title: DNaseI sensitivity/hypersensitivity Part I

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


title: Gene expression in fetal gubernaculum and testis of wildtype (LE/wt) and cryptorchid (LE/orl) rats

status: Public on Feb 03 2008

city: Wilmington

first: Julia

middle: S.

last: Barthold

state: DE

address: 1600 Rockland Road

department: Urology

country: USA

institute: Nemours/AI duPont Hospital for Children

summary:
The Long Evans/orl (LE/orl) rat is an animal model of inherited undescended testis (UDT).  To explore genetic mechanisms of UDT, we studied differential gene expression in LE/orl and LE wild type (LE/wt) fetal gubernaculum and testis.

Analyses of differentially expressed probe sets linked below as supplementary files:
Analysis_methods.txt [A description of the analysis]
gub.txt [Genes differentially expressed in between wt and orl gubernacula]
testes.txt [Genes differentially expressed between wt and orl testes]
wt.txt [Genes differentially expressed in wt gubernacular development]
Keywords: strain/condition predisposition, disease state analysis, developmental

overall_design: Fetuses were harvested from timed matings of LE/wt and LE/orl rats at gestational day (GD) 17, 18, 19, and 20.  Single gubernaculum and testis were removed from male fetuses and total RNA was isolated from each organ.  Left organs were used, except for GD 20 fetuses where both right and left gubernacula were included.   For female fetuses, the right and left gubernacula from a single fetus were pooled before RNA isolation.  A total of 54 samples were hybridized to GeneChips; 34 gubernacular samples and 20 testes samples.  There were 13 sample groups, each included biological replicate arrays.  The sample groups were (1) female LE/wt GD18 gubernacula n=4, (2) male LE/wt GD18 left gubernacula n=4, (3) male LE/wt GD19 left gubernacula n=4, (4) male LE/wt GD20 left gubernacula n=4, (5) male LE/wt GD20 right gubernacula n=3, (6) male LE/orl GD18 left gubernacula n=4, (7) male LE/orl GD19 left gubernacula n=4, (8) male LE/orl GD20 left gubernacula n=4, (9) male LE/orl GD20 right gubernacula n=3, (10) male LE/wt GD17 left testes n=5, (11) male LE/wt GD19 left testes n=5, (12) male LE/orl GD17 left testes n=5, and (13) male LE/orl GD19 left testes n=5.

middle: S

first: Suzanne

middle: M

last: McCahan

first: Amar

last: Singh

first: Thomas

last: Knudsen

first: Xiaoli

last: Si

first: Liam

last: Campion

first: Robert

middle: E

last: Akins


title: Genes in nonpermissive temperature-induced cell growth arrest and differentiation of astrocyte RCG-12 cells

status: Public on Apr 13 2007

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

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 astrocyte RCG-12 cells harboring temperature-sensitive simian virus 40 large T-antigen by using an Affymetrix GeneChip system. Astrocyte RCG-12 cells used in this study were derived from primary cultured rat cortical glia cells infecting with 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. Of the 15,923 probe sets analyzed, nonpermissive temperature differentially expressed 556 probe sets by >2.0-fold.
Keywords: Astrocyte cell; growth arrest; differentiation; temperature-sensitive simian virus 40 large T-antigen; nonpermissive temperature

overall_design: RCG-12 cells were cultured at permissive (33°C) or nonpermissive (39°C) temperature for 3 days. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with the Rat Expression Array 230A which was spotted with 15,923 probe sets. Sample preparation for array hybridization was carried out as described in the manufacture’s instructions.

first: Ichiro

last: Takasaki


title: DNaseI sensitivity/hypersensitivity

status: Public on Jun 22 2007

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Hippocampal pathways in cognitive impairment

status: Public on Mar 15 2007

city: Lexington

first: Veronique

last: Thibault

state: KY

address: 800 Rose Street

department: Pharmacology

institute: University of Kentucky

summary:
Although immediate early genes (IEGs) such as Bdnf, Arc and Egr1, have been implicated in plasticity, the larger pathways related to memory and memory disorders are not well understood. Here, we combined statistical Affymetrix microarray and behavioral analyses to identify key genes and pathways associated with aging-related cognitive impairment. Aged rats were separated into cognitively unimpaired (AU) or impaired (AI) groups, based on their Morris water maze performance relative to young-adult (Y) animals. Hippocampal gene expression was assessed in Y, AU and AI on the fifth (last) day of maze training or 21 days posttraining, and in non-trained aged and young animals (eight groups, overall n = 78, one chip/animal). ANOVA, linear contrasts, and overrepresentation analyses identified genes and pathways that differed from Y generally with aging (in both AU and AI) or selectively with cognitive status (only in AI or AU). Plasticity pathways, including insulin/cAMP/IEG signaling, and glycogenolytic and lipogenic pathways, were selectively downregulated (5 days) in AI, whereas Notch2 (regulating oligodendrocyte differentiation) and myelination pathways were upregulated (particularly at 21 days). Downregulation with general aging occurred in signal transduction and axonal growth/transport pathways, whereas upegulation occurred in immune/inflammatory, lipid metabolism/transport (e.g., Lxr-Srebf1), and lysosomal pathways. In AU, receptor/signal transduction genes were selectively upregulated, suggesting possible compensatory mechanisms. Immunohistochemistry confirmed and extended results to the protein level. Thus, this study identified novel cognition-linked processes, suggesting a new model in which energy-intensive, plasticity/lipogenic processes and energy-generating pathways necessary for learning are coordinately downregulated during training, while myelinogenic programs that impair cognition are concurrently activated.
Keywords: Immediate Early Genes, Insulin Signaling, Cholesterol, Myelination, Glia, Inflammation, Young and Old comparaison, behavioral-characterization, Aging-related cognitive impairment.

overall_design: Aged rats were separated into cognitively unimpaired (AU) or impaired (AI) groups, based on their Morris water maze performance relative to young-adult (Y) animals (NT, 5D, and 21D, N=10/group). Hippocampal gene expression was assessed in Y, AU and AI on the fifth (last) day of maze training or 21 days posttraining, and in non-trained aged and young animals (eight groups, overall n = 78, one chip/animal)

first: Wayne

middle: B

last: Rowe

first: Eric

last: Blalock

first: KueyChu

last: Chen

first: Inga

last: Kadish

first: Daguang

last: Wang

first: James

last: Barrett

first: Olivier

first: Nada

last: Porter

first: Gregory

last: Rose

first: Philip

middle: W

last: Landfield


title: experiment in midbrain primary cultures, enriched in dopaminergic neurons

status: Public on Mar 19 2007

city: Naples

first: Umberto

last: di Porzio

address: Via Pietro Castellino 111

department: neurobiology laboratory

country: Italy

institute: Istitute of genetics and biophysics

summary:
To identify novel Nurr1 target genes we have used microarrays strategies in rat midbrain primary cultures, enriched in dopaminergic neurons, by the action of  basic fibroblast growth factor (bFGF, 20ng/ml) and Sonic hedgedog (SHH), following upregulation of Nurr1 expression by depolarization.To this aim we have treated the cultures after 9 days in vitro for 2h with high KCl and collected 30 min or 2 h after the end of depolarization (2h + 30 min or 2h + 2h). With this experimental protocol we have identify a putative Nurr1 regulator and Nurr1 target
Keywords: depolarization, microarrays, time course.

overall_design:
cRNA triplicates of cultures treated for 2h with high KCl and collected 30 min or 2 h after the end of depolarization (2h + 30 min or 2h + 2h)  and control was hybridized on triplicate microarrays. The extrapolation of expression values from the images was carried out using different statistical filters and were compared up- and down-regulated
probesets showing significant change between depolarized and control samples
after 30 min or 2 h after the end of depolarization.

first: Floriana

last: Volpicelli

first: Dario

last: Greco

first: Massimiliano

last: Caiazzo

first: Claudia

last: Consales

first: Carla

last: Perrone Capano

first: Luca

last: Colucci D'Amato


title: Expression data from adrenal glands from normoxic and hypoxic neonatal rats

status: Public on Nov 14 2006

city: Milwaukee

middle: David

last: Bruder

state: WI

address: 2801 W. KK River Parkway, Suite 245

department: Endocrine Research

institute: Aurora St. Luke's Medical Center

summary:
We hypothesize that changes in adrenal gene expression mediate the increased plasma corticosterone and steroidogenesis in rat pups exposed to hypoxia from birth.
Keywords: effects of hypoxia on adrenal steroidogenesis in the neonatal rat

overall_design: In the current study, rat pups (with their dams) were exposed to hypoxia from birth and compared to pups from normoxic dams fed ad libitum.  Adrenal glands were collected from normoxic and hypoxic pups at PD7and pooled (N=24/sample; 4 samples per treatment group) for total RNA extraction.  Microarray analysis was performed, followed by verification with real-time PCR.  Furthermore, the expression of selected genes involved in adrenal function was analyzed by real-time PCR, regardless of microarray results.

first: E

middle: D

first: H

last: Raff


title: HNF1b, HNF4a2 and HNF6 targets

status: Public on Dec 03 2006

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie


title: Dietary effect of SPI or Genistein alters rat mammary epithelial global gene expression profiles

status: Public on Jan 31 2007

city: Little Rock

first: Ying

last: Su

state: AR

address: 1120 Marshall St. South Campus

department: physiology

institute: UAMS

summary:
The role of diet in the prevention of breast cancer is widely accepted, yet little is known on how early dietary effects mitigate adult cancer risk. Soy consumption is associated with reduced breast cancer risk in women, an effect largely attributed to the soy isoflavone genistein (GEN). We previously showed lower chemically-induced mammary tumor incidence in young adult rats with lifetime dietary intake of soy protein isolate (SPI), a highly refined soy product in infant formula, than in those fed the control diet Casein (CAS). To gain insight into signaling pathways underlying dietary tumor protection, we performed genome-wide expression profiling of mammary epithelial cells from young adult rats lifetime fed CAS, SPI, or supplemental GEN-based diets. We identified mammary epithelial genes regulated by SPI (79 total) and GEN (99 total) using Affymetrix rat 230A GeneChip arrays and found minimal overlap in gene expression patterns. We showed that the regulated transcripts functionally cluster in biochemical pathways involving metabolism, immune response, signal transduction, and ion transport. We confirmed the differential expression of Wnt (Wnt5a, Sfrp2) and Notch (Notch2, Hes1) signaling components by SPI and/or GEN using QPCR. Wnt pathway inhibition by GEN was supported by lower Cyclin D1 immunoreactivity in mammary ductal epithelium of GEN relative to CAS and SPI, despite their comparable levels of membrane-localized E-cadherin and β-catenin.  Identification of distinct GEN and SPI responsive genes in mammary epithelial cells may define early events contributing to tumor protection by diet relevant to the prevention of breast and other types of cancer.
Keywords: Comarative genomic hybridization

overall_design: Female Sprague-Dawley rats, fed one of the three purified diets, were studied at postnatal day50. Total RNA( each RNA samples were extracted from #4 mammary gland from two animals under the same diet group) purified from non-tumor tissue within the proximal half of each colon, was used to prepare biotinylated probes, which were hybridized to Affymetrix RAE230 rat microarrays.

first: Frank

last: Simmen

first: Rijin

last: Xiao

first: Rosalia

middle: C


title: Genetic basis of rare arterial and renal phenotypes in the Brown Norway rat

status: Public on Dec 16 2006

city: Berlin

first: Oliver

last: Hummel

department: Experimental Genetics of Cardiovascular Diseases

institute: Max-Delbrück-Center

summary:
The Brown Norway (BN) strain of rat is an inbred normotensive strain. BN rats of both sexes present some interesting pathophysiological phenotypes involving arteries and the kidneys. These include internal elastic lamina (IEL) ruptures in the abdominal aorta and iliac arteries, a deficit in aortic elastin content, a persistent ductus arteriosus, hydronephrosis and hematuria.
Spontaneous rupture of the internal elastic lamina occurs in various arteries during growth and aging, in different rat strains, both normotensive and hypertensive. Most strains present such ruptures in their caudal and renal arteries, although to different extents (Osborne-Pellegrin 1985; Coutard and Osborne-Pellegrin 1991). However, the BN strain is the only rat strain to spontaneously develop numerous IEL ruptures in the abdominal aorta and iliac arteries (Osborne-Pellegrin et al., 1989; Behmoaras J et al., 2005). In this respect, it is exceptional.
In this study samples of abdominal aortae of BN- and LOU-rats (here as control) were compared
Keywords: strain effect

overall_design:
10 chips were analyzed. They represent 2 groups of 5 replicates each.
The 2 groups are 2 different rat strains: BN and LOU.
Samples were prepared only from abdominal aortae (tissue).

first: Lalitha

last: Kota

first: Mary

last: Osbborne-Pellegrin

first: Herbert

last: Schulz

first: Norbert

last: Hubner


title: Reduced inflammatory response under candesartan pre-treatment  following transient focal ischemia in rats

status: Public on Dec 31 2006

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

institute: Max Planck Institute for Molecular Genetics

summary:
Large clinical studies have shown that AT1 receptor blockers (ARBs) reduce the incidence of stroke in patients at risk. However, there is controversy about the underlying pathomechanisms. To get a closer insight into the effects of ARBs in stroke on molecular level, gene expression pattern was compared in the ischemic brain areas of Candesartan pre-treated (0,2 mg/kg bwt., 5 days, s.c.) versus vehicle treated, normotensive, adult rats after middle carotid artery occlusion (MCAO).
Candesartan significantly improved neurological outcome (as estimated by Garcia-scale) 24 h and 48 h after stroke and reduced infarct volume by about 40% compared to vehicle.
Keywords: disease state analysis

overall_design: For gene expression profiling, RNA of two animals per group was pooled and forwarded to preparation of the labeled targets for the micro array experiment. For each biological condition two independent pools were hybridised onto Affymetrix RAE 230A arrays.

first: Christa

last: Thone-Reineke

first: Ute

last: Ungethuem

first: Patricia

last: Ruiz

first: Thomas

last: Unger


title: Octreotide LAR and the oxyntic mucosa

status: Public on Sep 27 2006

city: Trondheim

first: Sten

middle: Even

last: Erlandsen

address: Olav Kyrres gate 9, 5 etg.

department: Department of Cancer Research and Molecular Medicine

country: Norway

institute: NTNU

summary:
Previous studies have shown that treatment with the somatostatin analogue octreotide LAR causes regression of gastric ECL-cell carcinoids in patients with hypergastrinaemia due to chronic atrophic gastritis, reducing both the number and size of tumours. The main objective of the present study was to examine the molecular mechanisms behind the antiproliferative effect of octreotide in the oxyntic mucosa on a genome wide scale. Female Sprague-Dawley rats were dosed with octreotide LAR and control group were given the LAR vehicle for 21 days. Serum gastrin levels were measured and tissue samples for histology and RNA extraction collected from the oxyntic mucosa. Histomorphological examination showed a significant decrease in the number of gastric glands, cells per gland and length of glands, indicating a negative effect of octreotide on growth of the oxyntic mucosa. Further immunohistochemical studies showed a tendency towards increased apoptosis and decreased proliferation in the group receiving octreotide. Affymetrix GeneChip microarrays were used to detect differentially expressed genes. Many regulated genes could be related to regulation of apoptosis, fewer to proliferation, and the largest group of regulated genes was transcriptional factors several of which may be involved in regulation of growth. Control studies using quantitative real-time RT-PCR showed a high degree of consistency of the microarray results. In conclusion, octreotide exerts a negative effect on growth of the oxyntic mucosa, and extensive gene expression changes relevant to growth regulation can be detected.
Keywords: regulation, proliferation, Affymetrix GeneChip, qRT-PCR, immunohistochemistry.

overall_design: RNA from eigth animals (controls that received the LAR-vehicle) were pooled to produce a control affymetrix chip. Six animals (treatmentgroup) were given octreotide LAR and RNA from two and two animals were pooled to produce three affymetrix chips for comparison to the controlchip.

first: Vidar

last: Fykse

first: Helge

middle: L

last: Waldum

first: Arne

middle: K

last: Sandvik


title: The Spontaneously Hypertensive Rat: An Experimental Model of Sulfur Dioxide-induced Airways Disease

status: Public on Oct 03 2006

city: Research Triangle Park

first: Urmila

middle: P

last: Kodavanti

state: NC

address: 109 TW Alexander Drive

department: NHEERL, ETD

institute: USEPA

summary:
Chronic obstructive pulmonary disease (COPD) is diagnosed by airway obstruction and underlies a group of ailments such as bronchitis, emphysema and often asthma; however, rodent models do not resemble human pathology. Because genetically predisposed spontaneously hypertensive (SH) rats display phenotypes such as systemic inflammation, thrombosis, oxidative stress, and suppressed immune function, that are also apparent in COPD patients, we exposed SH and commonly used male Sprague Dawley (SD) to 0, 250, or 350 ppm sulfur dioxide (SO2), 5h/d for 4 consecutive days. Airways disease was characterized by pulmonary functional, pathological and molecular analysis. SO2 caused dose-dependent changes in breathing parameters in both strains with SH rats being slightly more affected than SD. Bronchoalveolar lavage fluid (BALF) total cells and neutrophilic inflammation were dose-dependent and significantly greater in SH than in SD rats. The recovery was incomplete 4-day following SO2 exposure in SH rats. Pulmonary protein leakage did not occur in either strain but lactate dehydrogenase and n-acetyl glucosaminidase activity was increased in BALF of SH rats. Lung pathology and morphometric evaluation of mucin production in the airways demonstrated significantly greater impact of SO2 in SH than in SD rats. Baseline differences in lung gene expression pattern suggested marked immune dysregulation, oxidative stress, and impairment cell signaling and fatty acid metabolism in SH rats. Gene expression pattern of SD and SH rats following SO2 exposure demonstrated greater effect on inflammation/immune markers, and oxidative stress. Thus, the SH rat may serve as a better and more susceptible rat strain to be used for experimental model of bronchitis which is relevant to human disease.
Keywords: strain and treatment differences

overall_design: Spontaneously hypertensive and Sprague Dawley rats were used in this experiment.  Each strain of rat was treated with either SO2 or AIR (control).  There were 4 biological replicates for each strain/treatment.

first: Mette

last: Schladweiler

first: Allen

last: Ledbetter

first: Roselia

middle: V

last: Ortuno

first: Marie

last: Suffia

first: Paul

last: Evansky

first: Judy

middle: H

last: Richards

first: Richard

last: Jaskot

first: Ronald

last: Thomas

first: Edward

last: Karoly

first: Yuh-Chin

middle: T

last: Huang

first: Daniel

last: Costa

first: Peter

last: Gilmour

first: Kent

last: Pinkerton


title: Effect of chronic ethanol consumption on rat pancreas

status: Public on Jul 01 2006

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

summary:
Male Wistar rats weighing 90-120 g were acclimatized for one week and fed standard laboratory chow, at which time the animals were divided into two groups.  Animals were then pair-fed for 8 weeks a regular laboratory chow and water “ad libitum” or Lieber-DeCarli diet (36% calories from ethanol). Control animals received the iso-caloric amount of dextrose to replace ethanol. After 8 weeks of differential feeding rats were euthanized, the pancreas immediately dissected and stored at -80?C until RNA isolation.  RNA expression was analyzed using Affymetrix RAE230A gene chips
Keywords: stress response, disease state analysis

overall_design: pancreas from 3 rats feed control diets and 3 rats feed ethanol diets were analyzed

first: Craig

last: Logsdon

first: Constanze

last: Kubisch

first: Ilya

last: Gukovsky

first: Aurelia

last: Lugea

first: Hidekazu

last: Tsukamoto

first: Stephen

middle: J

last: Pandol

first: David

last: Misek

first: Samir

last: Hanash


title: Gene expression profiles in lung tissue of rats following exposure to mainstream cigarette smoke

status: Public on Jul 28 2006

city: Hannover

first: Jürgen

last: Borlak

address: Nikolai-Fuchs-Straße 1

institute: Fraunhofer Institut für Toxikologie und Experimentelle Medizin

summary:
Expression data from rats exposed to cigarette smoke (CS) at three concentrations (sham, 300µgTPM/l and 600µgTPM/l) for 13 weeks (5d/week; 2hrs/day) after three different recovery times (2hrs, 6hrs and 20hrs after last treatment); lung tissue
Keywords: recovery time course and dose dependency

overall_design: Male Sprague-Dawley rats were nose-only-exposed for 13 weeks in total, 5d/week, 2h/day to following concentrations of mainstream cigarette smoke from the standard reference cigarette 2R4F: sham, 300µgTPM (Total particulate matter)/l or 600µgTPM/l.

first: Stephan

last: Gebel

first: Sabine

last: Glombitza


title: Long Term Thermal Injury Analysis

status: Public on Aug 30 2006

city: Piscataway

first: Tim

last: Maguire

state: NJ

address: 98 Brett Road, Engineering C252

department: BME

institute: Rutgers University

summary:
These samples comprise the full analysis of liver function during response to thermal injury.
Keywords: Time Course

overall_design:
 - 4 analysis days
 - three samples per day
 - burn (experimental)
 - sham (control)
 - all arrays were run as competitive (dual channel)
 - Affymerix Rat RAE230A arrays

first: Arul

last: Jayaraman

first: Francois

last: Berthiome

first: Martin

last: Yarmush

first: M

last: Vemula


title: Response of young and aged Mesenchymal Stem Cells to Dexamethasone

status: Public on Aug 08 2006

city: Tel Aviv

first: Dafna

last: Benayahu

department: Cellular and Developmental Biology, Sackler Faculty of Medicine

country: Israel

institute: Tel Aviv University

summary:
To explore the molecular events that underline skeletal physiology during aging we catalogued the profile of gene expression in ex vivo cultured MSCs derived from 3 and 15 month old rats and challenged with dexamethasone (Dex). RNA retrieved from these cells was analyzed using Affymetrix Gene Chips to compare the effect of Dex on gene expression.
Keywords: age effect, treatment

overall_design:
Mesenchymal Stem Cells were collected in the following manner: the bone marrow cells were flushed from the long bones, collected and prepared for single cells suspension.  Cell pooled from six rats in each group were cultured in 75 cm2 flasks (Falcon, USA) containing 20 ml of growth medium, Dulbecco’s Modified Essential Medium (DMEM) containing 10% heat-inactivated fetal calf serum (FCS). Under these conditions, the hematopoietic cells died and the cultures finally remained only with cells forming the adherent stromal fibroblast-like layer. Cells were plated and after one week of culturing were trypsinized, single cell suspensions were re-cultured for 7 days and were grown in absence or presence of 10-8 M Dexamethasone (Dex). On day 14 cells were harvested for RNA extraction.

The groups included: young (3 month) untreated females, young (3 month) untreated males, young treated (Dex) females, old (15 month) untreated rats, old treated (Dex) rats.

Total RNAs were extracted from the four experimental groups using the TRIzol and cRNA prepared according to Affymetrix protocols. Gene expression was measured by hybridization to Affymetrix RAE230A Gene Chip DNA microarrays .

first: Uri

last: Akavia

first: Irena

last: Shur

first: Gideon

last: Rechavi


title: DNA microarray reveals novel genes induced by mechanical forces in fetal lung type II epithelial cells

status: Public on Apr 29 2006

city: Providence

first: Juan

last: Sanchez-Esteban

state: RI

address: 101 Dudley Street

department: Pediatrics

institute: Women & Infants Hospital/Brown Medical School

summary:
Mechanical forces are essential for normal fetal lung development. However, the cellular and molecular mechanisms regulating this process remain largely unknown. In the present study, we used oligonucleotide microarray technology to investigate gene expression profile in cultured E19 rat fetal lung type II epithelial cells exposed to a level of mechanical strain similar to that observed in utero. Significance Analysis of Microarrays (SAM) identified 92 genes differentially expressed by strain. Interestingly, several members of the solute carrier family of amino acid transporters, genes involved in amino acid synthesis and development, and amiloride-sensitive epithelial sodium channel gene were induced by strain. These results were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). Thus, this study identifies genes induced by strain that may be important for amino acid signaling pathways, protein synthesis and development in fetal type II cells. In addition, these data suggest that mechanical forces may contribute to facilitate lung fluid reabsorption in preparation for birth. Taken together, the present investigation provides further insights into how mechanical forces may modulate fetal lung development.
Keywords: lung development, fetal type II epithelial cells, strain response, microarray

overall_design: Freshly isolated E19 fetal type II epithelial cells were plated on silastic membranes coated with collagen 1 and exposed to mechanical strain for 16 h to simulate mechanical forces in utero (5% cyclic strain, 60 cycles/min for 15 min + 2.5% continuous distention for the remaining 45 min of each hour) using the Flexercell FX-4000 Strain Unit. Cell grown on non-strained substrates were treated in an identical manner and served as controls. 3 pairs of control and strain samples were analyzed, using different litters for each pair (6 hybridizations).

first: Yulian

last: Wang

first: Benjamin

middle: S

last: Maciejewski

first: Gaia

last: Weissman

first: Ophira

last: Silbert

first: Hillary

last: Han


title: Gene expression profile of tungstate-induced beta cell mass increase in STZ rats

status: Public on Apr 01 2006

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary:
Background and Aims: It is well demonstrated that in the beta cell population of the pancreas there is a dynamic turnover, which results from the net balance of several processes; beta cell replication, apoptosis and neogenesis. These processes have been studied in partial pancreatectomy and glucagon-like peptide 1 treated animals, where an increase in pancreas regeneration has been observed. Similarly, sodium tungstate, which decreases hyperglycemia in several animal models of diabetes, promotes a rise in the beta cell mass of nSTZ and STZ animals. However, the molecular mechanisms underlying this pancreas regeneration remain unknown. Therefore the objective of this study is to identify which genes are up or down regulated in the increase of the beta cell population of STZ rats treated with sodium tungstate.
Materials and methods: Adult male Wistar (225-250 g) rats were kept under a constant 12-hour light-dark cycle and rats were kept under a constant 12-hour light-dark cycle and were allowed to eat and drink freely. Diabetes was induced by a single i.p. injection of streptozotocin (STZ) (70 mg/Kg body weight) in 0.9% NaCl with 100 mmol/L sodium citrate buffer (pH 4.5). Diabetes was confirmed by determination of its hyperglycaemia (>500mg/dL [Reflotron, Roche Diagnostic]). Healthy rats received an i.p. injection of the vehicle. Treatment started 7 days after the STZ or vehicle injection. Diabetic and healthy rats were divided into two groups. In the first (untreated), rats received deionized drinking water; in the second (treated) group, they were given a solution of sodium tungstate. During the first week of treatment, the rats received a solution of 0.7 mg/mL and in the next 4-5 weeks, the concentration was increased to 2 mg/mL. At the end of the experiment, the animals were sacrificed and pancreatic RNA isolated. Three chips (Affymetrix RAE-230A) were hybridized for each of the four experimental groups (untreated and treated healthy rats and untreated and treated diabetic rats). The raw intensity data obtained from the microarrays was normalized and summarized using the Bioconductor package RMA.
Keywords = pancreas regeneration
Keywords = STZ
Keywords = diabetes
Keywords = tungstate
Keywords = insulin-like agents
Keywords = beta cell plasticity
Keywords = neogenesis
Keywords: ordered

first: Albert

last: Barbera

first: Alexandre

last: Sanchez

first: Ramon

last: Gomis


title: High-Fat-Diet

status: Public on Jan 01 2006

city: MORIYA City

first: Yutaka

last: OHTA

department: Fundamental Research Lab

institute: ASAHI Breweries

summary:
High Fat Diet Experiment

SD rats fed either an AIN93G-based low fat diet or an AIN93G-based high fat diet.
Keywords: ordered

last: Ohta

first: Manabu

last: Sami

first: Kyoichi

last: Osada


title: Expression data from adult Rattus liver

status: Public on Jun 03 2006

city: Denver

first: Linda

last: Quattrochi

state: CO

department: Medicine

institute: University of Colorado at Denver and Health Sciences

summary:
Activation of the pregnane X receptor (NR1I2) by drugs and other xenobiotics stimulates (or suppresses) expression of numerous genes involved in the metabolic elimination of foreign compounds and some toxic endogenous substrates.
We used microarray analysis to identify genes whose expression in rat liver was significantly altered by pregnenolone 16alpha-carbonitrile (PCN) treatment.
Keywords: a single ip injection of PCN (100 mg/kg), 8 h treatment

overall_design: We chose to profile the gene expression pattern in the livers of adult rats to test the idea that PCN counteracts a wide variety of stresses by activating genes apart from drug metabolism.

first: Jeffrey

last: Guzelian

first: Joyce

last: Barwick

first: Lawrence

last: Hunter

first: Tzu

last: Phang

first: Philip


title: Genes associated with angiogenic response to Ang-1 or VEGF

status: Public on Mar 22 2006

city: Seattle

first: Alfred

last: Aplin

address: Box 357470 HSB-UW

department: Pathology

institute: University of Washington

summary:
Specific Aims
To identify novel transcriptional events associated with angiogenesis in VEGF and Ang-1 stimulated rat aortic rings.  Our studies take advantage of the capacity of rat aortic rings to generate new vessels in collagen gels.
Rat aortic rings embedded in collagen gel immediately after excision from the animal produce a self-limited angiogenic response under serum-free conditions and in the absence of exogenous stimuli.  This angiogenic response can be dose-dependently promoted by vascular endothelial growth factor (VEGF) and angiopoietin-1 (Ang-1), which are critical regulators of the angiogenic process during embryonal development and postnatal angiogenesis.  Aortic rings lose their capacity to spontaneously generate new vessels if embedded in collagen gels 10-14 days after excision. VEGF has the capacity to turn back “on” these quiescent rings producing florid angiogenesis.  Conversely, Ang-1 potentiates an existing angiogenic response, but is unable to turn the quiescent system “on”.  Since VEGF-mediated induction of angiogenic sprouting occurs 1-2 days of treatment, we hypothesize that this process is regulated by a unique set of “angiogenesis inducer genes” that are activated by VEGF and not by Ang-1.  Identification of the proteins encoded by these genes may advance our understanding of the molecular mechanisms that regulate the earliest stages of the angiogenic cascade.
Keywords: Response to growth factors

overall_design:
Rat thoracic aortic rings will be excised from 1 month old Fisher 344 rats and placed into suspension culture.  15-20 individual rings will be isolated from each animal and cultured in suspension in serum free medium.  The rings will be divided into three groups as described below.  (Assay is described in; Nicosia et al., 1997 Am.J.Pathol, 151).

All individual aortic rings isolated from a single animal will be split into three groups, VEGF treated, Ang-1 treated, and untreated controls.   Rings dissected from proximal and distal portions of the aorta will be mixed so that positional bias will not be carried through to the RNA preparation.

13 days post isolation, one set of aortic rings will be treated with 10ng/ml of recombinant human VEGF in serum free EBM media, a second set of rings will be treated with 100ng/ml of human recombinant Ang-1 (R&D Systems 923-AN) in conjunction with 5ug/ml poly-His antibody (R&D Systems MAB050), and a third set of rings will be incubated in serum free medium alone.

All samples were incubated for 18 hours post VEGF and Ang-1 treatment and then RNA was harvested.

With the number of aortic rings typically obtained, we anticipate having 4-6 individual rings from each animal for each experimental condition.   Furthermore, 10-100ng of total RNA will be collected per aortic ring, corresponding to 400-600ng of total RNA for each experimental condition per animal.

In order to have a minimum of three independent samples from each experimental condition, three animals were sacrificed, each of which gave rise to three individual RNA samples.  The resulting 9 individual RNA samples to be compared with respect to transcriptional profiles.

Total RNA will be extracted from each aortic ring using the Trizol reagent (Invitrogen) protocol. RNA will be stored at –80C until all 9 individual samples have been prepared.  Trizol extracted total RNA will be further purified/concentrated using the MicroRNAEasy Kit (Qiagen) with DNAseI digestion.

first: Roberto

middle: F

last: Nicosia


title: SHR-SP rats on Normal and High Salt+Fat diets, 2 vs. 8 weeks

status: Public on Oct 04 2005

city: Collegeville

first: Shawn

last: O'Brien

state: PA

address: 1250 Collegeville Rd

institute: GSK

summary:
Supporting microarray data for manuscript entitled "OSTEOPONTIN AND PAI-1 EXPRESSION IN MALIGNANT HYPERTENSION: SUPPRESSION BY p38 MAPK INHIBITORS" submitted to the HYPERTENSION journal.
Keywords: timecourse, diet

overall_design: Male spontaneously hypertensive stroke-prone rats (SHR-SP) were obtained from Charles River (Raleigh, NC). At 11 weeks of age, the SHR-SP were randomized into 2 groups, and fed either powdered chow diet (Purina 5001) with water ad lib; or a high-salt/high-fat diet consisting of 1% NaCl in the drinking water and 24.5% fat in the chow (from Harlan TekLad, Madison, Wisconsin). 6 replicate animals per diet per time point.

first: Alan

last: Olzinski


title: LECs from control and cirrhotic rats

status: Public on Nov 17 2005

city: Barcelona

first: Manuel

last: Morales-Ruiz

address: Villarroel 170

department: Biochemistry and Molecular Genetics

country: Spain

institute: Hospital Clinic

summary:
The study was performed in liver-endothelial cells (LECs) isolated from 6 adult male Wistar rats, undergoing a cirrhosis induction protocol as described previously by our group, and LECs isolated from 6 control Wistar rats, according to the criteria of the Investigation and Ethics Committee of the Hospital Clínic Universitari (Spain).The aim of this study was to evaluate differences in the gene expression pattern between LECs from control and cirrhotic rats. Methods: LECs were isolated from livers by collagenase perfusion, isopycnic centrifugation and incubation of cells with magnetic beads coated with specific antibodies (Ab).Total RNA was extracted from LECs with Trizol reagent (Life Technologies, Rockville, MD) after the cell-isolation step described above. RNA quality and concentration were confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). cRNA samples were hybridized to the Rat Expression 230A oligonucleotide microarray (Affymetrix). Microarray samples preparation and processing procedures where performed at the IDIBAPS Genomic Unit (Hospital Clinic Universitari, Barcelona) following the protocol as described in the Affymetrix GeneChip Expression Analysis Manual (Affymetrix, Inc, Santa Clara, CA).
Keywords: repeat sample


title: Effect of Trimethyltin on PC12 cells

city: Rome

first: camilla

last: bernardini

address: L.go F.Vito 1

department: Human Anatomy

institute: UCSC

summary:
The rat pheochromocytoma cell line PC12  cells were cultured in complete DMEM till 80% confluence, then placed at 5000 cells per squared cm. Cells were then plated in 24-well plates for cell viability assay and in T75 flasks for RNA isolation. Medium was replaced with serum-free fresh medium for 12 hours prior to TMT treatment.
Gene expression patterns were then analysed using Rat Expression Array 230A
Keywords: dose response, affymetrix chip

overall_design:
In this study we analize gene expression patterns in PC12 cells treated with Trimethyltin (TMT). We utilized control cells (untreated) and two different concentration (1 and 5 uM)
We used three biological replicates, for the three concentration tested, according to MIAME guidelines
(total 9 chips were used in this study).

first: Camilla

last: Bernardini

first: Wanda

last: Lattanzi


title: Burn Injury (1-7d)

status: Public on Oct 11 2005

city: Boston

first: Muralikrishna

last: Vemula

state: MA

department: Center for Engineering in Medicine/Department of Surgery

institute: Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children

summary:
Animal experiments were performed with male Sprague-Dawley rats (Charles River Laboratories, Boston, MA) weighing 150 ? 200 grams.  All experimental protocols used in this study were approved by the Subcommittee on Research Animal Care, Massachusetts General Hospital.  Rats were individually housed in a temperature-controlled (25oC) and light-controlled room (12h light-dark cycle) and allowed to adjust to their new surroundings for at least 5 days prior to the experiment.  Water and rat chow were provided ad libitum to the animals.  On the day of the treatment, the animals were randomly divided into two groups, burned and sham-burned.  The burn injury consisted of a full-skin-thickness scald burn of the dorsum, calculated to be ~ 20% of the rat?s total body surface area (TBSA), induced by immersing the designated area in boiling water for 10 s (45).  Rats were resuscitated with an intra-peritoneal injection of sterile saline solution (1.5 mL/Kg body weight/% TBSA) immediately after burn. The mortality rate of this treatment was negligible.  At each time point (1, 2, 4, and 7d), three animals belonging to each group were sacrificed, the liver and serum collected, and stored at ?80oC after being inflicted with 20% TBSA burn injury.  Sham-burn rats (n=3) considered as the control were treated identically except that they were immersed into a 37oC water bath and immediately sacrificed to collect the livers.
Keywords = Burn Liver microarray genechip time course
Keywords: time-course

first: Francois

last: Berthiaume

first: Arul

last: Jayaraman

first: Martin

last: Yarmush

first: Scott

last: Banta


title: Effect of Amoxicillin on the small intestine and colon of rats

city: Vers-chez-les-Blancs

first: Alexandra

last: Schumann

address: PO box 44

department: Nutrition and Health

institute: Nestle Research Center

summary:
Whole tissues corresponding to the proximal and distal small intestine and to the colon were dissected from each rat, washed with ice-cold saline solution and immediately frozen in liquid nitrogen. Rats were either control or treated with Amoxicillin (100mg/kg/day). Small intestine was divided in two identical length considered as the proximal and distal part. In each intestinal part 1 cm of tissue was taken in the middle of this part to perform the RNA extraction and then the GeneArray analysis.
Keywords: other

first: Sophie

last: Nutten

first: Dominique

last: Donnicola

first: Robert

last: Mansourian

first: Christine

last: Cherbut

first: Irène

last: Corthésy-Theulaz

first: Clara

last: Garcia-Rodens


title: Gene expression profile of cultured isolated UB in branching (BSN, PTN) and non-branching (HRG) conditions

status: Public on Sep 30 2005

city: La Jolla

first: Hiroyuki

last: Sakurai

state: CA

address: 9500 Gilman Drive 0693

institute: University of California, San Diego

summary:
Genes ontologically classified as proliferative and developmental were down-regulated by HRG, whereas those involved in transport were up-regulated. For example, the mRNA for the GDNF receptors, GFRa1 and ret9 were down-regulated while the mRNA for collecting duct transporters, such as urea transporter2, aquaporin3, sodium-hydrogen exchanger2 were up-regulated in HRG-treated UBs compared with UBs grown in the presence of branch-promoting factors
Keywords: Comparing different growth factor treatment

overall_design: Total RNA was extracted from 3 isolated ureteric buds in culture per one treatment condition (1 sample). Three samples (biological replicates) were used for one condition.

first: Kevin

last: Bush

first: Sanjay

last: Nigam


title: Age alters the gene expression profiles of rat oculomotor nucleus and spinal cord

status: Public on Sep 17 2005

city: Lexington

first: Colleen

last: McMullen

address: 800 Rose St MS508

department: Physiology

institute: University of Kentucky

summary:
Some of the most common neurodegenerative disorders have a strong association with aging. Curiously, these conditions tend to involve specific areas of the central and peripheral nervous system, at least initially. For example, amyotrophic lateral sclerosis preferentially targets spinal motor neurons and spares oculomotor neurons. This suggests that aging has divergent effects on brain stem and spinal cord, a factor that may explain differential susceptibility to certain neurodegenerative disorders. Therefore, for this study we asked whether aging induces a change in the evolution of the transcriptome of oculomotor nucleus (OMN) throughout the lifespan which would be different than that of the spinal cord aging.  Age induced a transcriptome shift to a pattern consistent with inflammation/immune response in both OMN and spinal cord. However, the response was more dramatic in the spinal cord. On the other hand, age repressed genes coding ion channels and transporters in OMN and cytoskeletal proteins in the spinal cord. The results indicate that OMN and spinal cord transcriptomes change differently with age. The results give an initial glimpse of how tissue-specific gene expression patterns may underlie the differential susceptibility to age-related neuromuscular dysfunction.
Keywords: time course, aging

overall_design: Total RNA was obtained with TRIzol (Invitrogen Carlsbad, CA) following the manufacturers recommended protocol. Tissues from 4 animals were combined into each RNA sample to decrease inter-subject variability. Biotinylated cRNA samples were hybridized to Affymetrix Rat Genome RA230 gene chips (n=18 chips) described previously [McMullen et al. 2004]. Microarrays were washed and stained with a streptavidin-bound marker and scanned. Data were analyzed with Affymetrix Microarray Suite 5.0 software. Only genes with consistent absent/present calls in all four independent replicates per group were considered for further analysis. Comparisons used the 6-mo transcriptome as the baseline and the one-sided Wilcoxon’s signed rank test to estimate “increase/no change/ decrease” difference calls for each pair-wise comparison. Only difference calls consistent in all pair-wise comparisons and with average changes > 1.70 were considered significant, resulting in a conservative list of genes with changed expression levels. Functional classification of genes was based on an extensive literature review.

first: Francisco

last: Andrade

first: Jorge

last: Gamboa


title: Burn-CLP

status: Public on Sep 20 2005

first: Muralikrishna

last: Vemula

institute: CEM, Mass Gen Hospital, Harvard Med School, Shriners Hospital for children

summary:
The experimental design included three biological replicates for each of the three conditions: Sham-Sham, Sham-CLP and burn-CLP. Liver samples were collected from the rats and the total RNA was analyzed on a Affymetrix RAE230A chip. No technical replicates were included in the study
Keywords: other

first: Tadaaki

last: Yokoyama

first: Francois

last: Berthiaume


title: Rat LAD IR study

status: Public on Mar 24 2006

city: Columbus

first: Sashwati

last: Roy

state: OH

department: Surgery

institute: Ohio State University

summary:
Rats underwent surgery for LAD ligation for 30 min followed by reperfusion. Heart ventricles were collected 2d or 7d after reperfusion.
Keywords: rat heart ventricles, LAD - left anterior descending coronary artery, IR - ischemia-reperfusion

overall_design:
rats were divided in following groups that underwent LAD occlusion or not (SHAM):

1. 7d-IR (n=3)
2. 7d-sham (n=3)
3. 2d-IR (n=3)
4. 7d-sham (n=3)

first: Chandan

last: Sen

first: Savita

last: Khanna


title: Rat mammary normal - tumor

status: Public on Apr 30 2005

first: Penelope

middle: Lyn

last: Miron

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary:
Rat mammary tumors induced by N-methyl-N-nitrosurea (NMU) and normal mammary gland
Keywords = breast cancer
Keywords = rat mammary tumor
Keywords = NMU
Keywords = animal model.
Keywords: other

first: M.

last: Chan

first: X.

last: Lu

first: F.

last: Merchant

first: J.

last: Iglehart

first: P.


title: Control vs Diabetic Penile Tissues

status: Public on Aug 23 2005

city: Sacramento

first: Chris

last: Sullivan

address: 6000 J Street

department: Biological Sciences

institute: California State University, Sacramento

summary:
Gene expression analysis in control and diabetic rats. Diabetes-induced erectile dysfunction in rat model of DM. 10 weeks of streptozotocin induced diabetes. F344 Rats.
Keywords: other

overall_design:
Sample with Title (Controls)
GSM46500  HWC13
GSM46503  HWC14
GSM46508  HWC16
GSM46512  HWC17
GSM46516  HWC7

Sample with Title (Diabetic)
GSM46518  HWS17
GSM46519  HWS18
GSM46520  HWS22
GSM46521  HWS23
GSM46522  HWS26

first: Hunter

last: Wessells


title: 12 Week Rat Jejunum

status: Public on Jul 11 2005

city: Tucson

first: James

middle: Forrest

last: Collins

state: AZ

address: PO Box 245073, 1501 N. campbell Ave.

institute: University of Arizona Health Sciences Center

summary:
12-week-old rats, iron-replete or iron-deficient. Three groups of each condition. 230A and 230B chips used with cRNA derived from jejunal scrapes.
Keywords: ordered


title: Global Gene Expression Profiles of Single-Cell Derived Fetal Rat Calvaria Cell Colonies with Adipocyte and Bone Markers

status: Public on Dec 09 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Single cell-derived colonies were obtained by sorting 21 days fetal Rat calvaria cells into microtitre wells using flow cytometry. Colonies were categorized according to a limited gene expression profiling for a specific bone (osteocalcin) and a specific adipocyte (adipsin) marker by real-time PCR. Colonies expressing neither, one or both bone and adipocyte markers are in the sample set. Microarray analysis will address the global gene expression profiles of CFU-O (bone marker only), CFU-F (neither bone nor adipocyte marker) and CFU-bipotential (both markers) derived from single cells. CFU-A (adipocyte marker only) samples are also available for analysis if warranted.
Keywords: other

overall_design: this experiment include 3 samples and 18 replicates


title: Reinnervation of rat muscle

status: Public on Apr 28 2005

city: Tuebingen

first: Antje

last: Bornemann

institute: Institute of Brain Research

summary:
Three male 8-week-old Wistar rats were used. The peroneal nerve of the animals was transected and sutured to the biceps femoris muscle. Four weeks later, the proximal stump was sutured to the distal stump. The animals survived for 8 weeks.
All experiments were performed under Ketanest (ketamine hydrochloride, Essex Pharma GmbH, Munich, Germany; 100 mg/kg) and Rompun (xylazine hydrochloride, Bayer, Leverkusen, Germany; 10 mg/kg) anesthesia. Both substances were injected intraperitoneally. RNA was extracted from the ipsilateral and contralateral tibialis anterior muscles of each animal. The gene array analysis compared the ipsilateral muscle with the contralateral muscle of each animal.
Keywords: parallel sample

first: Zhe

last: Zhou

first: Carl

last: Cornelius

first: Martin

last: Eichner


title: Profiling of D-PA Induced Idiosyncratic Drug Reactions

status: Public on Jun 21 2005

city: Toronto

first: Paul

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
Idiosyncratic drug reactions (IDRs) cause significant morbidity and mortality. In an animal model of IDRs, 50-80% of Brown Norway rats exposed to D-penicillamine develop an autoimmune syndrome after several weeks of treatment. The symptoms of the IDR are similar to that observed in humans who take D-penicillamine. The mechanism of this reaction is unknown, and no effective biomarkers have been identified to predict susceptibility. We postulate that cell stress caused by drugs is required to initiate the response. We used a highthroughput approach to identify factors that might represent danger signals by profiling hepatic gene expression 6 h after dosing with D-penicillamine (150 mg/kg). Our results show that the drug-treated animals cluster into two distinct groups. One group exhibits substantial expression changes relative to control animals. The most significantly altered transcripts have a role in stress, energy metabolism, acute phase response, and inflammation. We used quantitative reverse transcriptase polymerase chain reaction to measure transcript levels in liver biopsies of 33 rats and found that resistant animals cluster together. This 'resistant' cluster of animals contains 87.5% (7/8) resistant animals but only 48% (12/25) 'sensitive' animals. This separation is statistically significant at the p 0.01 level.
Keywords: Response to Drug

overall_design: Single-channel Affy arrays used to profile 4 control Brown Norway rats and 8 D-Penicillamine treated Brown Norway rats.

first: Beatrice

last: Seguin

first: Xujian

last: Li

first: Allan

middle: B

last: Okey

first: Jack

last: Uetrecht


title: PPAR gamma overexpression and activation in rat pancreatic islet

city: Research Triangle Park

first: Sujoy

last: GHOSH

institute: GLAXOSMITHKLINE

summary:
Impact of PPAR gamma overexpression and activation on rat pancreatic islet gene expression profile analyzed with oligonucleotide microarrays
Keywords: parallel sample

first: Laura

last: Parton

first: Frederique

last: Diraison

first: Suzanne

middle: E

last: Neill

last: Ghosh

first: Mark

middle: A

last: Rubino

first: John

last: Bisi

first: Celia

last: Briscoe

first: Guy

last: Rutter


title: Gene Expression for fetal kidneys of hyper insulinemia induced intrauterine growth restriction  rat model

status: Public on Aug 31 2005

city: Jerusalem

first: Yoav

middle: M

last: Smith

address: Hadassah Ein-Karem

department: Medical School

institute: Hebrew University

summary:
Inrauterine growth restriction was induced by chronic hyper insulinemia in pregnant rats and differential gene expression was studied using affymetrix rat genome RAE230A.Data was analysed using SAM.
Keywords: disease state analysis

overall_design: rna was isolated from 5 kidneys of growth restricted fetus and compared with 5 normal controls

first: Ilana

last: Ariel

first: Michael

last: Bursztyn


title: Gene expression in Hypotension

status: Public on Mar 12 2005

city: Berlin

first: Timm

last: Westhoff

address: Hindenburgdamm 30

department: Medizinische Klinik IV

institute: Charite, Campus Benjamin Franklin

summary:
Rat kidney in normo- and hypotensive animals.
Keywords: parallel sample

first: Stefanie

last: Scheid

first: Markus

last: Toelle

first: Bogac

last: Kaynak

first: Walter

last: Zidek

first: Silke

last: Sperling

last: Van der Giet


title: Steen-5R01NS042241-03

status: Public on Jul 06 2005

city: Phoenix

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
The adult somatosensory cortex undergoes reorganization in response to changes in peripheral input, such as limb usage patterns or denervation/amputation. This reorganization underlies important phenomena, such as phantom pain, recovery after stroke, and certain forms of learning.  Although cellular processes, such as LTP, receptor regulation, axonal growth and synaptic formation have been theorized and studied in relation to cortical reorganization, conclusive evidence remains elusive.  The identification of genes up- and down-regulated during reorganization will provide clues for which processes underlie reorganization.  Reorganization is likely to involve forms of signaling between cortical neurons (e.g. release of growth factors), which could be identified through gene chip studies.  Identification of genes modulated during reorganization will provide specific direction for further studies in the elucidation of the mechanism(s) underlying cortical reorganization.
To identify those genes with altered regulation during the cortical reorganization process.
We hypothesize that genes regulated during cortical reorganization will be components of the mechanism(s) underlying this important process, and that identification of these genes will provide insight for the design of further studies of cortical plasticity.
Cortical reorganization in rat somatosensory cortex (S1) will be induced at the forepaw/lower jaw border by partially denervating the paw.  The animals will be recovered and the reorganization allowed to proceed for 3, 7, 14 and 28 days.  Control animals will receive a sham denervation.  Following the allotted time, the border between the lower jaw and the now silent forepaw cortex will be mapped in vivo.  A 500 um wide strip of cortex surrounding the border area will be excised and stored in RNAlater (Qiagen) at 20oC until processed for RNA extraction.  The tissue will be dispersed using a disposable pestle and microcentrifuge tube and then homogenized in Qiashredder (Qiagen) columns.  RNA will be extracted using a RNeasy Micro Kit.  However, if the UCLA center has a rotor/stator homogenizer with a microcentrifuge tube sized probe, we would like to discuss the possibility of performing the RNA extraction there (we would expect a better yield, and cannot locate this equipment at UCR).  An initial portion of this study will done for 3 day experimental and sham control animals, plus non-operated animals, with four animals per group.  This will be to determine the variability among our samples and to familiarize our personnel with the process.  The number of samples/group necessary for the remaining time points may be modified based on the results of the 3 day study.
Keywords: time-course

overall_design: as above

first: P

last: Steen


title: Long-term Clofibric acid study

status: Public on Mar 01 2005

city: VITRY / SEINE

first: Cecile

last: Michel

address: 13, quai Jules Guesde

department: DSE

country: France

institute: Sanofi-Aventis

summary:
F344 rats were divided into 4 groups: vehicle control, DEN, DEN+CLO and CLO. After one week of basal diet, rats belonging to the groups DEN and DEN+CLO underwent intraperitoneal injection of DEN (30mg/kg body weight) dissolved in NaCl 9‰. The two other groups were injected with NaCl 9‰ alone. At 30mg/kg, DEN is non-necrogenic thus only exhibiting initiating properties. Twelve days after injection, diet from rats belonging to the groups CLO and DEN+CLO was changed for diet containing 5000ppm CLO for up to 608 days. Series of 5 rats from each group were necropsied at days 18, 46, 102, 264, 377, 447 (reverse phase from day 377: no more CLO in the diet for rats belonging to the DEN+CLO group), and for the CLO and Control group 524, and 608 days after the injection of DEN or saline. From day 524, half of the CLO-treated rats were kept on basal diet (reverse phase) until day 608.
Keywords = Clofibric acid
Keywords = Diethylnitrosamine
Keywords = Rat
Keywords: other

first: Ruth

last: Roberts

first: Chantal

last: Desdouets

first: Kevin

middle: R

last: Isaacs

first: Eric

last: Boitier


title: Effect of Isoflurane and LTM on basolateral amygdala

status: Public on Dec 31 2004

city: Stony Brook

first: Ira

last: Rampil

state: NY

institute: University at Stony Brook

summary:
Fear conditioning in rats leads to long term memory (LTM) formation. A central neural substrate for LTM is the basolateral amygdala. We sought the expression changes specific to LTM at 6h following anesthesia with isoflurane (a general anesthetic and an effective amnestic agent), following pain (a component of conditioning), and following conditioning in presence and absence of isoflurane.
Keywords = anesthesia, amygdala, LTM, Rampil, Isoflurane, fear, memory
Keywords: other

overall_design: For baseline control 9 samples were used. 5 samples each were used for all other experimental conditions: isoflurane, pain, conditioning and conditioning in presence of isoflurane.

first: Achim

last: Bell

first: Daryn

last: Moller


title: Bis-(2-chloroethyl) sulfide exposure time course and dose response in the rat lung

status: Public on Dec 20 2004

city: Aberdeen Proving Ground

first: James

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

summary:
Male Sprague-dawley rats were exposed to saline, isopropyl alcohol, 1mg/kg, 3mg/kg or 6 mg/kg sulfur mustard for 30 min, 1 hr, 3 hr, 6 hr, or 24 hr before analysis of lung tissue by oligonucleotide array analysis.
Keywords = sulfur mustard
Keywords = rat
Keywords = lung
Keywords = bis-(2-chloroethyl) sulfide
Keywords: ordered

first: Alfred

last: Sciuto

first: Christopher

last: Phillips

first: Linda

last: Dorsch

first: Alison

middle: I

last: Hege

first: Matthew

middle: D

last: Croxton

first: Albert

last: Sylvester

first: Theodore

last: Moran


title: A comparison of forskolin-induced mRNA vs. an inactive control in the rat PC12 cell pheochromocytoma cell line.

status: Public on Dec 16 2004

city: Portland

first: Soren

last: Impey

state: OR

institute: Vollum Institute

summary:
PC12 cells (passage 22) were cultured at 5% CO2 in a 37 C incubator. The growth medium was DMEM (high glucose, Invitrogen) supplemented with 25mM HEPES, 10% FCS, 5% FBS and 1x Pen/Strep (Invitrogen). 1x106 cells were starved overnight  in DMEM+25 mM HEPES and treated with 10 uM 1,9 dideoxy forskolin or forskolin for 60 min. The final DMSO concentration was 0.05%. Total RNA was purified using Trizol (Invitrogen) according to the manufacturers protocol. An additional round of purification was conducted using Rneasy columns (Qiagen) according to the manufacturers protocol. cRNA was synthesized and labeled according to standard Affymetrix protocols. 2 biological replicates for the forskolin and 1,9 dideoxy forskolin conditions were run on Affymetrix RAE230 A and B chips for a total of 8 hybridizations.
Keywords: repeat sample

first: S

last: McCorkle

first: H

last: Cha-Molstad

first: J

last: Dwyer

first: G

last: Yochum

last: Boss

last: McWeeney

last: Dunn

last: Mandel

first: R

last: Goodman


title: Rat mammary expression in individuals and pools

status: Public on Feb 25 2005

city: Madison

first: Christina

last: Kendziorski

state: WI

address: 1300 University Avenue (6729 MSC)

department: Biostatistics and Medical Informatics

institute: University of Wisconsin

summary:
Rat mammary glands were obtained from individual rats in RXR treated (a) and control (b) conditions (12 rats in each condition). The 24 samples were hybridized individually.  Also, in each condition, samples were combined into different pools of 2, pools of 3, pools of 12. Technical replicates were also run.
Keywords: other


title: Investigating learning disabilities: fetal alcohol exposed rats. Perrone-Bizzozero-5R01NS030255-12-2

status: Public on Nov 24 2004

first: Winnie

last: Liang

summary:
We are searching for common gene expression alteration in the hippocampus of animal models of learning disabilities and in post-mortem human tissues derived from patients with cognitive deficits. Our study has three phases. In phase I, we want to investigate the changes in gene expression in a transgenic mouse line that shows impairments in hippocampal-dependent learning. These animals are overexpressing the RNA-binding protein HuD in the forebrain under the control of the alpha CAMKinII promoter. For phase II, we plan to characterize the hippocampus of another animal model of learning disabilities: fetal alcohol exposed (FAE) rats. Last, for phase III, we would like to examine gene expression changes in the hippocampus and other tissues from patients with schizophrenia.
To test our hypothesis, in phase 2 of our project, we propose to compare the pattern of gene expression in our mouse model with that in the hippocampus of rats prenatally exposed to alcohol (FAE model).
Our hypothesis is that learning disabilities have common neural substrates regardless of the origin of the disability being genetic, environmental of a combination of these two. To test this hypothesis, we plan to examine the pattern of gene expression in the hippocampus of animals and humans with cognitive deficits and use bioinformatics tools to identify common changes in gene expression in three of such conditions: a genetic model (HuD transgenic mice), an environmental model (FAE rats) and a model for combined environmental and genetic effects (patients with schizophrenia).
All the animals are adult male Sprague-Dawley rats (age 90-100 days). Animals were divided in three diet groups and three experimental treatment conditions (9 conditions altogether). Three groups of pregnant rat dams were placed on different diet regimens: a liquid diet containing 5% alcohol (A) groups, a control group fed an isocaloric liquid diet without alcohol (B) and a group of rats fed lab chow ad libitum (C). Offspring from each of these groups were allowed to grow until adulthood and placed into each of three training groups: a contextual fear conditioned group (1), a non-learning stress control group (2) and a naive/unhandled group (3). Hippocampi were dissected and used to isolate total RNA from each rat diet and training condition. Initially, we will submit 18 samples as follows: 10 samples from training group 1 and 8 samples from training group 3 (training group 2 will be analyzed at a later date).  The diet assignment for the 18 samples is: 8 samples from group A, 6 samples of group B and 4 samples of group C. Please note that I was able to enter only the first 8 samples, as the sample list does not hold 18 samples altogether.
Keywords: dose response

first: Nora

last: Perrone-Bizzozero


title: Neuron susceptibility to seizure-induced injury. Dingledine-5R01NS031373-10-2

summary:
Neurodegenerative brain disorders become more common in the aged. Most of these disorders are associated with or caused by selective death of certain neuronal subpopulations. The mechanisms underlying the differential vulnerability of certain neuronal populations are still largely unexplored and few neuroprotective treatments are available to date. Elucidation of these mechanisms may lead to a greater understanding of the pathogenesis and treatment of neurodegenerative diseases. Moreover, preconditioning by a short seizure confers neuroprotection following a subsequent prolonged seizure. Our goal is to identify pathways that confer vulnerability and resistance to neurotoxic conditions by comparing the basal and preconditioned gene expression profiles of three differentially vulnerable hippocampal neuron populations.
Hippocampal CA1 and CA3 pyramidal neurons are highly susceptible to seizures and ischemia, whereas dentate gyrus granule cells are relatively resistant. A brief preconditioning seizure confers protection to the pyramidal cells. We will first determine gene expression profiles of untreated rat CA1 and CA3 pyramidal cells, and dentate granule cells, using laser capture microscopy to obtain region-specific neuronal mRNA. We will then determine the effect of a brief preconditioning seizure, which is neuroprotective in CA1 and CA3, on these expression profiles.
We hypothesize that common molecular mechanisms exist in neurons that determine their susceptibility to seizure-induced injury. Intrinsic differences in gene expression exist between hippocampal glutamatergic CA1 and CA3 pyramidal neurons, on the one hand, and dentate granule cells on the other, which contribute to the greater susceptibility of pyramidal neurons to degeneration in experimental stroke and epilepsy. We specifically hypothesize that differences in basal energy metabolism genes may confer differential susceptibility to neurodegeneration produced by seizures and ischemia.
Anesthetized animals will be sacrificed by decapitation, and frozen 10 micron sections will be lightly stained with cresyl violet to identify cell layers in the hippocampus. Approximately 1000 neurons from each of the three cell layers will be isolated by LCM.  Poly-A RNA will be amplified using a modified Eberwine protocol. The quality of our aRNA will be evaluated by quantitative RT-PCR of GluR6 and KA2 mRNA levels before we send the samples to the Center for labeling and hybridization to Affymetrix rat 230A arrays. We will provide a one-round amplification cDNA product to the center for labeling and hybridization.  This protocol is identical to a previously approved study by Jim Greene in our laboratory.
Keywords: other

first: Ray

last: Dingledine


title: Rat Adipose Tissue

status: Public on Nov 30 2004

city: London

first: Kaiping

last: Yang

institute: University of Western Ontario

summary:
Male 130 day old rat adipose tissue from control and obese rats
Keywords: ordered


title: INS-1 cell lines (FLP-In T-REx)

status: Public on Nov 05 2004

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
Four rat insulinoma cell lines (INS-1) were generated that contain a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the cell lines contain the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors or other signal tranduction molecules can be identified. The expression profiles of the parental INS-1 cell line and the four derivatives were determined on a RAE230A array, showing that the highly differentiated phenotype of the parental cell line was maintained in the clones.
Keywords: ordered

first: Heike

last: Thomas

first: Sabine

last: Senkel

first: Silke

last: Erdmann

first: Tanja

last: Arndt

first: Gülüzar

last: Turan

first: Gerhart

middle: U

last: Ryffel


title: Targets of HNF1b mutants in INS-1

summary:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors HNF1b and HNF1b mutants were identified. Two different clones containing the same transcription factor were analyzed in the non-induced and tet-induced (24 h) state.
Keywords: ordered


title: Targets of HNF1b, HNF4a2 and HNF6 in INS-1 cells

summary:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet) induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors HNF1b, HNF4a2, and HNF6 (onecut1) were identified.
Two different clones containing the same transcription factor were analyzed in the non-induced and tet-induced (24 h) state.
Keywords: ordered


title: Fibronectin Induced Cardiac Myocyte Hypertrophy

status: Public on Aug 19 2004

city: Pittsburgh

first: Jorge

middle: L

last: Sepulveda

address: S758 200 Lothrop

institute: University of Pittsburgh

summary:
Gene expression changes in neonatal rat ventricular myocytes plated in fibronectin (2 samples) or uncoated plates (2 samples).
Keywords = Hypertrophy Cardiac Myocyte Fibronectin
Keywords: repeat sample


title: Rat germ cells

status: Public on Mar 16 2004

city: New York

first: Nikolaus

last: Schultz

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

summary:
Rat germ cells
Keywords: other

first: F

middle: Kent

last: Hamra

first: Karen

last: Chapman

first: Dana

last: Grellhesl

first: Jennifer

last: Cronkhite

first: Robert

last: Hammer

first: David

last: Garbers


title: Laminar gene expression of rat extraocular orbital and global layers

status: Public on Oct 12 2004

city: Philadelphia

first: Murat

last: Budak

institute: University of Pennsylvania

summary:
Adult rat global and orbital layers of rectal extraocular muscles  microdissected using Arcturus Pixcell II LCM are gene profiled here using affymetrix rat RAE230A gene chip.
www.med.upenn.edu/cellbio/faculty/rubinstein/
www.uphs.upenn.edu/pmi/members/khurana/lab%20page.htm
Keywords: ordered

first: Sasha

last: Bogdanovich

first: Olga

last: Lozynska

first: Tejvir

last: Khurana

first: Neal

last: Rubinstein


title: A Comparison of Neonatal Rat Ventricular Myocytes Treated With Phenylephrine or PAMH

status: Public on Mar 02 2004

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

summary:
Neonatal rat ventricular myocytes cultured for 48 hours without stimulation, in the presence of twenty micromolar phenylephrine, or in the presence of one micromolar PAMH.
Keywords = Rattus
Keywords = Ventricular Myocytes
Keywords = Cardiomyocytes
Keywords = Hypertrophy
Keywords = Phenylephrine
Keywords = PAMH
Keywords = 5-hydroxytryptamine
Keywords = Pyridine
Keywords: repeat sample

first: Erik

last: Bush

first: Jens

last: Fielitz

first: Lawrence

last: Melvin

first: Michael

last: Martinez-Arnold

first: Timothy

last: McKinsey

first: Ryan

last: Plichta


title: Effect of environmental enrichment in reducing seizure-induced neuronal injury. Koh-7K08NS002068-05

status: Public on Oct 14 2004

first: Winnie

last: Liang

summary:
Neuropsychiatric consequences of poorly controlled seizures that begin in childhood can be devastating.  School failure or behavioral difficulty in a child with epilepsy is common and can become the focus of concern for families. Current antiepileptic drugs compound problems with their CNS side effects; effective therapy is currently limited as little is known about the cellular and molecular changes caused by seizures in the developing brain. This study will investigate transcriptional regulation induced by early-life seizures and explore alternative nonpharmacological therapeutic strategies in reversing damages of early-life seizures. We will study the therapeutic efficacy of environmental enrichment in reducing seizure-induced neuronal injury and in modifying gene expression alterations.  We will explore molecular mechanisms underlying the beneficial effects of enriched environment and examine how different genes act in concert to influence the outcome of seizure-induced damage.
To test the effect of environmental enrichment in modifying KA seizure-induced alterations in gene expression.
We hypothesize that environmental enrichment enhances plastic, homeostatic response of immature brain to excessive, dysregulating seizure activity and protect against maladaptive response of developing animals to seizures.
After inducing seizures by systemic injection of KA (8 mg/kg) or PBS injections (control) at P20, we will randomly assign P21 male Long Evans rats to 4 groups: enrichment housing (control-enriched; SE-enriched) or to standard vivarium cages (control; SE). Sixteen animals (8 control-enriched; 8 SE-enriched) will be housed as a group in a plastic rectangular cage measuring 115cm x 80 cm containing a running wheel, tunnels, rubber balls, a maze, a mirror, and a clock with a cyclist pendulum. Control and KA will be housed individually in a standard cage. Four litters will be used for each run of experiment and the experiment will be repeated once to obtain 16 animals per group. At P30, 240 h after KA or PBS, animals will be deeply anesthetized with isoflurane, decapitated for total RNA preparation (half brain for each, n = 12 per group). Total RNA will be isolated from each hippocampus individually, and equal amounts of RNA from 4 hippocampi will be pooled for each Genechip. Three independent hybridizations will be performed per condition (total of 12 Genechip Rat Expression Set 230).
Keywords: dose response

first: Sookyong

last: Koh