporine A (CsA).     Most studies about immunosuppressive effects of SFA took place on T and B lymphocytes. Unlike CsA, the cyclophilin-SFA-complex shows no effect on the calcium-dependent protein phosphatase calcineurin (Zenke, G. 2001). Unlike CsA and FK506, SFA shows no inhibition of IL-2 expression (Zenke, G. 2001; Zhang, L.H. 2001), nor does it suppress IL-2 receptor transcription (Zhang, L.H. 2001) in T lymphocytes. It could be shown that SFA reduces the Interleukin 12 production in dendritic cells (Steinschulte, C. 2003). IL-12p70 plays an important role in the pathogenesis of inflammation and autoimmune diseases. DCs generated in the presence of SFA show reduced macropinocytosis and lectin-mediated endocytosis. In contrast, CD89 und CD32 were increased by SFA. The effect of SFA on the expression of Ag uptake receptors and Ag capture by DCs makes SFA unique among other immunophilin-binding immunosuppressive drugs (Woltman, A. 2004).    Our goal is to investigate the gene expression profile of SFA treated mature human monocyte-derived dendritic cells.

overall_design: Comparison of SFA-stimulated versus unstimulated cells. 7 biological replicates

first: Holger

last: Hackstein

first: Sabrina

last: Immecke


title: Gene expression profiling in AML with normal karyotype: A multicenter study investigating molecular markers in 251 cases

city: New York

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

summary:
Acute myeloid leukemia (AML) is a heterogeneous disease and AML with normal karyotype (AML-NK) is categorized as an intermediate-risk group. Over the past years molecular analyses successfully identified biomarkers that will further allow to dissecting clinically meaningful subgroups in this disease. Thus far, somatic mutations were identified which elucidate the disturbance of cellular growth, proliferation, and differentiation processes in hematopoietic progenitor cells. In AML-NK, acquired gene mutations with prognostic relevance were identified for FLT3, CEBPA, and NPM1. FLT3-ITD mutations were associated with short relapse-free and overall survival, while mutations in CEBPA or NPM1 (without concomitant FLT3-ITD) had a more favorable outcome.
Here, we present a multicenter study investigating gene expression profiles of 251 cases of AML-NK. In three centers whole-genome microarray analyses were performed to delineate robust and common expression signatures for molecular markers in AML-NK.

overall_design: All samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation (Dresden, n=78; Munich, n=97; Ulm, n=77). Each laboratory performed its routine diagnostic algorithms, including the characterization of molecular markers.

first: Alexander

last: Kohlmann

first: Lars

last: Bullinger

first: Christian

last: Thiede

first: Markus

last: Schaich

first: Susanne

last: Schnittger

first: Konstanze

last: Döhner

first: Martin

last: Dugas

first: Hartmut

first: Gerhard

last: Ehninger

first: Torsten

last: Haferlach


title: Characterization of Populus Class III HDZIPs

city: Davis

first: Andrew

last: Groover

state: CA

address: 1100 West Chiles Rd

department: Institute of Forest Genetics

institute: USDA Forest Service

summary: Comparison of wild type Populus to transgenics expressing either a miRNA-resistant Populus ortholog of ATHB15/CORONA or miRNA-resistant Populus ortholog of REVOLUTA

overall_design: RNA was extracted from stem tissue of four biological replicates each for two mutants and wild type controls.  Mutants were lines HBMut2-4-1 (Populus ATHB15/CAN ortholog) and HBMut3-8-1 (Populus REVOLUTA ortholog).

first: Juan

last: Du

first: Eriko

last: Miura

first: Marcel

last: Robischon


title: Effect of PPARγ inhibition on pulmonary endothelial cell gene expression: Gene profiling in pulmonary hypertension

status: Public on Dec 28 2009

city: Augusta

first: Jing

last: Tian

state: GA

address: 1459 Laney Walker BLVD

department: Vascular Biology Center

institute: Medical College of Georgia

summary:
The loss of PPARγ is found to be associated with the development of pulmonary hypertension (PH). We hypothesize that  PPARγ inhibition induced gene expression changes may underscore the endothelial dysfunction in the disease process.
We utilized microarray analysis to determine gene expression changes in PPARγ inhibited ovine PAECs.

sample_organism:
Bos taurus
Ovis aries

overall_design: Ovine PAECs were treated with vehicle (DMSO) or GW9662 (5μM) for 24hrs, and total RNA was extracted for microarray analysis.

first: Anita

last: Smith

first: John

last: Nechtman

first: Robert

last: Podolsky

first: Saurabh

last: Aggarwal

first: Sanjiv

last: Kumar

first: Mona

last: Eglaish

first: Peter

last: Oishi

first: Agnes

last: Görlach

first: Sohrab

last: Fratz

last: Hess

last: Catravas

last: Verin

first: Jeffrey

last: Fineman

first: Jin-Xiong

last: She

first: Stephen

middle: M

last: Black


title: To Study the effects of antioxidant on allergic airways inflammations

status: Public on Nov 22 2009

city: Galveston

last: Sur

address: 301 University Blvd

institute: University of Texas Medial Branch

summary:
Ragweed challenge in Ragweed (RWE) sensitized animals generates Reactive oxygen species (ROS) in the airway epithelium and induces allergic airway inflammation. We want to study the genes induced by ROS generated by RWE. This goal can be achieved by comparing PBS challenge vs. RWE challenge.

Keywords: Infection

overall_design: There are two group of animals. Group 1 has Wild type mice(n=3) treated with PBS and Group 2 has Wild Type mice(n=4) treated with Ragweed

first: Nilesh

last: Mala


title: Gene expression data from infants (<1 year of age) diagnosed with Acute Lymphoblastic Leukemia (ALL)

status: Public on Dec 16 2009

city: Rotterdam

first: Ronald

last: Stam

address: Dr. Molewaterplein 60

country: Netherlands

institute: Erasmus MC - Sophia Children's Hospital

summary: Acute Lymphoblastic Leukemia (ALL) in infants (<1 year) is characterized by a poor prognosis and a high incidence of MLL translocations. Several studies demonstrated the unique gene expression profile associated with MLL-rearranged ALL, but generally small cohorts were analyzed as uniform patient groups regardless of the type of MLL translocation, while the analysis of translocation-negative infant ALL remained unacknowledged.

overall_design: We generated and analyzed primary infant ALL expression profiles (n=73) typified by translocations t(4;11), t(11;19) and t(9;11), or the absence of MLL translocations, in order to study translocation-specific gene expression between the different genetic subtypes of infant ALL.

middle: W

first: Rob

last: Pieters


title: DNA methylation data from human iPS cells and fibroblasts

status: Public on Nov 01 2009

city: Baltimore

first: Akiko

last: Doi

address: 855 N Wolfe St, Rangos 580

department: Medicine

institute: Johns Hopkins University School of Medicine

type: Methylation profiling by genome tiling array

summary:
DNA methylation is often inversely correlated with gene expression.
We used custom Nimblegen microarrays to determine the relationship between DNA methylation and gene expression in 6 iPS cell lines and the fibroblasts from which they were derived.

overall_design: We isolated genomic DNA from iPS cells and fibroblasts and hybridized to custom-designed Nimblegen microarrays (CHARM arrays).

first: In-Hyun

last: Park

first: Bo

last: Wen

last: Murakami

first: George

middle: Q

last: Daley

first: Andrew

middle: P

last: Feinberg


title: Metabolic switching in Streptomyces coelicolor Timeseries 1

status: Public on Dec 14 2009

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

institute: The Genome Analysis Centre

summary:
Background: During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples.
Results: Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis.
Conclusions: Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting.

Keywords: time course

overall_design:
F199: 32 samples, no replicates; one hour resolution from 20-44h; two hour resolution 44-60h; sample missing for 25h
F201: 8 samples, no replicates; four hour resolution from 24-48h; one sample at 60h
F202: 15 samples, no replicates; four hour resolution from 24-32h; one hour resolution from 34-40h; two hour resolution from 42-48h; one sample at 60h

SysMO STREAM Consortium

first: Kay

last: Nieselt

first: Florian

last: Battke

first: Alexander

last: Herbig

first: Per

last: Bruheim

last: Wentzel

first: Øyvind

last: Jacobsen

first: Håvard

last: Sletta

first: Tauqeer

last: Alam

first: Elena

last: Merlo

middle: D

first: Walid

last: Omara

first: Edward

last: Morrissey

first: Miguel

last: Juarez-Hermosillo

first: Antonio

last: Rodriguez-Garcia

first: Merle

last: Nentwich

first: Louise

last: Thomas

first: Roxane

last: Legaie

first: William

middle: H

last: Gaze

first: Gregory

middle: L

last: Challis

first: Ritsert

middle: C

last: Jansen

first: Lubbert

last: Dijkhuizen

first: David

last: Rand

last: Wild

first: Michael

last: Bonin

first: Jens

last: Reuther

first: Wolfgang

last: Wohlleben

first: Margaret

last: Smith

first: Nigel

last: Burroughs

first: Juan

last: Martin

last: Hodgson

first: Eriko

last: Takano

first: Rainer

last: Breitling

first: Trond

middle: E

last: Ellingsen

first: Elizabeth

last: Wellington


title: An Estrogen Receptor α-bound Human Chromatin Interactome

status: Public on Sep 11 2009

city: Singapore

first: Yijun

last: Ruan

state: Singapore

address: 60 Biopolis Street, #02-01 Genome, Singapore 138672

department: Research Computing Group

country: Singapore

institute: Genome Institute of Singapore

summary:
We developed Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) for de novo detection of global chromatin interactions, and comprehensively mapped the chromatin interaction network bound by estrogen receptor α (ERα) in the human genome. We performed 454 and Illumina sequencing analyses.

Keywords: Epigenetics

overall_design:
Using 454, we examined 3 libraries: IHM001 (Estrogen Receptor ChIA-PET), IHM043 (Estrogen Receptor ChIP-PET) and IHM062 (IgG ChIA-PET)

Using Illumina, we examined 4 libraries: IHM001 (Estrogen Receptor ChIA-PET replicate 1, Paired End Sequencing), IHH015 (Estrogen Receptor ChIA-PET replicate 2, Paired End Sequencing), H3K4me3 ChIP-Seq and RNA polymerase II ChIP-Seq

first: Melissa

last: Fullwood


title: Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs

status: Public on Aug 25 2009

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Expression profiling by genome tiling array

type: Genome binding/occupancy profiling by genome tiling array

summary:
Expression profile of mutant cells compared to wild-type cells:
Expression profile of Schizosaccharomyces pombe genome  in ∆pht1, ∆ago1, ∆clr4, rik1, ∆pht1rik1, ∆pht1∆ago1 and ∆pht1∆clr4 cells.
Expression profile of Schizosaccharomyces pombe genome  in ∆rrp6, ∆cid14, ∆swi6, ∆swr1, ∆set1, ∆pht1∆swi6 and ∆pht1∆set1 cells.
Expression profile of Schizosaccharomyces pombe genome  in ∆alp13, ∆cph1, ∆set2, clr6-1 and ∆cph1∆pht1 cells.

Occupancy profiling:
Occupancy profiling of RNA polymerase II, histone variant H2A.Z and ClrC subunit Rik1 in fission yeast Schizosaccharomyces pombe
Occupancy profiling of histone variant H2A.Z  in ∆msc1 cells.

overall_design:
Agilent 60mer oligonucleotide custom array containing probes spanning large portion of chromosome 2 at 50bp resolution was used to profile expression levels in mutant cells and to compare them to levels in wild-type cells.

Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  RNA polymerase II, H2A.Z or Rik1 from asynchronous culture of fission yeast.

Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  histone H2A.Z  from asynchronous culture of fission yeast.

first: Martin

last: Zofall

first: Tamás

last: Fischer

first: Ke

last: Zhang

first: Ming

last: Zhou

first: Bowen

last: Cui

first: Timothy

last: Veenstra

middle: I


title: Transcriptome analysis of rice in relation to infection with rice tungro spherical virus (RTSV)

status: Public on Aug 31 2009

city: Metro Manila

first: IL-RYONG

last: CHOI

address: DAPO Box 7777

country: Philippines

institute: International Rice Research Institute

summary:
Near-isogenic lines TW16-4 and TW16-69 were developed from the cross between TN1 (recurrent parent susceptible to RTSV) and Utri Merah (donor parent resistant to RTSV). TW16-4 is susceptible to RTSV, whereas TW16-69 is resistant to RTSV based on a serolog.

Keywords: time course, virus infection, disease response

overall_design: Comparison between RTSV and mock-infected rice. Biological replicates: 2 control (mock), 2 RTSV-infected, independently grown and harvested at 7 days after inoculation (DAI). Each sample was prepared using leaf tissues pooled from 5 plants grown under the same conditions.

first: Kouji

last: Satoh

first: Hiroaki

last: Kondoh

first: Setsuko

last: Kimura

first: Teresa

last: De Leon

first: Shoshi

last: Kikuchi


title: Comparative analysis of gene expression in the skin of WT and LynDeltaN mice

status: Public on Jun 01 2009

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary:
The caspase cleaved form of the tyrosine kinase Lyn (LynDeltaN) mediates a psoriasis-like inflammatory syndrome in mice.
To gain insights into the molecular mechanism of LynDeltaN in the control of this infllammatory process, we performed the pangenomic profile of  WT and LynDN skin from 5 day-old mice just before the entire inflammatory syndrom takes place.

overall_design: Skin samples from 3 wt and 3 LynDN  transgenic mice were compared in a dye-swap experiment.

first: Patrick

last: Auberger

first: Pascal

last: Barbry

first: Bernard

last: Mari

first: Sandrine

last: Marchetti

first: Sebastien

last: Grosso


title: Antiestrogen-resistant subclones of MCF-7 human breast cancer cells are derived from a common clonal drug-resistant progenitor

status: Public on Aug 27 2009

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Emergence of antiestrogen-resistant cells in MCF-7 cells during suppression of estrogen signaling is a widely accepted model of acquired breast cancer resistance to endocrine therapy. To obtain insight into the genomic basis of endocrine therapy resistance, we characterized MCF-7 monoclonal sublines that survived 21-day exposure to tamoxifen (T-series sublines) or fulvestrant (F-series sublines) and sublines unselected by drugs (U-series). All T/F-sublines were resistant to the cytocidal effects of both tamoxifen and fulvestrant. However, their responses to the cytostatic effects of fulvestrant varied greatly, and their remarkably diversified morphology showed no correlation with drug resistance. mRNA expression profiles of the U-sublines differed significantly from those of the T/F-sublines, whose transcriptomal responsiveness to fulvestrant was largely lost. A set of genes strongly expressed in the U-sublines successfully predicted metastasis-free survival of breast cancer patients. Most T/F-sublines shared highly homogeneous genomic DNA aberration patterns that were distinct from those of the U-sublines. Genomic DNA of the U-sublines harbored many aberrations that were not found in the T/F-sublines. These results suggest that the T/F-sublines are derived from a common monoclonal progenitor that lost transcriptomal responsiveness to antiestrogens as a consequence of genetic abnormalities many population doublings ago, not from the antiestrogen-sensitive cells in the same culture during the exposure to antiestrogens. Thus, the apparent acquisition of antiestrogen resistance by MCF-7 cells reflects selection of preexisting drug-resistant subpopulations without involving changes in individual cells. Our results suggest the importance of clonal selection in endocrine therapy resistance of breast cancer.

overall_design:
We picked well-isolated colonies from polyclonal MCF-7 cell culture to
establish sublines. All sublines characterized were confirmed as
monoclonal by their homogeneous morphology. The unselected
anti-estrogen-sensitive U-series sublines were derived from colonies
that emerged in low-density MCF-7 cultures without drug pressure.  The
anti-estrogen-resistant sublines were isolated by exposing
high-density MCF-7 cultures to fulvestrant (Fv, 10–100 nM) or
4-hydroxytamoxifen (Tam, 1M) for 21 days. Approximately 1 in 10^5 to
2 X 10^6 anti-estrogen-exposed cells survived this drug pressure. After
a 7-day drug-free recovery period, colonies were picked to establish
the Tam-selected T-series and the Fv-selected F-series sublines. All
T/F-sublines were maintained in the absence of anti-estrogens and were
characterized within 20 population doublings.

first: K

last: Coser

first: N

middle: F

last: Rosenthal

first: B

middle: S

first: S

last: Ramaswamy

first: T

last: Shioda


title: Rat liver.  Control vs. Chemical treated, 28 days

status: Public on Jun 21 2009

city: Kitakatsushika-gun

first: Hiroshi

last: Matsumoto

state: Saitama

address: 1600 Shimotakano, Sugito-machi

institute: Chemicals Evaluation and Research Institute, Japan

summary:
The final goal of this study is to develop a short term and highly accurate prediction method of carcinogenicity based on gene expression profile of rats administrated by carcinogens.
We conducted 3 days-, 14 days- and 28 days-repeated dose experiments in male F344 rats with 47 carcinogens and 26 non-carcinogens, and the gene expression profiles in liver were investigated by custom glass microarrays.

Supplementary file "73 Compounds for training" indicates 47 carcinogens and 26 non-carcinogens.
Supplementary file "15 Compounds for test" lists the other compounds which are for test.

overall_design: Two-condition experiment, control vs. chemical treated rat liver. Biological replicates: 4 control, 4 treated, control samples were pooled. One replicate per array.

first: Koji

last: Nakayama

first: Hideki

last: Miyaura

first: Kayo

last: Sumida

first: Fumiyo

last: Saito

first: Koichi

first: Masaru

last: Sekijima

first: Masanori

last: Otsuka

first: Yoshikuni

last: Yakabe

first: Tomoyuki

last: Shirai


title: Regulation of genes affecting body size and innate immunity by the DBL-1/BMP-like pathway in Caenorhabditis elegans

status: Public on Jul 28 2009

city: Bethesda

first: maocheng

last: yang

address: 10 Center Drive

department: NCI

institute: National Institutes of Health

summary: Compare the global gene expression profiles of Sma-6 and Dbl-1 in L4 stage C. elegans

overall_design: Sma-6 and Dbl-1  mutants compared

first: Andrew

last: Roberts

first: Tina

last: Gumienny

first: Ryan

middle: J

last: Gleason

first: Huang

last: Wang

first: Richard

last: Padgett


title: Avian duodenum tissues: primary vs. secondary E. acervulina infected

status: Public on May 27 2009

city: Beltsville

first: Hyun

last: Lillehoj

address: USDA-ARS, Bldg. 1040, BARC-East

department: Animal Research Service

institute: US Department of Agriculture

summary: Global transcriptional responses in duodenal intestinal epithelia of chickens following primary and secondary Eimeria acervulina infections.

overall_design: Simple loop hybridization (day 0 vs. days 1-2, days 1-2 vs. 3-4, days 3-4 vs. 5-6, and days 5-6 vs. 7-8) per primary or secondary infections.

first: Chul

last: Kim

first: Yeong

last: Hong

first: Calvin

last: Keeler Jr.


title: Gene expression profile of regenerating intestine in the sea cucumber H. glaberrima

status: Public on May 21 2009

city: Amherts

first: Pablo

middle: Andres

last: Ortiz-Pineda

address: 661 N Pleasant st

department: Veterinary & Animal Sciences

institute: University of Massachusetts

summary:
Regenerating intestine tissues were compared with normal (non-regenerating tissues) to determine the gene expression profile at early stages of regeneration (3, 7 and 14 days post- evisceration  (dpe)).

Immuno activated tissues with LPS were compared with Normal (non-regenerating tissues) and regenerating tissues (3 and 7 dpe) to determine the gene expression of immune related genes in the sea cucumber and it's expression during early stages of regeneration.

overall_design:
16 Total arrays.
8 comparisons with 8 dye swap replicates.
Normal Vs. (3, 7 and 14 days of regeneration), and Vs. (LPS)
2 microarray slides used.
Each slide with 8 Arrays (8 x 15k).
15,744 probes printed per array. (all 16 arrays are identically printed).
7,209 ESTs from Normal, 3 dpe and 7 dpe tissues were used to design the probes.
Two probes per EST from diferent regions of the sequence (as a technical replicate).
536 technical controls and more than 600 internal biological controls (from different species).

middle: A

first: Jose

last: Garca-Arraras


title: Gene expression profiling of experimental asthma reveals a possible role of paraoxonase-1 in asthma

status: Public on Jul 06 2009

city: Budapest

first: Gergely

last: Tolgyesi

address: Nagyvarad ter 4

country: Hungary

institute: Semmelweis University Budapest

summary:
Background: Several studies indicate that asthma is a polygenic disease, and its complexity originates from the interaction of an unknown number of genes with environmental factors.
Objective: In this study we aimed to identify new genes, gene groups and pathways involved in the pathogenesis of experimental asthma.
Methods: In an ovalbumin-induced murine model of asthma we applied microarray gene expression analysis of the lung at different time points in the asthmatic process. Advanced statistical methods were used to relate gene expression changes to cellular processes and to integrate our results into multiple levels of information available in public databases.
Results: According to the observed marked neutrophil infiltration found early, at 4 hours after the first allergen challenge, gene expression pattern reflected mainly an acute inflammatory response and strong chemotactic activity. At 24 hours after the third allergen challenge, gene set enrichment analysis revealed significant overrepresentation of gene sets corresponding to Th2 type inflammation models. Among the top downregulated transcripts, an antioxidant enzyme, paraoxonase-1 (PON1) was identified. Reduced PON1 protein expression in the lung was confirmed by immunohistochemical analysis. In human asthmatic patients we found that serum PON1 activity was reduced at exacerbation, but increased parallel with improving asthma symptoms. PON1 gene polymorphisms did not influence the susceptibility to the disease.
Conclusion: Our observations suggest that an altered PON1 activity might be involved in the pathogenesis of asthma, and PON1 might be a potential new therapeutic target as well as a new diagnostic tool for following up the effect of therapy.

overall_design:
Experimental design:
Three groups of mice (6 mice/group) were sensitized and challenged with allergen (OVA), one group (control group) was sensitized and challenged with placebo (PBS) and served as a control. On day 28 and 30, 4 h after the first and third allergen challenge, mice in groups 1 and 2 were anaesthetized by an intraperitoneal injection of ketamine and xylazine, BAL was isolated and the lungs were removed for further analysis. On day 31, 24h after the third (last) allergen challenge mice in group 3 and the controls were anaesthetized, and airway hyper-responsiveness (AHR) was assessed. After the AHR measurements, BAL sampling and lung tissue collection were performed, the same way as it was carried out in groups 1 and 2. Cellular composition of BAL, and lung histology were examined in all mice in all groups. AHR was measured in controls and group 3 on day 31. 1000 ng-1000 ng quality-checked total lung tissue RNA samples from OVA sensitized and challenged mice from group 1, 2 and 3 were identically labeled with Cy5 dye, while lung tissue RNA samples from group 4 (control, placebo sensitized and challenged) were pooled and labeled with Cy3 dye, and served as a common reference.

last: Tölgyesi

first: Viktor

last: Molnár

first: Zoltán

last: Wiener

first: Zsolt

last: Komlósi

first: Péter

last: Pócza

first: András

last: Falus

first: György

last: Losonczy

first: Csaba

last: Szalai


title: AML with mutated NPM1 carrying a normal or aberrant karyotype show overlapping features

first: Hans-Ulrich

last: Klein

institute: Columbia University Medical Center

summary:
AML with mutated NPM1 usually carries normal karyotype (NK) but it may harbor chromosomal aberrations whose significance remains unclear. We addressed this question in 631 AML patients with mutated/cytoplasmic NPM1. An abnormal karyotype (AK) was present in 93/631 cases (14.7%), the most frequent abnormalities being +8, +4, -Y, del(9q), +21. Chromosome aberrations in NPM1-mutated AML were similar to, but occurred less frequently than additional chromosome changes found in other AML with recurrent cytogenetic abnormalities according to WHO classification. Four of the 31 NPM1-mutated AML patients karyotyped at different time points had NK at diagnosis but AK at relapse: del(9q) (n=2), t(2;11) (n=1), inv(12) (n=1).
NPM1-mutated AML with NK or AK showed overlapping morphological, immunophenotypic (CD34-negativity) and gene expression profile (downregulation of CD34 and upregulation of HOX genes). No difference in survival was observed among NPM1-mutated AML patients independently of whether they carried a normal or abnormal karyotype, the NPM1-mutated/FLT3-ITD negative cases showing the better prognosis. Findings in our patients point to chromosomal aberrations as secondary events, reinforce the concept that NPM1 mutation is a founder genetic lesion and indicate that NPM1-mutated AML should be clinically handled as one entity, irrespective of the karyotype.

overall_design: All bone marrow samples were obtained from untreated patients at the time of diagnosis. Cells used for microarray analysis were collected from the purified fraction of mononuclear cells after Ficoll density centrifugation.

first: Claudia

last: Haferlach

first: Cristina

last: Mecucci

first: Susanne

last: Schnittger

first: Alexander

last: Kohlmann

first: Marco

last: Mancini

first: Antonio

last: Cuneo

first: Nicoletta

last: Testoni

first: Giovanna

last: Rege-Cambrin

first: Antonella

last: Santucci

last: Vignetti

first: Paola

last: Fazi

first: Maria

last: Martelli

first: Torsten

first: Brunangelo

last: Falini


title: Mammary tumors in transgenic mice expressing constitutively active and C-terminally truncated variants of STAT5

status: Public on Mar 06 2009

city: Rehovot

first: Tali

last: Eilon

address: Rehovot

country: Israel

institute: The Volcani Center

summary:
Stat5 is a latent transcription factor that regulates essential growth and survival functions in normal cells. Constitutive activity of Stat5 and the involvement of its C-terminally truncated variant have been implicated in blood cell malignancies and mammary or breast cancer.
To distinguish the individual contributions of the Stat5 variants to mammary tumorigenesis, global gene-expression profiling was performed on transgenic STAT5-induced tumors.

overall_design: Mammary tumors derived from transgenic mice carrying one of two Stat5 variants were collected for RNA extraction and hybridization on Affymetrix GeneChip® Mouse Genome 430A 2.0 array.

first: Itamar

last: Barash


title: Expression data from differentiating ventral otic Epithelial Cell line

status: Public on Apr 08 2009

city: Sheffield

first: Marta

last: Milo

state: South Yorkshire

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary:
The study of the gene expression during otic development is a source of important information for understanding the mechanism of inner ear development and subsequently create appropriate gene therapies both to prevent hearing loss and eventually to regenerate the damaged parts.This dataset contains data from temporal expression profiles in an epithelial cell line derived from the cochlear duct of a mouse inner ear at embryonic day E10.5. There are 6 time points across 14 days of in vitro differentiation in serum-free media.
We used microarrays to define patterns of expression in a differentiating otic cell line.

Keywords: Temporal gene expression of 14 days of differentiation in vitro.

overall_design: The model is based on the conditionally immortal cell line University of Sheffield/ventral otocyst-epithelial cell line clone 36 (US/VOT-E36), derived from ventral otic epithelial cells of the mouse at embryonic day 10.5. This cell ilines is recapitulates a coherent pattern of cell differentiation compared with in vivo cells and provide a convenient model for screening the effects of other extrinsic factors on the differentiation of cochlear epithelial cell types in vitro. The cell line VOT-E36 was weaned from the fetal calf serum (FCS), which was used to culture the parental cell line, by progressive serum dilution. The cell line was conditionally immortalized by a temperaturesensitive variant of the T antigen (tsA58), controlled by a c-interferoninducible promoter. Cell growth could then be arrested and the cells allowed to differentiate by culturing them at 39  C without c-interferon. Cultures were customarily set up under proliferative conditions (33  C, c-interferon) and allowed to grow for 2–3 days. To induce differentiation, the dishes were rinsed twice with Ultraculture and the medium was replaced without c-interferon and then transferred to 39  C. Medium was renewed every 4 days.

first: Matthew

last: Holley


title: SCFA-hexosamine scaffold

status: Public on May 08 2009

first: Kevin

last: Yarema

address: 3400 N. Charles St., Clark Hall 106A

department: Biomedical Engineering

institute: Johns Hopkins University

summary:
The purpose of this study was to characterize the gene expression profile of MDA-MB-231 breast cancer cells treated with various SCFA-hexosamine analogs to better understand the role of various modifications to this scaffold.
Keywords: SCFA-hexosamine analog comparison

overall_design: In total, six analogs were investigated in this study. For the relatively "toxic" C6-SCFA analogs, IC30 was selected to explore initial growth inhibitory and apoptotic gene expression changes.  Two independent biological replicates were analyzed for each analog-treated condition.  Three independent biological replicates were analyzed for the vehicle-treated control (EtOH).

first: Noha

last: Elmouelhi


title: Gene array prediction of AML transformation in MDS

status: Public on Jun 09 2009

city: Pleasanton

first: Wei-Min

last: Liu

address: 4300 Hacienda Drive

institute: Roche Molecular Systems

summary:
Microarray-based classifiers and prognosis models identify subgroups with distinct clinical outcomes and high risk of AML transformation of myelodysplastic syndrome (MDS)
An array-based Diagnostic Classifier (DC) model, developed for and evaluated during the MILE study, correctly identified ~50% of the unfractionated MDS specimens submitted to the study; predictions for the other samples were split between “none-of-the-targets” classes and AML signatures, but this distinction also reflected clinical outcome in terms of time to AML transformation. Furthermore, an improved Prognostic Classifier (PC) model was developed that correlated with both time to AML transformation and overall survival.

Keywords: Microarray-based gene expression profiling aimed at prediction of AML transformation in MDS

overall_design:
164 MDS, 202 AML and 69 non-leukemia bone marrow samples were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips.
This dataset is a subset of the MILE Study (Microarray Innovations In LEukemia) program, headed by the European Leukemia Network (ELN) and sponsored by Roche Molecular Systems, Inc.


title: INTRA_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor

city: Seattle

first: Tomas

last: Marques-Bonet

address: 1705 NE Pacific St,

department: Genome Sciences

institute: University of Washington

type: Genome variation profiling by genome tiling array

summary: Wilson and King were among the first to recognize that the extent of phenotypic change between humans and great apes was dissonant with the rate of molecular change. Proteins are virtually identical; cytogenetically there are few rearrangements that distinguish ape-human chromosomes; rates of single-basepair change and retroposon activity have slowed particularly within hominid lineages when compared to rodents or monkeys. Here, we perform a systematic analysis of duplication content of four primate genomes (macaque, orangutan, chimpanzee and human) in an effort to understand the pattern and rates of genomic duplication during hominid evolution. We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of basepairs and in terms of events. This duplication acceleration within the ancestral species is significant when compared to lineage-specific rate estimates even after accounting for copy-number polymorphism and homoplasy. We discover striking examples of recurrent and independent gene-containing duplications within the gorilla and chimpanzee that are absent in the human lineage. Our results suggest that the evolutionary properties of copy-number mutation differ significantly from other forms of genetic mutation and, in contrast to the hominid slowdown of single basepair mutations, there has been a genomic burst of duplication activity at this period during human evolution.

sample_organism:
Pan troglodytes
Pongo abelii
Pongo pygmaeus pygmaeus
Homo sapiens

overall_design: A total of 8 humans, 8 chimpanzees and 8 orangutans were hybridized against the reference (NA15510, Clint and Susie, respectively).

first: Jeffrey

middle: M

last: Kidd

first: Mario

last: Ventura

first: Tina

last: Graves

first: Ze

last: Cheng

first: LaDeanna

last: Hillier

first: Zhaoshi

last: Jiang

first: Carl

last: Baker

first: Ray

last: Malfavon-Borja

first: Lucinda

last: Fulton

first: Can

last: Alkan

first: Gozde

last: Aksay

first: Santhosh

last: Girirajan

first: Priscillia

last: Siswara

first: Lin

last: Chen

last: Cardone

first: Arcadi

last: Navarro

first: Elaine

middle: R

last: Mardis

first: Richard

middle: K

last: Wilson

first: Evan

last: Eichler


title: Changes in Gene expression mediated by Cyclic Mechanical Stress in Trabecular Meshwork Cells

status: Public on Mar 04 2009

city: Durham

first: Pedro

last: Gonzalez

state: NC

address: Erwin Road Box 3802

department: Ophthalmology

institute: Duke University

summary: Purpose: To investigate the changes in gene expression induced by cyclic mechanical stress (CMS) in trabecular meshwork (TM) cells.

overall_design: Methods: HTM cultures from three donors were plated on type I collagen-coated flexible silicone bottom plates and subjected to 15% stretching, 1 cycle per second for 6 hours. Non-stressed parallel control cultures were incubated under the same conditions in the absence of CMS. Total RNA from each culture was amplified (1 round amplification) and hybridized to Operon Human Oligo Arrays version 3.0 (35K). Control used was Universal Reference Human RNA from Stratagene. Differences in gene expression induced by CMS were analyzed using Genespring 7.2.

first: Coralia

last: Luna

first: Guorong

last: Li

first: Paloma

middle: B

last: Liton

first: David

last: Epstein


title: Gene expression data of skin from psoriatic patients and normal controls

status: Public on Jan 25 2009

city: Ann Arbor

first: Goncalo

last: Abecasis

state: MI

address: 1420 Washington Heights

department: Biostatistics

institute: University of Michigan

summary:
Gene expression has been proposed as an intermediate phenotype that can increase power in complex trait gene-mapping studies. Psoriasis, an immune-mediated, inflammatory and hyperproliferative disease of the skin and joints, provides an ideal model system to evaluate this paradigm, as conclusive evidence demonstrates that psoriasis has a genetic basis and the disease tissue is readily accessible.
To better understand the complex nature of processes in psoriasis, we characterize gene expression profiles in uninvolved and involved skin from affected individuals as well as normal skin from control individuals.

Keywords: disease state analysis

overall_design:
We extracted total RNA from punch biopsies taken from 58 psoriatic patients and 64 normal healthy controls. Two biopsies were taken from each patient; one 6mm punch biopsy was obtained from lesional skin of each patient (involved sample) and the other from non-lesional skin (uninvolved sample), taken at least 10 cm away from any active plaque. One biopsy was obtained from each healty control. Totally 180 samples were run on Affymetrix HU133 Plus 2.0 microarrays containing >54,000 gene probes.
The raw data from 180 microarrays were processed using the Robust Multichip Average (RMA) method. The expression values in the table were after adjustment of RMA expression values (on the log scale) to account for batch and sex effects.
Definition of abbreviations used in Sample records: NN = normal skin from controls; PN = uninvolved skin from cases; PP = involved skin from cases.

first: Johann

last: Gudjonsson

first: Jun

last: Ding

first: Rajan

last: Nair

first: Philip

last: Stuart

first: John

last: Voorhees

first: James

middle: T

last: Elder


title: A Burst of Segmental Duplications in the African Great Ape Ancestor

first: Tomas

last: Marques-Bonet

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Macaca mulatta
Gorilla gorilla
Pan paniscus
Pan troglodytes
Pongo abelii
Pongo pygmaeus pygmaeus
Homo sapiens

overall_design: Refer to individual Series


title: Microarray Innovations in LEukemia (MILE) study: Stage 1 data

status: Public on Sep 30 2009

first: Wei-Min

last: Liu

summary:
An International Multi-Center Study to Define the Clinical Utility of Microarray–Based Gene Expression Profiling in the Diagnosis and Sub-classification of Leukemia (MILE Study)

Established in 2005, the MILE (Microarray Innovations in LEukemia) study research program included 11 participating centers in three continents. This cohort of n=2,096 samples represents data on the retrospective whole-genome analysis phase.

This dataset is part of the MILE Study (Microarray Innovations In LEukemia) program, headed by the European Leukemia Network (ELN) and sponsored by Roche Molecular Systems, Inc.

overall_design: 2096 blood or bone marrow samples of acute and chronic leukemia patients were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips.


title: The role of PTEN/Akt1/PI3K signaling on the maintenance and viability of prostate cancer stem-like cell populations

status: Public on Dec 09 2008

city: San Diego

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
Self-renewing tumor initiating cells that are capable of differentiation and responsible for tumor growth have been isolated from cancers and cell lines. If such minor populations are associated with tumor progression, understanding molecular pathways that are required for viability and maintenance of these populations will allow to target these pathways to eradicate tumors that are resistant to existing therapies. In this study we enriched for prostate cancer progenitors (Pr. CP’s) expressing cell surface markers CD44/CD133/alpha 2 beta 1 integrin in non-adherent serum-free growth conditions maintained as spheres. Cells grown in these conditions have increased in vivo clonogenic and in vivo tumorigenic potential. microarray analysis of cells grown in sphere conditions compared with long term monolayer culture conditions revealed preferential activation of PI3K/AKT pathway in prostate cancer progenitors. PI3K p110 alpha and beta protein levels were high in sphere condition cultured cells, and PTEN knockdown lead to an increase in Pr.CP’s, and to increased clonogenic and tumorigenic potential. Inhibition of Akt1 phosphorylation target FoxO3a lead to inhibition of tumorigenic capacity in vivo for prostate cancer cells.  Inhibition of PI3K activity by PI3K inhibitor NVP-BEZ235 lead to a selective inhibition of Pr.CP’s, nuclear localization of FoxO3a and increase in GADD45a in prostate cancer cells. Taken together our data strongly suggest that PTEN and PI3K/Akt pathways are critical for prostate cancer stem-like cell maintenance and targeting the PI3K signaling by selective inhibitors may give an incredible advancement in prostate cancer treatment.
Keywords: multiple tissues

overall_design: sphere and monolayer cultures from two different prostate cancer cell lines

first: Anna

last: Dubrovska

last: Salamone

first: Peter

middle: G

last: Schultz

first: Venkateshwar

last: Reddy


title: GSK3 inhibition Induces Glioma Cell Death through c-MYC, NF-kB and Glucose Regulation

status: Public on Jan 01 2009

first: Yuri

last: Kotliarov

address: 4 Memorial Dr., room 134

department: CHI

institute: NHLBI

summary:
We identified GSK3 as a regulator of GBM cell survival using microarray analysis, small molecule and genetic inhibitors of GSK3 activity.  Various molecular and genetic approaches were then employed to dissect out the molecular mechanisms responsible for GSK3 inhibition-induced cytotoxicity.
Keywords: time course

overall_design: RNA extracted from U251 cells treated with DMSO or Enzastaurin for indicated time were hybridized to Affymetrix expression arrays (HG_U133-Plus_2) to detect changes in gene expression caused by Enzastaurin. Three replicates per sample were used.

first: Svetlana

last: Kotliarova

first: Sandra

last: Pastorino

first: Lara

last: Kovell

first: Rolanda

last: Bailey

first: Wei

last: Zhang

first: Hua

last: Song

first: Dragan

first: Jean-Claude

last: Zenklusen

first: Jeongwu

last: Lee

first: Howard

last: Fine


title: Gene Expression and Isoform Variation: Exon-level Analysis

status: Public on Oct 07 2008

city: Montréal

first: Amandine

last: Bemmo

state: Québec

address: 740, Dr Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

summary:
Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. Here, we use the well studied Microarray Quality Control (MAQC) dataset to benchmark the Affymetrix Exon Array, and compare it to two other popular platforms: Illumina, and Affymetrix U133.
Results:We show that at the gene expression level, the Exon Array performs comparably with the two 3’ targeted platforms. However, the interplatform correlation of the results is slightly lower than between the two 3’ arrays. We show that some of the discrepancies stem from the RNA amplification protocols, e.g. the Exon Array is able to detect expression of non-polyadenylated transcripts. More importantly, we show that many other differences result from the ability of the Exon Array to monitor more detailed isoform-level changes; several examples illustrate that changes detected by the 3’ platforms are actually isoform variations, and that the nature of these variations can be resolved using Exon Array data. Finally, we show how the Exon Array can be used to detect alternative isoform differences, such as alternative splicing, transcript termination, and alternative promoter usage. We discuss the possible pitfalls and false positives resulting from isoform-level analysis.
Conclusions:The Exon Array is a valuable tool that can be used to profile gene expression while providing important additional information regarding the types of gene isoforms that are expressed and variable. However, analysis of alternative splicing requires much more hands on effort and visualization of results in order to correctly interpret the data, and generally results in considerably higher false positive rates than expression analysis. One of the main sources of error in the MAQC dataset is variation in amplification efficiency across transcripts, which is not adequately corrected using existing statistical methods. We outline approaches to reduce such errors by filtering out potentially problematic data.

Keywords: Compare the Affymetrix Exon Array 1.0 ST to Illumina, and Affymetrix U133 platforms

overall_design: We used the Universal Human Reference RNA (catalog no. 740000) and human Brain Reference RNA (catalog no. 6050) forour analysis; five technical replicates of each sample were hybridized independently at two test sites (Virginia Tech and McGill university).

first: David

last: Benovoy

first: Tony

last: Kwan

first: Daniel

last: Gaffney

first: Roderick

middle: V

last: Jensen

first: Jacek

last: Majewski


title: Gene Expression and Isoform Variation: Gene-level Analysis

overall_design: We used the Universal Human Reference RNA (catalog no. 740000) and human Brain Reference RNA (catalog no. 6050) for our analysis; five technical replicates of each sample were hybridized independently at two test sites (Virginia Tech and McGill university).


title: Expression profile of PC-3-derived cell lines after transendothelial migration

status: Public on Jan 15 2009

city: Iowa City

first: Justin

last: Drake

state: IA

address: 6-509 Bowen Science Building

institute: The University of Iowa

summary: Metastatic colonization involves cancer cell lodgment or adherence in the microvasculature and subsequent migration of those cells across the endothelium into a secondary organ site.  To study this process further, we analyzed transendothelial migration of human PC-3 prostate cancer cells in vitro.  We isolated a subpopulation of cells, TEM4-18, that crossed an endothelial barrier more efficiently, but surprisingly, were less invasive than parental PC-3 cells in other contexts in vitro.  Importantly, TEM4-18 cells were more aggressive than PC-3 cells in a murine metastatic colonization model.  Microarray and FACS analysis of these cells showed that the expression of many genes previously associated with leukocyte trafficking and cancer cell extravasation were either unchanged or down-regulated.  TEM4-18 cells exhibited characteristic molecular markers of an epithelial-to-mesenchymal transition (EMT), including frank loss of E-cadherin expression and upregulation of the E-cadherin repressor ZEB1.  Silencing ZEB1 in TEM4-18 cells resulted in increased E-cadherin and reduced transendothelial migration.  TEM4-18 cells also express N-cadherin, which was found to be necessary, but not sufficient for increased transendothelial migration.  Our results extend the role of EMT in metastasis to transendothelial migration and implicate ZEB1 and N-cadherin in this process in prostate cancer cells.

overall_design: We wanted to compare the expression profiles of cells that had undergone transendothelial migration.  The parental, and reference cell line, PC-3 was plated onto a confluent human microvascular endothelial cell line from the lung and allowed to migrate across this monolayer.  A new cell line, TEM4-18, was isolated from this experiment.  We also performed this experiment a second time to isolate a biological replicate of the TEM4-18 cell line, termed TEM2-5.  All 3 cell lines, PC-3, TEM4-18, and TEM2-5 are analyzed as replicates in this experiment for a total of 6 samples in this microarray.  Both TEM4-18 and TEM2-5 were then compared to PC-3 cells for changes in gene expression.

first: Garth

last: Strohbehn

first: Thomas

last: Bair

first: Jessica

last: Moreland

first: Michael

middle: D

last: Henry


title: PUR alpha protein induces endoplasmic reticulum stress response and cell differentiation pathways in prostate cancer

status: Public on Jan 22 2009

city: Baltimore

first: Robert

middle: H

last: Getzenberg

address: 600 North Wolfe St., 121 Marburg

department: James Buchanan Bradey Urological Institute

institute: The Johns Hopkins School of Medicine

summary:
Following androgen ablation treatment for advanced prostate cancer, almost all men relapse after a period of initial response to therapy, which eventually is life threatening. We have previously found that purine-rich element binding protein, PUR alpha, was significantly repressed in androgen-independent prostate cancer cell lines in comparison to an androgen-dependent line.  Moreover, over-expressing PURa in androgen-independent prostate cancer cells attenuated their cell proliferation. The aim of the studies described here was to uncover some of the mechanisms by which over-expression of PURa attenuates cell proliferation.
A set of common genes induced by over-expressing PURa both in PC3 and LNCaP cells was analyzed by DNA microarray.  The results were then validated utilizing quantitative reverse transcription-PCR.  Using a 5.3-kb region of the PSA promoter containing androgen response elements, the participation of PURa in androgen regulated gene expression was determined.
Genes involved in stress response and cell differentiation were induced in cells over-expressing PURa.  Some of the genes that are targets of androgen regulation are also induced.  Most strikingly, ectopic expression of PURa induced transcriptional activity of the 5.3-kb PSA promoter containing androgen response elements, without androgen stimulation.
Based upon the consideration that some of the genes involved in cell stress and differentiation are also regulated by androgens our data suggest that PURa shares some common pathway regulated by the androgen receptor.  These findings suggest that regulation of PURa expression in prostate cancer cells may serve as a therapeutic target for hormone refractory prostate cancer.

overall_design:
PC3 cells (low in PURa expression) was stably over-expressed PURa.  Total RNA of the cells was collected simultaneously with that of PC3 transfected with mock vector.
LNCaP cells (Express PURa more than PC3 cells) was PURa-over-expressed with retrovirus vector (MSCV-PIG) and selected with puromycin for 72hr.  Total RNA of the cells was collected simultaneously with that of LNCaP cells infected with mock vector.
One set of RNA derived from PC3 cells and two independent RNA derived from LNCaP cells retrovirus infection were used for DNA microarray.  Quality and concentration of total RNA was verified using Agilent Bioanalyzer and Nanodrop Spectrophotometer, respectively.  T7 oligo(dT) primer (Sigma-Proligo, Boulder, CO) and 5ug total RNA are combined for first strand cDNA synthesis.  Following second strand cDNA synthesis and cDNA cleanup (Phase Lock Gel Light, Eppendorf, Hamburg, Germany) an in vitro transcription reaction was performed overnight using T7 RNA transcript labeling kit provided by Enzo Life Sciences, Inc. (Farmingdale, NY).  IVT reactions were cleaned using RNeasy Mini Kit (Qiagen) and concentration determined by Nanodrop Spectrophotometer.  15ug cRNA was fragmented using 5X fragmentation buffer (made in-house).  Hybridization cocktail was made in accordance with Affymetrix eukaryotic expression array protocol (Affymetrix, Santa Clara, CA) and combined with fragmented cRNA.  10ug cRNA was loaded onto Human U133Plus 2.0 genome arrays (Affymetrix, Santa Clara, CA) and hybridized overnight for 16 hours.  After hybridization, staining and washing of the arrays was performed following the Affymetrix eukaryotic expression array protocol, including staining with streptavidin-phycoerythrin, antibody stain, and a second streptavidin-phycoerythrin stain.  After washing and staining, all arrays were scanned with the Affymetrix GeneChip Scanner and data collected with GeneChip Operating System 1.4 (GCOS, Affymetrix, Santa Clara, CA).
  The quality of the microarray experiments was assessed with affyPLM and Affy, two Bioconductor packages for statistical analysis of microarray data.  To estimate the gene expression signals, data analysis was conducted on the chips’ CEL file probe signal values at the Affymetrix probe pair (perfect match (PM) probe and mismatch (MM) probe) level, using the statistical algorithm Robust Multiarray Analysis (RMA) expression measure (Irizarry RA et al. 2003) with Affy. This probe level data processing includes a normalization procedure utilizing the quantile normalization method (Bolstad BM et al. 2003) to reduce the obscuring variation between microarrays, which might be introduced during the processes of sample preparation, manufacture, fluorescence labeling, hybridization and/or scanning.  Exploratory data analysis (EDA) was performed with the preprocessed data above.  Between-treatment and between-replicate variations were examined with the pair-wise MvA plots, in which the base 2 log ratios (M) between two samples are plotted against their averaged base 2 log signals (A).  With the signal estimates, Principal Component analysis (PCA) was also performed to assess sample variability.
With the signal intensities obtained above, an empirical Bayes method with the Gamma-Gamma modeling, as implemented in the bioconductor package EBarrays, was used to estimate the posterior probabilities of the differential expression of genes between PURA and Vector only sample conditions (Newton MA et al. 2001, Kendziorski Cm et al. 2003, Newton MA et al. 2004).  The criterion of the posterior probability > 0.5, which means the posterior odds favoring change, was used to produce the differentially expressed gene list.
All Bioconductor packages are available at http://www.bioconductor.org and all computation was performed under R environment (http://www.r-project.org).

first: Takahiro

last: Inoue

first: Atsushi

last: Maeno

first: Conover

last: Talbot Jr.

first: Yu

last: Zeng

last: Yeater

first: Eddie

last: Leman

first: Prakash

last: Kulkarni

first: Osamu

last: Ogawa


title: Genes regulated by Meis1 in murine Mll-AF9 leukemia cells

status: Public on Dec 23 2008

city: Minneapolis

first: Ashish

last: Kumar

state: MN

address: 425 East River Road

institute: University of Minnesota

summary:
Leukemias with MLL-rearrangements are characterized by high expression of the homeo box gene MEIS1. In these studies, we knocked down Meis1 expression by shRNA lentivirus transduction in murine Mll-AF9 leukemia cells. Meis1 knockdown resulted in decreased proliferation and survival of murine Mll-AF9 leukemia cells. We also observed reduced clonogenic capacity and increased monocytic differentiation. The establishment of leukemia in transplant recipients was significantly delayed by Meis1 knockdown. Gene expression profiling of cells transduced with Meis1 shRNA showed reduced expression of genes associated with cell cycle entry and progression. shRNA mediated knockdown of MEIS1 in human MLL-fusion gene leukemia cell lines resulted in reduced cell growth. These results show that MEIS1 expression is important for MLL-rearranged leukemias and suggest that MEIS1 promotes cell cycle entry. Targeting MEIS1 may have therapeutic potential for treating leukemias expressing this transcription factor.

Keywords: Gene expression

overall_design: Murine Mll-AF9 leukemia (4166) cells were transduced with lentivirus expressing shRNA against Meis1 or control lentivirus (empty vector). Gene expression profiles were compared at 48 hours post transduction, using Puromycin as selection agent for transduced cells.

first: Quanzhi

last: Li

first: Wendy

last: Hudson

first: Weili

last: Chen

first: Thien

middle: N

last: Sam

first: Baolin

last: Wu

first: Qing

last: Yao

first: Erik

last: Lund

first: Branden

last: Kowal

first: John

last: Kersey


title: Microarray Innovations in LEukemia (MILE) study

first: Wei-Min

last: Liu


title: Normal human bone marrow CD34+ cells, promyelocytes, and neutrophils and PR9 cell line PML-RARA induction time course

status: Public on Sep 06 2008

city: St Louis

first: Jacqueline

last: Payton

state: MO

address: 4320 Forest Park Avenue, Suite 211

institute: Washington University School of Medicine

summary: To better understand the pathogenesis of acute promyelocytic leukemia (APL, FAB M3 AML), we identified genes that are expressed differently in APL cells compared to other acute myeloid leukemia subtypes, and to normal promyelocytes. Comparative gene expression analysis of 14 M3, 62 other AML (M0, M1, M2 and M4) and 5 enriched normal promyelocyte samples revealed a signature of 1,121 genes that are specifically dysregulated in M3 samples relative to other AML, and that do not simply represent normal promyelocyte expression (“M3-specific signature”). We used a novel, high throughput digital platform (Nanostring's nCounter system) to evaluate a subset of the most significantly dysregulated genes in 30 AML samples; 33 of 37 evaluable gene expression patterns were validated. In an additional analysis, we selected only genes that are dysregulated in M3 both compared to other AML subtypes, and to purified normal CD34+ cells, promyelocytes, and/or neutrophils, thereby isolating a 478 gene "composite M3 dysregulome". Surprisingly, the expression of only a few of these genes was significantly altered in PR-9 cells after PML-RARA induction, suggesting that most of these genes are not direct targets of PML-RARA. Comparison of the M3-specific signature to our previously described murine APL dysregulome revealed 33 commonly dysregulated genes, including JUN, EGR1, and TNF. Collectively, these results suggest that PML-RARA initiates a transcriptional cascade which generates a unique downstream expression signature in both primary human and mouse APL cells.

overall_design: 14 human APL/M3 AML samples were compared to 62 AML samples of other AML FAB subtypes (bone marrow aspirates collected at diagnosis, included in GSE10358), to fractionated cells from normal human bone marrow aspirates (5 CD34+ cells, 5 promyelocytes, 5 neutrophils/PMNs), and to PR9 cells before and after Zinc-induction of PML-RARA.

middle: E

first: Nicole

last: Grieselhuber

first: Timothy

last: Ley


title: Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays

first: Amandine

last: Bemmo

summary:
Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. Here, we use the well studied Microarray Quality Control (MAQC) dataset to benchmark the Affymetrix Exon Array, and compare it to two other popular platforms: Illumina, and Affymetrix U133.
Results:We show that at the gene expression level, the Exon Array performs comparably with the two 3’ targeted platforms. However, the interplatform correlation of the results is slightly lower than between the two 3’ arrays. We show that some of the discrepancies stem from the RNA amplification protocols, e.g. the Exon Array is able to detect expression of non-polyadenylated transcripts. More importantly, we show that many other differences result from the ability of the Exon Array to monitor more detailed isoform-level changes; several examples illustrate that changes detected by the 3’ platforms are actually isoform variations, and that the nature of these variations can be resolved using Exon Array data. Finally, we show how the Exon Array can be used to detect alternative isoform differences, such as alternative splicing, transcript termination, and alternative promoter usage. We discuss the possible pitfalls and false positives resulting from isoform-level analysis.
Conclusions:The Exon Array is a valuable tool that can be used to profile gene expression while providing important additional information regarding the types of gene isoforms that are expressed and variable. However, analysis of alternative splicing requires much more hands on effort and visualization of results in order to correctly interpret the data, and generally results in considerably higher false positive rates than expression analysis. One of the main sources of error in the MAQC dataset is variation in amplification efficiency across transcripts, which is not adequately corrected using existing statistical methods. We outline approaches to reduce such errors by filtering out potentially problematic data.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.


title: Heme homeostasis is regulated by the conserved and concerted functions of HRG-1 proteins

status: Public on Jun 13 2008

first: WeiPing

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary:
Hemes are essential but potentially  cytotoxic cofactors that participate in critical  and diverse biological processes. Although the  pathway and intermediates for heme biosynthesis  have been well defined, the intracellular  networks which mediate heme trafficking remain  unknown. Caenorhabditis elegans and related  helminths are natural heme auxotrophs requiring  environmental heme for growth and development.  We exploited this auxotrophy to identify HRG-1  and HRG-4 in C. elegans and show that they are  essential for heme homeostasis and normal  vertebrate development. We demonstrate that heme  deficiency upregulates expression of hrg-4 and  its evolutionarily conserved paralog hrg-1.  Depletion of either HRG-1 or HRG-4 in worms  results in disruption of organismal heme sensing  and abnormal response to heme analogs. HRG-1 and  HRG-4 are novel transmembrane proteins that bind  heme and have evolutionarily conserved functions.  Transient knockdown of hrg-1 in zebrafish leads  to hydrocephalus, yolk tube malformations, and,  most strikingly, profound defects in  erythropoiesis - phenotypes that are fully  rescued by worm HRG-1. These findings reveal  unanticipated and conserved pathways for cellular  heme trafficking in animals that defines the  paradigm for eukaryotic heme transport.  Uncovering the mechanisms of heme transport in C.  elegans will provide novel insights into human  disorders of heme metabolism and generate unique  anthelmintics to combat worm infestations.
Keywords: dose-response

overall_design: As a first-step toward understanding heme homeostasis at the molecular level, we performed genome-wide microarrays to identify genes that are transcriptionally regulated by heme. For microarray analysis, synchronized F2 larvae were re-inoculated in mCeHR-2 medium supplemented with 4, 20 or 500 uM hemin and harvested at the late L4 stage for mRNA prep and probe hybridization to Affymetrix C. elegans Whole Genome Expression Arrays. Total RNA from three biological replicates were used at each hemin concentration. Data from worms grown in mCeHR-2 medium with 4 and 500 uM hemin were compared to data from worms grown in 20 uM hemin. Microarray data were verified with Microarray Suite 5.0 (Affymetrix) and Robust Multichip Average Method (RMA, R package). Results from MAS 5.0 and RMA analyses provided with 375 genes that showed 1.6 fold change in 4 and 500 uM hemin when compared to data from 20 uM hemin samples. Statistical analyses identified changes in 375 genes from worms grown in either 4 or 500 µM heme (see Methods). The microarray results were validated by qRT-PCR (Supplementary Fig. 1) and the 375 heme-responsive genes were classified into eight categories based on their relative changes in gene expression (Table I). The data from the microarray study show that ‰1.9 % of genes in the worm genome are transcriptionally responsive to heme. Notably, of the 375 genes, 164 had some sequence identity in human genome databases at the amino acid level, and >90 % of the genes had no ascribed function in the C.

first: Abbhirami

last: Rajagopal

first: Anita

middle: U

last: Rao

first: Julio

last: Amigo

first: Caitlin

last: Hall

first: Suji

last: Uhm

first: Barry

last: Paw

first: Michael

last: Krause

first: Iqbal

last: Hamza


title: Expression data of hormone-responsive MCF-7 cells versus estrogen-deprived MCF-7:5C and MCF-7:2A breast cancer cells

status: Public on Mar 19 2008

city: Philadelphia

first: Dr Joan

last: Lewis-Wambi

state: PA

address: 333 Cottman Ave

department: Medical Sciences

institute: Fox Chase Cancer Center

summary:
Estrogen deprivation using aromatase inhibitors is currently the standard of care for patients with estrogen-receptor (ER)-positive breast cancer. Unfortunately, prolonged estrogen deprivation leads to drug resistance (i.e. hormone-independent growth). We therefore used DNA microarray analysis to study the gene expression profiles of wild-type MCF-7 cells (which are sensitive to antihormone therapy) and long-term estrogen deprived MCF-7:5C and MCF-7:2A breast cancer cells (which are resistance to estrogen-deprivation; aromatase inhibitor resistant).
Transcriptional profiling of wild-type MCF-7 cells and estrogen deprived MCF-7:5C and MCF-7:2A cells was performed using Affymetrix Human Genome U133 Plus 2.0 Array.
Keywords: breast cancer cells, estrogen

overall_design: We wanted to study the gene expression profiles of the different cell lines in their growth media without any drug treatment. Therefore, MCF-7, MCF-7:5C, and MCF-7:2A cells were grown in estrogen-free media (phenol red-free RPMI medium supplemented with 10% 4X dextran-coated charcoal-treated fetal bovine serum) until they were 70-80% confluent then RNA was extracted, labeled, and hybridized to the Affymetrix Human Genome U133 Plus 2.0 Arrays.

first: Joan

first: Heather

last: Cunliffe

first: Helen

last: Kim

first: Amanda

last: Willis

first: V

middle: C

last: Jordan


title: EXECUTER1- and EXECUTER2-dependent transfer of stress signals from the plastid to the nucleus of Arabidopsis thaliana

status: Public on Feb 14 2008

city: Zurich

first: Chanhong

address: Universitystr. 2

department: Plant Sciences

country: Switzerland

institute: ETH Zurich

summary:
Shortly after the release of singlet oxygen (1O2), drastic changes in  nuclear gene expression occur in the conditional flu mutant of  Arabidopsis that reveal a rapid transfer of signals from the plastid  to the nucleus. In contrast to retrograde control of nuclear gene  expression by plastid signals described earlier, the primary effect  of 1O2 generation in the flu mutant is not the control of chloroplast  biogenesis but the activation of a broad range of signaling pathways  known to be involved in biotic and abiotic stress responses.  This activity of a plastid-derived signal suggests a new function of  the chloroplast, namely that of a sensor of environmental changes  that activates a broad range of stress responses. Inactivation of the  plastid protein EXECUTER1 attenuates the extent of 1O2-induced  up-regulation of nuclear gene expression, but it does not fully  eliminate these changes. A second related nuclear-encoded protein,  dubbed EXECUTER2, has been identified that is also implicated  with the signaling of 1O2-dependent nuclear gene expression  changes. Like EXECUTER1, EXECUTER2 is confined to the plastid.  Inactivation of both EXECUTER proteins in the ex1/ex2/flu triple  mutant is sufficient to suppress the up-regulation of almost all  1O2-responsive genes. Retrograde control of 1O2-responsive genes  requires the concerted action of both EXECUTER proteins within  the plastid compartment.
Keywords: biotic and abiotic stress response, nuclear gene expression, plastid-derived signal, Col-0 ecotype, continuous light and then dark-incubated plants

overall_design:
Two individual biologica replicates, each containing material of five mature plants of wild  type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu, respectively, were used for  the microarray analysis. Plants were germinated on soil and kept  under continuous light until the beginning of bolting and then  transferred to the dark for 8 h. Dark-incubated mature plants were  reilluminated for 30 min and subsequently harvested for RNA extraction.

The EX1 (At4g33630) T-DNA insertion line SALK 002088 and EX2 (At1g27510) T-DNA insertion line  SALK 012127 were obtained from the European Arabidopsis Stock  Centre (NASC). Homozygous mutant lines were identified by PCR  analysis by using T-DNA-, EX1- and EX2-specific primers. Both  T-DNA-lines were crossed with a flu Col-0 line that had been  obtained by 5 backcrosses of flu1-1 in Landsberg erecta with  wild-type Columbia. The ex1/flu and ex2/flu mutant lines were  crossed, and within the segregating F2 population triple mutants  were identified by PCR-based genotyping. For the cultivation of mature plants, seeds of wild type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu,  all in Col-0 ecotype, were sown on soil and plants were grown under  continuous light (100  mol m 2 s 1).

first: Keun-Pyo

last: Lee

first: Klaus

last: Apel


title: INTER_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor

status: Public on Mar 06 2009

first: Tomas

last: Marques-Bonet

overall_design: A total of 3 chimpanzees, 2 bonobos, 3 gorillas, 1 orangutan and 1 macaque were hybridized against human (NA15510). Other hybridizations (other humans, and non-humans) were also used as a replicate.

first: Jeffrey

last: Kidd

first: Mario

last: Ventura

first: Tina

last: Graves

first: Ze

last: Cheng

first: LaDeanna

middle: W

last: Hillier

first: Zhaoshi

last: Jiang

first: Carl

last: Baker

first: Ray

last: Malfavon-Borja

first: Lucinda

last: Fulton

first: Can

last: Alkan

first: Gozde

last: Aksay

first: Santhosh

last: Girirajan

first: Priscillia

last: Siswara

first: Lin

last: Chen

last: Cardone

first: Arcadi

last: Navarro

first: Elaine

last: Mardis

first: Richard

last: Wilson

first: Evan

last: Eichler