title: Effect of two weeks erythropoietin treatment on monocyte transcriptomes of cardiorenal patients

status: Public on Aug 11 2009

city: Edmonton

first: Branko

last: Braam

department: Medicine / Nephrology

institute: Univ. of Alberta

summary: Patients with combined heart and renal failure, also termed the cardiorenal syndrome (CRS), have high cardiovascular morbidity and mortality.  Several key connectors between heart and kidney have been recognized, such as oxidative stress, inflammation, the renin-angiotensin system and the sympathetic nervous system. Monocytes are key players in the development of atherosclerosis and may act as a biosensor to detect changes in the systemic environment. Anemia, which occurs frequently in CRS, is partly due to an absolute and/or relative erythropoietin (EPO) deficiency. Until now, EPO treatment has largely been used to treat (renal) anemia, but recent research also showed beneficial non-hematopoietic effects such as anti-inflammatory and anti-oxidative capacities. The hypothesis of the present study was that monocyte gene expression profiles of cardiorenal patients compared to healthy controls reflect the systemic nature of CRS and are responsive to short-term treatment with Epo. The first aim was to investigate whether this short term treatment revealed non-hematopoietic EPO effects. The second aim was to address whether EPO dampens expression of genes involved in inflammation and oxidative stress. Given the variable response to EPO, the third aim was to test whether baseline gene expression profiles or the acute gene expression modulation by EPO are associated with EPO resistance.

overall_design:
This study was part of a larger clinical trial in which hematopoietic and non-hematopoietic effects of EPO treatment for short and long term are assessed in CRS patients. Therefore, patients were randomized into 3 groups: (1) EPO, patients are kept on baseline low hemoglobin levels by phlebotomy for 6 months; (2) EPO, patients may rise in hemoglobin levels to defined maximum for 6 months; (3) No EPO. This gene expression analysis is focussed on EPO's short-term (2wk) effects in a subset of included patients. Group (1) and (2) were grouped for analysis, since both groups received EPO and no phlebotomy had been performed in the first 2 weeks. Monocytes were positively isolated from peripheral whole blood with CD14+ immunomagnetic beads. Total RNA was isolated and prepared for genome wide analyses using Illumina HumanRef8 V3.0 Beadchips. In total, 48 arrays were analyzed including 12 healthy controls, 18 CRS patients at baseline and 2 weeks after study enrollment. Twelve out of 18 patients received EPO during the two weeks.

The supplementary file 'GSE17582_non-normalized_data.txt' contains non-normalized data for Samples GSM438053-GSM438100.

first: Carlo

last: Gaillard

first: Marianne

last: Verhaar

first: Kim

last: Jie

first: Sebastiaan

last: Wesseling

first: Karien

last: van der Putten


title: Topoisomerase I suppresses genomic instability by preventing interference between replication and transcription

status: Public on Aug 08 2009

city: Montpellier

first: Philippe

last: Pasero

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

type: Genome binding/occupancy profiling by genome tiling array

summary:
Topoisomerase I (Top1) is a key enzyme acting at the interface between DNA replication, transcription and mRNA maturation. Here, we show that Top1 suppresses genomic instability in mammalian cells by preventing conflicts between transcription and DNA replication. Using DNA combing and ChIP-on-chip, we found that Top1-deficient cells accumulate stalled replication forks and chromosome breaks in S phase and that breaks occur preferentially at gene-rich regions of the genome. Strikingly, these phenotypes were suppressed by preventing the formation of RNA-DNA hybrids (R-loops) during transcription. Moreover, these defects could be mimicked by depletion of the splicing factor ASF/SF2, which interacts functionally with Top1. Taken together, these data indicate that Top1 prevents replication fork collapse by suppressing the formation of R-loops in an ASF/SF2-dependent manner. We propose that interference between replication and transcription represents a major source of spontaneous replication stress, which could drive genomic instability during early stages of tumorigenesis.
Bed files contain the gamma-H2AX enrichment sites described in the paper

overall_design: Gamma-H2AX ChIPed vs. Input DNA in HCT116 shTop1 and shCtrl cells

first: Sandie

last: Tuduri

first: Laure

last: Crabbe

first: Chiara

last: Conti

first: Helene

last: Tourriere

first: Heidi

last: Holtgreve-Grez

first: Anna

last: Jauch

first: Veronique

last: Pantesco

first: John

first: Aubin

last: Thomas

first: Charles

last: Theillet

first: Yves

last: Pommier

first: Jamal

last: Tazi

first: Arnaud

last: Coquelle


title: Genome-wide HIF-1 binding sites in HepG2 cells

status: Public on Jun 02 2009

city: Boston

first: Xiaobo

last: Xia

state: MA

address: 44 Binney St, Mayer 649

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

summary: Adaptation to hypoxia is mediated through a coordinated transcriptional response driven largely by Hypoxia-Inducible Factor 1 (HIF-1). The direct transcriptional targets of HIF-1 play important roles in facilitating both short-term and long-term adaptation to hypoxia. Alignment of the sequences encompassing all well-characterized HIF-1 binding sites has revealed a consensus core HRE motif of 5'-RCGTG-3' (R = A or G). Since the consensus HIF-1 binding motif is too promiscuous to accurately predict binding a priori, we used ChIP-chip to define HIF-1 chromatin binding on a genome-wide level. We integrated these results with gene expression profiling to interrogate mechanisms regulating hypoxia-induced gene expression, and to more comprehensively identify direct targets of HIF-1 transactivation.

overall_design: HepG2 cells were cultured under normoxic (ambient) or hypoxic (0.5%O2, 4 h) conditions. HIF-1  ChIP was performed with a HIF-1 polyclonal Ab. Triplicate ChIPed DNA and inputs were amplified and hybridized onto the Affymetrix Gene-Chip Human Tiling 2.0R Array Set. The MAT algorithm was used to identify peaks of probe intensity (‘‘hits’’).


title: Human-specific transcriptional regulation of CNS development genes by FOXP2

status: Public on Nov 12 2009

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: The signaling pathways orchestrating both the evolution and development of language in the human brain remain unknown.  To date, the transcription factor FOXP2 is the only gene implicated in Mendelian forms of human speech and language dysfunction1,2.  It has been proposed, that the amino acid composition in the human variant of FOXP2 has undergone accelerated evolution, and this change occurred around the time of language emergence in humans3,4.  However, this remains controversial, and whether the acquisition of these amino acids in human FOXP2 has any functional consequence in human neurons remains untested.  Here, we demonstrate that these two amino acids confer new functionality in terms of differential transcriptional regulation, and extend these observations to in vivo brain, showing that several of the differential FOXP2 targets significantly overlap with genes different between human and chimpanzee brain.  We also identify novel relationships among the differentially expressed genes with additional critical regulators of neuronal development. These data provide support for the functional relevance of changes that occur on the human lineage by showing that the two amino acids unique to human FOXP2 can lead to significant differences in gene expression patterns across brain evolution, with direct consequences for human brain development and disease.  Since FOXP2 has an important role in the use of language in humans, the identified targets may have a critical function in the development and evolution of language circuitry in humans.

sample_organism:
Pan troglodytes
Homo sapiens

overall_design:
This study contains 2 microarray studies.
One study is in SH-SY5Y cells, and contained cells of three different genotypes:  control cells, cells overexpressing human FOXP2, and cells overexpressing chimpanzee FOXP2.  Three independent lines of each genotype were used and four biological replicates of each, for a total of 12 arrays per genotype (36 arrays total).
The second study is a comparison of human and chimpanzee brain in three brain regions:  frontal pole, caudate nucleus, and hippocampus.  Tissue from 3-6 individuals was utilized for each brain region for each species.

first: Jamee

middle: M

last: Bomar

first: Kellen

last: Winden

first: Giovanni

last: Coppola

first: Zophonias

middle: O

last: Jonsson

first: Fuying

last: Gao

first: Sophia

last: Peng

first: Todd

last: Preuss

first: James

middle: A

last: Wohlschlegel

first: Daniel

middle: H

last: Geschwind


title: Dietary soy effects on early rat mammary gland development

status: Public on Jul 23 2009

city: Little Rock

first: Ying

last: Su

state: AR

address: 1120 Marshall St. South Campus

department: physiology

institute: UAMS

summary: The linkage between nutrition and cancer prevention is an intriguing concept that is gaining widespread support based on epidemiological and animal studies. Multiple mechanisms likely underlie dietary protection against cancer, with effects influenced by target tissue response, cell-cell interactions and developmental context. Given the negative correlation between breast cancer incidence and intake of soy foods by Asian women, and the increasing consumption of soy protein-based formula by infants in the Western world, we have studied soy protein isolate (SPI) used in most infant formula as a paradigm to evaluate diet as a risk factor in a rodent model of mammary cancer. We previously demonstrated that lifetime exposure to dietary SPI reduced the incidence of N-methyl-N-nitrosourea-induced mammary tumors in young adult rats relative to those fed the control diet Casein (CAS). This protection was associated with increased tumor suppressor PTEN and decreased Wnt signaling component expression in mammary epithelial cells at postnatal day (PND) 50 prior to carcinogen insult. To identify early events contributing to mammary tumor suppression by diet, we used Affymetrix RAE230A GeneChips containing 14280 probe sets and the GeneSpring Robust Multi-array program to analyze genomic profiles of mammary glands of prepubertal (PND21) rats lifetime exposed to SPI or CAS.

overall_design: Female SD rats are exposed to either casein/soy protein isolate based AIN-93G diet since gestation day 4 till weaning. Whole mammary gland were harvested for the gene analysis by microarray.

first: Rijin

last: Xiao

first: Frank

last: Simmen

first: Rosalia

middle: C


title: Genomic Studies upon NeuroD6 overexpression in PC12 cells, in the presence or absence of an apoptotic stimulus

status: Public on May 05 2009

city: Washington

first: Anne

last: Chiaramello

state: DC

address: 2300 I Street N.W. Ross Hall 427

department: Anatomy and Regenerative Biology

institute: George Washington University Medical Center

summary: During neurogenesis, expression of the basic Helix-Loop-Helix NeuroD6/Nex1/MATH-2 transcription factor parallels neuronal differentiation, while maintaining the differentiated state in the mature nervous system. To further dissect NeuroD6 differentiation properties, we previously generated a NeuroD6-overexpressing stable PC12 cell line, PC12-ND6, which displays a neuronal phenotype characterized by spontaneous neuritogenesis, accelerated NGF-induced differentiation, and increased regenerative capacity. Furthermore, we reported that NeuroD6 promotes long-term neuronal survival upon oxidative stress triggered by serum deprivation. In this study, we identified the NeuroD6-mediated transcriptional regulatory pathways linking neuronal differentiation to survival, by conducting a genome-wide microarray analysis using PC12-ND6 cells and serum deprivation as a stress paradigm.  Through a series of filtering steps and a gene-ontology analysis, we found that NeuroD6 promotes distinct but overlapping gene networks, consistent with the differentiation, regeneration, and survival properties of PC12-ND6 cells.  Using a gene set enrichment analysis, we provide the first evidence of a compelling link between NeuroD6 and a set of heat shock proteins in the absence of stress, which may be instrumental to confer stress tolerance to PC12-ND6 cells.  Immunocytochemistry results showed that HSP27 and HSP70 interact with cytoskeletal elements, consistent with their roles in neuritogenesis and preserving cellular integrity. HSP70 also colocalizes with mitochondria located in the soma, growing neurites and growth cones of PC12-ND6 cells prior to and upon stress stimulus, consistent with its neuroprotective functions.  Collectively, our findings support the notion that NeuroD6 links neuronal differentiation to survival via the network of molecular chaperones and endows the cells with increased stress tolerance.

overall_design: The experimental design involved six replicates of serum-grown PC12 cells (control), serum-grown PC12-ND6 cells (t=0), and serum-deprived PC12-ND6 cells (t=48 hrs).

first: Martine

last: Uittenbogaard


title: Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures

status: Public on May 10 2009

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: In the mammalian central nervous system (CNS) an important contingent of dopaminergic neurons are localized in the substantia nigra and in the ventral tegmental area of the ventral midbrain. They constitute an anatomically and functionally heterogeneous group of cells involved in a variety of regulatory mechanisms, from locomotion to emotional/motivational behavior. Midbrain dopaminergic neuron (mDA) primary cultures represent a useful tool to study molecular mechanisms involved in their development and maintenance. Considerable information has been gathered on the mDA neurons development and maturation in vivo, as well as on the molecular features of mDA primary cultures. Here we investigated in detail the gene expression differences between the tissue of origin and ventral midbrain primary cultures enriched in mDA neurons, using microarray technique. We integrated the results based on different re-annotations of the microarray probes. By using knowledge-based gene network techniques and promoter sequence analysis, we also uncovered mechanisms that might regulate the expression of CNS genes involved in the definition of the identity of specific cell types in the ventral midbrain. We integrate bioinformatics and functional genomics, together with developmental neurobiology. Moreover, we propose guidelines for the computational analysis of microarray gene expression data. Our findings help to clarify some molecular aspects of the development and differentiation of DA neurons within the midbrain.

overall_design: 9 microarrays used. MesE11 x 3; MesPC x 6.

first: Floriana

last: Volpicelli

first: Antonio

last: Di Lieto

first: Damiana

last: Leo

first: Carla

last: Perrone Capano

first: Petri

last: Auvinen

first: Umberto

last: di Porzio


title: Transcriptional gene profile of peripheral blood derived mesenchymal stromal cells from GFP transgenic rat

status: Public on Apr 26 2009

city: Birmingham

first: Qiling

last: He

state: AL

address: 1825 University Blvd, Shelby Building

department: Microbiology

institute: University of Alabama at Birmingham

summary:
Using culture conditions similar to those defined for bone marrow derived mesenchymal stromal cells (BMMSCs), peripheral blood derived mesenchymal stromal cells (PBMSCs) from green fluorescent protein (GFP) transgenic rats were isolated and expanded. Despite the highly similar profile in the putative mesenchymal characteristics including fibroblastic morphology, molecular markers such as CD90, CD44, CD106, vimentin, etc., osteogenic and adipogenic differentiation potentials, significant differential expression between PBMSCs and BMMSCs was discovered in 167 genes by Affymetrix microarray. Of the 167 sequences, were there 81 genes up-regulated and 86 genes down-regulated in the PBMSCs vs BMMSCs. The gene ontological (GO) analysis further revealed that ontology terms such as cell differentiation, development, cell communication, extracellular region, etc., were significantly enriched in these 167 genes, implying potential different biological function of PBMSCs from their counterpart BMMSCs. These genes and associated proteins may also be used as markers for defining PBMSCs from BMMSCs, and more important, may provide further direction to study this elusive cell population.
Keywords: mesenchymal stromal cells (MSCs), peripheral blood (PB), bone marrow (BM), green fluorescent protein (GFP) transgenic rat, microarray

overall_design: Using the same culture conditions, 3 paired PBMSCs and BMMSCs were obtained from 3 different GFP rats. Total cellular RNA of the passage 2 cells was isolated using a total RNA extraction mini kit and processed for the comparative gene expression profile study. Thus, within the total 6 hybridizations, there were 2 comparative groups containing 3 samples in each and each of the 3 samples in one group were paired with one of the other 3 samples in the other group.

first: Chao

last: Wan

first: Xinmin

last: Li

first: Graham

last: Lee

first: Tom

last: Gardiner

first: Gang


title: Mouse Exon Atlas

status: Public on May 08 2009

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
The purpose of the study was to compare exon expression across a diverse collection of mouse tissues

Keywords: between tissue comparison

overall_design: between tissue comparison

first: Andrew

last: Su

first: Jay

last: Zhang


title: 5-methylcytosine ChIP-on-Chip (MeDIP) of sporadic amyotrophic lateral sclerosis and control human brains

status: Public on Apr 23 2009

city: University of Sydney

first: Roger

last: Pamphlett

address: Blackburn Bld

country: Australia

institute: University of Sydney

type: Methylation profiling by genome tiling array

summary:
This experiment series sought to detect genome-wide methylation in sporadic amyotrophic lateral sclerosis brains and compare it to normal control brains. Methylation across the whole genome was measured in brain DNA of 10 SALS patients and 10 neurologically-normal controls. Methylated DNA was immunoprecipitated and interrogated by Affymetrix GeneChip Human Tiling 2.0R Array Sets. Methylation calls were compared between SALS patients and controls at each methylated site.

Keywords: ChIP-Chip

overall_design: 10 sporadic amyotrophic lateral sclerosis brain (lateral frontal cortex, Brodmann area 46) and 10 normal control brain (lateral frontal cortex, Brodmann area 46). 1 replicate sample repeated at different time (19a).

first: Julia

last: Morahan


title: GBM cell lines derived and propagated according to Cambridge protocol

status: Public on Apr 28 2009

city: Cambridge

first: Talal

middle: M.

last: Fael Al-Mayhani

state: Cambridgeshire

address: Forvie Site, Robinson Way

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

summary: We screened the gene expression in GBM cell lines cultured under serum-free conditions. We have special interest in genes associated with glial development such as NG2, Olig2 and PDGFRa. This microarray data gave us an idea about the expression of these genes and made the basis for further investigation.

overall_design: Seven GBM cells were derived from 7 different patients under serum-free conditions according to Cambridge protocol as previously described (Fael Al-Mayhani et al, 2009). The RNA was extracted and its quality was assessed. The samples were sent for microarray screening using Illumina platform. The gene was considered as present when the detection value was greater than 0.99.

first: Colin

last: Watts


title: Gene expression of genetically related and unrelated human embryonic stem cell lines

status: Public on Mar 20 2009

city: New York

first: Dieter

last: Egli

state: NY

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

summary:
Gene expression of sibling human ES cell lines are more similar to each other than unrelated cell lines.
Undifferentiated human embryonic stem cells were used for analysis. We sought to determine whether genetic differences underly variations between different human ES cell lines. Sibling cell lines that are genetically closer than non-sibling cell provided the opportunity to determine this. We found that sibling cell lines are more similar in their gene expression patterns than unrelated cell lines.

overall_design: 16 Samples. HUES 55-58 are related, so are HUES 50 and HUES51, and so are HUES 62 and HUES 63.

first: Kun

first: Alice

last: Chen

first: Jie

last: Deng

first: Kevin

last: Eggan

first: Douglas

last: Melton


title: Transcriptional profiles of rodent hippocampal CA1 tissue during aging and cognitive decline

status: Public on Jan 18 2009

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary:
Recent microarray studies in the hippocampus of rodents or Alzheimer’s disease (AD) subjects have identified a substantial number of cellular pathways/processes correlated with aging and cognitive decline. However, the temporal relationships among these expression changes or with cognitive impairment have not been studied in depth.  Here, using Affymetrix microarrays, immunohistochemistry and Morris water maze cognitive testing across 5 age groups of male F344 rats (n=9-15/group, one microarray per animal), we systematically analyzed the temporal sequence and cellular localization of aging changes in expression.  These were correlated with performance scores on the hippocampus-dependent Morris Water Maze task. Significant microarray results were sorted in to Early, Intermediate, Midlife, and Late patterns of expression, and functionally categorized (Early- downregulated neural development, lipid synthesis and energy-utilization; upregulated ribosomal synthesis, growth, stress/inflammatory, lysosome and protein/lipid degradation. Intermediate- increased defense/inflammatory activation and decreased transporter activity; Midlife- downregulated energy-dependent signaling and neurite growth, upregulated astroglial activation, Ca2+-binding, cholesterol/lipid trafficking, myelinogenic processes and additional lysosome/inflammation; Late- further recruitment of genes in already-altered pathways). Immunohistochemistry revealed a primarily astrocytic localization of the processes upregulated in midlife, as well as increased density of myelin proteins. Evidence of cognitive impairment first appeared in the 12-month-old group (midlife) and was increased further in the 23-month-old group, exhibiting the highest correlations with some upregulated genes related to cholesterol transport (e.g., Apoe, Abca2), protein management and ion binding. Some upregulated genes for inflammation (Il6st) and myelinogenesis (Pmp22) also correlated with impairment. Together, the data are consistent with a novel sequential cascade model of brain aging in which metabolic alterations early in maturity are followed by inflammation and midlife activation of an astrocyte-centered cholesterol trafficking pathway that stimulates oligodendrocyte remyelination programs. Importantly, this cholesterol trafficking pathway also may compete for astroglial bioenergetic support of neurons, in turn, leading to downregulation of energy-dependent pathways needed to sustain cognitive functions.
Keywords: aging time course

overall_design: Fisher 344 rats aged 3 (n = 9), 6 (n = 9), 9 (n = 9), 12 (n = 9), or 25 (n = 15; but see below) months were behaviorally characterized on the Morris water maze. Briefly, animals were placed in a circular water bath chamber with a partially submerged platform. Three times per day for three days, animals were placed at randomized starting points with the goal of locating the hidden platform. Generally, animals became better at locating the platform, and by the third day of training, were reliably swimming directly to the platform despite randomized starting loci. On the fourth day, the platform was removed and the degree to which the animals focused their searches on the area that previously contained the platform was measured. On the last day of behavior, animals were given a cue trial in which the platform was raised above the water level so that the rats could see it. Measures taken from the behavior study included path length (how long did the animal swim prior to locating the platform/ platform area), latency to platform in seconds, and velocity (centimeters/ second; swim speed). Two aged animals (E2 and E12) were removed from the study for poor health, reducing the 23 month cohort (n = 13). Twelve to twenty four hours after the last behavioral session, animals were killed and their hippocampi removed. The right hippocampus went to immunohistochemistry for quantification and localization of selected protein products. The left hippocampus was dissected, the CA1 region removed and frozen in dry ice prior to microarray processing. mRNA was extracted from each animal's tissue by standard Affymetrix protocols (see Blalock et al., 2003) and hybridized to individual microarrays (RAE 230A; N = 49 arrays in total). Results were processed with the MAS5 algorithm and subjected to ‘all probe set’ scaling with a target intensity of 500. Probe sets were filtered for presence (> = 5 presence calls study wide) and gene symbol level annotation prior to statistical analysis. 1-ANOVA across age was used to identify aging-related probe sets/genes (p <= 0.05). Aging-related genes were subjected to post hoc template correlation to determine the pattern of age-related change, and further, within the 12 and 23 month old groups, Pearson's correlation with behavioral scores was used to identify genes whose expression levels correlated significantly (p <= 0.05) with behavior. Twelve and 23 month old groups were chosen for this correlation analysis as they showed the greatest variability among similarly aged animals, suggesting that these ages show important cognitive transition phases during aging-related cognitive decline. Functional grouping analysis was performed using the DAVID suite of on-line tools.

first: Inga

last: Kadish

first: Olivier

last: Thibault

first: Kuey-Chu

last: Gant

first: Nada

last: Porter

first: Philip

middle: W

last: Landfield


title: Exon analysis of HCV tumor promoting effect

status: Public on Mar 22 2009

city: Ramat-Gan

first: Mark

last: Katzenellenbogen

address: Ramat-Gan 52900, Israel

department: THE FACULTY OF LIFE SCIENCE, BIOINFORMATICS AND MICROARRAY UNIT

country: Israel

institute: Bar Ilan University

summary:
The hepatitis C virus (HCV) is one of the major risk factors for the development of hepatocellular carcinoma (HCC). Nevertheless, transgenic mice which express the whole HCV polyprotein (HCV-Tg) do not develop HCC. Whereas chronic HCV infection causes inflammation in patients, in HCV-Tg mice, the host immune reaction against viral proteins is lacking. We aimed to test the role of HCV proteins in HCC development on the background of chronic inflammation in vivo.
We crossed the HCV-Tg mice which do not produce HCC with the Mdr2-knockout (Mdr2-KO) mice which develop inflammation-associated HCC, to generate Mdr2-KO/HCV-Tg mice. We studied the effect of the HCV transgene on tumor incidence, hepatocyte mitosis and apoptosis, and on gene expression in the liver of produced mice.

overall_design: The expression profile of HCV-Tg and not HCV-Tg mice on the MDR2-KO and control MDR2-heterozygous background had been tested. The non-tumorous liver tissue from 4 non-HCV-Tg Mdr2-heterozygous female mice, 5 HCV-Tg Mdr2-heterozygous female mice, 5 non-HCV-Tg Mdr2-KO female mice, 5 HCV-Tg Mdr2-KO female mice and  6 tumors developed by  HCV-Tg MDR2-KO mice were submitted to the gene expression profiling. The non tumorous match of tumorous samples number 1-4 are HCV-Tg MDR2-KO samples 1-4, of tumorous sample 5,6 - HCV-Tg MDR2-KO sample 5.

first: Naama

last: Klopstock

first: Orit

last: Pappo

first: Miriam

last: Sklair-Levy

first: Devorah

last: Olam

first: Lina

last: Mizrahi

first: Eithan

last: Galun

first: Daniel

last: Goldenberg


title: EZH1 and H3K27me3 ChIP-chip data from mouse embryonic stem cells

status: Public on Mar 25 2009

first: Xiaohua

last: Shen

address: 44 Binney Street

institute: Dana Farber Cancer Institute

summary: Trimethylation on H3K27 (H3K27me3) mediated by Polycomb repressive complex 2 (PRC2) has been linked to embryonic stem cell (ESC) identity and pluripotency. EZH2, the catalytic subunit of PRC2, has been reported as the sole histone methyltransferase that methylates H3K27 and mediates transcriptional silencing. Analysis of Ezh2(-/-) ESCs suggests existence of an additional enzyme(s) catalyzing H3K27 methylation. We have identified EZH1, a homolog of EZH2 that is physically present in a noncanonical PRC2 complex, as an H3K27 methyltransferase in vivo and in vitro. EZH1 colocalizes with the H3K27me3 mark on chromatin and preferentially preserves this mark on development-related genes in Ezh2(-/-) ESCs. Depletion of Ezh1 in cells lacking Ezh2 abolishes residual methylation on H3K27 and derepresses H3K27me3 target genes, demonstrating a role of EZH1 in safeguarding ESC identity. Ezh1 partially complements Ezh2 in executing pluripotency during ESC differentiation, suggesting that cell-fate transitions require epigenetic specificity.

overall_design: We used ChIP-chip to reveal genome-wide locationation of Polycomb protein EZH1 and H3K27me3 mark in undifferentiated wild-type (CJ7) and Ezh2-/- mutant embryonic stem (ES) cells. DNA fragments pulled down by chromatin immunoprecipitation, amplified and hybridization on Affymetrix mouse Tiling 2.0R array sets.

first: Stuart

last: Orkin


title: Gene expression profiles in the cerebellum and hippocampus following exposure to neurotoxicant Aroclor 1254

status: Public on Jan 31 2009

city: Research Triangle Park

first: Jennifer

last: Fostel

state: NC

institute: NIEHS

summary:
Pregnant rats (Long-Evans) were dosed perinatally with 0 or 6 mg/kg/day of Aroclor 1254 from gestation day 6 through postnatal day (PND) 21. Gene expression in cerebellum and hippocampus from PND7 and PND14 animals was analyzed with an emphasis on developmental aspects. Changes in gene expression (≥ 1.5 fold) in control animals identified normal developmental changes. These basal levels of expression were compared to data from Aroclor 1254-treated animals to determine the impact of gestational PCB exposure on developmental parameters.
The results indicate that the expression of a number of developmental genes related to cell cycle, synaptic function, cell maintenance, and neurogenesis is significantly altered from PND7 to PND14. Aroclor 1254 treatment appears to dampen the overall growth-related gene expression levels in both regions with the effect being more pronounced in the cerebellum. Functional analysis suggests that Aroclor 1254 delays maturation of the developing nervous system, with the consequences dependent on the ontological state of the brain area and the functional role of the individual gene.

Keywords: time course, stress response

first: Prasada

last: Kodavanti

first: Joyce

last: Royland


title: Expt. B; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling

status: Public on Jan 15 2009

city: Bethesda

first: David

middle: C.

last: Klein

state: MD

address: 49 Convent Dr.

department: PDEGEN

institute: NICHD/NIH

summary:
Biological processes are optimized by circadian and circannual biological timing systems.  In vertebrates, the pineal gland plays an essential role in these systems by converting time into a hormonal signal, melatonin; in all vertebrates, circulating melatonin is elevated at night, independent of lifestyle.
We have analyzed the rat pineal transcriptome at mid-day and mid-night to identify genes that exhibit night/day changes in expression.

Keywords: Time course (2 points)

overall_design: Rat pineal glands were obtained at mid-day and mid-night for RNA extraction and hybridization to Affymetrix microarrays. Triplicates of pooled pineal glands were analyzed at each timepoint. A similar set of samples was taken from a transgenic rat line (DN-Fra-2; Smith et al. (2001) Mol. Cell. Biol. 21, 3704-3713).

first: Michael

middle: J

last: Bailey

first: Steven

middle: L

last: Coon

last: Carter

first: Ann

last: Humphries

first: Jong-so

last: Kim

first: Qiong

last: Shi

first: Pascaline

last: Gaildrat

first: Fabrice

last: Morin

first: Surajit

last: Ganguly

first: John

middle: B

last: Hogenesch

first: Joan

last: Weller

first: Martin

middle: F

last: Rath

first: Morten

last: Møller

first: Ruben

last: Baler

last: Sugden

first: Zoila

middle: G

last: Rangel

first: Peter

last: Munson


title: Gene expression profiling of LNCaP and PC-3 prostate cancer cell lines

status: Public on Apr 27 2009

city: Oklahoma City

first: Hsueh-Kung

last: Lin

state: OK

address: Room 462, 800 Research Parkway

department: Urology

institute: University of Oklahoma Health Sciences Center

summary:
BACKGROUND.  Human prostate cancer LNCaP and PC-3 cell lines have been extensively used as prostate cancer cell models to study prostate cancer progression and to develop therapeutic agents.  Although LNCaP and PC-3 cells are generally assumed to represent early and late stages of prostate cancer development, respectively, there is limited information regarding comprehensive gene expression patterns between these two cells lines and relating these cells to prostate cancer progression based on their gene expression.

METHODS.  Comprehensive gene expression analysis was performed in LNCaP and PC-3 cells.  Total RNA was isolated from cultured cells and hybridized to Illumina human Ref-8 version 3 BeadChips representing 24,526 transcripts.  Bioinformatics approach was applied to identify genes, their functional roles and interaction networks that are unique in either LNCaP or PC-3 cells.

RESULTS.  We observed large differences in gene expression between LNCaP and PC-3 cells.Using robust statistical analysis and very high significance criteria to identify tractable number of genes 115 and 188 genes were identified uniquely expressed in LNCaP and PC-3 cells, respectively. Genes uniquely expressed in LNCaP cells contained UDP-glucosyltransferases as a signature for this cell line. This cell line demonstrated upregulation of various metabolic pathways on gene expression level. Talα/β, GATA-1 and c-Myc/Max were identified by in silico analysis as possible transcription factors regulating unique LNCaP genes. PC-3 cells were characterized by cytosceleton-related genes, keratins in particular. Several other well known genes (VEGFC, IL8, TGFβ2 and others) scattered throughout literature were identified and summarized in the discussion.
CONCLUSIONS.  This study demonstrated that LNCaP and PC-3 cells represent two distinct prostate cancer cell lineages.  LNCaP cells retain many prostate cell specific properties, whereas PC-3 cells have acquired more aggressive bone-like characteristics following bone metastasis and show little resemblance to prostate cells.  Microarray studies confirmed previously published results and provided more information between these two prostate cancer cell lines.  Future studies need to consider their similarities and differences in gene expression between localized and metastasized prostate cancer.

overall_design: LNCaP and PC-3 human prostate cancer cell lines were grown on Plastic under normal conditions. Total RNA was isolated from LNCaP cells passaged 31-32 times and from PC-3 cells passaged 16-17 times. Four biological replicates for each cell line (each replicate from different passage) were run on Illumina HumanRef-8 v3.0 platform. Two groups were compared by using associative t-test (Dozmorov I. & Centola M, 2003) and differentially expressed genes were characterized.

first: Mikhail

last: Dozmorov

first: Robert

middle: E

last: Hurst

first: Daniel

last: Culkin

first: Bradley

middle: P

last: Kropp

first: Mark

last: Frank

first: Jeanette

last: Osban

first: Trevor

last: Penning


title: Cerebellar gene expression data from Mecp2-null and MECP2-transgenic mice

status: Public on Apr 07 2009

city: Houston

first: Maria

last: Chahrour

address: 1 Baylor Plaza, T836

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary:
We compared gene expression changes in the cerebellum of mice lacking MeCP2 (Mecp2-null) and mice overexpressing MeCP2 (MECP2-transgenic).

A group of postnatal neurodevelopmental disorders collectively referred to as MeCP2 disorders are caused by aberrations in the gene encoding methyl-CpG-binding protein 2 (MECP2). Loss of MeCP2 function causes Rett syndrome (RTT), whereas increased copy number of the gene causes MECP2 duplication or triplication syndromes. MeCP2 acts as a transcriptional repressor, however the gene expression changes observed in the hypothalamus of MeCP2 disorder mouse models suggest that MeCP2 can also upregulate gene expression. To determine if this dual role of MeCP2 extends beyond the hypothalamus, we studied gene expression patterns in the cerebellum of Mecp2-null and MECP2-Tg mice, modeling RTT and MECP2 duplication syndrome, respectively. We found that abnormal MeCP2 dosage causes alterations in the expression of hundreds of genes in the cerebellum. The majority of genes were upregulated in MECP2-Tg mice and downregulated in Mecp2-null mice, consistent with a role for MeCP2 as a modulator that can both increase and decrease gene expression. Interestingly, many of the genes altered in the cerebellum, particularly those increased by the presence of MeCP2 and decreased in its absence, were similarly altered in the hypothalamus.

Keywords: Comparison of cerebellar gene expression data between Mecp2-null mice and Mecp2-transgenic mice

overall_design: Total cerebellar RNA samples were collected from Mecp2-null male mice (n=5), MECP2-transgenic male mice (n=5), and their wild type male littermates at 6 weeks of age (n=5 for each group).

first: Shay

last: Ben-Shachar

first: Christina

last: Thaller

first: Chad

last: Shaw

first: Huda

middle: Y

last: Zoghbi


title: Gene expression profiling under low dose and short incubation time of cadmium in primary rat hepatocyte in culture

status: Public on Feb 25 2009

city: Kalamazoo

first: Susan

last: Stapleton

state: MI

address: 3425 Wood Hall

department: Chemistry

institute: Western Michigan University

summary:
The study was performed using primary rat hepatocyte in culture from 4 adult male Sprague-Dawley rats to investigate the changes in gene expression under low dose (4μM) and short exposure (3hrs) of cadmium chloride. By comparing the gene expression profiles of control and cadmium-treated cells, the most dramatic and significant changes were for those genes associated with transcriptional regulation, antioxidant response and control of protein integrity. Changes in other genes involved in cellular physiological responses such as inflammation, growth and apoptosis were also observed. Results were further confirmed by quantitative real time polymerase chain reaction (qRT-PCR).
Keywords: early protective responses

overall_design: Primary hepatocytes from four rats were isolated using the collagenase-hyaluronidase perfusion and digestion method. The cells of greater than 85% viability were used in this study. The cells were plated at 90% confluency on culture dishes coated with collagen and maintained in Waymouth's medium containing BSA for 4hrs prior to an overnight incubation with BSA free Waymouth's medium. Control samples and cadmium-treated samples from individual rats were hybridized to RAE 230A arrays (n=4 and 8 microarrays); data were generated and analyzed.

first: C

last: Hsiao

first: S


title: Genome-wide Binding Site Mapping of Retinoic Acid Receptors and Coregulators in Breast Cancer Cells

status: Public on Mar 16 2009

first: Sujun

last: Hua

state: Tx

address: 1901 East Rd

institute: MD Anderson Cancer Center

summary:
Retinoic acid (RA) triggers growth-suppressive effects in tumor cells and therefore RA and its synthetic analogs have great potential as anti-carcinogenic agents. RA effects are mediated by retinoic acid receptors (RARs), which regulate gene expression in an RA-dependent manner. To define the genetic network regulated by RARs in breast cancer cells, we identified RAR genomic targets using chromatin immunoprecipitation and expression analysis in a model breast cancer cell line MCF-7. Furthermore, we identified genomic binding sites for two putative RAR coregulators FoxA1 and GATA3.

Keywords: ChIP-Chip Analysis

overall_design: This series contains ChIP-Chip raw data for four transcription factors (RARA, RARG, FoxA1 and GATA3) in MCF-7 cells. All the experiments are done in triplicates. We mapped the binding sites of RARA, RARG and GATA3 in the bacterial artificial chromosome (BAC) transgenic MCF7 cells in which we tagged the transcription factors with a modified LAP (localization and affinity purification) tag containing green fluorescent protein (GFP). Goat anti-GFP (raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP) was used to perform ChIP experiments in those transgenic lines. To map the binding sites of RARs, MCF7 Cells were hormone-deprived for 3 days and then were treated with 100 nM AM580 (RARA-selective agonist) or 100 nM CD437 (RARG-selective agonist) for 1 hour at 80% confluence. FoxA1 binding sites were mapped using goat anti-FoxA1 antibodies (Abcam: ab5089). Control data include Input from MCF-7 cells. ChIP-Chip experiments with eGFP antibody in wide type MCF-7 cells are used to control eGFP antibody non-specific binding.

first: Ralf

last: Kittler

first: Kevin

last: White


title: Transcriptional re-programming of primary human macrophages by IRF-3 and IRF-7

status: Public on Nov 30 2008

city: Montreal

first: Eduardo

last: Hernandez

state: Quebec

address: 3755 Cote-Sainte-Catherine Road

department: Molecular Oncology Group

country: Canada

institute: Lady Davis Institute for Medical Research (JGH)

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

overall_design: Refer to individual Series


title: Immune response to the yellow fever vaccine 17D.

status: Public on Dec 01 2008

city: Montréal

first: Bastian

middle: Robert

last: Angermann

address: 264 René-Lévesque Est

institute: Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CR-CHUM) Saint-Luc

summary: Correlates of immune mediated protection to most viral and cancer vaccines are still unknown. This impedes the development of novel vaccines to incurable diseases such as HIV and cancer. In this study, we have used functional genomics and polychromatic flow cytometry to define the signature of the immune response to the yellow fever (YF) vaccine 17D (YF17D) in a cohort of forty volunteers followed for up to one year after vaccination. We show that immunization with YF17D leads to an integrated immune response that includes several effector arms of innate immunity including complement, the inflammasome and interferons, as well as adaptive immunity as shown by an early T cell response followed by a brisk and variable B cell response. Development of these responses is preceded, as demonstrated in three independent vaccination trials and in a novel in vitro system of primary immune responses (Modular IMmune In vitro Construct (MIMIC) system), by the coordinated up-regulation of transcripts for specific transcription factors including STAT1, IRF7 and ETS2 that are upstream of the different effector arms of the immune response. These results clearly show that the immune response to a strong vaccine is preceded by coordinated induction of masters transcription factors, that lead to the development of a broad, polyfunctional and persistent immune response that integrates all effector cells of the immune system.

overall_design: This study has 3 branches, two of which are in vivo vaccination studies in two different Locations (Montreal,Canada and Lausanne, Switzerland). The third branch is an in vitro system mimicing (VaxDesign Mimic experiment) the environment in a lymph node. The Montreal Cohort enrolled 15 donors, and sampled whole blood pre vaccination with the Sanofi-Pasteur YF17D-204 YF-VAX vaccine, and on days 3,7,10,14,28,60,365 post vaccination. In the Lausanne Cohort 11 donors were enrolled vaccinated with Stamail, wohle blood was sampled on days 0,3 and 7. The VaxDesign experiment used purified CD4+ T-cells and autologus DC from 3 different donors, YF17D stimulated and unstimulated control samples were analyzed on day 0,3 and 7 after the start of co culturing of T-Cells and DC.

first: Denis

last: Gaucher

first: Rene

last: Therrien

first: Genevieve

last: Boucher

first: Nadia

last: Kettaf

first: Abdelali

last: Filali-Mouhim

first: Janice

middle: M

last: Moser

first: Riyaz

middle: S

last: Mehta

first: Donald

last: Drake III

first: Erika

last: Castro

first: Rama

last: Akondy

first: Aline

last: Rinfret

first: Bader

last: Yassine-Diab

first: Elias

last: Said

first: Younes

last: Chouikh

last: Cameron

first: Robert

last: Clum

first: David

last: Kelvin

first: Roland

last: Somogyi

first: Larry

middle: D

last: Greller

last: Balderas

first: Peter

last: Wilkinson

first: Giuseppe

last: Pantaleo

first: Jim

last: Tartaglia

middle: K

last: Haddad

first: Rafick-Pierre

last: Sekaly


title: Transcriptional profiles of Ad-F7 transduced macrophages treated with anti-IFNAR2 antibody or control isotype (IgG)

first: Eduardo

last: Hernandez

summary: Determine the role of interferons in the transcriptional profile of Ad-F7 transduced primary human macrophages using neutralizing antibody for the type I IFN receptor (IFNAR2).

overall_design: Primary human macrophage preparations were transduced with Ad-GFP or Ad-F7 and treated with control isotype (IgG) or neutralizing antibody for the type I IFN receptor (IFNAR2). RNA was collected 24 hours later and subjected to microarray analysis. Data represents the average of 5 donors.

first: Delphine

last: Goubau

first: John

last: Hiscott


title: Subchronic inhalation of zinc sulfate induces cardiac changes in healthy rats

status: Public on Sep 22 2008

first: beena

last: vallanat

address: 109 Tw Alexanser Dr

institute: EPA

summary:
Zinc is a common metal in most ambient particulate matter (PM), and has been proposed to be a causative component in PM-induced adverse cardiovascular health effects. Zinc is also an essential metal and has the potential to induce many physiological and nonphysiological changes. Most toxicological studies employ high levels of zinc. We hypothesized that subchronic inhalation of environmentally relevant levels of zinc would cause cardiac changes in healthy rats. To address this question, healthy male WKY rats (12 wks age) were exposed via nose only inhalation to filtered air or 10, 30 or 100 ug/m3 of aerosolized Zn in sulfate form, 5 h/d, 3 d/wk for 16 wks. Necropsies occurred 48 h after the last exposure to ensure effects were due to chronic exposure rather than the last exposure. No significant changes were observed in neutrophil or macrophage count, total lavageable cells, or enzyme activity levels (lactate dehydrogenase, n-acetyl ?-D-glucosaminidase, ?-glutamyl transferase) in bronchoalveolar lavage fluid, indicating minimal pulmonary effect. In the heart, cytosolic glutathione peroxidase activity decreased, while mitochondrial ferritin levels increased and succinate dehydrogenase activity decreased, suggesting a mitochondria-specific effect. Although no cardiac pathology was seen, cardiac gene array analysis indicated changes in genes involved in cell signaling, a pattern concordant with known zinc effects. These data indicate that inhalation of zinc at environmentally relevant levels may induce cardiac effects. While changes are small in healthy rats, these may be especially relevant in individuals with pre-existent cardiovascular disease.
Keywords: dose response

overall_design: total 24 samples, control and 3 doses. 6 replicates per group.

first: J

last: Wallenborn

first: Paul

last: Evansky

first: Jonathan

middle: H

last: Shannahan

first: Beena

last: Vallanat

first: Allen

last: Ledbetter

first: Mette

middle: C

last: Schladweiler

first: Judy

last: Richards

first: Rajaram

middle: R

last: Gottipolub

first: Abraham

last: Nyska

first: Urmila

last: Kodavanti


title: Conserved Transcriptional Response of Rodent Liver to TCDD: Rat

status: Public on Sep 19 2008

city: Toronto

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
Background
Mouse and rat models are mainstays in pharmacology, toxicology and drug development – but differences between strains and between species complicate data interpretation and application to human health. Dioxin-like polyhalogenated aromatic hydrocarbons represent a major class of environmentally and economically relevant toxicants. In mammals dioxin exposure leads to a broad spectrum of adverse affects, including hepatotoxicity of varying severity. Several studies have shown that dioxins extensively alter hepatic mRNA levels. Surprisingly, though, analysis of a limited portion of the transcriptome revealed that rat and mouse responses diverge greatly (Boverhof et al. Toxicol Sci 94:398–416, 2006).

Results
We employed oligonucleotide arrays to compare the response of 8,125 rat and mouse orthologs. We confirmed that there is limited inter-species overlap in dioxin-responsive genes. Rat-specific and mouse-specific genes are enriched for specific functional groups which differ between species, conceivably accounting for species-specificities in liver histopathology. While no evidence for the involvement of copy-number variation was found, extensive inter-species variation in the transcriptional-regulatory network was identified; Nr2f1 and Fos emerged as candidates to explain species-specific and species-independent responses, respectively.

Conclusion
Our results suggest that a small core of genes is responsible for mediating the similar features of dioxin hepatotoxicity in rats and mice but non-overlapping pathways are simultaneously at play to result in distinctive histopathological outcomes. The extreme divergence between mouse and rat transcriptomic responses appears to reflect divergent transcriptional-regulatory networks. Taken together, these data suggest that both rat and mouse models should be used to screen the acute hepatotoxic effects of drugs and toxic compounds.

overall_design: Wild-type Long-Evans(Kuopio) rats were treated with 100 ug/kg TCDD (n=4) or with cornoil vehicle as control (n=4) for 19 hours. Their livers were then excised, RNA extracted, and the resulting samples hybridized to Affymetrix RAE230A arrays to survey changes in the transcriptome profile.

first: Raimo

last: Pohjanvirta

first: Allan

last: Okey


title: RNA mapping and ChIP with tiling arrays in FGF-stimulated NIH3T3 cells

status: Public on Jul 01 2008

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

type: Expression profiling by genome tiling array

summary:
Transcription initiation in mammals is assumed to be independently controlled among nearby genes. On the other hand, recent large-scale transcriptome analyses have shown that the genome is pervasively transcribed, such that the majority of its DNA gives rise to RNAs. A simple question therefore arises: is it possible to pinpoint and activate a particular locus without perturbing numerous neighboring transcripts? Here we show that intensive transcription of immediate-early genes (IEGs) in response to growth factor stimulation is often accompanied by co-upregulation of their neighboring genes. Profiling primary transcripts in the nucleus with whole-genome tiling arrays delineated simultaneous activation of transcription centered on IEGs. Even in surrounding intergenic regions, which lack annotated protein-coding genes, transcriptional upregulation took place at the same time. We further found that acetylation levels of histone H3 and H4 are elevated along with the IEG induction and neighbouring co-upregulation, and that inhibition of the mitogen-activated protein kinase (MAPK) pathway or the transcription factor SRF suppresses all these transcriptional upregulation. These results suggest that transcriptional activation has a ripple effect, and causes a substantial fluctuation in multiple intragenic and intergenic transcripts.

Keywords: Time course and ChIP-chip

overall_design: The following RNA mapping and ChIP experiments were performed using tiling arrays in FGF-stimulated NIH3T3 cells.  1) Expression time course of nuclear RNA  2) Expression time course of total RNA  3) Effect of the MEK inhibitor U0126  4) ChIP-chip with anti-acetylated histone H3 antibody  5) ChIP-chip with anti-SRF antibody

first: Miki

last: Ebisuya

first: Takuya

last: Yamamoto

first: May

last: Nakajima


title: Htt-N171 HD in vitro

status: Public on Aug 14 2008

city: Lausanne

first: Ruth

last: Luthi-Carter

address: AI 2138, Station 15

country: Switzerland

institute: EPFL

summary:
4 Treatment groups:
A) Uninfected
B) Infected 6 weeks prior with GFP-expressing recombinant lentivirus
C) Infected 6 weeks prior with Htt-N171-19Q-expressing recombinant lentivirus
D)Infected 6 weeks prior with Htt-N171-82Q-expressing recombinant lentivirus
Keywords = huntington
Keywords: parallel sample

first: Diana

last: Zala

first: Etienne

last: Regulier

first: Patrick

last: Aebischer

first: Beate

last: Sick

first: Nicole

last: Deglon


title: Rapid encoding of information alters the profile of plasticity related mRNA transcripts in the hippocampal CA1 region.

status: Public on Jun 01 2008

city: Baltimore

first: Carlo

last: Colantuoni

address: 733 N Broadway

department: Neurology

institute: Johns Hopkins Univ. School of Medicine

summary:
A theoretical framework for the function of the medial temporal lobe system in memory defines differential contributions of the hippocampal subregions with regard to pattern recognition retrieval processes and encoding of new information. To investigate molecular programs of relevance, we designed a spatial learning protocol to engage a pattern separation function to encode new information. After background training, two groups of animals experienced the same new training in a novel environment, however only one group was provided spatial information and demonstrated spatial memory in a retention test. Global transcriptional analysis of the microdissected subregions of the hippocampus exposed a CA3 pattern that was sufficient to clearly segregate spatial learning animals from control. Individual gene and functional group analysis anchored these results to previous work in neural plasticity. From a multitude of expression changes, increases in camk2a, rasgrp1 and nlgn1 were confirmed by in situ hybridization. Furthermore, siRNA inhibition of nlgn1 within the CA3 subregion impaired spatial memory performance, pointing to mechanisms of synaptic remodeling as a basis for rapid encoding of new information in long-term memory.
Keywords: behavioral intervention: spatial learning paradigm

overall_design: RNA samples from animals subjected to a spatial learning paradigm were compared to controls using Affymetirx RAE230a chips. An N of 6 was used in each of the two experimental conditions.

first: Rebecca

last: Haberman

first: Hongjoo

last: Lee

first: Ming

middle: T

last: Koh

first: Michela

last: Gallagher


title: J82 human bladder cell line treated with frankincense oil

status: Public on Feb 10 2009

first: Bart

last: Frank

institute: OMRF

summary: Frankincense oil is prepared from aromatic hardened wood resin obtained by tapping Boswellia trees.  For thousands of years, it has been important both socially and economically as an ingredient in incense and perfumes.  Frankincense oil is a botanical oil distillate made from fermented plants that contains boswellic acid, a component known to have anti-neoplastic properties.  We evaluated frankincense oil-induced cytotoxicity in bladder cancer cells.  With a window of concentration, frankincense oil suppressed cell viability and induced cytotoxicity in bladder transitional carcinoma J82 cells but not normal bladder urothelial UROtsa cells immortalized with SV40 large T antigen.  However, frankincense oil-induced J82 cell death did not result in DNA fragmentation.  Microarray and bioinformatics analysis confirmed that frankincense oil activated cell cycle arrest, suppressed cell proliferation, and activated apoptosis in J82 cells through a series of potential pathways.   These finding suggest that bladder cancer can be treated through intravesical administration of pharmaceutical agents similar to direct application on melanoma.

overall_design: 2E05 J82 cells were untreated or treated with a 1/1000 dilution of frankincense oil for 0.5, 1, 2, or 3 hours prior to RNA extraction.

first: Mark

first: Qing

last: Yang

first: Jeanette

last: Osban

first: Joseph

last: Azzarello

first: Marcia

last: Saban

first: Ricardo

first: Jan

last: Welter

first: Hsueh-Kung

last: Lin


title: Rapid encoding of new information alters the profile of plasticity related mRNA transcripts in the hippocampal region


title: Response of Drosophila cell lines to 5 hr ecdysone treatment

status: Public on Mar 20 2009

city: Bloomington

first: Lucy

last: Cherbas

state: IN

department: CGB

institute: Indiana University

summary:
The changes in transcript titers are described for different Drosophila cells following 5 hr treatment with 20-hydroxyecdysone.
Keywords: hormone response

overall_design: RNA from ecdysone-treated cells was compared to RNA from cells treated with carrier alone. A total of 3-13 slides were analyzed for each cell line.  Each slide represents separate biological sample; dye-swaps were included.

first: Yi

last: Zou

first: Peter

first: Phillip

last: Knollman

first: Tyler

last: Iams


title: Rapid encoding of information alters the profile of plasticity related mRNA transcripts in the hippocampal DG region.

first: Carlo

overall_design: RNA samples from animals subjected to a spatial learning paradigm were compared to controls using Affymetirx RAE230a chips. An N of 7 was used in each of the two experimental conditions.

first: Rebecca

first: Hongjoo

middle: J


title: Rapid encoding of information alters the profile of plasticity related mRNA transcripts in the hippocampal CA3 region

summary:
A theoretical framework for the function of the medial temporal lobe system in memory defines differential contributions of the hippocampal subregions with regard to pattern recognition retrieval processes and encoding of new information. To investigate molecular programs of relevance, we designed a spatial learning protocol to engage a pattern separation function to encode new information. After background training, two groups of animals experienced the same new training in a novel environment, however only one group was provided spatial information and demonstrated spatial memory in a retention test. Global transcriptional analysis of the microdissected subregions of the hippocampus exposed a CA3 pattern that was sufficient to clearly segregate spatial learning animals from control. Individual gene and functional group analysis anchored these results to previous work in neural plasticity. From a multitude of expression changes, increases in camk2a, rasgrp1 and nlgn1 were confirmed by in situ hybridization. Furthermore, siRNA inhibition of nlgn1 within the CA3 subregion impaired spatial memory performance, pointing to mechanisms of synaptic remodeling as a basis for rapid encoding of new information in long-term memory.
Keywords:behavioral intervention: spatial learning paradigm

first: Ming

first: Michela


title: Genome-wide Binding Site Mapping of Estrogen Receptor alpha and c-MYC in Breast Cancer Cells

status: Public on Mar 13 2008

first: Sujun

last: Hua

summary:
Estrogens are steroid hormones that play critical roles in the initiation, development, and metastasis of breast and uterine cancers.  The estrogen (E2) response in breast cancer cells is predominantly mediated by the estrogen receptor-alpha (ER alpha), a ligand-activated transcription factor.  ER alpha regulates transcription of target genes through direct binding to its cognate recognition sites, known as estrogen response elements (EREs), or by modulating the activity of other DNA-bound transcription factors at alternative DNA sequences.  The proto-oncogene c-myc is upregulated by ER¦Á in response to E2 and encodes a transcription factor, c-MYC, which regulates a cascade of gene targets whose products mediate cellular transformation.  This study aims at mapping the binding sites of these two transcription factors (ER alpha and c-MYC) in one ER alpha positive breast cancer cell line (MCF7 cell line).
Keywords: ChIP-Chip Analysis

overall_design: This series contains ChIP-on-Chip data sets for two transcription factors (ER alpha and c-MYC) and control samples (INPUT). All the experiments are done in triplicates. MCF7 Cells were E2-deprived for 3 days and then were treated with 10 nM E2 (45 minutes and 2 hours for mapping ER alpha and c-MYC binding sites, respectively) at 80% confluence.

first: Kevin

last: White


title: Hypothalamic gene expression data from Mecp2-null and MECP2-transgenic mice

status: Public on May 30 2008

first: Maria

last: Chahrour

summary:
We compared gene expression changes in the hypothalamus of mice lacking MeCP2 (Mecp2-null) and mice overexpressing MeCP2 (MECP2-transgenic). Mutations in the gene encoding the transcriptional repressor methyl-CpG binding protein 2 (MeCP2) cause the neurodevelopmental disorder Rett syndrome. Loss of function as well as increased dosage of MECP2 gene cause a host of neuropsychiatric disorders.

To explore the molecular mechanism(s) underlying these disorders, we examined gene expression patterns in the hypothalamus of mice that either lack or overexpress MeCP2. In both models, MeCP2 dysfunction induced changes in the expression levels of thousands of genes, but surprisingly the majority of genes (~85%) appeared to be activated by MeCP2. We selected six genes and confirmed that MeCP2 binds to their promoters. Furthermore, we showed that MeCP2 associates with the transcriptional activator CREB1 at the promoter of an activated target but not a repressed target. These studies suggest that MeCP2 regulates the expression of a wide range of genes in the hypothalamus and that it can function as both an activator and repressor of transcription.

overall_design: Total hypothalamic RNA samples were collected from Mecp2-null male mice (n=4), MECP2-transgenic male mice (n=4), and their wild type male littermates at 6 weeks of age (n=4 for each group).

first: SungYun

last: Jung

first: Chad

middle: A

last: Shaw

first: Xiaobo

last: Zhou

first: Stephen

last: Wong

first: Jun

last: Qin

first: Huda

last: Zoghbi


title: Molecular Mechanisms of Early Response in Adaptive Cerebral Arteriogenesis

status: Public on Sep 01 2008

city: Berlin

first: Philipp

last: Hillmeister

state: Berlin

address: Hessische Straße 3-4

department: Center for Cardiovascular Research

country: Germany

institute: Charité Mitte Berlin

summary:
This study aims at a comprehensive understanding of the genomic program activated during early-phase of collateral vessel growth in a rat model for cerebral adaptive arteriogenesis (3-VO). While arteriogenesis constitutes a promising therapeutic concept for cerebrovascular ischemia, genomic profiles essential for therapeutic target identification were analysed solely for collateral arteries of the heart and periphery. Despite challenging anatomical conditions of the brain the 3-VO model allows identification of differentially expressed genes during adaptive cerebral arteriogenesis by selective removal of the posterior cerebral artery (PCA).
Keywords: early response time course, selective collateral growth, brain

overall_design: Using an established rat model of nonischemic cerebral hypoperfusion (3-VO) (Busch, Buschmann; 2003), RNA was extracted from isolated ipsilateral PCA. Pooled RNAs from groups of intact (0h), sham and 3-VO animals 24h and 3 days after surgery, were hybridised repeatedly for an extensive genome screen of 15866 genes applying standardized Affymetrix technology. For each Array total RNA from 8 animals was processed, pooled and hybridized to a Rat230A GeneChip per group. These groups were classified as follows: intact control (N=3), 24h3VO (N=3); 24h sham (N=3), 3days3VO (N=3); and 3days sham(N=3). Hybridization, washing, antibody amplification, staining, and scanning of probe arrays were performed according to the Affymetrix Technical Manual. Probe arrays were scanned using the GeneChip System (Hewlett-Packard, Santa Cruz, CA)(Affymetrix) and raw data were processed using GCOS and normalized to a global intensity of 500.

first: Kerstin

last: Lehmann

first: Ivo

last: Buschmann


title: Tissue/Cell DNaseI sensitivity/hypersensitivity screening II

status: Public on Apr 30 2008

city: SEATTLE

first: John

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary:
DNaseI hypersensitivity using DNase-array method on Affy platform overall design
Per DNase-array method (Sabo et al Nature Methods 3:511,2006) PMID: 15782197
This study is part of an ongoing screening process designed to obtain high quality cell-lines/tissues for further high throughput sequencing analysis.
Bed files based on hg17 genome build
Keywords: genomic

overall_design:
This deposit consists of 74 experimental samples (DNaseI enriched). Each experimental sample is analyzed, by cell type, with a set of 3 averaged control replicate samples. PBLC controls consist of the 3 replicates full set of seven Affymetrix 2.0R arrays, each of the other control sets consist of only 1 component array (denoted by the first value in the CEL file name and as a component of the characteristics).
3 BJ controls where combined via Affymetrix TAS (tiling array software) for control analysis vs. each of the 4 BJ experimental samples
3 CACO controls where combined via Affymetrix TAS (tiling array software) for control analysis vs. each of the 7 CACO experimental samples
3 GM12878 controls where combined via Affymetrix TAS (tiling array software) for control analysis vs. both of the GM12878 experimental samples
3 OVCAR controls will be used in future experimental analysis (TBD)
18 PBLC controls where combined via Affymetrix TAS (tiling array software) for control analysis vs. each of the of the 11 SKMC, 1 HMEC and 1 NHBE experimental samples.
3 SKNS controls where combined via Affymetrix TAS (tiling array software) for control analysis vs. each of the 16 SKNS samples
Previous GEO submission comprise the control samples for the remaining experimental samples:
GSM227018, GSM227019, GSM227020 combined via Affymetrix TAS for control analysis vs. each of the 3 ESER, 3 FLER, 3 ESER, 5 GM69 experimental samples
GSM172647, GSM172673, GSM172681 combined via Affymetrix TAS for control analysis vs. each of the 12 HeLa experimental samples
GSM227015, GSM227016, GSM227017 combined via Affymetrix TAS for control analysis vs. each of the 3 HEPG experimental samples
GSM227012, GSM227013, GSM227014 combined via Affymetrix TAS for control analysis vs. each of the 3 HL60 experimental samples


title: Regulation of the gonadal transcriptome during sex determination and testis morphogenesis: comparative candidate genes

status: Public on Feb 20 2008

city: Pullman

first: Michael

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

summary:
Embryonic day 13 (E13), E14, and E16 rat testes and ovaries were used for microarray analysis, as well as E13 testis organ cultures that undergo testis morphogenesis and develop seminiferous cords in vitro. A list of 109 genes resulted from a selective analysis for genes present in male gonadal development and with a 1.5-fold change in expression between E13 and E16. Characterization of these 109 genes potentially important for testis development revealed that cytoskeletal-associated proteins, extracellular matrix factors, and signaling factors were highly represented. Throughout the developmental period (E13-E16), sex-enriched transcripts were more prevalent in the male with 34 of the 109 genes having testis-enriched expression during sex determination. In ovaries, the total number of transcripts with a 1.5-fold change in expression between E13 and E16 was similar to the testis, but none of those genes were both ovary enriched and regulated during the developmental period. Genes conserved in sex determination were identified by comparing changing transcripts in the rat analysis herein, to transcripts altered in previously published mouse studies of gonadal sex determination. A comparison of changing mouse and rat transcripts identified 43 genes with species conservation in sex determination and testis development. Profiles of gene expression during E13-E16 rat testis and ovary development are presented and candidate genes for involvement in sex determination and testis differentiation are identified. Analysis of cellular pathways did not reveal any specific pathways involving multiple candidate genes. However, the genes and gene network identified influence numerous cellular processes with cellular differentiation, proliferation, focal contact, RNA localization, and development being predominant.
Keywords: expression analysis, testis, ovary, sex determination

overall_design: RNA samples from two different groups of 20-40 pooled gonads for each sample.  Embrionic testis and ovaries  of age E13, E14, or E16, and E13 testis cultured for three days were compared to each other

first: Tracy

last: Clement

first: Mathew

last: Anway

first: Mehmet

last: Uzumchu


title: SMA mouse tissue exon array analysis

status: Public on May 16 2008

city: Philadelphia

first: Gideon

last: Dreyfuss

state: PA

address: 415 Curie Blvd

institute: HHMI/ University of Pennsylvania

summary:
We used Affymetrix exon arrays to identify potential changes in alternative splicing between mice affect with spinal muscular atropy (SMA) and their unaffected littermates.
Keywords: disease state analysis

overall_design: Total RNA was extracted from spinal cord, brain and kidney of three SMA and three control mice on postnatal day 11


title: Global Control of cell cycle transcription by coupled CDK and network oscillators

status: Public on May 07 2008

city: Durham

first: Steven

middle: B

last: Haase

address: Duke University, Department of Biology, Box 90338

department: Biology

institute: Duke University

summary:
Yeast cell cycle transcription dynamics in two S. cerevisae strains: BF264-15DU (MATa ade1 his2 leu2-3, 112 trp1-1 ura3Dns, bar1) [referred to as wild type] and a mutant of the wild type strain, clb1,2,3,4,5,6 GAL1-CLB1, [referred to as cyclin mutant] that does not express S-phase and mitotic cyclins.  Both strains were synchronized by elutriation and released into YEP 2% dextrose/1M sorbitol at 30c. 15 samples were taken at 16 min intervals covering ~2 cycles in wild-type and ~1.5 cycles for the mutants.
A significant fraction of the Saccharomyces cerevisiae genome is transcribed periodically during the cell division cycle, suggesting that properly timed gene expression is important for regulating cell cycle events.  Genomic analyses of transcription factor localization and expression dynamics suggest that a network of sequentially expressed transcription factors could control the temporal program of transcription during the cell cycle.  However, directed studies interrogating small numbers of genes indicate that their periodic transcription is governed by the activity of cyclin-dependent kinases (CDKs).  To determine the extent to which the global cell cycle transcription program is controlled by cyclin/CDK complexes, we compared genome-wide transcription dynamics in wild type budding yeast to mutants that do not express S-phase and mitotic cyclins.
Keywords: cell cycle, strain comparison

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Cell cycle synchrony/time series experiments. G1 cells collected by elutriation was examined over time for 2 cell cycles. Strains compared: wild type vs cyclin mutants. 15 samples per time course at 16 min resolution. 2 biological replicates per strain.

first: David

last: Orlando

first: Charles

last: Lin

first: Jean

last: Wang


title: Comparative GeneChip expression profiling of four brain regions

status: Public on Feb 24 2008

city: Lawrence

first: Xinkun

state: KS

address: 2099 Constant Ave

department: Genomics Facility

institute: The University of Kansas

summary:
Study on selective vulnerability of certain brain regions to oxidative stress. Here we selected 4 brain regions (hippocampal CA1 and CA3, cerebral cortex, and cerebellar granular layer) to study this phenomenon.
Keywords: Comparative analysis of different regions of the brain.

overall_design: Neurons were collected from the 4 regions of the rat brain and subjected to Affymetrix RAE230A analysis, in order to identify genes related to the differential vulnerability of the neurons to oxidative stress.

first: Elias

last: Michaelis


title: Heart in Diabetes

status: Public on Jan 26 2008

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

summary:
8 week old rats injected with streptozotocin or buffer alone at age of 8 weeks, heart obtained at 12 weeks (thus animals were diabetic for 4 weeks).  Left vent of heart.
Keywords: Disease state analysis (diabetes)

overall_design:
Three control rats (normal heart #1, 2, 3)
Three diabetic rats (diabetic heart #1, 2, 3)

first: Michelle

last: Moyer


title: Differential susceptibility of Wistar Kyoto and spontaneously hypertensive rats to diesel exhaust particle exposure.

status: Public on Jun 23 2008

city: Research Triangle Park

first: Urmila

last: Kodavanti

address: 109 TW Alexander Drive

department: NHEERL, ETD

institute: USEPA

summary:
DEP exposure is linked to increases in cardiovascular effects. This effect is enhanced in individuals with pre-existing disease. Animal models of cardiovascular disease are used to study this susceptibility. The heart is rich in mitochondria, which produce high levels of free radicals, leading to inactivation of tricarboxylic acid cycle enzymes. We hypothesized that a 4-wk DEP inhalation would result in strain-related structural impairment of cardiac mitochondria and changes in these enzyme activities in WKY and SHR. Male rats (12-14 wks age) were exposed whole body to air or 0.5 or 2.0 mg/m3 DEP for 6h/d, 5 d/wk for 4 wks. Neutrophilic influx was noted in the bronchoalveolar lavage fluid in both strains. A slightly lower level of baseline cardiac mitochondrial aconitase activity was seen in SHR than WKY. Aconitase activity appeared to be decreased in an exposure related manner in both strains. Significantly higher baseline levels of cardiac cytosolic ferritin and aconitase activity were seen in the SHR than WKY. No exposure-related changes were noted in either of these measures. Mitochondrial succinate and isocitrate dehydrogenase activities were not changed following DEP exposure in either strain. Transmission electron microscopy images of the heart indicated abnormalities in cardiac mitochondria of control SHR but not control WKY. No exposure related ultrastructural changes were induced by DEP in either strain. In conclusion, strain differences in cardiac biomarkers of oxidative stress and structure of mitochondria exist between SHR and WKY. DEP exposure results in small changes in cardiac mitochondrial and cytosolic markers of oxidative stress. (Abstract does not represent USEPA policy.)
Keywords: strain differences, exposure differences

overall_design: Two strains of rats (Wistar Kyoto (WKY) and spontaneously hypertensive (SH) rats were exposed to either diesel exhaust particles or clean air.  Four biological replicates were used for each strain/treatment exposure.  Total number of chips equals 16.

first: Edward

last: Karoly


title: gene profiling in carcinoma cell during EMT

city: Villejuif cedex

first: Marianne

last: Tuefferd

address: 16 avenue Paul Vaillant Couturier

institute: INSERM

summary:
Modulation of several waves of gene expression during FGF-1 induced Epithelial-mesenchymal transition of carcinoma cells . In vitro FGF-1 induced EMT study using NBTII rat bladder carcinoma cells
Keywords: time course ; EMT ; cancer cell line ; FGF-1

overall_design: NBTII and NBTII-FGFR1 cells were induced by FGF-1. Total RNA were prepared from stimulated and control cells at time 0.5, 2, 6, 24 and 48 hours. Except for control and 0.5 hour stimulated cells, the experiment was done in duplicate for each cell line type

first: Clotilde

last: Billottet

last: Gentien

first: Audrey

last: Rapinat

last: Thiery

first: Philippe

last: Broët

first: Jacqueline

last: Jouanneau


title: Normal Heart vs Normal Diaphragm

status: Public on Jan 24 2008

summary:
Comparison of gene expression of heart (left vent) and diaphragm of normal Sprague Dawley rats, young adult
Keywords: Cell type comparison

overall_design:
6 diaphragm samples
6 heart samples

first: Sarah

last: Spiegler


title: Gene expression in a resistance artery in 2 models of hypertension in the rat

status: Public on Nov 28 2007

city: Canberra

first: Stephen

middle: John

last: Ohms

state: Australian Capital Territory

address: Garran Road

department: John Curtin School of Medical Research

institute: Australian National University

summary:
We investigated morphometric structure and gene expression by microarray analysis in a small diameter artery, branch of the saphenous artery (a resistance artery), in representative models of renin-angiotensin system (RAS)-dependent and glucocorticoid hypertension, using the spontaneously hypertensive rat (SHR) and adrenocorticotropic hormone (ACTH)-induced hypertensive rat, respectively.
Sixteen-week-old male Wistar-Kyoto (WKY) and age-matched spontaneously hypertensive rats (SHR) were used.
Keywords: Comparison of global gene expression in resistance arteries of normotensive and genetically hypertensive rats and ACTH-treated rats.

overall_design: There were 3 experimental groups: Group 1: 16-week male Wistar-Kyoto rats; Group 2: 16-week male Wistar-Kyoto rats treated with ACTH (0.1mg/kg/day) subcutaneously, for 4 weeks prior to sampling  (i.e. during weeks 12-16 of life) ; Group3: 16-week male SHR (spontaneously hypertensive) rats. There were 3 replicate hybridizations in each experimental group. Due to the low yield of total RNA obtained from the arterial sections, each replicate was composed of RNA pooled from 2-3 different rats.

first: Caryl

last: Hill

first: T

last: Grayson


title: Time-dependent response of hippocampal CA1 and CA3 to oxidative stress

status: Public on Jan 08 2008

last: Wang

summary:
Mechanistic study on the differential responses of the two hippocampal adjoining regions, i.e., CA1 and CA3, to elevated oxidative stress.
Keywords: Time course stress response study

overall_design: Time course study. Involved four time points and comparison of two brain regions.


title: An E2F1-Dependent Gene Expression Program That Determines the Balance Between Proliferation and Cell Death

status: Public on Nov 02 2007

city: Minneapolis

first: Timothy

middle: C.

last: Hallstrom

state: MN

address: MMC 366

department: Pediatrics

institute: University of Minnesota

summary:
E2F1 has been shown to induce both proliferation and apoptosis.
We now show that PI3K/Akt signaling regulates the balance of these events by specifically blocking expression of genes in the E2F1 apoptotic program but not the proliferative program.
Keywords: PI3K dependent modulation of E2F1 gene expression measured by Affymetrix gene expression analysis

overall_design: 11 samples total, two replicates each (except Sample 1 which is represented once)

first: Seiichi

last: Mori

first: Joseph

last: Nevins


title: Expression data from brain tissue of Rattus norvegicus treated with chlorpyrifos (CPF)

status: Public on Dec 04 2007

city: WPAFB

first: Victor

last: Chan

address: 2729 R St. Area B Bldg. 837

department: Applied Biotechnology Branch

institute: Air Force Research Laboratory

summary:
Chlorpyrifos is an organophosphorus insecticide that despite imposed restricitions on its use by the EPA, is one of the most commonly used insecticides.  Although CPF is so widely used little is known about its effect on overall gene expression in vivo.
DNA microarray technology was used to determine differential gene expression resulting from chlorpyrifos (CPF) exposure.
Keywords: Dose course

overall_design: Male Fisher 344 rats aged 11-12 weeks were treated with varying doses of chlorpyrifos (CPF) and terminally sacced at 96 hours post-exposure in three separate experiments.  An approximate 30mg section of the frontal lobe of the brain was processed for total RNA extraction.

first: Andrea

last: Stapleton


title: Paradoxical role of zinc in cardiac injury: a potential link to air pollution mortality?

status: Public on Nov 15 2007

last: Kodavanti

summary:
Zinc (Zn) is a major elemental component of respirable ambient particulate matter (PM) detected often at alarming levels in urban air. Exposure to PM has been widely associated with increased cardiovascular morbidity and mortality, however, it is not known what components or sources of PM are causative. We recently demonstrated that long-term episodic inhalation of combustion PM, having similar amount of Zn found in urban PM, caused myocardial lesions in rats. We further demonstrated that a single pulmonary exposure to Zn at high concentration is associated with disturbances in cardiac mitochondrial function, ion channel regulation, calcium homeostasis, and cell signaling. Therefore, in this study we investigated the role of PM-associated Zn in cardiac injury using multiple exposure scenarios. Male Wistar-Kyoto (WKY) rats of 12-14 wks age were intratracheally exposed (once per wk x 8 or16 wks) to either (1) saline (control); (2) PM having no soluble Zn; (3) combustion PM suspension containing 14.5 ug/mg water-soluble Zn at high and (4) low dose levels, (5) the aqueous fraction of this suspension devoid of solid insoluble particulate fraction (14.5 ug/mg soluble Zn), or (6) Zn sulfate. Zn concentrations were identical in groups 3, 5 and 6. Pulmonary toxicity was apparent in all exposure groups when compared to saline as determined by recovery of cells in bronchoalveolar lavage fluid. Long-term exposure to PM with or without soluble Zn, or Zn sulfate caused distinct myocardial lesions characterized by subepicardial and randomly distributed myocardial inflammation, degeneration, and fibrosis. The lesion severity was higher in those groups receiving Zn PM. Because cardiac mitochondria are likely the primary target of inhaled metal or other absorbed PM components, we analyzed mitochondrial DNA damage using QPCR and found that all exposure groups except those exposed to PM without Zn caused variable degree of damage. Aconitase activity, sensitive to inhibition by oxidative stress was inhibited slightly but significantly in rats receiving zinc sulfate. Although modest, microarray (Affymetrix) analysis revealed expression changes in the heart reflective of effects on cell signaling, inflammation/oxidative stress, mitochondrial fatty acid metabolisms and cell cycle regulation in rats exposed to zinc sulfate. However, these changes were minimal following exposure to PM devoid of soluble metals. We demonstrate that episodic subchronic pulmonary exposure to zinc sulfate causes cardiac injury and mitochondrial DNA damage. Thus, water-soluble PM-associated zinc may be one of the PM components responsible for cardiovascular morbidity.
Keywords: Pulmonary exposure, Cardiac gene expression

overall_design: Group 1 received Saline to serve as a control. Group 2 received Mount St. Helen’s ash, which does not contain any water-soluble zinc or other metals such that we can delineate any cardiac effect secondary to pulmonary deposition of these particles as these fine mode particles themselves are not likely to translocate to the heart. Group 3 received whole saline suspension of the same fugitive oil combustion particle sample used in the previous study, which contained insoluble components plus water-soluble zinc (Kodavanti et al., 2003; 14.5 ug/mg zinc) and also a small amount of water-soluble nickel (3.0 µg/mg). Elemental composition of this PM is comparable to Ottawa urban PM (Kodavanti et al., 2003). Group 4 also received same particle sample but at half the dose than group 3. Group 5 received saline-soluble or leachable fraction of PM-HD devoid of any solid material but contained soluble components including zinc and nickel. And, group 6 received zinc sulfate at concentration that was present in groups 3 or 5.  This design allowed us to test if cardiac injury in rats was due to leached of zinc or solid particles.  There were 4 replicates per treatment group.

last: Karoly

first: Mette

last: Schladweiler

first: Peter

last: Gilmour

first: J

middle: G

last: Wallenborn

first: Bhaskar

last: Mandavilli

first: Allen

last: Ledbetter

first: David

last: Christiani

first: Judy

last: Richards

first: Marschall

last: Runge

first: Daniel

middle: L

last: Costa

first: Abraham

last: Nyska


title: Sex differences in gene expression profiles during hantavirus infection of rats

status: Public on Oct 30 2007

first: Sabra

middle: Lynn

last: Klein

address: 615 North Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins Bloomberg School of Public Health

summary:
Gene expression profiles were examined in whole lung tissue collected from male and female Long-Evans rats at different time points after inoculation with Seoul virus (i.e., the species-specific hantavirus that infects Norway rats)
We used microarray analyses to analyze global gene expression differences between the sexes during hantavirus infection
Keywords: time course

overall_design: Gonadally-intact male and female rats were inoculated with 10^4 pfu of Seoul virus (strain SR-11) and lung samples were collected 0, 3, 15, and 40 days post-inoculation (p.i.) to assess gene expression patterns during the acute (i.e., days 3-15 p.i.) and persistent (i.e., day 40 p.i.) phases of infection


title: Comparison between conventionally-isolated and laser capture microdissected glomeruli

status: Public on Sep 11 2007

city: Chicago

first: Jian

last: Zhou

state: IL

address: 5841 S Maryland Ave

department: functional Genomics Facility

institute: University of Chicago

summary:
We compared the gene expression  analysis of 2 different glomerular isolation techniques  (laser capture microdissection with 2 rounds of RNA amplification and unamplified glomerular RNA after iron perfusion with glomerular sieving) and  obtained different results depending on the glomerular isolation technique that was used
Keywords: time course

overall_design: Paired kidneys from Lewis-Hsd rat kidneys were collected. The glomeruli of one kidney was obtained by LCM with 2 rounds of RNA amplification while the unamplified glomerular RNA of the contralateral kidney was obtained after perfusion with iron oxide and isolated by magnetic purification and a glomerular sieving technique. The RNA was analyzed using the Affymetrix  Rat 230A microarrays.

first: Anthony

last: Chang

first: Andrew

middle: W

last: Minto

first: Richard

last: Quigg


title: Expression data from Aristolochic Acid and Ochratoxin A treated Tsc2 mutant (Eker) and corresponding wild type rats

status: Public on Aug 23 2007

city: Konstanz

middle: R.

last: Dietrich

address: Jakob-Burckhardt-Str. 25

department: Environmental Toxicology

institute: University of Konstanz

summary:
Renal gene expression profiles of Eker and wild type rats, gavaged with AA or OTA, respectively for 1, 3, 7 or 14 days
We used Affymetrix RAE230A microarrays for the analysis of early gene expression changes in the renal cortex_ outer medulla of carcinogen treated Eker and corresponding wild type rats
Keywords: time course

overall_design: Eker and wild type rats were gavaged daily with OTA (210µg_ kg BW) or AA (10mg_ kg BW), dissolved in 0,1M sodium bicarbonate. Time-matched vehicle controls were gavaged with 0,1M sodium bicarbonate. Following 1, 3, 7, and 14 days of treatment, Narcoren (pentobarbital) anesthetized rats were sacrificed by exsanguination subsequent to retrograde perfusion with PBS. Left kidneys were collected, cross-sectioned into 5mm slices and stored in RNAlater for subsequent RNA isolantion and chip hybridisation

first: Kerstin

last: Stemmer

first: Heidrun

last: Ellinger-Ziegelbauer

first: Hans-Juergen

last: Ahr


title: Tissue/Cell DNaseI sensitivity/hypersensitivity screening

status: Public on Sep 30 2007

first: John

last: Stamatoyannopoulos

summary:
DNaseI hypersensitivity using DNase-array method on Affy platform overall design Per DNase-array method (Sabo et al Nature Methods 3:511,2006) PMID: 15782197
Keywords: genomic

overall_design: Per DNase-array method (Sabo et al Nature Methods 3:511-18,2006) PMID: 15782197

last: Haydock


title: Salt Induced Hypertensive Disease Results in Over Expression of Matricellular Genes in Cerebral Arteries

status: Public on Aug 09 2007

city: Burlington

first: Karen

middle: M.

last: Lounsbury

state: VT

address: 89 Beaumont Avenue

department: Pharmacology

institute: University of Vermont

summary:
The Dahl salt-sensitive (S) rat model develops chronic hypertensive disease when fed a high salt diet that ultimately results in renal and heart failure, as well as prevalent cerebrovascular pathologies.  Phenotypic changes in the cerebral vasculature are preceded by changes in gene expression, and evidence supports a role for extracellular signal-regulated kinase 1/2 (ERK1/2) in vascular cell proliferation, yet little is known regarding ERK1/2 –regulated gene transcription in cerebrovascular smooth muscle during hypertension.  Findings presented here support the hypothesis that salt-induced hypertensive disease results in upregulation of ERK1/2 activity and ERK1/2-regulated genes that promote remodeling in cerebral resistance arteries.  Dahl S rats were fed either a 0.4% NaCl (low salt, LS) or 8% NaCl (high salt, HS) diet until evidence of left ventricular dysfunction.  Gene expression profiling using oligonucleotide array analysis detected a significant fold-change of 1.5 or greater in 133 out of 15,923 genes examined.  Mitogen-activated protein kinase (MAPK)-regulated genes were overrepresented and provided a link to genes involved in proliferation and extracellular matrix signaling including plasminogen activator inhibitor I (PAI-1), osteopontin (OPN) and junB.  These data suggests that salt induced hypertensive disease promotes hyperplasia and changes in matricellular genes that are likely important in vascular remodeling.
Keywords: Normotensive vs. Hypertensive Disease

overall_design: Analysis was based on a comparison between the Low Salt and High Salt groups.  Arteries from 3 animals were pooled for each sample, thus there were 9 animals/group.  Analysis of significance amongst all genes as well as prospective hypotheses correlating to disease were performed.

first: Patricia

last: Rose

first: Scott

last: Tighe

first: Michael

last: Toth

first: Theresa

last: Wellman

first: Jeffrey

last: Bond

first: Martin

middle: M

last: Lewinter


title: NGF Treatment of PC12 Cells

status: Public on Mar 27 2007

city: Ann Arbor

first: Christin

last: Carter-Su

address: 1301 Catherine St.

institute: University of Michigan

summary:
Expression profiling of PC12 cells stably transfected with GFP, GFP-SH2-Bb, or GFP-SH2-Bb(R555E), treated with or without NGF for 6h
Keywords: response to NGF

overall_design:
Total RNA was obtained from PC12 cells
-stably transfected with GFP (G0)
-stably transfected with GFP and treated for 6h with NGF (G6)
-stably transfected with GFP-SH2-Bb (F0)
-stably transfected with GFP-SH2-Bb and treated for 6h with NGF (F6)
-stably transfected with GFP-SH2-Bb(R555E) (R0)
-stably transfected with GFP-SH2-Bb(R555E) (R6)

first: Linyi

last: Chen


title: Perirenal and epididymal preadipocytes from young and old rats.

status: Public on Jan 09 2008

city: Boston

first: Marc

middle: E.

last: Lenburg

state: MA

address: 715 Albany Street, E613B

department: Genetics and Genomics

institute: Boston University School of Medicine

summary:
Inherent depot- and age-dependent preadipocyte characteristics may contribute to age-related fat redistribution. Both aging and depot origin affect preadipocyte replication and adipogenesis. To define responsible mechanisms, we analyzed genome-wide expression profiles in epididymal (E) and perirenal (P) preadipocytes cultured from young (3 month) and old (30m) rats. Differences between depots were distinct from and more dramatic than those that occur with aging.
Keywords: cell type and age comparison

overall_design: Preadipocytes were isolated from perirenal and epididymal fat depots of 3 young (3 month) and 3 old (30 month) Brown Norway rats for a total of 12 samples from 6 different animals.

middle: E

last: Schlauch

first: James

last: Kirkland

first: Mark

last: Cartwright

first: Tamara

last: Pirstskhalava

last: Tchkonia


title: ChIP-chip analysis of transcription factors GABP, SRF, TAF, and NRSF on Affymetrix whole genome tiling arrays 2.0R

status: Public on Jul 19 2007

city: Stanford

first: David

middle: Scott

last: Johnson

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

summary:
As part of the ENCODE consortium project (NIH, NHGRI), we conducted genome-wide location analysis for various transcription factors in various cell types.  The long-term goal of this project is to determine the function of each DNA nucleotide in the genome.  Measurement of transcription factor binding events is an important part of this effort.  Here we measure genome-wide binding events for a variety of important transcriptional regulators.
Keywords: ChIP-chip

overall_design:
ChIP-chip analyses were performed for the following transcription factors (TFs) and cell types:

1) transcriptional regulators GA-binding protein (GABP) and serum response factor (SRF) in GMO6990 cells
2) transcriptional regulators GABP, SRF, and TBP-associated factor 1 (TAF250) in HeLa cells
3) transcriptional regulators GABP and SRF in HepG2 cells
4) transcriptional repressor neural restrictive silencer factor (NRSF/REST) using two different antibodies in Jurkat cells
5) transcriptional regulators GABP, SRF, and TAF250 in k562 cells

Each Sample (GSMxxx) record comprises data from biological replicates.

middle: S

first: Richard

last: Myers

first: Elizabeth

last: Anton

first: Loan

last: Nguyen

first: Catherine

last: Medina


title: Expression data from rat mammary tumors with varying invasive phenotyes

status: Public on Apr 20 2007

first: Penelope

middle: Lyn

last: Miron

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary:
We used microarrays to identify genes implicated in breast cancer progression
Keywords: tumor progression

overall_design: By serially transplanting initial carcinogen induced rat mammary tumors (PR for primary tumor) through five generations of syngeneic hosts, we generated a series of tumors (T1 through T5) with varying invasive and metastatic phenoytpes

first: Maren

last: Chan

first: Xin

last: Lu

first: Faisal

last: Merchant

middle: D

last: Iglehart


title: Genes in nonpermissive temperature-induced cell growth arrest and differentiation of tracheal epithelial RTEC11 cells

status: Public on Jul 17 2007

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
We performed global scale microarray analysis to identify detailed mechanisms by which nonpermissive temperature induces cell growth arrest and differentiation in tracheal epithelial RTEC11 cells harboring temperature-sensitive simian virus 40 large T-antigen by using an Affymetrix GeneChip system. Tracheal epithelial RTEC11 cells used in this study were derived from transgenic rats harboring a temperature-sensitive simian virus 40 large T-antigen. Although the cells grew continuously at the permissive temperature, the nonpermissive temperature led to cell growth arrest and differentiation.
Keywords: rat tracheal epithelial RTEC11; growth arrest; differentiation; gene expression

overall_design: A rat conditionally immortalized tracheal epithelial cell line, RTEC11, derived from transgenic rats harboring a temperature-sensitive simian virus 40 large T-antigen was used. RTEC11 cells were cultured at permissive (33°C) or nonpermissive (39°C) temperature for 3 days.

first: Takeshi

last: Doi

first: Ichiro

last: Takasaki


title: DNaseI sensitivity/hypersensitivity Part II

status: Public on Jun 23 2007

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

summary:
DNaseI sensitivity/hypersensitivity using  DNase-array method (Sabo et al Nature Methods 3:511-18, 2006) on Affymetrix whole-genome tiling DNA microarrays.  Background:  Focal alteration in chromatin structure in vivo, detectable through hypersensitivity to DNaseI and other nucleases, is the sine qua non of diverse transcriptional regulatory elements including enhancers, promoters, insulators, and locus control regions.
Keywords: genomic

overall_design: Per DNase-array method (Sabo et al Nature Methods 3:511,2006) PMID: 15782197