title: Differential gene expression between WT and ERRa-null hearts

status: Public on Mar 08 2007

city: Montréal

first: Vincent

last: Giguère

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

summary:
Total RNA was isolated from 3 WT and 3 ERRa null hearts and independent hybridizations were performed using MOE430 2.0 microarrays. Expression profiling was conducted to determine changes in gene expression in hearts lacking ERRa. The expression of genes involved in heart and muscle development, muscle contraction, lipid metabolism, OxPhos, protein metabolism and transcription were affected by the loss of ERRa.
Keywords: microarray and genetic modification

overall_design: 3 hearts from WT and 3 hearts from ERRa-null mice were used in the study. The expression of genes in the ERRa KO hearts were compared to the reference WT hearts.

first: Catherine

middle: R

last: Dufour

first: Brian

last: Wilson


title: Embryonic Ovary Developmental Time Course

status: Public on Feb 05 2007

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

country: USA

institute: Washington State University

summary:
Time course of gene expression in the murine embryonic ovary from the time of the indifferent gonad (11.5dpc) to birth (18.5dpc)
Keywords: Time course

overall_design: Independent embryonic ovary preps were used for array analysis. Duplicates were provided for each sample.

first: Christopher

middle: L

last: Small

first: Michael

middle: D

last: Griswold


title: Gene expression in the mouse brain during spontaneous sleep and prolonged wakefulness

status: Public on Feb 11 2007

city: Philadelphia

first: Miroslaw

last: Mackiewicz

state: PA

address: 2124 TRL 125S 31st Street

department: Medicine

institute: University of Pennsylvania

summary:
These studies address temporal changes in gene expression during spontaneous sleep and extended wakefulness in the mouse cerebral cortex, a neuronal target for processes that control sleep; and the hypothalamus, an important site of sleep regulatory processes. We determined these changes by comparing expression in sleeping animals sacrificed at different times during the lights on period, to that in animals sleep deprived and sacrificed at the same diurnal time.
Keywords: gene expression, temporal changes, brain, behavior, sleep,

overall_design: Experiments were performed on male mice (C57/BL6), 10 weeks of age ±1 week. Animals were housed in a light/dark cycle of 12 hrs, in a pathogen free, temperature- and humidity-controlled room (22°C and 45-55%, respectively) with water available ad libitum. Food was accessible for 12 hrs only during the active period. Animals were subjected to 14 days of acclimatization during which a nighttime feeding pattern was established. This was done to avoid differential food intake between mice that were subsequently sleep deprived during the lights on period and those allowed to sleep.  Mice were sacrificed following 3, 6, 9 and 12 hrs of total sleep deprivation (n=5 at each time point). Deprivation was initiated at lights-on, and performed through gentle handling. Sleeping animals, which were left undisturbed, were sacrificed at the same diurnal time points as sleep deprived mice (n=5 at each time point). An additional control group of mice were sacrificed at time zero, i.e., at the time of lights-on (n=5). All mice were behaviorally monitored using the AccuScan infrared monitoring system that detects movement when the mouse crosses electronic beams (Columbus Instruments).  Mice were sacrificed by cervical dislocation. Brain sectioning was performed according to the mouse brain atlas of Franklin and Paxinos . The primary and secondary motor areas (M1 and M2) of the cerebral cortex and broadly defined regions and zones of the hypothalamus were sampled. RNA was isolated with Trizol (Invitrogen) and further purified using RNeasy columns (Qiagen) as per the manufacturer's instructions.

first: M

first: K

last: Shockley

middle: A

last: Romer

first: R

middle: J

last: Galante

first: J

middle: E

last: Zimmerman

first: N

last: Naidoo

first: D

last: Baldwin

first: S

middle: T

last: Jensen

first: G

last: Churchill

first: A

middle: I

last: Pack


title: Embryonic Testis/Ovary Developmental Time Courses

status: Public on Jan 31 2007

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

overall_design: Refer to individual Series


title: Gene expression profiles of P1 ureter isolated from SMGA (Actg2) transgenic mice. (GUDMAP Series ID: 14)

status: Public on Feb 08 2007

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

summary:
The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing urogenital tract.  The central thesis is straightforward. The combination of microdissected and laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of postnatal day 1 ureters.
Keywords: Gene expression analysis of the postnatal day 1 mouse ureter

overall_design: Ureters were isolated from postnatal day 1 SMGA/EGFP transgenic mice and RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

first: James

last: Lessard

first: John

middle: C

last: Szucsik


title: Expression data from wild type (wt) and Ikbke knockout (Ikke) embryonic fibroblasts (EF)

city: Cambridge

first: Benjamin

middle: Robert

last: tenOever

state: MA

address: 7 Divinity Avenue

department: MCB

institute: Harvard University

summary:
WT and Ikbke-/- EF cells were stimulated with recombinant interferon beta for 6 hours.  Cells lacking IKKe kinase show a defect in a subset of interferon stimulated gene transcription
Keywords: comparative study

overall_design: WT and Ikbke cells were either stimulated and left untreated to compare their response to interferon.

first: Sze-Ling

last: Ng

first: Mark

last: Chua

first: Sarah

last: McWhirter

first: Adolfo

last: Garcia-Sastre

first: Tom

last: Maniatis


title: Effect of X-linked hypophosphatemia (the Hyp mutation) on gene expression in the mid-shaft of the mouse femur

status: Public on Feb 06 2007

city: Charlotte

first: Ralph

middle: A.

last: Meyer

state: NC

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

summary:
The pathophysiology of the osteomalacia in X-linked hypophosphatemia is uncertain.  In this project, genomic DNA microarrays were used to identify novel genes with abnormal mRNA expression levels in mice with the dominant Hyp mutation of the Phex gene.  Femoral shafts from five-week-old C57BL/6J mice, male and female, normal and Hyp (hemizygous male and heterozygous female), were flushed with saline to remove the marrow.  RNA was extracted from each bone, pooled between two mice for each array, processed to cRNA, and hybridized to Affymetrix Mouse 430 2.0 GeneChip microarrays with probe sets for 45,101 genes.  Twenty microarrays (40 mice) were done with 5 arrays for each treatment group (normal male, Hyp male, normal female and Hyp female).  For each gene, factorial analysis of variance was performed for the main effects of genotype (normal vs. Hyp), sex (male vs. female), and genotype-by-sex interaction.  The mRNA levels for 54 % of the genes on each array were scored as present.  At P < 0.01, 2,635 genes were significant for genotype, 1,488 for sex, and 509 for genotype-by-sex interaction.  There were two probes sets for the Phex gene.  Probe 1450445, at the 3’ end of the coding sequence, was low in normal samples (246 ± 37 (10), mean ± SEM (n)) and absent in Hyp samples.  Probe 1421979, at the far 3’ end of the untranslated region of the cDNA, 3,000 base pairs from the coding sequence, was high in normal mice (3,915 ± 315 (10); 8x brighter than the average gene), undetectable in Hyp males, and 725 ± 93 (5) in Hyp females.  Both probe sets were scored as absent in kidney tissue.  In Hyp bone, male and female, there was significant down-regulation of markers of osteoblasts and bone matrix synthesis with significant up-regulation of markers of blood vessel formation and cytoskeleton.  No prominent skeletal gene was up-regulated in Hyp to attempt to compensate for the low skeletal mineralization.  The genes with significant genotype-by-sex interaction did not show a marked fold difference between male and female Hyp mice.  In conclusion, male and female Hyp mice showed similar depression of mRNA levels of genes related to bone synthesis in the femoral shaft.  There was a high signal level from probes for a sequence in the 3’ untranslated region of the Phex gene of normal, but not Hyp, mice, suggesting the need for further study of the molecular organization of this gene.
Keywords: 2x2 factorial design with complete blocks

overall_design: Equal amounts of RNA from two mice, matched for genotype and sex were pooled to create each sample for microarray analysis.  Four treatment groups were done:  (1) Normal male mice, (2) Hyp male mice, (3) normal female mice, and (4) Hyp female mice.   Five replicates were done with each replicate containing one sample from each of the four treatment groups for a total of 20 independent samples (40 mice total).  Each replicate was matched for littermates and parallel processing.

first: Martha

middle: H


title: Transcriptional comparison between whole kidneys from E14.5 Wnt4 mutants and wildtype mice (Mouse430_2 platform). (GUDMAP Series ID: 13)

status: Public on Feb 03 2007

summary:
Our laboratory's interest is in understanding the molecular principles that underlie the regional organization of the mammalian metanephric kidney. Our goal is to generate a detailed spatial map of the cellular expression of selected regulatory genes during mammalian kidney development.  The goal of this study is to identify a population of genes that are enriched in the renal vesicle (RV) and its derivatives using Wnt4 mutants.
Keywords: mutant comparison

overall_design: Wnt4 is required for renal vesicle (RV) induction.  Therefore, RV and the derivatives (s-shaped body and eventually the mature nephron) are missing in Wnt4 mutants.  At E14.5, these structures are present in wildtype kidneys.  Transcriptional profile comparison between E14.5 wildtype and Wnt4 mutants therefore identify genes expressed in the RV and derivatives. Minimally pooled kidney samples were used as single biological replicates.  Total RNA was isolated from these pools and subjected to a single round of amplification for use on Affymetrix arrays.

first: Andrew

middle: P

last: McMahon

first: M

last: Valerius


title: Embryonic Testis Developmental Time Course

first: Lizhong

last: Yang

summary:
Time course of gene expression in the murine embryonic testis from the time of the indifferent gonad (11.5dpc) to birth (18.5dpc)
Keywords: Time Course

overall_design: Independent embryonic testis preps were used for array analysis. Duplicates were provided for each sample.

first: Christopher

last: Small

first: Michael

last: Griswold


title: FoxO are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress

status: Public on Jan 25 2007

city: Boston

last: Sears

address: 300 Longwood Avenue

institute: HMS/CHB

summary:
To investigate the role of FoxO transcription factors as mediators of hematopoietic stem cell resistance to oxidative stress.
Keywords: Hematopoietic stem cells, myeloid progenitors, oxidative stress, ROS, Affymetrix Mouse Genome 430 2.0

overall_design: Study the effect of the deficiency of FoxO1, FoxO3, and FoxO4 in murine bone marrow hematopoietic stem cells and myeloid progenitors on expression of genes involved in reactive oxygen species (ROS) metabolism.

first: Z

last: Tothova

first: R

last: Kollipara

first: BJ

last: Huntly

first: BH

last: Lee

first: DH

last: Castrillon

first: DE

last: Cullen

first: EP

last: McDowell

first: S

last: Lazo-Kallanian

first: IR

last: Williams

first: C

first: SA

last: Armstrong

first: E

last: Passegue

first: RA

last: DePinho

first: DG

last: Gilliland


title: Expression data in the absence of Notch1 in hair follicles

status: Public on Jan 26 2007

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

summary:
Notch1 deficient hair matrix keratinocytes have lower mitotic rates, resulting in smaller follicles with fewer cells. In addition, the ratio of melanocytes to keratinocytes is greatly reduced. Microarray was performed to study downstream mechanism of Notch1-deficiency
Keywords: genetic modification

overall_design: Microarray was first performed using HF_emN1-1 and HF_anN1-1 samples. Later, HF_emN1-2, HF_anN1-2, HF_WT-1, and HF_WT-2 were used to perform another set of microarray. anN1s and WTs were used as wild-type controls.


title: Development of Regulatory T cell Precursors in the Absence of a Functional Foxp3 Protein

city: Los Angeles

first: Marc

middle: Richard John

last: Carlson

state: CA

address: 695 Charles E. Young Dr. S.

department: Department of Human Genetics

institute: UCLA

summary:
To analyze gene expression in in regulatory T cell precursors that develop in the absence of a functional Foxp3 protein as compared to that of normal regulatory T cells
Keywords: Cell type comparison

overall_design: Murine wild-type and mutant (delta) Foxp3 alleles were tagged with EGFP reporters. CD4 positive T cells expressing the respective tagged Foxp3 allele (Foxp3/EGFP and delta Foxp3/EGFP) were isolated from hemizygous male mice by cell sorting using FACS. CD4 positive cells that did not express the EGFP tag were a isolated. Total RNA was prepared and used in the array studies.

first: Wen

last: Lin

first: Dipica

last: Haribhai

first: Lance

middle: M

last: Reland

first: Nga

last: Truong

first: Calvin

middle: B

first: Talal

last: Chatila


title: Aeromonas caviae infection, 24 hours

status: Public on Jan 20 2007

first: Samuel

last: Hayes

state: OH

address: 26 W. Martin Luther King Dr.

institute: United States Environmental Protection Agency

summary:
Aeromonas caviae has been associated with human gastrointestinal disease.  Strains of this species typically lack virulence factors (VFs) such as enterotoxins and hemolysins that are produced by other human pathogens of the Aeromonas genus.  Microarray profiling of murine small intestinal extracts, 24 hours after oral infection with an A. caviae strain, provides evidence of a Th1 type immune response.  A large number of gamma-interferon (γ-IFN) induced genes are up-regulated as well as several tumor necrosis factor-alpha (TNF-α) transcripts.  A. caviae has always been considered an opportunistic pathogen because it lacks obvious virulence factors.  This current effort suggests A. caviae colonizes murine intestinal tract and causes what has been described by others as a dysregulatory cytokine response leading to an irritable bowel-like syndrome.  This response would explain why a number of diarrheal waterborne outbreaks have been attributed to A. caviae even though it lacks obvious enteropathogenic properties.
Keywords: Aeromonas caviae, infection, disease mechanism, TH1 resposne

overall_design: Biological replicates (n=5), controls are uninfected mice, test replicates are infected with organism

first: Stephen

last: Vesper

first: Mark

last: Rodgers

first: Dennis

last: Lye

first: Gerard

last: Stelma

first: Maura

last: Donohue


title: Stabilization of b-catenin induces lymphomas

status: Public on Feb 17 2007

first: Fotini

last: Gounari

address: 75 Kneeland, 12th floor

department: molecular oncology research institute

institute: Tufts-New England Medical Center

summary:
Activation of b-catenin has been causatively linked to the etiology of colon cancer. Conditional stabilization of this molecule in pro-T-cells promotes thymocyte development without the requirement for preTCR signaling. We show here that activated b-catenin stalls the developmental transition from the double-positive (DP) to the single-positive (SP) thymocyte stage and predisposes DP thymocytes to transformation. b-Catenin induced thymic lymphomas have a leukemic arrest at the early DP stage. Lymphomagenesis requires Rag activity, which peaks at this developmental stage, as well as additional secondary genetic events. A consistent secondary event is the transcriptional upregulation of c-Myc, whose activity is required for transformation since its conditional ablation abrogates lymphomagenesis. In contrast, the expression of Notch receptors as well as targets is reduced in DP thymocytes with stabilized b-catenin and remains low in the lymphomas indicating that Notch activation is not required or selected for in b-catenin induced lymphomas. Thus, b-catenin activation may provide a mechanism for the induction of T-ALL that does not depend on Notch activation.
Keywords: Lckcre, CD4Cre-Ctnnbex3, lymphoma, gene expression

overall_design: This study was used to compare gene expression patterns of LckCre mice, CD4Cre-Ctnnbex3 mice before and after T-cell transformation. 5 independent Lckcre (control), 5 independent CD4Cre-Ctnnbex3 mice and 8 independent mice with lymphomas were used. Thymocytes or tumor masses were collected from Lckcre, CD4Cre-Ctnnbex3 mice. Total RNA isolation and purification followed by synthesis of dscDNA, Biotinylated cRNA and purification of Biotinylated cRNA. Then the hybridization to Affymetrix  “Mouse Expression Array 430 Genechips” was done. Data was analysed by dchip.

first: Zhuyan

last: Guo

first: Marei

last: Dose

first: Damian

last: Kovalovsky

first: Rui

last: Chang

first: Jennifer

last: O'Neil

first: Thomas

last: Look

first: Harald

last: von Boehmer

first: Khashayarsha

last: Khazaie


title: Foxp3 ablation in peripheral mature regulatory T cells

city: Seattle

first: Alexander

last: Rudensky

address: 1959 Pacific St

department: Immunology

institute: University of Washington

summary:
Analysis of Foxp3 ablated peripheral regulatory T cells. Regulatory T cells require the expression of the transcription factor Foxp3 for thymic development. It is not known whether continuous expression of Foxp3 is required for the maintained function of mature regulatory T cells in the periphery. Results indicate changes to the regulatory T cell developmental program in the absence of Foxp3.
Keywords: genetic modification

overall_design: Compare Cre recombinase treated peripheral regulatory T cells possessing a Cre sensitive Foxp3 locus to Cre treated regulatory T cells with a wild type Foxp3 locus. Cre exposure is observed via the Cre sensitive expression of the yellow flourescent protein molecule.

first: Luke

last: Williams

middle: Y


status: Public on Jan 19 2007

city: Kennett Square

first: K.

middle: John

last: McLaughlin

address: 382 West Street Rd

department: Animal Biology; School of Veterinary Medicine

summary:
Identification of imprinted genes expressed in adult CD3+ splenocytes
Keywords: imprinted gene; hematopoietic; transplantation

overall_design: For analysis of imprinted gene expression of uniparental-derived cells in adult recipients we chose eGFP/CD3-double positive splenocytes as a defined cell type, and first identified imprinted genes that are normally expressed in this cell type by microarray analysis of normal eGFP/CD3-double positive splenocytes from an eGFP transgenic B6129 mouse.


title: Palmitoyl protein thioesterase-1 knockout mice hofma-affy-mouse-370000

status: Public on Jan 09 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Infantile neuronal ceroid lipofuscinosis (aka infantile Batten disease) is a severe neurodegenerative disorder of early childhood characterized by cortical atrophy, blindness and seizures, leading to premature death in the first decade. The disorder is caused by deficiency in a soluble lysosomal enzyme, palmitoyl protein thioesterase-1 (PPT1). PPT1 knockout mice faithfully reproduce the features of the human disease, with motor deterioration, blindness, seizures, and death before 10 months of age. The progression of events leading from enzyme deficiency to organ failure is poorly defined. The neuronal ceroid lipofuscinoses are of particular interest because of the similarities between the accumulated material and lipofuscin that is associated with normal aging.
We will determine changes in gene expression that occur during the course of neurodegeneration in PPT1 knockout as compared to control mice.
Gene expression profiling of brain tissue from PPT1 knockout mice as compared to normal controls will provide insights into the mechanism of neurodegeneration. Comparison of this profile with gene expression profiles associated with normal aging may provide insights into the contribution of lipofuscin to aging and neurodegeneration.
PPT1 knockout mice on a C57BL/6 background will be sacrificed under CO2 and whole brains removed and frozen under liquid nitrogen.  Three mice will be used for each time point. Data points will be collected at 3 months, 5 months and 8 months of age. Normal age- and sex-matched C57BL/6 mice will be used as controls.
Keywords: gene knockout

first: Sandra

middle: L

last: Hofmann


title: Gene Expression Data in HDAC2 KO Myocardium

status: Public on Jan 18 2007

first: Jonathan

last: Epstein

address: 421, Curie Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania, School of Medicine

summary:
We used microarrays to detail the global programme of gene expression underlying cardiac development by HDAC2 and identified distinct classes of up-regulated and down-regulated genes during this process.
Keywords: Genetic Modification

overall_design: Embryonic heart ventricles were dissected at E17.5 for RNA extraction and hybridization on Affymetrix microarrays. Wild type and HDAC2-deficient littermates were used.  Tissue from 2-3 individual animals of identical genotype was pooled for each micro-array.

first: Chinmay

last: Trivedi

first: Yang

last: Luo

first: Zhan

last: Yin

first: Maozhen

last: Zhang

last: Floss

first: Martin

last: Goettlicher

first: Patricia

middle: R

last: Noppinger

first: Wolfgang

last: Wurst

first: Victor

last: Ferrari

first: Charles

middle: S

last: Abrams

first: Peter

last: Gruber


title: Comparison of corneas from wildtype mice to those from mice under the influence of high doses of TGF-beta russe-affy-mouse-372894

summary:
Characteristic structural details of the cornea are transparency, the absence of blood vessels, and the presence of numerous sensory nerve endings. The corneal epithelium is one of the most densely innervated tissues of the body. The characteristics of the cornea are established during fetal development, and are lost in adult life when the cornea regenerates after injury. The common reaction of the cornea to injury is the formation of opaque scars, the ingrowth of blood vessels, and distinct changes in the innervation pattern. Scar formation of the cornea is critically modulated by the expression of transforming growth factor-beta (TGF-beta).
To identify genes that are important for corneal transparency, dense innervation and absence of blood vessels by comparing corneas from wildtype mice with those that are under the influence of high doses of TGF-beta.
Transparency, dense innervation, and absence of blood vessels in the cornea all depend on the expression of a critical set of genes that are not expressed when TGF-beta is present.
Mice were generated that overexpress TGF-beta under control of a strong lens-specific promoter. These mice developed opaque corneas that are vascularized and lack sensory nerves. In addition, these corneas were densely populated with cells expressing neural cell adhesion protein.
RNA was isolated from corneas of transgenic animals and wildtype littermates in order to analyze differentially expressed genes and to identify those that are only expressed in transparent, avascular, and densely innervated wildtype corneas.
Keywords: TGF-beta overexpression

first: Paul

last: Russell


title: Astroglial gene expression program elicited by fibroblast growth factor-2 mande-affy-mouse-307080

summary:
Astroglia, the star-shaped cells found throughout the central nervous system are the most numerous cell type in the brain.   The astroglial response to injury, generically termed reactive astrogliosis, is classically defined by cellular hypertrophy and process extension, increased glial filament production, and some degree of proliferation.  Astrogliosis and its functional outcomes, glial scar formation and neuroinflammation, are often viewed as detrimental to recovery.  However, increasing evidence points to neuroprotective roles of reactive astroglia in the setting of brain injury.  Therapeutic modulation of this double-edged sword will require detailed knowledge of mechanisms by which specific signals induce detrimental and beneficial phenotypes.
This proposal is is a logical extension of a published, peer reviewed study  (Heffron DS and Mandell JW, Opposing roles of ERK and p38 MAP kinases in FGF2-induced astroglial process extension.  Mol Cell Neurosci 2005, 28:779-90).   The downstream gene expression changes underlying these pathway-specific responses are largely unknown.  The data generated from the proposed project will delineate pathway-specific gene expression responses of astroglia to fibroblast growth factors.  This information  will allow a rational approach to pharmacological approaches to modulate reactive astrogliosis in brain and spinal cord injury.
Determine the astroglial gene expression program elicited by fibroblast growth factor-2, and dissect specific contributions of the ERK and p38 MAP kinase pathways using highly specific pharmacological inhibitors.
FGF2, acting via two distinct intracellular signaling pathways, ERK- and p38 MAPK, leads to pathway-specific gene expression changes in astrocytes which promote the morphological plasticity (ERK-dependent) and pro-inflammatory properties (p38-dependent) of reactive astroglia.
Cell culture
Neonatal primary astrocyte cultures are prepared exactly as previously described (Heffron and Mandell, 2005), using slight modifications of established protocols (McCarthy and de Vellis, 1980).
Astrocytes prepared with these methods comprised greater than 95% of cell cultures as determined by GFAP staining. Microglia are present as a contaminating cell type at a percentage of 3.6 ± 0.9% as determined by CD11B staining.
For process induction experiments, cells are trypsinized and replated in DMEM with 1% fetal bovine serum. This low serum concentration is necessary for good adhesion of the cells. Pharmacological inhibitors are dissolved in DMSO and added 2 h later. P38 MAP kinase inhibitors SB202190  (Calbiochem) and the MEK inhibitor U0126 (Promega) are used at 20 µM.  We previously determined that the inactive analog of SB 202190, SB202474 (Calbiochem) had no effects on pathway activation or astrocyte morphology.  Therefore, the inactive drug analog will not be used in the array experiments.
Final DMSO concentration in the drug treatments and vehicle controls is  0.2%.  Human recombinant FGF2 (obtained from the National Cancer Institute Preclinical Repository) is used at 25 ng/ml, based on extensive dose/response analyses in our published work.
Keywords: fibroblast growth factor-2 treatment

first: James

middle: W

last: Mandell


title: Gene expression study in 1 and 2 cell cloned mice embryos

status: Public on Jan 01 2007

first: Keith

middle: E

last: Latham

address: 3307 N Broad St

department: The Fels Institute for Cancer Research and Molecular Biology

institute: Temple University School of Medicine

summary:
Cloned embryos produced by somatic cell nuclear transfer (SCNT) display a plethora of phenotypic characteristics that make them different from fertilized embryos, indicating defects in the process of nuclear reprogramming by the recipient ooplasm.  To elucidate the extent and timing of nuclear reprogramming, we used microarrays to analyze the transcriptome of mouse SCNT embryos during the first two cell cycles.  We identified a large number of genes mis-expressed in SCNT embryos.  We found that genes involved in transcription and regulation of transcription are prominent among affected genes, and thus may be particularly difficult to reprogram, and these likely cause a ripple effect that alters the transcriptome of many other functions, including oxidative phosphorylation, transport across membrane, and mRNA transport and processing.  Interestingly, we also uncovered widespread alterations in the maternal (i.e. non transcribed) mRNA population of SCNT embryos. We conclude that gene expression in early SCNT embryos is grossly abnormal, and that this is at least in part the result of incomplete reprogramming of transcription factor genes.
Keywords: embryo kind comparison

overall_design: for both 1 and 2 cell stage we analyzed 4 samples each of fertilized embryos cultured with and without a-amanitin, scnt embryos cultured with and without a-amanitin, and parthennogenic embryos.

first: Rita

last: Vassena

first: Zhiming

last: Han

first: Shaorong

last: Gao

first: Don

middle: A

last: Baldwin

first: Richard

last: Schultz


title: Transcriptional Biomarkers to Predict Female Mouse Lung Tumors in Rodent Cancer Bioassays - A 13 Chemical Training Set

status: Public on Feb 14 2007

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

summary:
The primary goal of toxicology and safety testing is to identify agents that have the potential to cause adverse effects in humans.  Unfortunately, many of these tests have not changed significantly in the past 30 years and most are inefficient, costly, and rely heavily on the use of animals.  The rodent cancer bioassay is one of these safety tests and was originally established as a screen to identify potential carcinogens that would be further analyzed in human epidemiological studies.  Today, the rodent cancer bioassay has evolved into the primary means to determine the carcinogenic potential of a chemical and generate quantitative information on dose-response behavior in chemical risk assessments.  Due to the resource-intensive nature of these studies, each bioassay costs $2 to $4 million and takes over three years to complete.  Over the past 30 years, only 1,468 chemicals have been tested in a rodent cancer bioassay.   By comparison, approximately 9,000 chemicals are used by industry in quantities greater than 10,000 lbs and nearly 90,000 chemicals have been inventoried by the U.S. Environmental Protection Agency as part of the Toxic Substances Control Act.  Given the disparity between the number of chemicals tested in a rodent cancer bioassay and the number of chemicals used by industry, a more efficient and economical system of identifying chemical carcinogens needs to be developed.
Keywords: toxicology, chemical carcinogenesis, lung

overall_design: Five-week old female B6C3F1 mice were exposed for 13 weeks in the following dose groups: 1) 1,5-Naphthalenediamine, CAS No. 2243-62-1, feed, 2000 ppm, positive lung carcinogen; 2) 2,3-Benzofuran, CAS No. 271-89-6, gavage, 240 mg/kg, positive lung carcinogen; 3) 2,2-Bis(bromomethyl)-1,3-propanediol, CAS No. 3296-90-0, feed, 1250 ppm, positive lung carcinogen; 4) N-Methylolacrylamide, CAS No. 924-42-5, gavage (water), 50 mg/kg, positive lung carcinogen; 5) 1,2-Dibromoethane, CAS No. 106-93-4, gavage (corn oil), 62 mg/kg, positive lung carcinogen; 6) Coumarin, CAS No. 91-64-5, gavage (corn oil), 200 mg/kg, positive lung carcinogen; 7) Benzene, CAS No. 71-43-2, gavage (corn oil), 100 mg/kg, positive lung carcinogen; 8) N-(1-naphthyl)ethylenediamine dihydrochloride, CAS No. 1465-25-4, feed, 2000 ppm, negative lung carcinogen; 9) Pentachloronitrobenzene, CAS No. 82-68-8, feed, 8187 ppm, negative lung carcinogen; 10) 4-Nitroanthranilic acid, CAS No. 619-17-0, feed, 10000 ppm, negative lung carcinogen; 11)  2-Chloromethylpyridine hydrochloride, CAS No. 6959-47-3, gavage (water), 250 mg/kg, negative lung carcinogen; 12) Diazinon, CAS No. 333-41-5, feed, 200 ppm, negative lung carcinogen; 13) Malathion, CAS No. 121-75-5, feed, 16000 ppm, negative lung carcinogen; 14) Corn oil control, gavage; 15) Water control, gavage; 16) Rodent diet control, feed.  Feed animals were exposed 7 days/week and gavage animals were exposed 5 days/week (5 ml/kg). After 13 weeks, animals were euthanized and lungs were collected.  The right lobe was used for microarray analysis.  Microarray analysis was performed on the lungs of three to four mice per treatment group.

first: Linda

middle: J

last: Pluta

first: Longlong

last: Yang

first: Thomas

last: Halsey


title: mECK36: a cell and animal model of virally induced Kaposi's sarcoma

city: Miami

first: Enrique

last: Mesri

state: FL

address: 1550 NW 10th Ave, PAP-109B

department: Microbiology and Immunology

institute: University of Miami

summary:
Transfection of a Kaposi's sarcoma (KS) herpesvirus (KSHV) Bacterial Artificial Chromosome (KSHVBac36) into mouse bone marrow endothelial lineage cells generated a cell (mECK36) that induced KS-like tumors in mice. mECK36 formed KSHV-harboring vascularized spindle-cell sarcomas that were LANA+ and displayed a KSHV and host transcriptomes reminiscent of KS tumors.
Keywords: Cell type comparison

overall_design: There are three biological replicates per sample. Tumors (mKS) were compared the the human KS signature. mECK36 and mEC-V were compared to putative BM lineage cells.

first: Lucas

last: Cavallin


title: Gnotobiotic mouse cecal epithelium; B.thetaiotaomicron-B. longum mono- versus bi-association, PR chow, NMRI

city: Saint Louis

first: Justin

middle: L.

last: Sonnenburg

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

summary:
Laser captured cecal epithelium from gnotobiotic mice colonized with B. thetaiotaomicron or B. longum (mono-association) or B. thetaiotaomicron bi-association with B. longum.   Samples were derived from 10d colonizations of NMRI  mice fed a standard-chow polysaccharide rich (PR) diet.
Keywords: Germ-free vs. Mono-associations or Bi-association, in vivo

platform_organism:
Homo sapiens
Mus musculus

overall_design: Total RNA was prepared from laser captured cecal epithelium of 10 day associated gnotobiotic mice, double amplified, and hybridized to 430 2.0 GeneChips or to GlycoGeneChipsv1.

first: Christina

middle: T

last: Chen

first: Jeffrey

middle: I

last: Gordon


title: Transcriptome Analysis Multipotent Adult Progenitor Cells (Affy)

city: Leuven

first: Fernando

last: Ulloa Montoya

address: Herestraat 49 bus 804

country: Belgium

institute: Katholieke Universiteit Leuven

summary:
We compare the transcriptome of two different clones of multipotent adult progenitor cells (MAPCs) using Affymetrix arrays.
Keywords: mRNA expression profiling, oligonucleotide microarrays, stem cells

overall_design: Three mRNA samples (biological replicates) per cell type taken at different passage number were compared. Two independently isolated MAPC clones were used.

middle: U

last: Montoya

first: Wei-Shou

last: Hu

first: Catherine

last: Verfaillie


title: static vs simulated microgravity

status: Public on Dec 31 2006

city: Atlanta

first: Mamta

last: Patel

state: GA

address: 101 Woodruff Circle #315

department: Biomedical Engineering

institute: Georgia Tech and Emory University

summary:
The below table includes a smaller list of data that was analyzed by dChip and filtered by pvalue such that a file with about 4600 genes was obtained, which allowed for ease of use from 40,000 genes.
Keywords: static vs simulated microgravity

overall_design: The total RNA was extracted from 2T3 pre-osteoblast cells exposed to static or simulated microgravity (Rotating Wall Vessel) conditions.  The RNA was then sent to Affymetrix microarray core facility at Baylor College of Medicine (Houston, TX) for microarray analysis.

first: Wenbin

last: Liu

first: Michelle

last: Sykes

first: Semyon

last: Risin

first: Diana

first: Hanjoong

last: Jo


title: Gene expression profiles of components isolated from developing kidney at E15.5 using LCM. (GUDMAP Series ID: 12)

status: Public on Dec 23 2006

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary:
The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney.  The central thesis is straightforward. The combination of laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in laser capture microdissected components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.
Keywords: Comparison of kidney components.

overall_design: At specific developmental time points we isolate discrete elements of the kidney by using laser capture  microdissection and then define their gene expression profiles with microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Comparison between gene expression in heart from Emd KO and control mice

status: Public on Dec 02 2006

city: New York

first: antoine

last: Muchir

state: NY

address: 630W 168th street

institute: columbia university

summary:
The present research is devoted to the identification of gene(s) severely affected by EMD mutations, leading to striated muscle laminopathies and more specifically the cardiomyopathy. For this purpose, we developped a large-scale gene expression approach on heart and skeletal tissues from Emd KO mouse model.
Keywords: disease state modification

overall_design: In the project presented here we performed differential expression in heart from a mouse model of EDMD: a Emd KO mouse created via homologous recombination by Y.Hayashi in Japan (Ozawa, 2006). The emd knock-out mouse showed significantly delayed PR time, that could correspond to impaired atrial-ventricle node conduction. Genes were identified as differentially expressed if they met a false discovery rate threshold of 0.05 in a two-sample t-test (q-value) and showed at least a two-fold difference in expression independent of absolute signal intensity.

first: paul

last: Pavlidis

first: yukiko

middle: k

last: Hayashi

first: howard

middle: j

last: Worman


title: ß-catenin Plays a Dual Role in the Generation and Maintenance of Immortalized Hematopoietic Stem Cells

status: Public on Dec 06 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
Hematopoietic stem cells (HSCs) are characterized by their ability to give rise to all mature blood lineages and to renew themselves. Despite their potential for the therapeutic use in cell replacement therapy, the cell fate decisions of HSCs controlled by extrinsic and intrinsic mechanisms remain poorly understood. In summary, our results provide a number of novel and important observations illustrating and enlightening the importance of ß-catenin in hematopoiesis. Specifically, we show that ß-catenin plays an essential role in the immortalization of HSCs.
Keywords: hematopoietic stem cells , immortalization, ß-catenin, genetic modification, time course

overall_design: One objective of our study was to understand the molecular targets of ß-catenin in controlling the immortalization of hematopoietic stem cells (HSCs). Using a microarray screening approach, we had identified candidate genes that might potentially regulate ß-catenin mediated immortalization of HSCs. A special focus was given to transcription factors (TFs), since they play myriad functions in basic cellular processes. The strategy of our experimental design utilized a combination of a pair wise comparison and time course microarray experiments that include the expression profiles of TFs in 4 different samples:

first: R

first: C

last: Templin

first: D

last: Kotlarz


title: Impact of endurance training in MHC-I over-expressed Mice

status: Public on Dec 21 2006

city: Jacksonville

first: Yan

middle: W.

last: Asmann

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary:
Myosine heavy chain I was overexpressed in mouse skeletal muscle. The transgenic mice, as well as the wild type mice, were endurance trained on treadmill for 5 days/week over  8 weeks at 80% peak aerobic capacity in comparison with untrained mice. The gene expression profiles of the skeletal muscles from wild-type trained (WTT) and untrained (WTUT), and transgenic trained (TGT) and untrained (TGUT) were measured using Affymetrix Mouse430A 2.0 GeneChips.
Keywords: genetic modification

overall_design: There were 5 WTT, 5 WTUT, 5 TGT, and 5 TGUT mice used in microarray studies.

first: Lisa

last: Chow

first: Laura

last: Greenlund

first: Kevin

last: Short

first: Shelly

middle: K

last: McCrady

first: James

last: Levine

first: K

last: Nair


title: Comparison between gene expression in heart from Lmna H222P homozygous and control mice

summary:
The present research is devoted to the identification of gene(s) severely affected by LMNA mutations, leading to striated muscle laminopathies and more specifically the cardiomyopathy. For this purpose, we developped a large-scale gene expression approach on heart and skeletal tissues from Lmna H222P heterozygous Knock-In mouse model.
Keywords: disease state modification

overall_design: In the project presented here we performed differential expression in heart from a mouse model of EDMD: a LmnaH222P knock-in mouse created via homologous recombination by Gisele Bonne in Paris, France (Arimura et al., 2005). The mutant male LmnaH222P knock-in homozygous mice display reduced locomotion activity with abnormal stiff walking posture and all of them die by 9 months of age. As for cardiac phenotype, they develop chamber dilation and hypokinesia with conduction defects. These results demonstrate that LmnaH222P knock-in homozygous mice represents a good model for studying laminopathies affecting striated muscles as they develop a dystrophic condition of both skeletal and cardiac muscles reminiscent of the human diseases. Genes were identified as differentially expressed if they met a false discovery rate threshold of 0.05 in a two-sample t-test (q-value) and showed at least a two-fold difference in expression independent of absolute signal intensity.

first: valerie

last: Decostre

first: Alan

last: Herron

first: takuro

last: Arimura

first: gisele

last: Bonne


title: Comparison between gene expression in heart from Lmna H222P heterozygous and control mice

first: antoine

last: Muchir

first: paul

last: Pavlidis

first: alan


title: Gene Expression Profiling Reveals Unique Pathways Associated with Differential Severity of Lyme Arthritis

status: Public on Dec 14 2006

city: Salt Lake City

first: Janis

last: Weis

state: UT

address: 15 North Medical Drive East

department: Pathology

institute: University of Utah

summary:
	The murine model of Lyme disease provides a unique opportunity to study the localized host response to similar stimulus, B. burgdorferi, in the joints of mice destined to develop severe arthritis (C3H) or mild disease (C57BL/6).  Pathways associated with the response to infection and the development of Lyme arthritis were identified by global gene expression patterns using oligonucleotide microarrays.  A robust induction of IFN responsive genes was observed in severely arthritic C3H mice at one week of infection, which was absent from mildly arthritic C57BL/6 mice.  In contrast, infected C57BL/6 mice displayed a novel expression profile characterized by genes involved in epidermal differentiation and wound repair, which were decreased in the joints of C3H mice.  These expression patterns were associated with disease state rather than inherent differences between C3H and C57BL/6 mice, as C57BL/6-IL10-/- mice infected with B. burgdorferi develop more severe arthritis that C57BL/6 mice and displayed an early gene expression profile similar to C3H mice.  Gene expression profiles at two and four weeks post infection revealed a common response of all strains that was likely to be important for the host defense to B. burgdorferi and mediated by NF-kB-dependent signaling.  The gene expression profiles identified in this study add to the current understanding of the host response to B. burgdorferi and identify two novel pathways that may be involved in regulating the severity of Lyme arthritis.
Keywords: disease state analysis, time course

overall_design: Expression profiling of ankle tissues of C3H, C57BL/6, and C57BL/6-IL10-/- mice infected with B. burgdorfer (0, 1, 2, and 4 weeks post-infection)

first: Hillary

last: Crandall

first: Diane

middle: M

last: Dunn

first: Ying

last: Ma

first: R

last: Wooten

middle: F

last: Zachary

first: John

middle: H

first: Robert

middle: B


title: Hypomorphic Mutation in PGC1beta causes mitochondrial dysfunction and liver insulin resistance

first: Michael

last: Huntgeburth

address: 99 Brookline Ave.

department: Endocrinology, Diabetes and Metabolism

institute: Beth Israel Deaconess Medical Center

summary:
PGC1beta is a transcriptional coactivator that potently stimulates mitochondrial biogenesis and respiration of cells. Here, we have generated mice lacking exons 3 to 4 of the Pgc1beta gene (PGC1beta E3,4-/E3,4- mice). These mice express a mutant protein that has reduced coactivation activity on a subset of transcription factors, including ERRalpha, a major target of PGC1beta in the induction of mitochondrial gene expression. The mutant mice have reduced expression of OXPHOS genes and mitochondrial dysfunction in liver and skeletal muscle as well as elevated liver triglycerides. Euglycemic-hyperinsulinemic clamp and insulin signaling studies show that PGC1beta mutant mice have normal skeletal muscle response to insulin, but have hepatic insulin resistance. These results demonstrate that PGC1beta is required for normal expression of OXPHOS genes and mitochondrial function in liver and skeletal muscle. Importantly, these abnormalities do not cause insulin resistance in skeletal muscle but cause substantially reduced insulin action in the liver.
Keywords: Liver and quadricpes muscle gene expression, WT vs. PGC1beta mutant

overall_design: Gene expression levels in liver tissue and quadriceps muscle were compared between WT/Control and PGC1beta mutant tissue. Total RNA was extracted from liver and skeletal muscle using RNAeasy kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions. Synthesis of cRNA, hybridization and scanning of the Affymetrix Murine 430 2.0 chip was performed by Dana Farber Cancer Institute Microarray Core Facility. The microarray data was analyzed by Clustering Analysis using the d-Chip software (Li and Wong, 2001).


title: Gene expression profiles of components isolated from developing kidney at E11.5, E12.5 & E15.5 using LCM. (GUDMAP Series ID: 10)

status: Public on Nov 18 2006

city: Edinburgh

first: GUDMAP

last: Developers

overall_design: At different developmental time points we isolate discrete elements of the kidney by using laser capture microdissection and then define their gene expression profiles with microarrays.

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Gene expression profiles of E14 bladder, urogenital sinus and urethra isolated from SMGA (Actg2) transgenic mice. (GUDMAP Series ID: 6)

summary:
The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder. The central thesis is straightforward. The combination of microdissected and laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of the embryonic day 14 bladder, urogenital sinus, and urethra.
Keywords: Gene expression comparison from developing regions of the mouse embryonic day 14 urogenital system

overall_design: Bladder, urogenital sinus, and urethra regions from embryonic day 14 SMGA/EGFP animals were microdissected and total RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

first: James

last: Lessard

middle: C

last: Szucsik


title: Comparative analysis of gene expression in A/J CB versus DBA/2J

city: Baltimore

first: Alexander

last: Balbir

state: MD

address: 615 N. Wolfe St.  Room E7610

department: Environmental Health Sciences

institute: Johns Hopkins Bloomberg School of Public Health

summary:
We hypothesize that gene expression in the CBs of these two strains of mice are divergent thus contributing to the disparity in the phenotypes. More specifically, (1) genes related to CB function are expressed less in the A/J mice compared to DBA/2J mice; (2) gene expression levels of morphogenic and trophic factors of the CB maybe significantly lower in the A/J mice than the DBA/2J mice.  In order to test these hypotheses, we utilized microarray analysis to examine transcriptional differences between CBs of both strains of mice.
Keywords: comparative expression profiling

overall_design: . This study utilizes microarray analysis to test these hypotheses. Three sets of CBs were harvested from both strains.  RNA was isolated and used for global gene expression profiling (Affymetrix Mouse 430 2.0 array). Statistically significant gene expression was determined as a minimum 6 counts of 9 pairwise comparisons, minimum 1.5-fold change, and p < 0.05.

first: Hannah

last: Lee

first: Mariko

last: Okumura

first: Shyam

last: Biswal

last: Fitzgerald

first: Machiko

last: Shirahata


title: HOXB4 target genes in adult hematopoietic stem and progenitor cells (HSC/HPCs)

status: Public on Sep 11 2007

city: Hannover

first: Bernhard

last: Schiedlmeier

department: Experimental Hematology

institute: Hannover Medical School

summary:
HOXB4 mediates expansion of adult and embryo-derived hematopoietic stem cells (HSCs) when expressed ectopically. To define the underlying molecular mechanisms, we performed gene expression profiling in combination with subsequent functional analysis using enriched adult HSCs  expressing inducible HOXB4. A substantial number of the identified HOXB4 target genes are involved in signaling pathways important for controlling self-renewal, maintenance and differentiation of stem cells. Functional assays performed on selected pathways confirmed the biological coherence of the array results. HOXB4 activity protected adult HSCs from the detrimental effects mediated by the proinflammatory cytokine TNF-alpha.  Furthermore, we demonstrate that HOXB4 activity and FGF-signaling are intertwined. HOXB4-mediated expansion of adult  HSCs was enhanced by specific and complete inhibition of FGF-receptors. Based on our results we propose that HOXB4 governs pivotal cell-intrinsic pathways involved in the regulation of cell cycle, differentiation and apoptosis. Our results strongly suggest that HOXB4 modulates the response of HSCs to multiple extrinsic signals in a concerted manner, thereby shifting the balance towards stem cell self-renewal.
Keywords: plus/minus induction of HOXB4 activity by treatment with 4-hydroxytamoxifen (TMX)

overall_design: To understand the mechanisms of HOXB4 activity, we wished to identify target genes of HOXB4 in adult hematopoietic stem and progenitor cells (HSC/HPCs). We thus transduced murine HSC/HPCs with a retroviral vector that co-expresses EGFP and a tamoxifen-inducible form of HOXB4 (HOXB4-ER). Upon addition of 4-hydroxytamoxifen (TMX), the HOXB4-ER fusion protein translocates from the cytoplasm to the nucleus, consequently being capable of modulating gene expression. Transduced cell populations were expanded for 14 days in the presence of TMX. Thereafter, HOXB4-ER+LSK (GFP+ , lineage negative, Sca1+, ckit+) cells were flow cytometrically isolated and cultivated either with or without TMX for 1 or 4 hours. Inactivation of HOXB4 activity by TMX withdrawal was intended to mimic the naturally occurring down-regulation of HOXB4 in differentiating stem cells. RNA was prepared after the aforementioned times and the transcriptional profiles of HOXB4-ER+LSK +/- TMX analyzed using the Affymetrix™ platform. As a control, profiling was also performed with LSK cells expressing unmodified constitutively active HOXB4 (HOXB4const) ± TMX, to exclude changes in gene expression due to unknown effects of tamoxifen itself.  RNAs from adult LSK cells were processed for use on Affymetrix GeneChips Mouse Genome 430 2.0. All quality parameters for the arrays were confirmed to be in the recommended range.

first: B

first: H

last: Auer

first: K

last: Kornacker

first: W

last: Ostertag

first: C

last: Baum

last: Klump

first: Moises

last: Mallo


title: Gene expression profiles of P1 and adult bladders isolated from SMGA (Actg2) transgenic mice. (GUDMAP Series ID: 11)

status: Public on Dec 08 2006

last: Developers

summary:
The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing bladder.  The central thesis is straightforward. The combination of microdissected and laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of the adult and postnatal day 1 bladder.
Keywords: Gene expression comparison between postnatal day 1 and adult bladders

overall_design: Bladders, from postnatal day 1 and adult transgenic mice in which EGFP is driven by a SMGA promoter/EGFP, were isolated by dissection and total RNA was extracted and underwent 2-round amplification (Epicentre® Biotechnologies) for gene expression analysis using the Affymetrix MOE430 microarray chip

first: John


title: ernst-affy-mouse-264940

status: Public on Nov 14 2006

first: Winnie

last: Liang

summary:
Inherited mutations of calcium ion channels exhibit neurological defects, such as epilepsy, ataxia, and migraine, and these phenotypes are shared among humans and mouse models.  Absence epilepsy and ataxic phenotypes are present in the calcium channelopathy mutants stargazer (stg-gamma2 subunit), tottering (tg-alpha1 subunit), and lethargic (lh-beta4 subunit). These mutations of high-voltage-activated (HVA) calcium channel subunits initiate increases in membrane excitability of low-voltage-activated (LVA) calcium channels in thalamic neurons, thus enhancing LVA currents.  Elevated LVA currents, produced from T-type calcium channels, induce rhythmic thalamocortical burst firing and spike-wave seizures.  The changes in gene expression originating from the different mutations result in similar T-type channel function; however, the network of gene modifications causing altered molecular plasticity and the emergence of pathological phenotypes remain unknown.  We would like to understand how loss of 3 different subunits of a calcium ion channel differentially alter gene expression in the brain.  Characterizing the gene expression profiles of the mutant stg, tg, and lh mice will provide evidence of the epileptic and ataxic mechanisms, which may identify potential therapeutic targets.
We will compare the gene expression profiles among adult mutant stg, tg, and lh mice, which display the ataxic and epileptic phenotypes, along with their wildtype, litter-mate controls, in the cerebellum and brain (without cerebellum).
We propose that the neuronal dysfunction associated with the ataxic and epileptic phenotypes develops from a common network of interacting gene alterations within the mutant stg, tg, and lh brain.  The changes dictated by the initial mutations leading to the ataxic and epileptic phenotypes are hypothesized to be localized to the cerebellum and the remaining areas of the brain, including the thalamus and cortex, respectively.
Adult mutant stg, tg, and lh mice, between 2 and 5 months of age, along with wildtype, litter-mate controls, will be sacrificed. Two brain regions responsible for two phenotypes will be examined. The cerebellum (ataxia) will be dissected from remainder of the forebrain (generalized epilepsy). Each tissue set will be collected in triplicate (3 separate mice per set) to account for biological variance, and total RNA isolated via standard Trizol procedure (Invitrogen) and purified with the RNeasy cleanup kit (Qiagen).  RNA samples will be stored at -80 C until sent for analysis using the Affymetrix GeneChip Mouse Genome 430 2.0 whole genome array.
Keywords: other

first: Wayne

middle: L

last: Ernst


title: C-type natriuretic peptide regulates endochondral ossification through p38 MAP kinase-dependent pathways_2

status: Public on Dec 15 2006

city: London

first: Claudine

last: James

email: claudinegj@hotmail.com, fbeier@uwo.ca

state: Ontario

address: 1151 Richmond Street, Suite 2

department: Physiology and Pharmacology

country: Canada

institute: University of Western Ontario

summary:
C-type natriuretic peptide (CNP) has been recently identified as an important anabolic regulator of endochondral bone growth, but the molecular mechanism mediating these effects are not completely understood. Here we demonstrate that CNP activates the p38 MAP kinase pathway in chondrocytes and that pharmacological inhibition of p38 blocks the anabolic effects of CNP in a tibia organ culture system. We further show that CNP stimulates endochondral bone growth largely through expansion of the hypertrophic zone of the growth plate, while delaying mineralization. Both effects are reversed by p38 inhibition. We performed Affymetrix microarray analyses to identify CNP target genes in the organ culture system. These studies confirmed that hypertrophic chondrocytes are the main targets of CNP signaling in the growth plate, potentially because cGMP-dependent kinases I and II, important transducers of CNP signaling and are expressed at much higher levels in these cells than in other areas of the tibia. One of the genes most strongly induced by CNP was the Ptgs2 gene, encoding Cox2. Real-time PCR confirmed that Cox2 expression was induced by CNP in hypertrophic chondrocytes, but surprisingly in a p38-independent manner. Moreover, Cox2 inhibition – in contrast to p38 inhibition - did not block the anabolic effects of CNP. In summary, our data identify novel target genes of CNP and demonstrate that the p38 pathway is a novel, essential mediator of CNP effects on endochondral ossification, with potential implications for numerous skeletal diseases.
Keywords: Growth plate zone comparison and treatment response analysis

overall_design: Tibiae from E15.5 day old embryonic mice were isolated and cultured in minimal media in the presence of vehicle, BSA/HCl (1mM), or C-type natriuretic peptide, CNP (10-6M). On the sixth day of treatment cultured tibias were micro-dissected into the resting/proliferating, hypertrophic, and mineralized areas. Distinct zones from approximately 24 bones were pooled together, from which RNA was isolated using the Qiagen RNeasy Lipid Extraction Kit. Once the quality of total RNA from three independent trials was determined using the Agilent 2100 bioanalyzer, microarray analyses were performed at the London Regional Genomics Centre using MOE430_2.0 Affymetrix arrays. Results were analyzed using GeneSpring 7.2 software.

first: Hanga

last: Agoston

first: Sameena

last: Khan

middle: G

first: Rosa

last: Serra

first: Lee-Anne

last: Stanton

first: Frank

last: Beier


title: Sense-antisense transcript comparison in mouse brain and kidney

status: Public on Nov 07 2006

city: Newcastle

first: Andreas

last: Werner

address: Framlington Place

department: Cell and Molecular Biosciences

institute: Newcastle University

summary:
Comparison of sense (forward probes) and antisense (reverse probes on U74 v1 gene arrays) transcripts in mouse kidney and brain.
Positive calls related to antisense transcripts were compared to the cognate signals on the 430 version of mouse genome arrays to obtain genes that co expressed sense and antisense transcripts. This had to be done manually because divergent probe IDs on the two chip generations.
Keywords: Qualitative comparison of expression

overall_design: The first Affymetrix U74 mouse gene chips contains reversely oriented probe sets. These probes will hybridize to natural antisense transcripts that overlap with the sense transcript in the cognate area. Affymetrix provided a mask to identify the reverse probes. Positive calls with these reverse probes will give an estimate of the antisense transcriptome in that particular tissue. Comparison of the reversely oriented probes with correctly annotated probes will reveal the expression ratio of sense and antisense transcripts.

first: Heiko

last: Peters

first: Michael

middle: S

last: Jackson

first: Maria

middle: A

last: Lastowska


title: PTEN-deficient intestinal stem cells initiate intestinal polyposis

city: Kansas City

first: Linheng

last: Li

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary:
Intestinal polyposis, a precancerous neoplasia, results primarily from an abnormal increase in the number of crypts. Crypts contain intestinal stem cells (ISCs). Thus intestinal polyposis provides an ideal condition for studying stem cell involvement in polyp/tumor formation. Using a conditional knock-out mouse model, we found that the tumor suppressor Phosphatase of Tension homolog (PTEN) governs the proliferation rate and number of ISCs and loss of PTEN results in an excess of ISCs. In PTEN mutants, excess ISCs initiate de-novo crypt formation and crypt fission, recapitulating crypt production in fetal/neonatal intestine. Microarray studies were used to profile the changes in gene expression that occurred   when PTEN was knocked out in the intestine.
Keywords: Disease state analysis, genetic modification, Intestinal polyposis, PTEN mutant, Cowden disease mouse model

overall_design: A conditional PTEN mutant allele [Groszer, M. et al. Negative regulation of neural stem/progenitor cell proliferation by the Pten tumor suppressor gene in vivo. Science 294, 2186-2189 (2001).] was combined with in interferon inducible Mx1-Cre [Kuhn, R., Schwenk, F., Aguet, M. & Rajewsky, K. Inducible gene targeting in mice. Science 269, 1427-1429 (1995).] to enable PTEN to be deleted from the intestine by administration of polyinosinic–polycytidylic acid (Poly I:C). PolyI:C was administered at weaning (every other day, five times total) to three PTEN mutant (Mx1-Cre positive:PTENfx/fx) and two control (Mx1-Cre negative:PTENfx/+) animals. Intestinal polyps (from PTEN mutants) and equivalent regions of intestine (from controls) were isolated 30 days after the final polyI:C injection. Microarray analysis compared the gene expression profiles of PTEN mutant polyps and control intestines. Genes were considered up-regulated or down-regulated if all of the following conditions were met: 1) There was at least a two-fold change in the average probe signal measured between controls and mutants; 2) There was no overlap between the range of mutant and control data; and 3) The control mean was outside the 95% confidence interval of the PTEN-mutant mean.

first: Xi

last: He

first: Tong

last: Yin

first: Justin

last: Grindley

first: Tosiro

last: Sato

first: Mark

last: Hembree

first: Leanne

last: Wiedemann


title: SM by NZB Female Liver Gene Expression

status: Public on Nov 03 2006

city: Bar Harbor

first: Ioannis

last: Stylianou

state: ME

address: 600 Maine Street

institute: The Jackson Laboratory

summary:
3 x 3 comparison of the inbred strains SM/J and NZB/BinJ.
Keywords: Comparitive mRNA

overall_design: Simple comparison of native untreated gene expression profiles of female 8wk old SM mice (x3) by female 8wk old NZB mice (x3)

first: Jason

middle: J

last: Affourtit

first: Keith

last: Shockley

first: Fadi

last: Abdi

first: Gary

last: Churchill

first: Beverly

last: Paigen


title: Murine host cell response to Aeromonas infection

status: Public on Oct 21 2006

city: Cincinnati

first: Samuel

last: Hayes

address: 26 W. Martin Luther King Dr.

institute: United States Environmental Protection Agency

summary:
Aims: To assess the virulence of multiple Aeromonas spp. using two models, a neonatal mouse assay and a mouse intestinal cell culture.
Methods and Results:  Transcriptional responses to both infection models were evaluated using microarrays.  After artificial infection with a variety of Aeromonas spp., mRNA extracts from the two models were processed and hydridized to murine microarrays to determine host gene response.  Definition of virulence was determined based on host mRNA production in murine neonatal intestinal tissue and mortality of infected animals.  Infections of mouse intestinal cell cultures were then performed to determine whether this simpler model system's mRNA responses correlated to neonatal results and therefore be predictive of virulence of Aeromonas spp.  Virulent aeromonads up-regulated transcripts in both models including multiple host defense gene products (chemokines, regulation of transcription and apoptosis, cell signaling).  Avirulent species exhibited little or no host response in neonates.  Mortality results correlated well with both bacterial dose and average fold change of up-regulated transcripts in the neonatal mice.
Conclusions:  Cell culture results were less discriminating but showed promise as potentially being able to be predictive of virulence.  Jun oncogene up-regulation in murine cell culture is potentially predictive of Aeromonas virulence.
Significance and Impact of the Study: Having the ability to determine virulence of waterborne pathogens quickly would potentially assist public health officials to rapidly assess exposure risks.
Keywords: Aeromonas; Virulence; Gene expression; Host response

overall_design: Two infection models were assessed, live, whole animals (neonatal Swiss Webster mice) and a murine small intestinal cell culture. Biological replicates (n=5) were infected with different Aeromonas species/strains and compared to uninfected controls.

first: Stephen

last: Vesper

middle: R

last: Rodgers

first: Dennis

last: Lye

first: Gerard

middle: N

last: Stelma


title: E14.5 wild type mouse embryo microarray results

status: Public on Oct 20 2006

city: Göttingen

first: Murat

last: Cankaya

address: Am Faßberg 11

department: Department of Genes and Behavior

institute: Max Planck Institute for Biophysical Chemistry

summary:
This series contains two microarrays for E14.5 wild type mouse embryos.
We purified total RNA with RNAzol. Please check www.rzpd.de for
labeling, hybridization and scanning protocols.
Keywords: other

overall_design: We worked with www.rzpd.de. We prepared total RNA with RNAzol.

first: Gregor

last: Eichele

first: Axel

last: Visel


title: Expression differences in the liver of a congenic mouse with low serum IGF-1

status: Public on Oct 29 2006

first: Cheryl

middle: Lynne

last: Ackert-Bicknell

address: 600 Main Street

summary:
Several studies have shown that bone mineral density (BMD), a clinically measurable predictor of osteoporotic fracture, is the sum of genetic and environmental influences.  In addition, serum IGF-1 levels have been correlated to both BMD and fracture risk.  We previously identified a Quantitative Trait Locus (QTL) for Bone Mineral Density (BMD) on mouse Chromosome (Chr) 6 that overlaps a QTL for serum IGF-1.  The B6.C3H-6T (6T) congenic mouse is homozygous for C57BL/6J (B6) alleles across the genome except for a 30 cM region on Chr 6 that is homozygous for C3H/HeJ (C3H) alleles.  This mouse was created to study biology behind both the BMD and the serum IGF-1 QTLs and to identify the gene(s) underlying these QTLs.   Female 6T mice have lower BMD and lower serum IGF-1 levels at all ages measured. As the liver is the major source of serum IGF-1, we examined differential expression in the livers of fasted female B6 and 6T mice by microarray.
Keywords: Genetic variation

overall_design: The experimental design of this experiment was a simple two-factor experiment, with three biological replicates of each factor (in this case mouse strain, B6.C3H-6T vs. C57BL/6J).  Each sample represented one mouse; no samples were pooled.   No technical replicated were done.

first: Wesley

last: Beamer

first: Clifford

last: Rosen


title: A profile of murine gastric epithelial cells:  Parietal, Zymogenic, Pit

city: Houston.

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

summary:
Continuous regeneration of digestive enzyme (zymogen) secreting chief cells is a normal aspect of stomach function that is disrupted in pre-cancerous lesions. Regulation of zymogenic cell (ZC) differentiation is poorly understood.  Here we profile Parietal, Pit, and Zymogenic cells for comparison and study.
Keywords: Bhlhb8, Mist1, mucous neck cell, laser-capture microdissection, zymogenic, gastric cell differentiation

overall_design:
Samples were obtained through Laser-capture microdisection of gastric epithelium.  The three samples come from enrichments for Zymogenic Cells (ZC), Parietal Cells (PC), and Mucus Pit Cells (Pit).
	Individual parietal cells (visualized by DBA-positivity and autofluorescence) from well-oriented gastric units were dissected (PixCell II LCM apparatus, 7.5-µm spot diameter; CapSure HS LCM caps, Arcturus, Mountain View, CA) one-at-a-time from the pit zone and collected for GeneChips. Pit cells (E-cadherin-positive, DBA-negative) were then collected from the same gastric units. Only the pit cells in a 2-3-cell-thick region at the apex of the gastric unit – but not yet upon the gastric surface – were taken. ZCs (E-cadherin-positive, GSII/DBA-negative cells in the base zones) were collected from different slides in corpus gastric units after potentially contaminating basal parietal cells had first been dissected and discarded. 3000-5000 individual cells from each cell lineage were isolated from 4-5 individual mice, and RNA was purified by PicoPure kit (Arcturus). RNA integrity was verified, and RNAs for each lineage were pooled from multiple mice and multiple dissections to make 20 ng total RNA, which was then amplified, labeled, and fragmented (by the Arcturus RiboAmp HS kit followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences). The resulting biotinylated cRNA probes were hybridized to Affymetrix (Santa Clara, CA) GeneChip® Mouse Genome 430 2.0 microarrays.

first: Victoria

last: Ramsey

last: Doherty


title: Cellular Mechanisms of Fatal Early-Onset Autoimmunity in Mice with the T Cell-Specific Targeting of TGFβ Receptor

status: Public on Oct 17 2006

city: Seattle

first: Jeffrey

last: Rasmussen

state: WA

institute: University of Washington

summary:
Transforming growth factor-β (TGF-β) has been implicated in the control of differentiation and proliferation of multiple cell types. However, a role for TGF-β in the control of immune homeostasis is not fully understood because of its pleiotropic action. Here we report that complete ablation of the TGF-β signaling in T cells engendered aggressive early-onset, multiorgan, autoimmune-associated lesions with 100% mortality. Peripheral CD4+ and CD8+ T cells with TGF-β-receptor II (TGF-βRII) deficiency activated cytolytic and T helper 1 (Th1) differentiation program in a cell-intrinsic T cell receptor (TCR)-specific fashion. Furthermore, TGF-βRII deficiency blocked the development of canonical CD1d-restricted NKT cells. Instead, it facilitated generation of a highly pathogenic T cell subset exhibiting multiple hallmarks of NK cells and sharply elevated amounts of FasL, perforin, granzymes, and interferon-γ. Thus, TGF-β signaling in peripheral T cells is crucial in restraining TCR activation-dependent Th1, cytotoxic, and NK cell-like differentiation program which, when left unchecked, leads to rapidly progressing fatal autoimmunity.
Keywords: Cell type comparison

overall_design:
To better understand the basis for pathogenicity of TGF-βRII-deficient NK1.1+ T cells, we performed gene expression profiling of NK1.1+ and NK1.1− T cell subsets from Tgfbr2fl/fl x CD4-Cre mice. We limited our analysis to CD8+ T cell subsets because NK1.1+ CD8 T cells made up 70% of total NK1.1+ T cells in Tgfbr2fl/fl x CD4-Cre mice, and this T cell subset showed the greatest numerical increase compared to littermate control mice. Thus, in these experiments we used FACS-sorted NK1.1+ and NK1.1− CD8+ T cells from 15- to 17-day-old mutant mice and total CD8+ T cells from Tgfbr2fl/wt x CD4-Cre littermate controls.

mRNA expression profiles of NK1.1+ and NK1.1− CD8+ T cells from Tgfbr2fl/fl x CD4-Cre (KO) mice were compared to NK1.1− T cells from littermate control Tgfbr2fl/WT x CD4-Cre (Control) mice.

first: Julien

last: Marie

first: Denny

last: Liggit

first: Alexander

middle: Y

last: Rudensky


title: Methylglyoxal treatment of MH-S cell line induces apoptosis and immune response

status: Public on Oct 31 2006

city: Berlin

first: Helmy

last: Rachman

address: Schumannstrasse 21-22

institute: MPIIB

summary:
Mycobacteria-induced apoptosis of macrophages plays an important role in modulation of the host immune response involving TNF-alpha as major cytokine. The underlying mechanisms are still ill-defined. Here, we show for the first time that methylglyoxal (MG) and AGEs levels were elevated during mycobacterial infection of macrophages and that their increased levels mediated mycobacteria-induced apoptotic and immune response of macrophages. Moreover, we show that high levels of AGEs were formed at the sites of pulmonary tuberculosis. This observation represents the first evidence of the potential involvement of AGEs in tuberculosis and in infectious diseases in general. Global gene expression profiling of MG-treated macrophages reveals diversified potential roles of MG in cellular processes, including apoptosis, immune response, and growth regulation.   The results of this study provide new insights into intervention strategies to develop therapeutic tools against infectious diseases in which MG and AGE production plays critical roles.
Keywords: time course, replicates, immune response, apoptosis

overall_design: MH-S cells (ATCC Number: CRL-2019), an alveolar macrophage cell line, was treated with 0.8 mM MG. At different time points after treatment (30 min, 4 h, and 8 h) the cells were harvested for total RNA preparation. As negative control the cells without treatment were included. RNA preparation was performed using Trizol method. Totally three independent experiments were performed, so that each time point consists of biological triplicates.

first: Ralf-Juergen

last: Kuban

first: Stefan

last: Kaufmann


title: Gene expression profile of BAFF-stimulated B cells

status: Public on Oct 24 2006

first: Alina

last: Patke

address: 1230 York Avenue

institute: Rockefeller University

summary:
The aim of the study was to illucidate how BAFF mediates B cell survival and growth through the identification of BAFF-regulated genes.
Keywords: cell stimulation

overall_design: RNA was isolated from unstimulated B cells ("minus") or after 36 hours of treatment with 25 ng/ml of BAFF ("plus"). A fraction of cell lysate was used for extraction of total RNA (samples Total_minus and Total_plus). The rest of the cell lysate was used for polysome purification as described (Patke et. al., 2006; samples Polysome_minus and Polysome_plus)

first: Ingrid

last: Mecklenbrauker

first: Hediye

last: Erdjument-Bromage

first: Paul

last: Tempst

last: Tarakhovsky


title: p53 family members in myogenic differentiation and rhabdomyosarcoma development

status: Public on Oct 16 2006

city: Wuerzburg

first: Christof

last: Burek

address: Josef-schneider-Str. 2

department: Pathologie

institute: Universitaet Wuerzburg

summary:
The p53 family comprises the tumor suppressor p53 and the structural homologs p63 and p73. How the three family members cooperate in tumor suppression remains unclear. Here, we report different but complementary functions of the individual members for regulating retinoblastoma protein (RB) function during myogenic differentiation. Whereas p53 transactivates the retinoblastoma gene, p63 and p73 induce the cyclin-dependent kinase inhibitor p57 to maintain RB in an active, hypophosphorylated state. DeltaNp73 inhibits these functions of the p53 family in differentiation control, prevents myogenic differentiation, and enables cooperating oncogenes to transform myoblasts to tumorigenicity. DeltaNp73 is frequently overexpressed in rhabdomyosarcoma and essential for tumor progression in vivo. These findings establish differentiation control as a key tumor suppressor activity of the p53 family.
Keywords: oligonucleotide

overall_design: DeltaNp73 alpha expressing C2C12 myoblasts examined 6 and 24 hours after shifting the cells to a differentiation medium.

first: Hakan

last: Cam

first: Heidi

last: Griesman

first: Thorsten

last: Stiewe


title: primary FDC

status: Public on Oct 04 2006

city: Tsurumi, Yokohama

first: Masaki

last: Hikida

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: RCAI

country: Japan

institute: RIKEN

summary:
expression profiles of FDC and BMDC are compared
Keywords: cell type comparison

first: Yumiko

last: Nishikawa

first: Hiroshi

last: Kitamura

first: Hitoshi

last: Ohmori

first: Tomohiro

last: Kurosaki


title: Essential role of Jun family transcription factors in PU.1-induced leukemic stem cells

status: Public on Oct 15 2006

city: Boston

first: Ulrich

last: Steidl

state: MA

address: 77 Avenue Louis Pasteur

department: Hematology/Oncology

institute: Harvard Institutes of Medicine

summary:
Knockdown of the transcription factor PU.1 (Spi1) leads to acute myeloid leukemia (AML) in mice. We examined the transcriptome of PU.1 knockdown hematopoietic stem cells (HSC) in the preleukemic phase by linear amplification and genome-wide array analysis to identify transcriptional changes preceding malignant transformation. Hierarchical cluster analysis and principal component analysis clearly distinguished PU.1 knockdown from wildtype HSC. Jun family transcription factors c-Jun and JunB were among the top downregulated targets. Retroviral restoration of c-Jun expression in bone marrow cells of preleukemic mice partially rescued the PU.1-initiated myelomonocytic differentiation block. Lentiviral restoration of JunB at the leukemic stage led to reduced clonogenic growth, loss of leukemic self-renewal capacity, and prevented leukemia in transplanted NOD-SCID mice. Examination of 305 AML patients confirmed the correlation between PU.1 and JunB downregulation and suggests its relevance in human disease. These results delineate a transcriptional pattern that precedes the leukemic transformation in PU.1 knockdown HSC and demonstrate that decreased levels of c-Jun and JunB contribute to the development of PU.1-induced AML by blocking differentiation (c-Jun) and increasing self-renewal (JunB). Therefore, examination of disturbed gene expression in HSC can identify genes whose dysregulation is essential for leukemic stem cell function and are targets for therapeutic interventions.
Keywords: genetic modification

overall_design: Total RNA of HSC of PU.1 knockdown or wildtype animals (3 pools of 3 animals each) was amplified by two rounds of RT and T7 promoter-based in-vitro transcription and the resultant biotinylated cRNA was then hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

first: Frank

last: Rosenbauer

first: Roel

last: Verhaak

first: Xuesong

last: Gu

first: Alexander

last: Ebralidze

first: Hasan

last: Otu

first: Steffen

last: Klippel

first: Christian

first: Ingmar

last: Bruns

first: Daniel

last: Costa

first: Katharina

last: Wagner

first: Manuel

last: Aivado

first: Guido

last: Kobbe

first: Peter

last: Valk

first: Emmanuelle

last: Passegue

first: Towia

last: Libermann

first: Ruud

last: Delwel

last: Tenen


title: Gene Expression Profiling of PGC-1a KO mouse striata

status: Public on Oct 05 2006

city: Charlestown

first: Dimitri

last: Krainc

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital

summary:
Huntington’s Disease (HD) is an inherited neurodegenerative disease caused by a glutamine repeat expansion in huntingtin protein.  Transcriptional deregulation and altered energy metabolism have been implicated in HD pathogenesis. We report here that mutant huntingtin causes disruption of mitochondrial function by inhibiting expression of PGC-1a, a transcriptional coactivator that regulates several metabolic processes including mitochondrial biogenesis and respiration.  Mutant huntingtin represses PGC-1a  gene transcription by associating with the promoter and interfering with the CREB/TAF4-dependent transcriptional pathway critical for the regulation of PGC-1a gene expression.  Crossbreeding of PGC-1a knockout mice with HD knock-in mice leads to increased neurodegeneration of striatal neurons and motor abnormalities in the HD mice.  Importantly, expression of PGC-1a partially reverses the toxic effects of mutant huntingtin in cultured striatal neurons.  Moreover, lentiviral-mediated delivery of PGC-1a in the striatum provides neuroprotection in the transgenic HD mice.  These studies suggest a key role for PGC-1a in the control of energy metabolism in the early stages of HD pathogenesis.
Keywords: PGC-1a, striatum

overall_design: Total RNA was extracted from striata of 3 pgc1α KO mice and 3 littermate controls using the RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol. Samples were analyzed using RNA 6000 Nano LabChip kit on a 2100 Bioanalyzer (Agilent Technologies) to ensure integrity of RNA.

first: Libin

last: Cui

first: Hyunkyung

last: Jeong

first: Fran

last: Borovecki

first: Christopher

last: Parkhurst

first: Naoko

last: Tanese


title: Differentiated somatic cells are more efficient than adult stem cells for cloning by somatic cell nuclear transfer

status: Public on Oct 01 2006

city: Storrs

first: Xiuchun

last: Tian

state: CT

address: 1392 Storrs Rd. Unit 4243

department: Center for Regenerative Biology

institute: University of Connecticut

summary:
Since the creation of Dolly, the first sheep cloned via somatic cell nuclear transfer (SCNT), in 1997, more than a dozen species of mammals have been cloned using this technology. One hypothesis for the limited success of cloning  via SCNT (1-5%) is that the clones are likely derived from adult stem cells, which form an extremely small fraction in most adult tissues. Support for this hypothesis is that the cloning efficiency of full term development using embryonic stem (ES) cells as nuclear donors is 5-10 times higher than that for somatic cells as nuclear donors. Additionally, cloned pups could not be produced directly from cloned embryos derived from nuclei of differentiated B and T cells or neuronal cells. The question remains: can SCNT-derived animal clones be derived from truly differentiated somatic cells? We tested this hypothesis with mouse hematopoietic cells at different differentiation stages: hematopoietic stem cells (HSCs), progenitor cells (HPCs), and granulocytes. Surprisingly, we found that cloning efficiency increases over the differentiation hierarchy. The terminally differentiated post-mitotic granulocytes yielded the greatest cloning efficiency and we produced two cloned pups from granulocytes. We conclude that cloned mammals could be directly derived from post-mitotic differentiated somatic cells.
Keywords: cell type comparison

overall_design: single channel Affymetrix arrays to confirm cell-type specific gene expression profiles

first: Li-Ying

last: Sung

first: Shaorong

last: Gao

first: Hongmei

last: Shen

first: Hui

last: Yu

first: Yifang

last: Song

first: Sadie

last: Smith

first: Ching-Chien

last: Chang

first: Kimiko

last: Inoue

first: Lynn

last: Kuo

first: Jin

last: Lian

first: Ao

last: Li

first: Cindy

first: David

middle: P

last: Tuck

first: Sherman

last: Weissman

first: Xiangzhong

last: Yang

first: Tao

last: Cheng


title: Expression data from mouse IRF6 null and wt skin

city: St. Louis

middle: Michael

last: Alvarado

address: 4565 Scott Ave

department: Genetics

institute: Washington University in St. Louis

summary:
Transcription factor paralogs may share a common role (e.g. Hox) in staged or overlapping expression in specific tissues.   In other examples, members have distinct roles in a range of embryologic, differentiation or response pathways (e.g. Tbx, Pax). For the Interferon Regulatory Factor (IRF) family of transcription factors, mice deficient in Irf1, Irf2, Irf3, Irf4, Irf5, Irf7, Irf8 or Irf9, have defects in the immune response but display no embryologic abnormalities. Mice deficient for Irf6 have not been reported, but in humans, mutations in IRF6 cause two Mendelian orofacial clefting syndrome, and genetic variation in IRF6 confers risk for isolated cleft lip and palate.
Mice deficient for Irf6 have abnormal skin, limb and craniofacial development. Histological and gene expression analyses indicate that the primary defect is in keratinocyte differentiation and proliferation.  This study describes a novel role for an IRF family member in epidermal development.
Keywords: Comparison of tissue from two genotypes

overall_design: Skin from E17.5 mice was removed and flash frozen for RNA extraction and hybridization on Affymetrix microarrays.

first: Christopher

last: Ingraham

first: Akira

last: Kinoshita

first: Shinji

last: Kondo

first: Baoli

first: Samin

last: Sajan

first: Kurt

last: Trout

first: Margaret

last: Malik

first: Martine

last: Dunnwald

first: Stephen

last: Goudy

first: Michael

last: Lovett

first: Jeffrey

last: Murray

first: Brian

last: Schutte


title: marsh-affy-mouse-232749

status: Public on Sep 12 2006

city: Phoenix

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Malformations of cortical development are the underlying eitiology of many cases of Mental Retardation and Epilepsy.  Subtle, below the resolution of current MRI, cortical dysplasias are probably involved in many cases of MR, Epilepsy and Autism for which no diagnosis can currently be made.  Therefore, understanding the process of cortical development will be vital in diagnosing and eventual treatment of many patients with these conditions.  More specifically, the cortex forms from two major populations of neuroblasts which reach their final destination in the cortex by differerent mechanisms.  One is radial migration from ventricular neuroblasts to the cortical plate.  These cells are excititory projection neurons and glia.  The second pathway is from the ventral ganglionic eminences and tangential migration of the interneuronal population of primarily inhibitory neurons.  Much less is known about the control of the latter process, and many of these currently undiagnosed subtle malformations may stem from abnormalities of this tangential migration.  This project focuses on the understanding the control of the tangentially migrating inhibitory interneurons.
We aim to uncover the transcriptional differences between two distinct neuronal populations, GFP positive cells in the ganglionic emience and GFP positive cells within the cortical plate, in order to understand the genetic control of tangential migration.  We will acomplish this aim by targeting two different labeled transcripts againts the affymetrix mouse genome arrays.
We hypothesis that there will be distinct differences in mRNA transcription profiles between the ganglionic eminence and cortical plate within developing interneurons.  The differences in transcript profiles will be genes that regulate the migration and differentiation of these developing neurons.
Transgenic mice have been generated which express green flourscent protien (GFP) based on the activity of the Dlx 5-6 promotor.  Dlx 5-6 are highly regulated genes, and are expressed only in developing interneurons with in the embryonic brain.  The expression of this gene begins at around E8 within the medial and lateral ganglionic eminence (GE) and then remain present as cells born within these regions migrate out into the developing cortex.  Therefore, we can take advantage of these mice by harvesting embryos at a midpoint in their development (E13.5-14.5) and dissect out GFP positive cells from the ganglionic eminence and from the cortical plate.  In order to obtain enough cells to extract sufficent mRNA, we have choosen to perform microdisction of the entire GE and entire cortical plate then break up the tissue into single cell suspension and Florescent activated cell sort (FACs) the populations of GFP + and GFP - cells.  We then will extract the total RNA from the GFP postive cell populations using a Trizol based method and purify the RNA with a Quiagen column purification method.  The purified RNA will then be amplified using the Affymetrix 1 or 2 round T7 based amplification procedure in order to generate the microgram quantities of labelled cRNA.  The labelled biotin cRNA will be sent to the microarray consortium for hybridization againt the Affy mouse genome chip.  Three embryos will be pooled in order to obtain sufficent RNA and 6 GFP positive GE and cortical plate samples will be used.  The six replicates will be obtained from at least 3 different pregnant mice.
Keywords: other

first: Eric

last: Marsh


title: Expression data from mouse brain region bed nucleus of the stria terminalis, nucleus accumbens, and dorsal striatum.

status: Public on Sep 10 2006

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary:
To identify distinct transcriptional patterns between the major subcortical dopamine targets commonly studied in addiction we studied differences in gene expression between the bed nucleus of the stria terminalis (BNST), nucleus accumbens (NAc), and dorsal striatum (dStr) using  microarray analysis. We first tested for differences in expression of genes encoding transcripts for common neurotransmitter systems as well as calcium binding proteins routinely used in neuroanatomical delineation of brain regions. This a priori method revealed differential expression of corticotropin releasing hormone (Crh), the GABA transporter (Slc6a1), and prodynorphin (Pdyn)  mRNAs as well as several others. Using a gene ontology tool, functional scoring analysis, and Ingenuity Pathway Analysis, we further identified several physiological pathways that were distinct  among these brain regions. These two different analyses both identified calcium signaling, G15 coupled protein receptor signaling, and adenylate cyclase-related signaling as significantly different among the BNST, NAc, and dStr. These types of signaling pathways play important roles in, amongst other things, synaptic plasticity. Investigation of differential gene expression revealed several instances that may provide insight into reported differences in synaptic plasticity between these brain regions. The results support other studies suggesting that crucial pathways involved in neurotransmission are distinct among the BNST, NAc, and dStr, and provide insight into the potential use of pharmacological agents that may target region-specific signaling pathways. Further, these studies provide a framework for future mouse-mouse comparisons of transcriptional profiles after behavioral/pharmacological manipulation.
Keywords: Tissue type comparison

overall_design: The genome-wide geen expression of mouse brain region bed nucleus of the stria terminalis, nucleus accumbens, and dorsal striatum were analyzed by Affymetrix Mouse430_2 chip. The expression and functional profiles were compared between these 3 tissues and cross-validated from independant data published before.

last: Olsen

first: Shirlean

last: Goodwin

first: Daniel

last: Ciobanu

first: Lu

last: Lu

first: Thomas

last: Sutter

first: Danny

last: Winder


title: Differential transcript abundance in NPAS2 mutant mouse at ZT14

status: Public on Dec 16 2006

city: Philadelphia

first: Radu

middle: Daniel

last: Rudic

state: PA

address: 421 Curie Boulevard

department: Center of Experimental Therapeutics

institute: University of Pennsylvania

summary:
Investigation of RNA transcript abundance in aortic tissue of NPAS2 mutant versus wild type mice at ZT14
Keywords: Differential RNA abundance in genetic mutant

overall_design: One-way ANOVA design with Strain (NPAS mutant/WT) as the independent variable and five replicates in each group

first: Anne

last: Curtis

first: Yan

last: Cheng

last: Price

first: Dermot

last: Reilly

first: Shiv

last: Kapoor

first: Garret

last: FitzGerald


title: Nuclear organization of active and inactive chromatin domains revealed by 4C technology

status: Public on Sep 22 2006

city: Rotterdam

first: Wouter

last: de Laat

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: Erasmus MC

type:
Expression profiling by array
Other

summary:
The spatial organization of DNA in the cell nucleus is an emerging key contributor to genomic function. We have developed 4C technology, or 3C-on-chip, which allows for an unbiased genome-wide search for DNA loci that contact a given locus in the nuclear space. We demonstrate here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts. The active b-globin locus in fetal liver contacts mostly transcribed, but not necessarily tissue-specific, loci elsewhere on chromosome 7, while the inactive locus in fetal brain contacts different, transcriptionally silent, loci. A housekeeping gene in a gene dense region on chromosome 8 forms long-range contacts predominantly with other active gene clusters, both in cis and in trans, and many of these intra- and interchromosomal interactions are conserved between the tissues analyzed. Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture.
Keywords: 4C technology

overall_design: Gene expression arrays were performed in triplicate, according to standard procedures (Affymetrix). 4C experiments were performed in duplo (biologically independent samples), dye swap was included. Hybriisation was performed on dedicated micro-arrays. Probes (60-mers) were selected from the sequences 100 bp up –and downstream of HindIII sites. To prevent cross-hybridization, probes that had any similarity with highly abundant repeats (RepBase 10.09) were removed from the probeset. In addition, probes that gave more than two BLAST hits in the genome were also removed from the probeset. Sequence alignments were performed using MegaBLAST using the standard settings. A hit was defined as an alignment of 30 nt or longer.

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