title: Htt14A2.5 induced verses uninduced

status: Public on May 30 2005

city: Irvine

first: Barbara

last: Apostol

state: CA

department: Psychiratry and Human Behavior

institute: University of California Irvine

summary:
Htt14A2.5 is a clonal rat pheochromocytoma (PC12) cell line, that expresses a truncated form of expanded repeat Htt exon 1 protein fused at the C-terminus to enhanced green fluorescent protein (EGFP).  For total RNA preparation, ~3 x 105 cells were plated on 150 mm plates and the following day either induced with 5 microM PA or treated with ethanol alone (uninduced) for 48 hrs followed by direct lysis using the RNeasy total RNA prep as described by the manufacturer (Qiagen, Valencia, CA).  Cells were harvested at approximately 40-60% confluency.  RNA was quantitated spectrophotometrically and integrity tested by capillary electrophoresis (Agilent 2100 Bioanalyzer).  25 micrograms total RNA was used to generate target cRNAs for hybridization to Affymetrix Rat Genome U34A oligonculeotide arrays (UCI DNA Array Core Facility).  Four separate cell growths were performed for the PA induced verses uninduced comparisons.  Target cRNA was synthesized separately for each of these cell growths and hybridized individually to the oligonucleotide microarrays.
Keywords = huntingtin
Keywords = PC12
Keywords: repeat sample

first: Leslie

last: Thompson

first: J

last: Marsh

first: Katalin

last: Illes

first: Judit

last: Pallos

first: Margaret

last: Roark

first: Shetia

last: Washington

first: Laszlo

last: Bodai

first: Jun

last: Wu

first: Andrew

last: Strand

first: Erik

last: Schweitzer

first: James

last: Olson

first: Aleksey

last: Kazantsev

first: Jeffrey

last: Vaught

first: J.


title: Fukuhara-2U54NS034194-09

status: Public on Jul 06 2005

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

country: USA

institute: Translational Genomics

summary:
There is growing appreciation that the feeling of well-being, alterations in mood and susceptibility to a variety of medical disorders depend on the proper expression of the master circadian clock and the synchrony among the other oscillators found in many peripheral tissues.  To improve our understanding of the role of peripheral oscillators, an improved understanding of the molecular machinery sub-serving the circadian variation in gene expression is essential.  Our long-term goal is to understand the molecular mechanisms that initiate circadian gene expression following external stimulation in the mammalian pineal gland.
Are all or just some of the "circadian clock" genes induced by NE, cAMP, or cGMP? In this project we compare a series of gene expression patterns using DNA microarray in response to cAMP, cGMP and NE stimulation to understand why NE does not initiate circadian rhythms in the rat pineal gland.  As a preliminary experiment we will compare gene expression 0, 1, and 4 h after start of chemical stimulation.
A failure of NE to initiate circadian rhythms is due to failure of activation of certain "circadian clock" genes. We found that circadian rhythms are initiated by stimulation of cAMP or cGMP analogue in the rat pineal gland, while norepinephrine (NE) stimulation only moderately induce Period1 mRNA (one of "circadian clock" genes) 24 h after start of stimulation.  From these results we hypothesize that external stimulation activates some "circadian clock" genes simultaneously, and that failure of circadian rhythm initiation following NE stimulation is due to insufficient "circadian clock" genes activations.
Male rats of wistar strain are kept in 12h-12h light dark cycles at least for one week before start of experiments.  Pineal glands are removed from animals and placed in the culture dish. Rat pineal glands are cultured for 3 days before chemical stimulation.  On the day of experiment, the pineal cultures are stimulated using one of NE, cAMP and cGMP analogues for 1 or 4 h before harvest.  The samples are immediately frozen and total RNA are extracted from each group which are from a pool of 8 pineal glands using Trizol reagent (Invitrogen).  Concentrations of total RNA are determined using spectrophotometer, and six microgram of total RNA is aliquoted in each sample tube for further analysis.  Since we already have Affymetrix Rat Genome U34A array GeneChips, we would like to send Chips as well as our total RNA samples.
Keywords: time-course

overall_design: as above

first: Chiaki

last: Fukuhara


title: Transcriptional profile of an acs2Ts1 mutant yeast

status: Public on Oct 01 2006

city: Baltimore

first: Hidekazu

last: Takahashi

state: Maryland

address: 339 Broadway Research Building, 733 North Broadway

department: High Throughput Biology Center

institute: Johns Hopkins University School of Medicine

summary:
Wild-type and the acs2Ts1 mutant yeasts were shifted from 25deg to 37deg. After 60 minutes, Yeasts were harvested and divided into 2 x 2 cell samples. Total RNAs were purified from 4 populations.
Keywords: WT vs mutant

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: microarray data of 2 x 2 = 4 samples were background-corrected with RMA. Because of a global change in expression, the data were taken as 1 x 2 = 2 means and normalized with controls using lowess curve.

first: Rafael

middle: A

last: Irizarry

first: Jef

middle: D

last: Boeke


title: Vitamin A-deficient diet

status: Public on Jun 30 2005

city: Indianapolis

first: Howard

last: Edenberg

state: IN

institute: Indiana University School of Medicine

summary:
Analysis of livers from 74-day old male rats fed vitamin A sufficient or vitamin A deficient diet for 53 days. Either 10ug or 2ug of total RNA used in standard Affymetrix protocol
Keywords = rat
Keywords = liver
Keywords = vitamin A deficiency
Keywords: other

first: Jeanette

middle: N

last: McClintick

first: David

middle: W

last: Crabb

first: Huijun

last: Tian

first: Jane

last: Pinaire

first: Ronald

middle: E

last: Jerome

middle: J


title: Rat liver response to Clofibrate, DEHP or VPA

status: Public on Jun 02 2005

first: Keith

middle: M

last: Goldstein

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

summary:
The project had 2 goals:
1) To evaluate the transcriptional response of 3 prototypical toxicants (Clofibrate, VPA, and DEHP) on rat lever.
2) To evaluate the impact pooling samples has on data analysis.

Keywords = Clofibrate
Keywords = Diethylhexyl phthalate
Keywords = Phthalic acid bis(2-ethylhexyl ester)
Keywords = Sodium Valproate
Keywords = Valproic Acid
Keywords = VPA
Keywords = vehicle
Keywords: other

overall_design:
Male SD rats were given a single dose of one of 3 prototypical toxicants or dosed with vehicle. The toxicants used were:
1000mg/kg Clofibrate (in 0.9% saline)
2000mg/kg Sodium Valproate (in distilled water)
20g/kg DEHP (in distilled water)

Animals were sacrificed at 4, 24, 48, or 168hrs post-dosing (only 48 and 168hrs for vehicle-treated animals)

One of the goals of this study was to assess the impact pooling RNA samples has on the array data. For each treatment and vehicle group there are 3-5 individual samples, as well as 1 pooled sample.

10ug of total RNA were hybridized to Affymetrix RG_U34A arrays according to the manufacturer's protocol. Signal intensities were generated using MAS5, with global scaling set to 1500.

first: Robert

last: Jolly

first: Tao

last: Wei

first: Hong

last: Gao

first: Peining

last: Chen

first: Shuguang

last: Huang

first: Jean-Marie

last: Colet

first: Timothy

middle: P

last: Ryan

first: Craig

last: Thomas

first: Shawn

middle: T

last: Estrem


title: CCg Progenitors

status: Public on Jun 16 2005

city: La Jolla

first: James

middle: Bradley

last: Aimone

address: 10010 N. Torrey Pines Rd

department: Laboratory of Genetics

institute: Salk Institute

summary:
Experiment comparing Low-density, CCg derived, progenitors (LDP) with high-density progenitors (HDP), and neurons (LDN) and astrocytes (LDA) derived from the LDP condition
Keywords: other

first: Vi

last: Chu

first: Alysson

middle: R

last: Muotri

first: Fred

middle: H

last: Gage


title: Hippocampal gene expression after brain injury

status: Public on Jul 01 2005

city: Memphis

first: Eldon

last: Geisert

state: TN

address: 855 Monroe Avenue

department: Ophthalmology

institute: University of Tennesse

summary:
RNA samples were prepared from ipsilateral rat hippocampi 3 hr and 24 hr following lateral cortical impact injury and compared to samples from sham-operated controls.  For details please see Matzilevich et al., J Neurosci Res 2002 Mar 1;67(5):646-63.
Keywords = Brain injury
Keywords: time-course

first: Anthony

last: Moore

first: Pramod

middle: K

last: Dash


title: Expression profiling in perinatal Ductus Arteriosus (DA) and Aorta (Ao).

status: Public on Sep 13 2005

city: Pisa

first: Flavio

last: Coceani

address: Piazza Martiri della Libertà, 33

department: Settore di Scienze Mediche

country: Italy

institute: Scuola Superiore S. Anna

summary:
Compared the gene expression profiles of two contiguous vessels pre and post - birth, namely the Ductus Arteriosus (DA), committed to become a fibrous ligament, and the Aorta (Ao), which conversely takes on a permanent activity.  The effect of artificially enhanced O2 tension was analyzed in DA in the pre-birth condition.
Keywords: Comparison gene expression

overall_design:
5 experimental conditions:
1)	DA of 19 days post coitum (dpc) fetuses  (DA19)
2)	DA of 19 dpc fetuses from dams kept at 100% O2  for three hours prior to cesarian section  (DA 19 O2)
3)	DA of 3 hrs newborn rats (DA3)
4)	Ao of 19 dpc fetuses (Ao19)
5)	 Ao of 3 hrs newborn rats (Ao3)

5 total hybridizations

Hybridization design:

Multiple comparisons among pre-birth DA, post-birth DA, pre-birth Ao and post-birth Ao to identify specific markers for each of these conditions; triple comparison between  artificially oxygenated pre-birth DA and post-birth DA using normal prebirth-DA as reference sample; comparison between pre-birth DA and post-birth DA (supplementary data, table 2); Comparison between pre-birth Ao and post-birth Ao

first: Mario

last: Costa

first: Silvia

last: Barogi

first: Nicholas

last: Socci

first: Debora

last: Angeloni

first: Margherita

last: Maffei

first: Barbara

last: Baragatti

first: Chiara

last: Chiellini

first: Emanuela

last: Grasso


title: DRG from CCI and Seltzer models of neuropathic pain and sham operated animals

status: Public on May 21 2005

city: London

first: Jakir

last: Ullah

country: United Kingdom

institute: Novartis

summary:
L5 DRG samples from CCI, Seltzer and sham models collected at 14, 21 and 50 days after surgery from ipsilateral hind limb.  Note that all replicates are techincal, i.e., there were no biological replicates in this study as samples were pooled for each group
Keywords: ordered


title: Chronic contusion spinal cord injury in rats

status: Public on May 03 2005

first: James

last: Aimone

summary:
Excerpt from a larger study which characterized the transcriptional effects of a spinal cord contusion injury in rats.  This is the data from the almost chronic contusion state (35 days) at the injury site (Thoracic 8) - where we saw significant changes in several areas, including cholesterol metabolism genes.  Other spinal cord areas (rostral, caudal) and time-points (3 hours, 24 hours, 7 days and 35 days) were analyzed as well and are discussed in our paper and at www.crpf.org/microarray.
Keywords = Spinal Cord Injury
Keywords = chronic
Keywords = thoracic
Keywords = cholesterol
Keywords: repeat sample

middle: B

first: Leigh

last: Leasure

first: Victoria

last: Perreau

first: Michaela

last: Thallmair


title: Gene expressing profiling of PC12 cells expressing the FGFR3 mutation responsible for thanatophoric dysplasia type II

status: Public on May 06 2005

last: Apostol

summary:
To investigate signaling pathways activated by FGFR3 mutations through an analysis of altered expression of downstream transcriptional targets, we performed gene expression profiling of stably transfected inducible PC12 cells expressing a chimeric receptor (PFR3) consisting of the extracellular domain of human platelet derived growth factor receptor (PDGFR) and the transmembrane and intracellular domains of human FGFR3 under the control of the zinc inducible metalliothionein promoter.  Cells expressing the wildtype receptor (i.e. zinc induced) were compared to cells expressing the mutant receptor PFR3K650E, which contains the thanatophoric dysplasia type II mutation, K650E.  See PubMed ID for further description of samples.

Keywords = thanatophoric dysplasia
Keywords = FGFR3
Keywords = PC12
Keywords = ERK1/2
Keywords: repeat sample

first: Nakisa

last: Nowroozi

first: Simona

last: Raffioni

first: Tracy

last: Wang

middle: L

first: Ralph

last: Bradshaw

first: Leslie

last: Thompson


title: Portal Hypertension Induced Changes in Mesenteric Artery Gene Expression

status: Public on Apr 12 2005

city: Chicago

first: David

last: Machado-Aranda

state: IL

address: 240 E Huron St. McGaw Pav. #2, Rm 2530

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

summary:
Differential gene expression in small meseteric arteries under sham operated and portal hypertensive conditions
Keywords: ordered

first: Joseph

last: Benoit

first: Hai-Ying

last: Zhang

last: Dean


status: Public on Mar 22 2005

city: Gothenburg

first: Per-Arne

last: Svensson

department: Department of molecular and clinical medicine

country: Sweden

institute: institute of medicine

summary:
Effects of voluntary exercise in rat aorta. Spontaneously hypertensive rats (SHR) performed 5 weeks of voluntary exercise (wheel-cage running). Aortic tissue was collected and samples were pooled (3 aortae/chip). Aortae from running rats were compared to aortae from non-running rats.
Keywords: parallel sample

first: Ulrika

last: Hägg

first: Maria

last: Johansson

first: Julia

last: Grönros

first: Andrew

middle: S

last: Naylor

first: Ingibjörg

last: Jonsdottir

first: Göran

last: Bergström

first: Li-ming

last: Gan


title: High Reproducibility Using Sodium Hydroxide Stripped Long Oligonucleotide DNA Microarrays

status: Public on Feb 23 2005

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary:
Recently, long oligonucleotide (60-70mer) microarrays for two-color experiments have been developed and are gaining widespread use. In addition, when there is limited availability of mRNA from tissue sources, RNA amplification can and is being used to produce sufficient quantities of cRNA for microarray hybridization. Taking advantage of the selective degradation of RNA under alkaline conditions, we have developed a method to “strip” glass-based oligonucleotide microarrays that use fluorescent RNA in the hybridization, while leaving the DNA oligonucleotide probes intact and usable for a second experiment. Replicate microarray experiments conducted using stripped arrays showed high reproducibility, however, we found that arrays could only be stripped and reused once without compromising data quality. The intraclass correlation (ICC) between a virgin array and a stripped array hybridized with the same sample showed a range of 0.90-0.98, which is comparable to the ICC of two virgin arrays hybridized with the same sample. Using this method, once stripped oligonucleotide microarrays are usable, reliable, and should help to reduce costs.
Keywords = Agilent microarray
Keywords = Stripped arrays
Keywords = Replicate reproducibility
Keywords: other

first: Zhiyuan

last: Hu

first: Melissa

last: Troester


title: Gene Microarrays in Hippocampal Aging

status: Public on Jan 10 2005

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary:
Male Fischer 344 rats aged 4 months (young, n=10), 14 months (mid-aged, n=10), and 24 months (aged, n=10) were trained sequentially on two tasks: Morris Spatial Water Maze (SWM) and Object Memory Task (OMT). The training/testing sequence lasted 7 d, and hippocampal tissue was collected 24 hr later. Training and testing occured on each day except for days 2 and 3 of the 7 d sequence.
(01/10/05: Series was updated to correct mislabeling of all sample signal values within the Young Treatment Group)
Keywords = bioinformatics
Keywords = gene expression
Keywords = memory
Keywords = synaptic plasticity
Keywords = myelin
Keywords = inflamation
Keywords = aging
Keywords: repeat sample

first: Kuey-Chu

last: Chen

first: Keith

last: Sharrow

first: James

last: Herman

first: Nada

last: Porter

first: Thomas

middle: C

last: Foster

first: Phillip

last: Landfield


title: Terminal heart failure

status: Public on Jan 03 2005

city: Berlin

first: Maren

last: Wellner

address: Robert-Rössle-Str. 10

country: Germany

summary:
Rats overexpressing the human renin and angiotensinogen genes die after seven weeks of end organ damage. They develop hypertension, heart hypertrophy and proteinuria.We compared terminal heart failure, these are indeed terminally ill to double transgenic animals suffering on hypertension, proteinuria and heart hypertrophy. In addition, Losartan-treated animals (10 mg/kg/d)showed similar physiological parameters (normotension, no proteinuria and no heart hypertrophy compared to control sprague dawley rats.
Keywords: other

first: Ralf

last: Dechend

first: Joon-Keun

last: Park

first: Erdenechimeg

last: Shagdarsuren

first: Nidal

last: Al-Saadi

first: Silke

last: Meiners

first: Torsten

last: Kirsch

first: Anette

last: Fiebeler

first: Hermann

last: Haller

first: Friedrich

last: Luft

first: Dominik

last: Muller


title: Genomic and Phenotypic Evidence for a Causative Role of Calcineurin in the Astrogliosis of Aging and Alzheimer's Disease

first: Eric

last: Blalock

summary:
Micorarray analysis was performed on RNA samples from hippocampal cultures infected with either Ad-aCaN or Ad-LacZ or uninfected. Each sample was applied to its own GeneChip (Rat RG-U34A; n=7-9 chips/group). Chips were then processed and scanned using Agilent Affymetrix GeneArray Scanner. MAS5 was used to determine signal intensity and presence/absence calls for the data.
Keywords = bioinformatics
Keywords = gene expression
Keywords = calcineurin
Keywords = calcium
Keywords = Alzheimer's
Keywords = inflamation
Keywords = Adenovirus
Keywords = astrocytes
Keywords = microarray
Keywords: parallel sample

first: Christopher

last: Norris

first: I

last: Kadish

first: Kuey-Chu

last: Chen

first: Veronique

last: Thibault

first: Philip

first: Susan

middle: D

last: Kraner


title: Rat diaphyseal femoral fracture healing:  Plate fixation vs. intramedullary nail

status: Public on Jan 01 2005

city: Charlotte

first: Ralph

middle: A.

last: Meyer

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

summary:
This is a study of femoral fracture healing in female rats 16 weeks old at fracture to compare intramedullary nailing, screw and plate fixation, and sham surgery.  The sham surgery group received a surgical exposure of the femur, but no fracture, no plate, and no nail.  Samples were collected at 1 day, 3 days, 1 week, 2 weeks, 4 weeks, and 6 weeks after surgery.  Each sample is a pool of RNA from three rats from the same surgery group at the same time point after fracture.  The middle third of the femur was collected with the cortical bone, fracture callus, and marrow elements.  Mid-diaphyseal, simple, transverse fractures were induced by a Gigli saw.  The no fracture sample was a time 0 control collected on the day of surgery from intact rats.
Keywords = rat
Keywords = fracture
Keywords = plate
Keywords = nail
Keywords = time
Keywords = femur
Keywords: time-course

middle: A

first: Martha

first: Daniel

last: Heiner

first: Steven

last: Frick

first: James

last: Fiechtl

middle: F

last: Kellam


title: Hippocampal development in fetal alcohol exposed rats. Perrone-Bizzozero-5R01NS030255-12-3

status: Public on Nov 24 2004

first: Winnie

last: Liang

summary:
Study the effect of fetal alcohol exposure (FAE) on hippocampal development
Compare the pattern of gene expression in the hippocampus of FAE and control rats fed either an isocaloric diet or a normal diet, at post-natal day 5 of development.
FAE will delay the maturation of the hippocampus
Rats were fed one of three diet, a liquid diet with 5% ethanol (FAE group), an isocaloric liquid diet (Isocalorc group) or nomal lab chao (normal group)
Keywords: dose response

first: Nora

middle: I

last: Perrone-Bizzozero


title: Cardiac cells after mechanical stress, ionising radiation or UV

status: Public on Dec 03 2004

city: Little Rock

first: Marjan

last: Boerma

state: AR

address: 4301 West Markham, Slot 725

institute: University of Arkansas for Medical Sciences

summary:
Rationale: During excessive pressure or overload, cardiac cells are subjected to increased mechanical stress. We investigate how the stress response of cardiac cells to mechanical stress can be compared to genotoxic stresses induced by DNA damaging agents.
Methods: Cultures enriched for cardiomyocytes and cultures of fibroblasts were derived from ventricles of neonatal rat hearts. In three independent experiments, both cell cultures were subjected to mechanical stress (cyclic stretch at 60 cycles/min), UV irradiation (10 J/m2), or X-rays (8.5 Gy). Cells were harvested 24 h. after (the onset of) treatment. Total RNA was isolated using an RNeasy® kit (Qiagen). Single stranded cDNA was synthesized from RNA from myocyte-enriched populations (10-14 microgram) and populations of fibroblasts (7.5-14 microgram), using Superscript II reverse transcriptase and T7-oligo(dT)24 primers at 42ºC for 1 h. Double stranded cDNA was obtained by using DNA ligase, DNA polymerase I and RNAse H at 16ºC for 2 h, followed by T4 DNA polymerase at 16ºC for 5 min. cRNA was synthesized from cDNA using the BioArray HighYield® RNA transcript labeling kit (Enzo) in the presence of biotin-labeled CTP and UTP. cRNA was fragmented in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM KAc and 30 mM MgAc, at 94ºC for 35 min. Fragmented cRNA was hybridized to GeneChip RG-U34A arrays (Affymetrix) at 45ºC for 16 h. Arrays were washed and incubated with a streptavidin-phycoerythrin complex. Fluorescent signals were determined with a GeneChip scanner.
Keywords: other

first: Caroline

middle: G

last: Van der Wees

first: Harry

last: Vrieling

first: Peter

last: Svensson

first: Jan

last: Wondergem

first: Arnoud

last: Van der Laarse

first: Leon

last: Mullenders

first: Albert

last: Van Zeeland


title: Comparison of  SNc and VTA dopaminergic neurons. Greene-5P50NS038399-050001

status: Public on Oct 14 2004

summary:
The cardinal clinical features of Parkinson's disease (PD) (rigidity, rest tremor, bradykinesia, and postural instability) result from selective loss of midbrain dopaminergic neurons.  More specifically, dopaminergic neurons in the substantia nigra pars compacta (SNc) are much more susceptible to damage than the adjacent dopaminergic neurons in the ventral tegmental area (VTA).  This dichotomy is not only seen in human Parkinsons disease, but also in many animal models of PD, including administration of the mitochondrial toxin rotenone to rats, which replicates many of the behavioral and neuropathological features of PD.  The factors underlying this selective vulnerability are unknown, but could be related to differences in neuronal circuitry, differences in glial support, or intrinsic differences between the neuronal populations of the two regions.  Elucidation of these factors may lead to a greater understanding of the pathogenesis and treatment of Parkinson's disease.
We will determine gene expression profiles of untreated rat SNc and VTA dopaminergic neurons using laser capture microscopy to obtain region-specific neuronal mRNA.
There are intrinsic differences in gene expression between dopaminergic neurons in the rat SNc and VTA that result in greater susceptibility of SNc neurons to degeneration in experimental parkinsonism.  These differences may be related to dopamine metabolism, oxidative metabolism and stress, protein aggregation, or other unforseen pathways.
We will compare gene expression profiles between SNc and VTA dopaminergic neurons in normal rats.  No treatment or time points will be studied in this experiment.  Animals will be anesthetized, sacrificed by decapitation, and brains frozen on dry ice.  Frozen sections will be collected onto glass microscope slides and rapidly immunostained for tyrosine hydroxylase to identify dopaminergic neurons.  SNc and VTA neurons (approx. 200 per sample) will be isolated using laser capture microscopy.  Total RNA will be extracted and poly-A RNA will be amplified using a modified Eberwine protocol.  aRNA will be sent to the centers for labeling and hybridization to Affymetrix rat U34A arrays.  We have confirmed with the center that our aRNA protocol is compatible with the centers amplification protocols; in fact, it is essentially identical.  We will be providing a two-round amplification product to the center for labeling and hybridization.  We recognize that using RNA after three rounds of amplification  may decrease sensitivity for low copy number transcripts, but favor this approach versus pooling our samples (which are inherently paired) at this point.  We have discussed this point in detail with the center. SNc and VTA samples from eight animals (16 samples total) will be provided to mitigate differences specific to individual animals.  With the assisatnce of the center, paired t-tests will be used to determine differential expression between the two regions.  Permutational t-test analysis and/or Benjamini and Hochberg analysis of expression ratios will be used to protect against multiple comparisons.  Selected differentially expressed genes will be validated on separate tissue samples using quantitative RT-PCR or in situ hybridization.

WARNING: These data are identical to those represented in GEO Series GSE1157.

last: Greene


title: Comparison of rat alveolar epithelial type I cells and type II cells

status: Public on Nov 01 2004

city: San Francisco

first: Leland

last: Dobbs

institute: UCSF

summary:
Comparison of rat freshly-isolated alveolar epithelial type I cells, freshly-isolated type II cells, and type II cells cultured for 7 days
Keywords = rat, alveolar epithelial type I cells, cultured type II cells
Keywords: parallel sample


title: passive avoidance trained rats

status: Public on Dec 01 2004

city: Dublin

first: Niamh

last: O'Sullivan

country: Ireland

institute: University College Dublin

summary:
Gene expression in the rat dentate gyrus following passive avoidance training.
Keywords: time-course

first: Ciaran

middle: M

last: Regan

first: Keith

middle: J

last: Murphy


title: Effect of Diabetes on Retinal Müller Cells

status: Public on Nov 17 2004

city: Boston

first: Chiara

last: Gerhardinger

state: MA

address: 20 Staniford Street

institute: Schepens Eye Research Institute

summary:
Rat Retinal Müller cells from diabetic rats (diabetes duration 6 months) compared to Rat Retinal Müller cells from healthy rats.  Diabetes was induced by streptozotozine.  Diabetic rats were treated with small doses of insulin to prevent catabolism.
Keywords: ordered

first: Paul

last: Grosu


title: Temporal analysis of  P15 hippocampus in kainate-induced seizures. Koh-2K08NS002068-04

city: Phoenix

last: Liang

institute: Translational Genomics

summary:
Early childhood convulsions have been correlated with hippocampal neuron loss in patients with intractable temporal lobe epilepsy. Using  a "two-hit" rat seizure model, we have shown that animals subjected to kainate (KA)- or hypoxia-induced seizures during early postnatal period showed no cell death, yet sustained more extensive neuronal death after second seizures in adulthood. An early life seizure, without causing overt cellular injury, predisposes the brain to the damaging effect of seizures in later life. Cellular and molecular changes that accompany early seizures and that lead to subsequent epileptogenesis and increased susceptibility to seizure-induced neuronal injury, however, remain poorly understood. We propose to investigate age-specific, time-dependent changes in gene expression that may underlie this priming effect of early-life seizures.
We will determine the sequence of gene expression pattern in the hippocampus at various times following KA induced seizures at postnatal day (P) 15.
Previous studies have shown that AMPA receptor subtype of glutamate receptors play a crucial role in the age-specific vulnerability and in the long-term epileptogenic effects of perinatal hypoxia seizures. We found that AMPA receptor antagonists block the increased susceptibility caused by early life seizures to later seizures and seizure-induced brain damage.  We hypothesize that an alteration of AMPA receptor composition is one of many changes caused by early-life seizures that leads to an increase in Ca2+ permeability, which then results in cascade of downstream events and modifies array of gene expression that promote epileptogenesis and susceptibility to neuronal death in later life.
We will examine three time points: 1hr, 72 hr, and 15 days following systemic KA-induced seizures at P15 as we have previously observed structural changes within the hippocampus at these time points. Within an hour of KA seizures, a marked swelling of dendrites, disassembly of dendritic microtubules and glycogen depletion are observed by electron microscopy. Within 5 days, basal dendrites of CA3 hippocampal pyramidal neurons show abnormal spine morphology and decreased branching pattern.  15 days after the seizures, aberrant growth of mossy fibers in the CA3 stratum oriens is observed in animals exposed to KA. Ten hippocampi will be pooled from five animals treated with KA (3mg/kg i.p.) and from five littermate controls injected with PBS. Animals will be decapitated and hippocampi will be rapidly dissected from the brain, flash frozen in liquid nitrogen, and stored at -80C until extraction of total RNA, which will be sent to the center. We will provide 4 tissue samples-2 controls and 2 KA, each a pool of five animals - for each time points. Mixing tissues from multiple rats will normalize single nucleotide polymorphisms and tissue heterogeneity.
Keywords: time-course

first: Sookyong

last: Koh


title: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells: Comparison to Long-Evans Rat SCN

status: Public on Oct 09 2004

city: College Station

first: Gus

middle: John

last: Menger

state: TX

department: Anatomy and Neurobiology

institute: Texas A&M Health Science Center

summary:
To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips.  In this comparison, adult male Long-Evans rats (175-200g; N=45) were housed under a standard 12h light:12h dark photoperiod (LD 12:12; lights-on at 0600 hr). At 1800 hr (circadian time [CT] 12), animals were exposed to constant darkness (DD) and 12 hours later (0600 hr or CT 0), sacrificed under isoflurane anesthesia at 6-hr intervals (N=5) for 48 hours by decapitation using an infrared viewer.  After the eyes were removed in the dark, SCN tissue was immediately dissected under dim light, frozen in liquid nitrogen, and stored at –800C. SCN tissue from individual animals was separately homogenized in TRIzol reagent by aspiration through a 25-gauge needle and then extracted cellular RNA for all animals at each timepoint was pooled into a single sample. RNA samples were subjected to on-column treatment with DNAse-1 to digest genomic DNA and then were stored at –80°C before routine processing for GeneChip analysis.
Keywords: other

first: Kim

last: Lu

first: Terry

last: Thomas

first: Vincent

last: Cassone

first: David

last: Earnest


title: Temporal analysis of  hippocampus in kainate-induced seizures. Koh-7K08NS002068-05-3

first: Winnie

summary:
Mesial temporal lobe epilepsy (MTLE) is the most common medically refractory epilepsy syndrome; kainic acid (KA) induced seizures have been studied as a MTLE model as limbic seizures produced by systemic injections of KA result in a distinctive pattern of neurodegeneration in the hippocampus that resembles human hippocampal sclerosis. In our "2-hit" seizure model, animals subjected to seizures during week 2 of life become more susceptible to seizures later in life and sustain extensive hippocampal neuronal injury after second KA seizures in adulthood. Using high-density oligonucleotide gene arrays, we began to elucidate the molecular basis of this priming effect of early-life seizures and of the age-specific neuroprotection against seizure-induced neuronal injury. We seek to identify target genes for epileptogenesis and cell death by selecting transcripts that are differentially regulated at various times in the P15 and P30 hippocampus.
To screen for and identify candidate genes responsible for epileptogenesis and seizure-induced cell death.
We hypothesize that active process of cell death signaling and long-term synaptic changes leading to chronic epilepsy is mediated by distinct transcriptional responses in mature brain that are different from those in immature brain.
We will select for transcripts that are highly regulated at 1, 6, 24, 72 and 240 hours (h) after KA-induced seizures at P30 compared to P15. These differentially regulated genes will serve as  potential target genes for therapeutic intervention. Highly regulated genes identified in our array analysis will then be confirmed by real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). Causative roles of select genes will be directly tested by gene silencing using RNA interference technology or by gene delivery using viral vectors.
Keywords: time-course


title: Exposure to urban particulate matter (EHC-93)

city: Bilthoven

first: Jeroen

last: Pennings

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: Natl. Inst. Public Health & Environment

summary:
We isolated total lung RNA from spontaneously hypertensive male rats 2–40 h after exposure to reference EHC-93. Three animals were exposed to EHC-93 in saline(10 mg/kg body weight) or saline at each time via intratracheal instillation or no instillation at all. RNA from different times was pooled for array hybridization as indicated.
Keywords: time-course

first: I

last: Kooter

first: J

first: A

last: Opperhuizen

first: F

middle: R

last: Cassee


title: Circadian Profiling of the Transcriptome in Immortalized Rat SCN Cells (3 biological replicates)

status: Public on Oct 08 2004

summary:
To determine whether immortalized cells derived from the rat SCN (SCN 2.2) retain intrinsic rhythm-generating properties characteristic of the SCN, oscillatory properties of the SCN2.2 transcriptome were analyzed and compared to those found in the rat SCN in vivo using rat U34A Affymetrix GeneChips. SCN2.2 cells were expanded in 6-well plates. At 6-hour interval across 2 circadian cycles, cells from single 6-well plates were harvested and pooled for total RNA extraction.
Keywords: other


title: Effect of Age on Fracture Healing in the Rat:  Series 3

status: Public on Oct 06 2004

first: Ralph

last: Meyer

summary:
A study of rat femoral fracture healing in young (6 weeks old at fracture), adult (26 weeks old at fracture), and old (52 weeks old at fracture) rats.  Samples were collected at time of surgery (intact controls) and at 3 days, 1 week, 2 weeks, 4 weeks, and 6 weeks after fracture.  Samples were the mid third of the femoral length including the external callus, cortical bone and marrow elements.  Fracture was stabilized with an intramedullary rod prior to fracture with a Bonnarens and Einhorn device.
Keywords: time-course

first: Martha

middle: H


title: Orotic acid induced fatty liver disease

status: Public on Sep 16 2004

city: Cambridge

first: Julian

last: Griffin

address: Tennis Court Road

department: Biochemistry

institute: University of Cambridge

summary:
A time course of orotic acid induced fatty liver disease. Kyoto and Wistar strain rats were exposed to orotic acid for days 1, 3 and 14. Controls are also included.
Keywords = Wistar
Keywords = Kyoto
Keywords = orotic acid
Keywords: time-course

first: Stephanie

last: Bonney

first: Chris

last: Mann

first: Abdul

last: Hebbachi

first: Geoff

last: Gibbons

first: Carol

last: Shoulders

first: James

last: Scott

last: Nicholson


title: Expression Profiling of DA, COP, and F1(COPxDA) rat left ventricles

status: Public on Sep 30 2004

city: Toledo

first: Justin

last: Ways

state: OH

address: 3035 Arlington Ave.

department: Physiology and Cardiovascular Genomics

institute: Medical College of Ohio

summary:
We used high density oligonucleotide arrays to measure the relative expression levels of ~27,000 probe sets in the left ventricles of inbred rat strains; DA (high performing), Copenhagen (COP, low performing), as well as F1(COPxDA) rats bred from these two strains whose performance was intermediate relative to both parental strains.  DA and COP rats differ for both intrinsic aerobic running capacity (assessed with a treadmill exercise test to exhaustion) and intrinsic cardiac performance (as assessed by the Langendorff-Neeley working heart model). Previous work also showed a strong correlation between intrinsic aerobic running capacity and intrinsic cardiac performance. The inbred rats were maintained under specific pathogen free conditions and had access to pelleted rat chow (diet #5001, Purina Mills, Richmond, IN) and water ad libitim. The rats were housed with a target room temperature and humidity of 22oC and 40%, respectively, and 12:12 hour light dark cycle,with the light cycle occurring in the daytime (6 A.M. – 6 P.M.). The aerobic running capacity of the rats used in this study was assessed using a single week of treadmill endurance running tests, occurring at 11 weeks of age, and the rats were allowed 4 weeks to recover. Rats were killed at 15 weeks of age and their left ventricles were dissected. RNA was isolated by homogenizing the left ventricles of the heart in an ice cold guanidine thiocyanate/phenol solution (Ultraspec, Biotecx Laboratories, Houston, TX), extracted with chloroform and isolated using RNA Tack Resin (Biotecx Laboratories). Total RNA was further purified by ethanol precipitation and absorption to a column (RNeasy, Qiagen, Valencia, CA). Double-stranded cDNA was synthesized from 15 micrograms total RNA from each rat (four rats per strain) using reverse transcriptase (SuperScript II, InVitrogen, Carlsbad, CA) and T7-(dT)24 as the oligonucleotide primer. Biotinylated cRNA was synthesized using a kit (Enzo Bioarray High Yield RNA transcript Labeling Kit, Enzo Diagnostics, Farmingdale, NY) according to the manufacturer’s instruction and cRNAs were purified on columns (RNeasy mini kit, Qiagen). Each cRNA was fragmented according to the protocol in the Affymetrix GeneChip Expression Analysis manual and their quality was assessed by hybridization of a 5 microgram aliquot to a test chip (TestChip3, Affymetrix). 15 micrograms of the probe was hybridized to each of a set of three rat GeneChips (U34A, B, and C; Affymetrix). Hybridization, washing, staining with streptavidin-phycoerythrin, and scanning were performed at the Medical College of Ohio Core Facility according to the manufacturer's (Affymetrix) instructions. Complete transcription and hybridization were validated with bacterial sequences as an external control and several housekeeping genes as an internal control. Absolute analysis of data were conducted using the default settings of the Affymetrix software (GeneChip Software MAS-5.0).  Microarray images were scaled to an average hybridization intensity of 150 to normalize the signals between individual chips.
Keywords = quantitative real-time RT-PCR
Keywords = insulin receptor substrate 2 (Irs2)
Keywords = phosphatidylinositol 3-kinase
Keywords = regulatory subunit 1
Keywords = (Pik3r1)
Keywords = endurance running
Keywords = treadmill running
Keywords: parallel sample

first: Soon

last: Lee

first: John

last: Barbato

first: Krista

last: Pettee

last: Essig

last: Weaver

first: Sarah

last: DeRaedt

first: Siming

last: Yang

first: Lauren

last: Koch

first: George

middle: T

last: Cicila


title: Genomics of preconditioning

status: Public on Jul 30 2004

city: Zurich

first: Michael

last: Zaugg

address: Raemistrasse 100

department: Anesthesiology

country: Switzerland

institute: Anesthesiology, University Hospital Zurich

summary:
Isolated perfused rat hearts exposed to isoflurane or ischemic preconditioning, a subgroup followed by 40 minutes of ischemia and 3 hours of reperfusion. Exact protocol available from the authors.
Keywords = preconditioning
Keywords = anesthetics
Keywords = ischemia/reperfusion
Keywords: other

first: Rafaela

last: da Silva

first: Eliana

last: Lucchinetti

first: Thomas

last: Pasch

first: Marcus

last: Schaub


title: Exercise induced cardiac hypertrophy

status: Public on Jul 12 2004

city: Copenhagen

first: Claes

last: Strøm

address: 20, Juliane Mariesvej

department: Department of Medicine B

country: Denmark

institute: H:S Rigshospitalet, University of Copenhagen Medical School

summary:
Cardiac hypertrophy was induced by treadmill running. Sedentary animals served as controls. Gene expression was determined by Affymetrix RGU34A GeneChip's to identify genes with differential expression in an adaptive model of cardiac hypertrophy.
Keywords: other


title: Effect of Angiotensin II on gene expression in SHRSP cerebral microcapillaries

status: Public on Aug 31 2004

city: Hannover

first: Torsten

last: Kirsch

institute: Medical School Hannover

summary:
Renin-angiotensin system (RAS) inhibition reduces stroke and improves brain capillary integrity in stroke prone spontaneously hypertensive rats (SHRSP). We tested the hypothesis that treatment with an angiotensin II receptor subtype 1 (AT1R) antagonist has different effects, compared to an angiotensin converting enzyme (ACE) inhibitor, on gene expression in blood-brain barrier (BBB) capillaries. Six weeks old SHRSP were treated with either olmesartan (4 mg/kg, n=20), lisinopril (6 mg/kg , n=20) or remained untreated (n=20). Blood pressure was controlled by tail-cuff measurement. After 5 weeks the animals were sacrificed and cerebral capillaries were isolated. mRNA was extracted and analyzed with rat GeneChip DNA arrays. Additionally, brain histology and monocyte/macrophage infiltrates were determined. Both treatments similarly reduced neurological signs of stroke, stroke mortality, and monocyte/macrophage infiltration, compared to controls. Blood pressure was not influenced significantly by both drugs. We found 42 transcripts that were regulated by both treatments in the same manner. These genes were mostly related to inflammation. We also observed 39 differentially expressed genes between the two treatment groups that typically contribute to cell growth and differentiation. This study demonstrates that, despite similar effects on cerebral pathology and outcome, ACE inhibition and AT1R blockade have distinct molecular effects on gene expression in BBB capillaries.
Keywords = angiotensin II
Keywords = gene expression
Keywords = microarrays
Keywords = brain capillaries
Keywords = SHRSP
Keywords = olmesartan
Keywords = lisinopril
Keywords: other

first: Maren

last: Wellner

first: Faikah

last: Gueler

first: Joon-Keun

last: Park

first: Michaela

last: Beese

first: Hermann

last: Haller

first: Andrea

last: Lippoldt


title: Expression profiling of fast glial cells

status: Public on Sep 01 2004

city: Muenster

first: Lars

last: Tatenhorst

address: Domagkstr. 19

institute: Institute of Neuropathology

summary:
Identification of genes mediating glioma invasion promotes the understanding of glia motility and might result in biologically based therapeutic approaches. To evaluate migration mechanisms operating in vitro versus in vivo, we used C6 rat glioma cells for selecting highly migratory cells in a monolayer migration assay (C6) as well as in brains of nude mice (C6SPGFP), and analyzed in each paradigm the expression profiles of these "fast" cells versus those of the original "slow" cells.
Keywords: other

first: Sylvia

last: Püttmann

first: Volker

last: Senner

first: Werner

last: Paulus

last: Püttmann-Cyrus


title: Comparison of renal transcript levels in Dahl Salt-sensitive (S) rat with S.R congenic rat containing a BP QTL

status: Public on Sep 20 2004

first: Bina

last: Joe

summary:
Kidney samples from three Dahl Salt-sensitive S rats were compared with kidney samples from three S.R(9)x3A congenic rats.
Keywords = Blood Pressure
Keywords = Quantitative trait locus
Keywords = QTL
Keywords = hypertension
Keywords = rat
Keywords = congenic
Keywords: parallel sample


title: ischemic tolerance time course

status: Public on May 05 2004

city: Meguro-ku

first: Makoto

last: Kano

state: Tokyo

address: 4-6-1 Komaba

country: Japan

institute: Research Center for Advanced Science and Technology, University of Tokyo

summary:
Comparison of time-series gene expression pattern in hippocampus of hypoxia tolerant or sensitive rats. At 12 time-points ({0h, 1h, 3h, 12h, 24h, 48h} x 2) after ischemia operation, microdissected CA1 regions of the two groups were respectively subjected to oligonucleotide-based microarray analysis. MIAME information can be obtained at the web link.
Keywords = Rattus norvegicus
Keywords = hippocampus
Keywords = ischemic tolerance
Keywords: time-course

first: Kano

last: Makoto

first: Tsutsumi

last: Shuichi

first: Kawahara

last: Nobutaka

first: Wang

last: Yan

first: Mukasa

last: Akitake

first: Kirino

last: Takaaki

first: Aburatani

last: Hiroyuki


title: retina injury timecourse

status: Public on Mar 29 2004

city: Memphis

first: Eldon

middle: E

last: Geisert

institute: University of Tennesse

summary:
Sprague-Dawley rat retina post-injury and control samples
Keywords = Gliosis, CNS injury

first: Felix

last: Vazquez-Chona

first: Bruce

middle: K

last: Song


title: age-related changes in neonatal rat spinal cord

status: Public on Mar 25 2004

city: Stony Brook

first: Lorne

last: Mendell

state: NY

department: Neurobiology & Behavior

institute: Stony Brook University

summary:
we compared L4-L6 section of spinal cord in 2 days old and 12 days old rat
Keywords: parallel sample

first: Victor

middle: L

last: Arvanian


title: Comparison between aortic and endocardial endothelial cells expression profiles

status: Public on Jun 17 2004

city: Antwerp

first: Jan

last: Hendrickx

address: Groenenborgerlaan 171

department: Pharmacology

country: Belgium

institute: University of Antwerp

summary:
Endocardial (EE) and Aortic (AE) endothelial cells were isolated from the same two rats, pooled (EE and AE kept separately) and cultured for 2 passages. Culture conditions and confluence of EE and AE cell cultures were kept as identical as possible. RNA was isolated and the expression profile of both endothelial cell types was compared using the Affymetrix rat genome U34A array.
Keywords: parallel sample

first: Kris

last: Doggen

first: Ellen

last: Weinberg

first: Pascale

last: Van Tongelen

first: Paul

last: Fransen

first: Gilles

last: De Keulenaer


title: Rat models of cardiac hypertrophy

status: Public on Mar 12 2004

first: Claes

last: Strøm

summary:
Cardiac hypertrophy was induced by aortic banding (6, 12, 16, and 30 weeks), myocardial infarction (3 and 9 weeks), an av-fistula (aorta abd. to v. cava inf.. 3 and 8 weeks), or hormone infusion (two weeks either angiotensin 2 or a thyroxin analogue). Sham operated or saline infused animals served as controls. Gene expression was determined by Affymetrix RGU34A GeneChip's to identify genes with common regulation in the different models of cardiac hypertrophy.
Keywords: other


title: EOM and hindlimb muscle development

status: Public on Apr 01 2004

city: Cleveland

first: Henry

middle: J.

last: Kaminski

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

summary:
Conserved and muscle group-specific gene expression patterns shape postnatal development of the novel extraocular muscle phenotype.  Comparison of postnatal development of extraocular and hindlimb muscle between birth and P45.
Keywords: parallel sample

first: Georgiana

last: Cheng

first: Anita

middle: P

last: Merriam

first: Bendi

last: Gong

first: Patrick

last: Leahy

first: Sangeeta

last: Khanna

first: John

last: Porter


title: Hindlimb unloading alters wound healing in ligaments

status: Public on Mar 10 2004

city: Houston

first: Steven

last: Strasnick

address: 369 Science and Research Bldg. II

department: Dept. of Biology and Biochemistry

institute: University of Houston

summary:
A recent physiological study established that hindlimb unloading of rats at 3 and 7 weeks inhibits healing of injured ligaments, resulting in a badly aligned, discontinuous collagen matrix. Using tissue from these rats, we focused on the 3-week time point employing microarray analysis to identify what cellular processes or lack of processes could account for these observed deficiencies. We used the Afyymetrix RG_U34A GeneChip and performed image analysis with Microarray Suite 5.0. For normalization we used the MAS global normalization protocol with a default target mean signal of 500. Gene expression in medial collateral ligament tissue under 4 different treatment conditions was measured: loaded control, loaded wound healing, unloaded control, and unloaded wound healing. From our results, it appears that unloaded tissue lags behind loaded tissue in its progression through the healing process and at 3 weeks is still engaged in the proliferative phase, whereas loaded tissue is actively remodeling its collagen matrix.

Summary tables below: Affymetrix MAS comparative analysis data for the 1778 genes qualified for further analysis as a result of detection call values.
Keywords: other

first: Daniel

last: Martinez

first: Pachiappan

last: Manickam

first: Richard

last: Grindeland

first: Charles

last: Wade


title: Dietary salt and renal function

status: Public on Feb 14 2004

city: Chicago

first: Bryan Angelo

last: Roxas

address: 900 S. Ashland Ave.

institute: University of Illinois at Chicago

summary:
Serum and glucocorticoid-induced kinase 1 (SGK1) activates the epithelial sodium channel (eNaC) in tubules. We examined renal SGK1 abundance in salt-adaptation and in salt-sensitive hypertension. Sprague-Dawley and Dahl salt-sensitive rats were placed on either 8% or 0.3% NaCl diets for 10 days. Plasma aldosterone levels were approximately 2.5-fold greater on 0.3% versus 8% NaCl diets in both rat strains. Both serum and glucocorticoid-induced kinase 1 transcript and protein abundance were less (P<0.01) in Sprague-Dawley rats and greater (P<0.01) in Dahl salt-sensitive rats on 8% versus 0.3% NaCl diets. The cDNA sequences of serum and glucocorticoid-induced kinase 1 in both strains of rat were the same. The present results provide evidence that the abundance of serum and glucocorticoid-induced kinase 1 in rat kidney may play a role in salt adaptation and the pathogenesis of hypertension and suggests that aldosterone is not the primary inducer of SGK1 in the Sprague-Dawley rat.
Keywords = Rattus norvegicus, Sprague Dawley, Dahl SS/Jr, kidney, NaCl diet
Keywords: other

first: M

last: Farjah

first: B

first: D

last: Geenen

first: R

middle: S

last: Danziger


title: Comparison of microarray to RT-PCR

status: Public on Feb 01 2004

city: Charlotte

first: Ralph

middle: A.

last: Meyer

institute: Carolinas Medical Center

summary:
mRNA used for the analysis of these microarrays were previously analyzed for 34 genes by reverse transcription - polymerase chain reaction in Desai BJ et al., J.Orthop.Trauma 17: 689-698, 2003.  These two data sets were subsequently studied to compare the results from these two different methods for mRNA quantitation.  The comparison was publised in "Comparison of mRNA gene expression by RT-PCR and DNA microarray" by W. Etienne, M.H. Meyer, J. Peppers, and R.A. Meyer, Jr., BioTechniques 36 (4): 618-626, April 2004.
Keywords = rat
Keywords = fracture
Keywords = age
Keywords = time
Keywords = femur
Keywords = RT-PCR
Keywords: time-course

first: Martha

first: Wiguins

last: Etienne

first: Bhaloo

last: Desai

first: Johnny

last: Peppers


title: Effect of Age on Fracture Healing in the Rat

status: Public on Jan 10 2004

summary:
mRNA gene expression was measured in intact female Sprague-Dawley rats at 6 (young), 26 (adult) and 52 (older) weeks of age at the time of fracture. Samples were collected at 0, 0.4, 1, 2, 4, and 6 weeks after fracture. RNA from two rats were pooled for each Affymetrix Rat U34A array.  Mid-shaft, simple, transverse left femoral fractures were induced after retrograde intramedullary rod fixation with a Bonnarens and Einhorn device.  Samples were collected from one third of the femoral length, centered on the fracture site, including the external callus, cortical bone, and marrow elements.
Keywords = rat
Keywords = fracture
Keywords = age
Keywords = time
Keywords = femur
Keywords: other

middle: A


title: Transcriptome analysis in rat

status: Public on Jan 27 2004

city: San Diego

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
Large scale transcriptome analysis of Wistar and Sprague Dawley rat tissues.
Keywords: other

first: Andrew

last: Su

first: David

middle: W

last: Self

middle: B

last: Hogenesch

first: Hilmar

last: Lapp

first: Rainer

last: Maier

last: Hoyer

first: Graeme

last: Bilbe


title: Effect of Age on Fracture Healing in the Rat:  Series 2

summary:
Study of rat femur fracture healing in young (6 weeks old), adult (26 weeks old), and older (52 weeks old) rats with samples collected at 0 time (no fracture) and at 0.4, 1, 2, 4, and 6 weeks after fracture.  RNA from two rats were pooled for each array.
Keywords = rat, femur, fracture, age, time
Keywords: time-course


title: Effect of Age on Fracture Healing in the Rat:  Series 1

summary:
mRNA gene expression was measured in rats at 6 (young), 26 (adult) and 52 (older) weeks of age at the time of fracture.  Samples were collected at 0, 0.4, 1, 2, 4, and 6 weeks after fracture.  RNA from two rats were pooled for each Affymetrix Rat U34A array.
Keywords = rat
Keywords = fracture
Keywords = age
Keywords = time
Keywords = femur
Keywords: time-course


title: MastomysRat

status: Public on Jan 07 2004

city: New Haven

first: Mark

last: Kidd

state: CT

address: 333 Cedar Street

department: Surgery

institute: Yale University School of Medicine

summary:
Analysis of gene expression in an enriched ECL cell population from the agstric mucosa of Mastomys treated with Loxtidine for 8-16 weeks, and from an animal that spontaneously developed an ECL cell carcinoid
Keywords = ECL Mastomys Affymetrix Carcinoid Gene
Keywords: other

first: Toshinori

last: Hinoue

first: Kevin

middle: D

last: Lye

first: Yi

last: Wen

first: Irvin

last: Modlin


title: Physiologic cardiac hypertrophy

status: Public on Oct 24 2003

first: Martina

last: Schinke

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

institute: Harvard University

summary:
Dahl salt-sensitive (DS) rats were obtained from Harlan Sprague Dawley Laboratory at 5 weeks of age. At 6 weeks of age, physiologic cardiac hypertrophy was generated by a
vigorous daily exercise regimen for 6 weeks (e group). The exercise protocol is based on those described previously with modifications (Wisloff U et al., 2001; Jin H et al., 1994). Rats were exercised daily for 6 weeks on a rodent treadmill (Exer-6M; Columbus Instruments). The exercise program consisted of three weeks of progressively strenuous exercise regimens; followed by three weeks of maintenance period, during which the rats were exercised at 16 m/min at a 5o incline for 90 minutes/day. All rats completed the exercise protocol. Pathological cardiac hypertrophy was generated by feeding a 6% NaCl diet to DS rats at 6 weeks of age (h group) (Inoko M et al., 1994). Control rats (c group) were age matched and sedentary DS rats fed normal rat chow.
Read more at http://cardiogenomics.med.harvard.edu/groups/proj1/pages/rat_home.html
Keywords: other

first: Peter

last: Kang

first: Jeffrey

last: Brown

first: Seigo

last: Izumo


title: Control LG vs Px LG

status: Public on Nov 30 2003

city: New Orleans

first: Doan

last: Nguyen

state: LA

institute: LSU Eye Center/LSUHSC

summary:
Control rat lacrimal gland samples representing a normal unoperated, a sham, and paired contralateral controls. Experimental LG samples representing paired and unpaired contralateral controls.  Paired contralateral control LGs represent LG from the same animal, one side was operated and the other side unoperated.
Keywords: repeat sample

first: Hiroshi

last: Toshida

first: Jill

last: Schurr

first: Roger

last: Beuerman

first: Beuerman

last: Roger


title: Allylamine Dose Response

status: Public on Sep 02 2003

city: Louisville

first: Kenneth

middle: S.

last: Ramos

department: Biochemistry and Molecular Biology

institute: University of Louisville School of Medicine

summary:
Response to Oxidative Stress via administration of Allylamine
Keywords: dose response

first: Charles

last: Partridge

first: Mahalet

middle: G

last: Tadesse

last: Johnson

first: Kim

last: Lu


title: Expression Profiles of Rats Treated with Clofibric Acid: Comparison of Whole and Laser Capture Microdissected Liver

status: Public on Dec 03 2003

city: Vitry sur Seine

first: Cecile

last: Michel

address: 13, quai Jules Guesdes

department: Drug Safety Evaluation

country: France

institute: Aventis Pharma France

summary:
This is an evaluation of the impact of the successive steps of LCM procedure on gene expression profiling by comparing profiles from LCM samples to those obtained with non-microdissected liver samples collected after a one month CLO treatment in the rat. We showed that the H&E staining used for identifying PP-foci and the laser microdissection itself do not impact on RNA quality.
Keywords = Microdissection
Keywords = Clofibric Acid
Keywords: other

first: Chantal

last: Desdouet

first: Beatrice

last: Sacre-Salem

first: Jean-Charles

last: Gautier

first: Ruth

last: Roberts

first: Eric

last: Boitier


title: Kidneys of Dahl salt sensitive rats

status: Public on Aug 20 2003

city: Montreal

first: Alan

middle: Y

last: Deng

country: Canada

institute: Research Centre-CHUM

summary:
Gene expression profiling of kidney tissue from 5 week old Dahl salt sensitive rats and congenic strain of Chr.10 Dahl salt sensitive rats.
Keywords: other


title: Syracuse High/Low Avoidance Learning in Rats

status: Public on Dec 31 2003

city: Dallas

first: Shumin

last: Zhang

institute: UT Southwestern

summary:
Comparisons of hippocampi of Syracuse High Avoidance (SHA) and Syracuse Low Avoidance (SLA) learning rats
Keywords: other

first: Tara

last: Amstein

first: F Robert

last: Brush

first: Howard

last: Gershenfeld


title: Halothane/Isoflurane Repetitive Exposures

status: Public on Oct 20 2003

city: Philadelphia

first: Roderic

last: Eckenhoff

state: PA

institute: University of Pennsylvania

summary:
Rats were exposed to 90 minutes of 0.8% halothane or 1.0% isoflurane twice a day for a total of 5 or 10 exposures. Animals did not require intubation.  All exposures and hybridizations were performed at the Univ. of Pennsylvania.
Keywords = anesthetics
Keywords: other

first: Maryellen

middle: F

first: James

last: Hecker


title: Halothane Repetitive Exposure

status: Public on Jun 26 2003

summary:
12 Controls, 3 5-exposures, 3 10-exposures. Rats were exposed to 90 minutes of 0.8% halothane twice a day for a total of 5 or 10 exposures. Animals did not require intubation. All exposures and hybridizations were performed at the Univ. of Pennsylvania.
Keywords: time-course


title: Effect of age on skeletal  muscle

status: Public on Sep 05 2003

city: Columbia

first: Scott

last: Pattison

state: MO

institute: University of Missouri

summary:
Comparison of gene expression in young soleus muscle (3-4 months) with old soleus muscle (30-31 months).
Keywords: parallel sample

first: J

first: T

last: Childs

first: L

middle: C

last: Folk

first: R

last: Madsen

first: F

last: Booth


title: Isoflurane Repetitive Exposure

summary:
12 Controls, 3 5-exposures, 3 10-exposures. Rats were exposed to 90 minutes of 1.0% isoflurane twice a day for a total of 5 or 10 exposures. Animals did not require intubation. All exposures and hybridizations were performed at the Univ. of Pennsylvania.
Keywords: time-course


title: Isoflurane Single Exposures

summary:
3 controls, 2 1-hr exposure, and 3 2-hr exposure. RNA extractions and microarray hybridization were performed at the University of of California, Davis. Male Sprague Dawley rats were used in this study and were intubated during the exposures.
Keywords = Eckenhoff
Keywords = anesthetics
Keywords: time-course

first: Uta

last: Jenny

first: Leon

last: Hall


title: Gene expression in follicle-stimulating hormone-treated rat Sertoli cells

status: Public on Jul 16 2003

city: Pullman

first: Derek

middle: J

last: McLean

state: WA

department: School of Molecular Biosciences

institute: Washington State University

summary:
Spermatogenesis requires the presence of functional somatic Sertoli cells in the seminiferous tubules of the testis. Sertoli cells provide support and factors necessary for the successful progression of germ cells into spermatozoa. Sertoli cells are regulated to a large degree by the glycoprotein hormone FSH, which is required for the testis to acquire full size and spermatogenic capacity. Signaling events initiated by the binding of FSH to its receptor lead to an alteration of Sertoli cell gene expression. To characterize the changes in gene expression in FSH-treated Sertoli cells, we used the mRNA from these cells to screen Affymetrix U34A rat GeneChip oligonucleotide microarrays. Sertoli cells from 20-d-old rats were cultured in the presence of 25 ng/ml ovine FSH. At 0, 2, 4, 8, and 24 h after the addition of FSH, total RNA was purified and used to prepare biotinylated target, which was hybridized to the U34A rat microarray containing approximately 9000 rat genes. Analysis identified 100-300 transcripts at each time point that were up-regulated or down-regulated by 2-fold or greater. Genes previously reported to be FSH or cAMP regulated in rat Sertoli cells were identified, in addition to numerous genes not reported to be expressed or FSH regulated in Sertoli cells. The expression patterns of five of these genes, encoding nerve growth factor inducible gene B, PRL-1, PC3 nerve growth factor-inducible antiproliferative putative secreted protein, diacylglycerol acyltransferase, and an expressed sequence tag, in FSH- and N,O'-dibutyryl cAMP-treated rat Sertoli cells were confirmed and characterized by Northern blot analysis. Thus, we have begun to define the transcriptome induced and repressed by FSH in rat Sertoli cells, and we have generated datasets of genes available for further analysis in regard to spermatogenesis and Sertoli cell signaling.
Keywords: other

first: Patrick

last: Friel

last: Pouchnik

first: Michael

last: Griswold


title: Colon carcinoma cell line CC531 response to butyrate and aspirin

status: Public on May 19 2003

city: Heidelberg

first: Anja

last: Germann

department: Department of Pathology

institute: University Heidelberg

summary:
Temporal analysis of colon carcinoma cell line CC531 response to 4.5 mM butyrate or 3 mM aspirin. Samples taken at 2, 6, 12, 16 and 24 hours.

The CC531 cell line has been widely used to study different aspects of tumor growth and metastasis and provides an excellent experimental platform to develop novel antitumor strategies. To characterize the CC531 model at the molecular level, we screened for mutations in genes covering important signal-transduction pathways that are known to play major roles during colon carcinogenesis, the wnt and the ki-ras signaling pathways. We found both a prototypic beta-catenin (Ctnnb1) mutation (Thr(41)Ile) and a ki-ras (G12D) mutation, providing unambiguous evidence for the constitutive activation of these pathways in CC531 cells. We further established comprehensive gene expression profiles of CC531 cells and investigated the molecular response to 2 antitumor drugs, butyrate and aspirin. Using oligonucleotide microarrays, we screened the expression levels of 7,700 genes and identified a total of 398 genes whose expression was significantly changed upon treatment with butyrate. When using aspirin, 121 genes were significantly altered. Interestingly, 36 genes were regulated by both butyrate and aspirin and 35 of them were regulated in the same direction. We found 7 differentially expressed genes, cyclin D1, cyclin E, c-myc, Fosl1, c-fos, Cd44 and follistatin, which are known targets of the beta-catenin and/or the ras pathway. In all cases, butyrate and aspirin reversed the changes in expression normally found in response to active signaling of these oncogenic pathways.
Keywords: other

first: A

first: S

last: Dihlmann

first: M

last: Hergenhahn

last: von Knebel Doeberitz

last: Koesters


title: Skin irradiation and vitamin A supplements

status: Public on Mar 20 2003

city: New York

first: Fredric

last: Burns

address: 550 First Ave.

department: Environmental Medicine

institute: NYU School of Medicine

summary:
Analysis of gene expression in skin of rats subjected to electron irradiation and the effect of vitamin A supplements.
Keywords: other


title: Aging in rat heart

status: Public on Aug 28 2003

city: Boston

first: Richard

middle: E.

last: Pratt

address: 75 Francis Street

department: Medicine

institute: Brigham and Women's Hospital

summary:
Myocardial aging leads to a reduction of beta-adrenergic receptor-induced metabolic and contractile responsiveness. We hypothesize that a change in the patterns of gene expression is important in these age-related events. To test this, hearts were harvested from young and aged male rats (3-4 and 20-22 mo, respectively). Total mRNA was extracted and prepared for hybridization to Affymetrix U34A GeneChips. Filtering criteria, involving fold change and a statistical significance cutoff were employed, yielding 263 probe pairs exhibiting differential signals. Of the 163 annotated genes, at least 56 (34%) were classified as signaling/cell communication. Of these 56, approximately half were directly involved in G protein-coupled receptor signaling pathways. We next determined which of these changes might be involved in anti-adrenergic activity and identified 19 potentially important gene products. Importantly, we observed a decrease in beta1-adrenergic receptor and adenylyl cyclase mRNAs, whereas the mRNA encoding beta-arrestin increased. Furthermore, the results demonstrate an increase in mRNAs encoding the adenosine A1 receptor and phospholipase D, which could increase anti-adrenergic effects. Moreover, the mRNAs encoding the muscarinic M3 receptor, nicotinic acetylcholine receptor beta3, and nicotinic acetylcholine receptor-related protein were increased as was the mRNA encoding guanylate kinase-associated protein. Interestingly, we also observed eight mRNAs whose abundance changed three- to sixfold with aging that could be considered as being compensatory. Although these results do not prove causality, they demonstrate that cardiac aging is associated with changes in the profiles of gene expression and that many of these changes may contribute to reduced adrenergic signaling.
Keywords = aging
Keywords = heart
Keywords: other

first: James

last: Dobson

first: John

last: Fray

first: Jack

last: Leonard


title: Cocaine Study

status: Public on Mar 13 2003

city: Pittsburgh

first: Rajan

last: Munshi

address: W1041 Biomedical Science Tower, 200 Lothrop Street

department: Center for Computational Biology and Bioinformatics

institute: University of Pittsburgh School of Medicine

summary:
The 10 samples below represent a study where gene expression levels were measured in 5 different parts of the rat brain under cocaine-treated (GSM4696, GSM4698 - GSM4701) and saline-treated control (GSM4702 - GSM4706) conditions. The regions studied were amygdala (amy), caudate putamen (cpu), nucleus acumbens (na), prefrontal cortex (cpu), and the ventral tegmental area (vta). The data were analyzed using two different computational techniques, viz. singular value decomposition (SVD) and self-organizing maps (SOM), to identify a common set of genes that were regulated by cocaine administration.
Keywords = cocaine
Keywords = oligonucleotide microarrays
Keywords = svd
Keywords = som
Keywords: repeat sample

first: Ozlem

last: Keskin

first: Chunyan

last: Xu

first: Peter

last: Silverman

first: David

last: Peters

first: Robert

middle: E

last: Ferrell

first: Ivet

last: Bahar


title: Rat muscle tissue group comparisons (skeletal-extraocular, skeletal-hindlimb, smooth-stomach, and cardiac; Porter lab)

status: Public on Apr 02 2003

city: Cleveland

first: Sangeeta

last: Khanna

institute: Case Western Reserve University

summary:
Comparison of normal adult rat extraocular muscle, cardiac muscle, leg (gastrocnemius-soleus) muscle and smooth muscle (stomach wall).  Affymetrix microarray chip RG-U34A was used. MAS version 5 was used to analyze the muscle group differences.  Data form part of publication: FASEB Journal 17: 1370-1372, 2003 (full length article available at http://www.fasebj.org/cgi/doi/10.1096/fj.02-1108fje).
Keywords: other

first: J

last: Porter

last: Merriam

first: P

last: Leahy

first: B

last: Gong