title: Contribution of Nuclear and Extranuclear PolyQ to Neurological Phenotypes in Mouse Models of Huntington’s Disease

city: Seattle

first: Andrew

last: Strand

state: WA

address: 1100 Fairview Ave N.

institute: Fred Hutchinson Cancer Research Center

summary:
To dissect the impact of nuclear and extranuclear mutant htt on the initiation and progression of disease, we generated a series of transgenic mouse lines in which nuclear localization (NLS) or nuclear export sequences (NES) have been placed N-terminal to the htt exon 1 protein carrying 144 glutamines. Our data indicate that the exon 1 mutant protein is present in the nucleus as part of an oligomeric or aggregation complex. Increasing the concentration of the mutant transprotein in the nucleus is sufficient for, and dramatically accelerates the onset and progression of behavioral phenotypes. Furthermore, nuclear exon 1 mutant protein is sufficient to induce cytoplasmic neurodegeneration and transcriptional dysregulation. However, our data suggests that cytoplasmic mutant exon 1 htt, if present, contributes to disease progression.
Keywords: Trangenic mouse brain gene expression

overall_design: Five lines of transgenic mice and normal littermate controls were compared using Affymetrix MG-U74Av2 A arrays to examine gene expression in cerebellum. Each line had 3 or 4 replicates.  Profiles were made at the first age that rotorod deficits could be detected.  Some lines were also profiled at a later age when neurological impairment was more pronounced.

first: Caroline

last: Benn

first: Gillian

last: Bates

first: James

last: Olson

middle: D

first: Ben

last: Woodman


title: Assessment of gene expression changes during palatal adherence and epithelial-mesenchymal transformation

status: Public on Jul 18 2005

city: Boston

first: Damian

last: LaGamba

state: MA

address: 220 Longwood Ave.

department: Cell Biology

country: USA

institute: Harvard Medical School

summary:
Genomic analysis was performed to distinguish expression changes in murine medial edge epithelial cells during both palatal adherence and epithelial-mesenchymal transformation (EMT). Assessment of changes between sample 0 hours and sample 12 hours represent palatal adherence. Changes between sample 12 hours and sample 24 hours represent EMT.
During adherence, we found that genes necessary for TGF-beta/LEF-1 signal transduction upregulate, as well as those necessary for cell adhesion. During EMT, we observed the loss of epithelial markers and upregulation of many genes necessary to promote the transition to mesenchyme and cell migration.
Keywords = EMT
Keywords = palate
Keywords = LEF-1
Keywords = TGF-beta
Keywords = craniofacial development
Keywords: time-course

first: Ali

last: Nawshad

first: Elizabeth

last: Hay


title: Transcriptional changes during neuronal death and replacement in the adult olfactory epithelium

status: Public on Aug 01 2005

city: Lexington

first: Ranjit

middle: S

last: Shetty

state: KY

address: 800 Rose Street

department: Physiology

institute: University of Kentucky

summary:
Expression profiling of mRNA abundance in the adult mouse olfactory epithelium during replacement of OSNs forced by the bilateral ablation of the olfactory bulbs.  The experiment was done on 6 week old male C57Bl/6 mice.  Olfactory epithelium tissue samples were collected on days 1, 5, and 7 after bulbectomy.  The cellular processes activated by bulbectomy include apoptosis of mature olfactory sensory neurons, infiltration of macrophages and dendritic cells, stimulation of proliferation of basal cell progenitors, and differentation of new sensory neurons.
Keywords = olfaction
Keywords = apoptosis
Keywords = immune response
Keywords = neurogenesis
Keywords = gene silencing
Keywords = microarray
Keywords = transcription factor
Keywords = spermatogenesis
Keywords: time-course

first: Soma

middle: C

last: Bose

first: Melissa

last: Nickell

first: Jeremy

last: McIntyre

first: Debra

middle: H

last: Hardin

middle: M

last: Harris

first: Timothy

last: McClintock


title: MyoD, Myf5, myogenin, or hrGFP expressed in 2C5/7 myoD-/-;myf5-/- fibroblast cells

status: Public on Sep 07 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Gene expression changes induced by MyoD or Myf5 were examined in a double-knockout fibroblast cell line lacking endogenous functional myoD or myf5 genes. Use of this cell line precluded the possibility of auto- or cross-activation of endogenous myoD or myf5. Myogenin or hrGFP were expressed in parallel samples as controls. Following infection with retrovirus - expressing the relevant myogenic regulatory factor (MRF) from the viral LTR promoter and hrGFP through an IRES element in the same mRNA transcript - GFP+ cells were sorted by FACS and harvested for total RNA.
Keywords: other

overall_design: this experiment include 4 samples and 12 replicates


title: Gene Expression Profiles of Nondiabetic and Diabetic Obese Mice--Adipose tissue, Liver, Muscle and Islets

status: Public on Jul 12 2005

city: Madison

first: Alan

last: Attie

state: WI

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

summary:
Obesity is a strong risk factor for the development of type 2 diabetes. We have previously reported that in adipose tissue of obese (ob/ob) mice, the expression of adipogenic genes is decreased. When made genetically obese, the BTBR mouse strain is diabetes susceptible and the C57BL/6J (B6) strain is diabetes resistant. We used DNA microarrays and RT-PCR to compare the gene expression in BTBR-ob/ob versus B6-ob/ob mice in adipose tissue, liver, skeletal muscle, and pancreatic islets. Our results show: 1) there is an increased expression of genes involved in inflammation in adipose tissue of diabetic mice; 2) lipogenic gene expression was lower in adipose tissue of diabetes-susceptible mice, and it continued to decrease with the development of diabetes, compared with diabetes-resistant obese mice; 3) hepatic expression of lipogenic enzymes was increased and the hepatic triglyceride content was greatly elevated in diabetes-resistant obese mice; 4) hepatic expression of gluconeogenic genes was suppressed at the prediabetic stage but not at the onset of diabetes; and 5) genes normally not expressed in skeletal muscle and pancreatic islets were expressed in these tissues in the diabetic mice. We propose that increased hepatic lipogenic capacity protects the B6-ob/ob mice from the development of type 2 diabetes. Diabetes 52:688–700, 2003
Keywords: Genetic modifications

overall_design: Four B6-ob/ob and four BTBR-ob/ob male mice at 14 weeks of age were used in the microarray study.  RNA samples from two individuals were pooled for each tissue, and each pooled RNA sample was applied to an Affymetrix MGU74AV2 array.  Because of the scarcity of islets in the BTBR-ob/ob mice, 4 additional mice were pooled to obtain islet RNA from these animals.  Sixteen MGU74Av2 arrays (2 strains X 4 tissues X 2 replicates = 16 arrays) were used to monitor the expression level of ≈12,000 genes or ESTs.

first: Hong

last: Lan

first: Mary

middle: E

last: Rabaglia

first: Jonathan

middle: P

last: Stoehr

first: Samuel

middle: T

last: Nadler

first: Kathryn

middle: L

last: Schueler

first: Fei

last: Zou

first: Brian

last: Yandell


title: Negative control of keratinocyte differentiation by Rho/CRIK signaling coupled with up-regulation of KyoT1/2 expression

status: Public on Aug 18 2005

city: Epalinges

last: Dotto

state: VD

address: 153 Chemin de Bovaress

country: Switzerland

institute: Lausanne University

summary:
Rho GTPases integrate control of cell structure and adhesion with downstream signaling events. In keratinocytes, RhoA is activated at early times of differentiation and plays an essential function in establishment of cell-cell adhesion. We report here that, surprisingly, Rho signaling suppresses downstream gene expression events associated with differentiation. Similar inhibitory effects are exerted by a specific Rho effector, CRIK (Citron kinase), which is selectively down-modulated with differentiation, thereby allowing the normal process to occur. The suppressing function of Rho/CRIK on differentiation is associated with induction of KyoT1/2, a LIM domain protein gene implicated in integrin-mediated processes and/or Notch signaling. Like activated Rho and CRIK, elevated KyoT1/2 expression suppresses differentiation. Thus, Rho signaling exerts an unexpectedly complex role in keratinocyte differentiation, which is coupled with induction of KyoT1/2, a LIM domain protein gene with a potentially important role in control of cell self renewal.
Keywords: epithelial cell differentiation | gene expression | Rho signaling | stem cell

overall_design:
Total RNA from primary mouse keratinocytes infected with
adeno-GFP, adeno-RhoV14, or adeno-CRIK-SK for 48 h was
used for biotin-labeled cRNA probe preparation and hybridization
to Affymetrix U74A gene chips. cRNA
probes from each condition were tested in duplicate.

first: Maddalena

last: Grossi

first: Agnès

last: Hiou-Feige

first: Alice

last: Tommasi di Vignano

first: Enzo

last: Calautti

first: Paola

last: Ostano

first: Sam

last: Lee

first: Giovanna

last: Chiorino

first: GianPaolo


title: Gene expression profile in B cells from Xid and Btk KO mice

status: Public on Jun 21 2005

city: Huddinge

first: Jessica

last: Lindvall

address: Hälsovägen 7

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary:
Bruton's tyrosine kinase (Btk) is important for B lymphocyte development. To identify genes that are differentially expressed in primary B cells lacking functional Btk, splenocytes from X-linked immunodeficiency (Xid), Btk knockout (KO) and immunocompetent CBA mice, were used in microarrays containing more than 12,000 genes and expressed sequence tags (ESTs). We found 4515 transcripts expressed in duplicate experiments in all three strains. Out of these, 38 were differentially expressed genes (21 up-regulated >2 fold and 17 down-regulated <-2 fold) between CBA and Btk defective mice. Ten out of these genes were selected and quantitative Real-Time PCR was conducted for validation and further investigation. Real-Time experiments correlated nicely with the microarray data.

No definitive phenotypic difference has previously been reported between Xid and Btk KO mice. We found 7 genes, whose expression differed (>2 fold) between the two strains. Moreover, when the 38 genes, which differed between immunocompetent CBA and Btk defective mice were ranked according to fold-increase, the levels in Btk KO mice were significantly more altered. This suggests that the defect in Btk KO mice is more severe and demonstrates that the mutant Btk protein in Xid mice does not generally function as dominant negative form.
Keywords: Btk, DNA microarray, Xid, Btk KO, Real-Time PCR

overall_design: 6 Affymetrix U74Av2 GeneChip arrays was run. Three initially with CBA, Xid and Btk KO mice and then additional three chips with new RNA preperations from new CBA, Xid and Btk KO mice.

first: K. Emelie

last: Blomberg

first: Anna

last: Berglöf

first: Qian

last: Yang

first: C. I. Edvard

last: Smith

first: Tahmina

last: Islam


title: Pressure overload cardiac hypertrophy

status: Public on Jun 29 2005

city: Durham

first: Maria

last: Mirotsou

state: NC

institute: Duke University

summary:
Expression profiling of hearts from FVB males subjected to cardiac pressure overload by transverse aortic constriction (TAC). TAC performed on 8-10 weeks month old males and females. Hearts examined  30 weeks after surgery.
Keywords: ordered


title: Gene-Expression Profiles in IRS Knockout Brown Preadipocytes

status: Public on Jun 01 2005

first: Atul

last: Butte

address: 300 Longwood Avenue

institute: Children's Hospital, Boston

summary:
Insulin and IGF-1 promote adipocyte differentiation via complex and overlapping signalling networks.  Here we used microarray analysis of brown preadipocytes derived from wild-type and insulin receptor substrate (IRS) knockout (KO) animals, which exhibited progressively impaired differentiation, to define the set of genes that predict adipogenic potential in these cells.  374 genes/ESTs were identified whose expression in preadipocytes correlated with their ultimate ability to differentiate.  Many of these genes were related to early adipogenic events, including genes involved in extracellular matrix, cytoskeletal organization, growth arrest, post-mitotic clonal expansion, and inhibitors of adipogenesis, including preadipocyte factor-1 and multiple members of the Wnt-signalling pathway.  Reconstitution of IRS-1 KO cells with IRS-1 reversed these changes and restored the ability to differentiate.  Several of these genes showed concordant changes in brown adipose tissue in vivo.  Necdin was markedly increased in IRS-1 KO cells that could not differentiate, and knockdown of necdin restored brown adipogenesis with down-regulation of Pref-1 and Wnt10a expression.  We demonstrated a necdin-E2F4 interaction repressing PPARg transcription.  IRS proteins regulated necdin via a CREB dependent pathway, defining a signalling network involved in brown preadipocyte determination.
Keywords = brown fat
Keywords = preadipocyte
Keywords = adipogenesis
Keywords = mouse
Keywords: parallel sample

first: Yu-Hua

last: Tseng

middle: J

first: Efi

last: Kokkotou

first: Vijay

middle: K

last: Yechoor

first: Cullen

last: Taniguchi

first: Kristina

last: Kriauciunas

first: Aaron

last: Cypess

first: Michio

last: Niinobe

first: Kazuaki

last: Yoshikawa

first: Mary

last: Patti

first: C

middle: R

last: Kahn


title: Cardiac hypertrophy and failure

status: Public on Jun 15 2005

summary:
Analysis of cardiac specific AT1 transgenic mice undergoing cardiac failure, cardiac hypertrophy and wild type aged matched controls. For detailed description of the AT1 Tg mice please refer to:
Paradis P, Dali-Youcef N, Paradis FW, Thibault G, Nemer M.
Overexpression of angiotensin II type I receptor in cardiomyocytes induces cardiac hypertrophy and remodeling.
Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):931-6. PMID: 10639182 [PubMed - indexed for MEDLINE]
Keywords: ordered


title: Cardiac and skeletal muscle gene expression profiles in dysferlin deficient mice

status: Public on Jul 10 2005

city: Berlin

first: Oliver

last: Hummel

department: Experimental Genetics of Cardiovascular Diseases

country: Germany

institute: Max-Delbrück-Center

summary:
Dysferlin is expressed in skeletal and cardiac muscle. However, dysferlin deficiency, namely limb girdle muscular dystrophy 2B (LGMD2B) and Myoshi myopathy, results in skeletal muscle weakness and spares the heart. This dichotomy could be caused by differential regulation of protective mechanisms. Therefore, we compared intraindividual mRNA expression profiles between cardiac and skeletal muscle in dysferlin-deficient SJL/J mice  and normal C57BL/6 mice.
Keywords: parallel sample

overall_design:
20 chips were analyzed. They represent 4 groups of 5 replicates each.
The 4 groups are cardiac (LV) and skeletal muscle of normal and dysferlin deficient mice.
Tissues from normal mice are the controls in comparison to tissues of dysferlin deficient mice.

first: Wenzel

last: Katrin

first: Spuler

last: Simone


title: Donarum-3R01NS040270-03S1

status: Public on Jul 06 2005

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Succinate semialdehyde dehydrogenase (SSADH) deficiency is a rare autosomal recessive disorder effecting approximately 350 people around the world. Patients suffering from SSADH deficiency experience language acquisition failure, memory deficiencies, autism, increased aggressive behaviors, and seizures. There is a chemical buildup of both gamma-aminobutyric acid (GABA) and gamma-hydroxybutyric acid (GHB) in the neurological system of these patients. The Aldh5a1-/- knock out mouse model of SSADH deficiency shows the same chemical imbalances as the human disease, with additional fatal tonic-clonic seizures at three weeks of age.  The elucidation of seizure causing pathways will facilitate treatment of seizure phenotypes in diseases with related epilepsy.
Gene expression patterns within the hippocampus, cerebellum, and cortex of SSADH deficient mice (Aldh5a1-/- mice) will be compared to wild type mice at a time point immediately prior to fatal seizures.
We hypothesis that the SSADH deficient mice experience a dysfunction of glutamate/GABA/ glutamine neurotransmitter cycle linked to astroglial metabolism and/or uptake of neuronally-released glutamate. The increased levels of GHB and GABA lead to down regulation of GABA-B-Receptor leading to seizures. The SSADH deficient phenotype may also be caused by ongoing oxidative damage and the pathological role of succinic semialdehyde.
SSADH deficient mice (Aldh5a1-/- knock out) exhibit fatal seizures around three weeks of age. Mutant and wild type mice will be sacrificed between 17 and 19 days of life, and brain sections will be extracted and frozen (using a standard protocol). Hippocampus, cerebellum, and cortex from three mutant mice and three wild type mice will individually be expression profiled on the Affymetrix platform, giving a total of eighteen arrays. Comparative analysis will then be carried out, evaluating the transcript differences between mutant and wild type mice in each brain region.
Keywords: other

overall_design: as above

first: E

middle: A

last: Donarum


title: Wild type and Ppara KO, CL time course

status: Public on Jun 10 2005

city: Detroit

first: James

last: Granneman

state: MI

institute: Wayne State University

summary:
Time course og gene expression changes in white fat of wildtype and Ppara KO mice during treatment with the adrb3 agonist CL 316,234.
Keywords: time-course


title: C57Bl6 3nmol/hr CL 316243 Time course

summary:
TIme course of gene expression changes in epididymal white adipose tissue of  3-4 month old male Bl6 mice treated with CL 316243 for 0,1,3 or 6 days
Keywords: time-course


title: Dysferlin deficiency modulates the proximal-distal muscle transcriptome

status: Public on May 06 2005

city: Newcastle-upon-Tyne

first: Steve

last: Laval

country: United Kingdom

institute: Institute of Human Genetics

summary:
By comparing the transcriptome from proximal (quadriceps femoris, QF) and distal (tibialis anterior, TA)muscle groups in dysferlin deficient mouse muscle (the SJL mutation bred onto C57BL/10 to produces C57BL/10-SJL.Dysf) with proximal and distal muscle groups from control C57BL/10 mice of an equivalent age (3-weeks old, prior to the onset of overt pathology) we aim to address the issues of muscle selectivity in this this form of muscular dystrophy.
Keywords: parallel sample

first: Maja

last: von der Hagan

first: Reginald

last: Bittner

first: Volker

last: Straub

first: Louise

middle: V

last: Anderson

first: Kate

last: Bushby


title: Fetal mouse heart, TCDD dose-response series

city: Albuquerque

first: Evan

middle: A.

last: Thackaberry

state: NM

address: 2502 Marble N.E.

department: College of Pharmacy

institute: University of New Mexico

summary:
Pregnant C57Bl6N mice were treated with 0 (corn oil), 1.5, 3.0, or 6.0 ug/kg TCDD on gd14.5.  Fetal hearts were collected on gd17.5.  Hearts from each litter were pooled onto one chip.  4 replicates of each condition were run on affymetrix MG_U74Av2 chips, using standard affymetrix protocols and controls.
Keywords: dose-response, 3 doses plus corn oil control, 4 replicates

overall_design: 0 (corn oil), 1.5, 3.0, or 6.0 ug/kg TCDD, 4 replicates of each

last: Walker


title: Comparative Analysis of MMTV-neu tumors, preneoplastic MMTV-neu mammary gland, and Wild-type controls

status: Public on May 03 2005

city: Cleveland

first: Melissa

last: Landis

state: OH

address: 2109 Adelbert

department: Pharmacology

institute: Case Western Reserve School of Medicine

summary:
To identify early events of erbB2-induced mammary tumorigenesis, we compared datasets from 14 genechip experiments including MMTV-neu tumors, preneoplastic neu mammary gland (adjacent neu), and age-matched, wild-type control mammary glands

Keywords = transgenic mouse
Keywords = MMTV-neu
Keywords = erbB2
Keywords = HER2
Keywords = mammary tumor
Keywords: ordered

first: Darcie

last: Seachrist

first: Marjorie

last: Montanez-Wiscovich

first: David

last: Danielpour

first: Ruth

last: Keri


title: Ikaros mutant thymic tumors

city: Illkirch

first: Susan

last: Chan

address: 1, rue Laurent Fries

country: France

institute: IGBMC

summary:
The experiment was to compare leukemic T cells from thymic lymphomas from homozygote mice for the IkL/L hypomorphic mutation and non-transformed thymocytes, either of WT or IkL/L genotype. The aim was to identify a gene expression signature specific to the IkL/L tumors.
Keywords = thymic lymphoma Ikaros
Keywords: other

first: Philippe

last: Kastner


title: Ablation of Telomerase and Ku86

status: Public on May 12 2005

city: Madrid

first: Peter

last: Klatt

department: Molecular Oncology Program

country: Spain

institute: Spanish National Cancer Center (CNIO)

summary:
Transcriptome of murine testis from wild type mice and mice lacking telomerase for three generations (G3-Terc), Ku86 or  both telomerase and Ku86.
Keywords: ordered

first: Sonia

last: Franco

first: Andrés

last: Canela

first: María

last: Blasco


title: Whole brain gene expression in X-monosomic and normal female mice

status: Public on May 02 2005

city: Storrs

first: Adam

last: Raefski

state: CT

address: 354 Mansfield Road

department: MCB

institute: University of Connecticut

summary:
Whole brain gene expression was examined in the following strains of mice:
1. P0 maternal monosomic 39,Xm females, C57BL/6J x C3H/Paf
2. P0 paternal monosomic 39, Xp females, In(X)/C3H x C57BL/6J
3. P0 normal 40,XX females, In(X)/C3H x C57BL/6J
4. P0 normal 40,XX females, C57BL/6J x C3H/Paf
Keywords = imprinting
Keywords = mammalian genetics
Keywords = X-linked
Keywords = brain
Keywords: other


title: promiscuous gene expression in the mouse thymus

status: Public on Apr 28 2005

city: Heidelberg

first: Benedikt

last: Brors

institute: German Cancer Research Center (DKFZ)

summary:
Gene expression in different thymic stromal cells and subsets thereof was analyzed in 6-12 week old wild type (C57BL/6) and Aire knock-out (mixed background) mice. Thymic stromal cells were purified by sequential enzymatic digestion (collagenase, collagenase/dispase and trypsin) followed by gradient centrifugation and FACS sorting. Sort criteria were as follows: dendritic cells (CD11c+, F4/80 -), macrophages (F4/80+, CD11c-), cTECs (CD45–/lo, CDR1/Ly51+, Ep-CAM+) and mTECs (CD45–/lo, CDR1/Ly51–, Ep-CAM+). mTECs of wild-type and Aire knock-out mice were further subdivided according to CD80 expression levels.
For microarray analysis total RNA from thymic stromal cell samples of two independent experiments was pre-amplified and biotinylated by two rounds of cDNA synthesis and in vitro transcription. Fluorescence readings were evaluated by using Microarray Suite 5.0 software.
Keywords = thymus
Keywords = promiscuous gene expression
Keywords = AIRE
Keywords: ordered

first: Jens

last: Derbinski

first: Jana

last: Gaebler

first: Sascha

last: Tierling

first: Sunitha

last: Jonnakuty

first: Manfred

last: Hergenhahn

first: Leena

last: Peltonen

first: Jörn

last: Walter

first: Bruno

last: Kyewski


title: Aging Liver Profiles of Long Lived Pit-1 Mutant Mouse (Snell) and Wild Type Controls

status: Public on Aug 16 2005

city: Galveston

first: James

last: DeFord

state: TX

address: 301 University Blvd.

department: Human Biological Chemistry and Genetics

institute: University of Texas at Galveston

summary:
To compare and contrast genetic signatures from livers of young and aged Snell dwarf mice with their wild type controls.
Keywords: Aging

overall_design: 25 micrograms of liver RNA was isolated from each of 6 aged (3 dwarf, 3 wild type) and 8 young (4 dwarf, 4 wild type) mice for use in hybridization of Affymetrix gene chips according to Affymetrix protocols.

first: Michelle

last: Guigneaux

first: William

last: Boylston

first: John

last: Papaconstantinou


title: Expression profile of conditional knock out of beta-catenin by K19-CRE at E7.5

status: Public on Apr 13 2005

city: Toronto

first: Brian

last: Cox

state: Ontario

address: University Ave, Rm. 884

institute: Samuel Lunenfeld Research Institute

summary:
expression profile of conditional knock out of beta-catenin by K19-CRE at E7.5. Tested a wild type with two alleles of beta-catenin, a heterzyote with one deleted allele and the conditional null in the domain on cytokeratin 19 driven CRE expression
Keywords: other

first: Heiko

last: Lickert

first: Christian

last: Wehrle

first: Makoto

last: Taketo

first: Rolf

last: Kemler

first: Janet

last: Rossant


title: Effect of LIF on ES cells overexpressing Akt

status: Public on Apr 12 2005

city: Suita

first: Shoko

last: WATANABE

country: Japan

institute: Osaka university

summary:
Embryonic stem (ES) cells can self-renew indefinitely without losing their differentiation ability to any cell types. Phosphoinositide-3 kinase (PI3K)/Akt signaling plays a pivotal role in various stem cell systems, including the formation of embryonic germ (EG) cells from primordial germ cells and self-renewal of neural stem cells. Here, we show that myristoylated, active form of Akt (myr-Akt) maintained the undifferentiated phenotypes in mouse ES cells without the addition of leukemia inhibitory factor (LIF). The effects of myr-Akt were reversible, because LIF dependence and pluripotent differentiation activity were restored by the deletion of myr-Akt. In addition, myr-Akt-Mer fusion protein, whose enzymatic activity is controlled by 4-hydroxy-tamoxifen, also maintained the pluripotency of not only mouse but also cynomolgus monkey ES cells. These results clearly demonstrate that Akt signaling sufficiently maintains pluripotency in mouse and primate ES cells, and support the notion that PI3K/Akt signaling axis regulates 'stemness' in a broad spectrum of stem cell systems.
Keywords: other


title: PGA_Mouse_Rat_Lung_MV

status: Public on Mar 08 2005

city: Baltimore

first: Shwu-Fan

last: Ma

state: MD

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins University

summary:
This series contain mouse and rat lung samples treated with mechanical ventilation and corresponded controls.
Keywords: other

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

first: Dmitry

middle: N

last: Grigoryev

first: Angela

last: Taylor

first: Stephanie

last: Nonas

first: Saad

last: Sammani

first: Shui

last: Ye

first: Joe

middle: G

last: Garcia


title: Pre-Neoplastic Stage of Medulloblastoma

status: Public on Mar 22 2005

city: Chicago

first: Simon

last: Lin

state: IL

department: Bioinformatics Core

institute: Northwestern University

summary:
SUMMARY

Medulloblastoma is the most common malignant brain tumor in children. It is thought to result from transformation of granule cell precursors (GCPs) in the developing cerebellum, but little is known about the early stages of the disease. Here we identify a pre-neoplastic stage of medulloblastoma in patched heterozygous mice, a model of the human disease. We show that pre-neoplastic cells are present in the majority of patched mutants, although only 16% of these mice develop tumors. Pre-neoplastic cells, like tumor cells, exhibit activation of the Sonic hedgehog pathway and constitutive proliferation. Importantly, they also lack expression of the wild-type patched allele, suggesting that loss of patched is an early event in tumorigenesis. While pre-neoplastic cells resemble GCPs and tumor cells in many respects, they have a distinct molecular signature. Genes that mark the pre-neoplastic stage include regulators of migration, apoptosis and differentiation, processes critical for normal development but previously unrecognized for their role in medulloblastoma. The identification and molecular characterization of pre-neoplastic cells provides insight into the early steps in medulloblastoma formation, and may yield important markers for early detection and therapy of this disease.

ANIMALS

Patched heterozygous mice (Goodrich et al., 1997) were obtained from Matthew Scott's lab at Stanford, and maintained by breeding with 129X1/SvJ mice from Jackson Laboratories. Math1-GFP transgenic mice (Lumpkin et al., 2003) were provided by Jane Johnson at UT Southwestern Medical Center. Math1-GFP/patched+/- mice were generated by crossing patched heterozygotes with Math1-GFP mice, and then backcrossing to Math1-GFP mice three times before further analysis. All mice were maintained in the Cancer Center Isolation Facility at Duke University Medical Center.

ISOLATION OF CELLS

Granule cell precursors (GCPs) were isolated from 7-day-old (P7) patched+/- mice; preneoplastic cells were obtained from 6 week-old patched mutants; and tumor cells were obtained from 10-25-week old patched mutants displaying physical and behavioral signs of medulloblastoma. Cells were isolated from each source using a protocol described in (Wechsler- Reya and Scott, 1999). Briefly, cerebella were digested in solution containing 10 U/ml papain Oliver et al. Pre-Neoplastic Stage of Medulloblastoma - 8 - (Worthington, Lakewood, NJ) and 250 U/ml DNase (Sigma) and triturated to obtain a cell suspension. This suspension was centrifuged through a step gradient of 35% and 65% Percoll (Amersham Biosciences, Piscataway, NJ), and cells were harvested from the 35%-65% interface. Cells were resuspended in serum-free culture medium consisting of Neurobasal containing B27 supplement, sodium pyruvate, L-glutamine, and penicillin/streptomycin (all from Invitrogen, Carlsbad, California) and counted on a hemacytometer. Cells used for RNA isolation were centrifuged and flash frozen in liquid nitrogen. For proliferation assays or immunostaining, cells were plated on poly-D-lysine (PDL)-coated tissue culture vessels and incubated in serum-free culture medium.

MICROARRAY HYBRIDIZATION AND ANALYSIS

RNA from GCPs, pre-neoplastic cells and tumor cells (isolated as described above, but not FACS-sorted) and from normal adult cerebellum (not dissociated) was converted to cDNA using the Superscript Choice cDNA kit (Invitrogen) and a T7-dT(24) primer (Genset/Proligo, Boulder, CO). cRNA was generated using a T7-transcription/labeling kit from Enzo Life Sciences and hybridized to Affymetrix U74Av2 chips (Affymetrix, Santa Clara, CA). Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA).

CORRESPONDING AUTHOR

Robert J. Wechsler-Reya*
Dept. of Pharmacology & Cancer Biology,
Duke University Medical Center Box 3813, Durham, NC 27710
Phone: 919-613-8754. Fax: 919-668-3556. Email: rw.reya@duke.edu
Keywords = medulloblastoma
Keywords = brain tumor
Keywords = pre-neoplastic
Keywords = patched
Keywords = hedgehog
Keywords = migration
Keywords = differentiation

first: R

last: Wechsler-Reya

first: Trudy

last: Oliver

first: Tracy

last: Read

first: Jessica

middle: D

last: Kessler

first: Anriada

last: Mehmeti

first: Jonathan

middle: F

last: Wells

first: Trang

last: Huynh

first: Robert


title: Targets of Wnt-1 in C57MG

status: Public on Apr 07 2005

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
RNA from murine mammary C57MG cells transfected with an empty control vector (PLNCx) or an expression vector encoding Wnt-1 was isolated and analyzed on Affymetrix MG-U74Av2 arrays. Sample preparation was done as recommended by the manufacturer. Images were analyzed using Affymetrix Microarray Suite 4.0 software. Comparison of Wnt-1 expressing and control cells revealed Wnt-1 targets.
Keywords: ordered

first: Slava

last: Ziegler

first: Sonja

last: Röhrs

first: Tarik

last: Möröy

first: Ingrid

last: Vetter

first: Oliver

last: Müller


title: Anergy Induction

status: Public on Feb 23 2005

first: Michael

last: Lutz

department: Oncology

institute: Johns Hopkins

summary:
pooled mRNA (2, 4, 6 hrs) from A.E7 T cells under conditions which promote or inhibit anergy induction
Keywords: ordered

last: Powell

first: Charles

last: Drake

first: Jeanne

last: Kowalski

first: Ronald

last: Schwartz


title: PTH regulation of genes in osteoblastic cells (OB-6)

status: Public on Mar 01 2005

city: Little Rock

first: Xiao-Dong

last: Chen

state: AR

institute: University of Arkansas for Medical Sciences

summary:
The level of 12,488 transcripts in osteoblastic OB-6 cells was quantified with Affymetrix U74A chips under basal conditions (0 time), and after addition of 50 nM PTH for 30 or 60 minutes
Keywords: time-course

first: Scott

last: Stewart

first: Stavros

middle: C

last: Manolagas

last: Jilka


title: Thymocyte Negative Selection

status: Public on Apr 05 2005

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
Fetal thymic organ culture (FTOC)  DC2.5 CD4+CD8+ thymocytes from B6g7 or NOD background.  0 or 16 hour after addition of the BDC mimitope
Keywords = BDC2.5 FTOC thymocyte
Keywords: dose response

first: Silvia

last: Zucchelli

first: Phil

last: Holler

first: Tetsuya

last: Yamagata

first: Matthew

last: Roy

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: A Bioinformatics Analysis of Memory Consolidation Reveals Involvement of the Transcription Factor c-Rel

status: Public on Mar 30 2005

city: Pasadena

first: Sangdun

last: Choi

state: CA

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

summary:
Consolidation of long-term memory (LTM) is a complex process requiring synthesis of new mRNAs and proteins. Many studies have characterized the requirement for de novo mRNA and protein synthesis; however, few studies have comprehensively identified genes regulated during LTM consolidation. We show that consolidation of long-term contextual memory in the hippocampus triggers altered expression of numerous genes encompassing many aspects of neuronal function. Like contextual memory formation, this altered gene expression required NMDA receptor activation and was specific for situations in which the animal formed an association between a physical context and a sensory stimulus. Using a bioinformatics approach, we found that regulatory elements for several transcription factors are over-represented in the upstream region of genes regulated during consolidation of LTM. Using a knock-out mouse, we found that c-rel, one of the transcription factors identified in our bioinformatics study, is necessary for hippocampus-dependent long-term memory formation.
Keywords: other

first: Jonathan

last: Levenson

first: Sun-Young

last: Lee

first: Yun Anna

last: Cao

first: Kim

last: Worley

first: Hui

last: Zheng

first: Melvin

middle: I

last: Simon

first: David

last: Sweatt


title: Cross-platform comparability of microarray data

status: Public on Apr 21 2005

city: Research Triangle Park

first: Kenneth

middle: Lyon

last: Phillips

institute: Paradigm Array Labs

summary:
To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms and methods to accommodate this variability.  RNA expression data were generated in seven laboratories, comparing two standard RNA samples using twelve microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories.  Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor.  Reproducibility between laboratories dramatically increased when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization.  Nonetheless, concordance could be found across different laboratories and platforms when data were analyzed in terms of enriched Gene Ontology categories.  These findings indicate that microarray results generated by multiple sites and platforms can be comparable, and that multi-investigator teams will maximize data comparability by adopting a common platform and a common set of procedures to generate compatible data.

Keywords: other

first: Theodore

last: Bammler

first: Richard

last: Beyer

first: Fredrico

middle: M

last: Farin

first: Terrance

last: Kavanagh

first: Sean

last: Quigley

first: Roger

last: Bumgarner

first: Kathleen

last: Kerr

first: Lixuan

last: Qin

first: Sanchita

last: Bhattacharya

first: Rebecca

last: Fry

last: Milton

first: Leona

last: Samson

first: Shirley

last: Xuan

first: Gary

last: Boorman

first: Michael

last: Cunningham

first: Abee

last: Boyles

first: Holly

last: Dressman

middle: H

last: Freedman

first: Yu-Ju

last: Li

last: Schwartz

first: Susan

last: Slifer

first: Marcy

last: Speer

first: Blair

middle: U

last: Bradford

first: Shibing

last: Deng

first: William

last: Kaufmann

first: Charles

last: Perou

first: Ivan

last: Rusyn

first: Yan

last: Shi

first: James

last: Swenberg

first: Ru

last: Tian

first: Pierre

last: Bushel

first: Rickie

last: Fannin

first: Jianying

middle: S

last: Paules

first: Stella

middle: O

last: Sieber


title: Mouse ES cells versus XEN cells

status: Public on Jan 29 2005

city: Edinburgh

first: Tilo

last: Kunath

address: 5 LIttle France Drive

department: Centre for Regenerative Medicine

institute: University of Edinburgh

summary:
Comparison of mouse ES cells and three different XEN cell cultures.

Three XEN cell cultures: Two different strains (IM8A1 is PO, and XEN1-3 is ICR). And two different culture conditions (IM8A1-I versus IM8A1-II).

Three biological replicates of XEN cell RNA were submitted to the Centre for Applied Genomics at the Hospital for Sick Children (Toronto, Canada) for preparation of cRNA and hybridization to the mouse U74Av2 Affymetrix gene array. QIAGEN RNeasy midi kit (QIAGEN Inc., Santa Clarita, CA) was used to extract total RNA from all samples according to manufacturer's instructions. The samples were (1) XEN1-3 cells at passage 18 (ICR strain, male) cultured on gelatin with 70% EMFI-CM, (2) IM8A1 cells at passage 27 (PO strain) cultured on gelatin with 70% EMFI-CM, (3) IM8A1 cells at passage 27 cultured on tissue culture plastic in RPMI 1640 (Gibco) supplemented with 20% FBS (CanSera, Rexdale, Canada), 1 mM sodium pyruvate, 2 mM L-glutamine, 50 mg/ml each of penicillin/streptomycin (all from Gibco), 100 uM b-mercaptoethanol (Sigma) for 4 days. RNA was also obtained from R1 ES cells grown in the absence of EMFIs in the above medium with LIF.
Keywords = ES cells
Keywords = XEN cells
Keywords: ordered

first: Janet

last: Rossant


title: Progression to Islet Destruction in a Cyclophosphamide-Induced Transgenic Model

status: Public on Feb 09 2005

first: CBDM

last: Lab

state: MA

summary:
BDC2.5/NOD mice were treated with cyclophosphamide to induce type 1 diabetes.  Their pancreatic islets were analyzed before treatment (Day 0) and as treatment progressed (Days 1 through 3)
Keywords = type I diabetes
Keywords = cyclophosphamide
Keywords = BDC2.5
Keywords = NOD
Keywords = pancreas
Keywords = islets
Keywords: time-course

first: Michael

last: Matos

first: Richard

last: Park

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Phenotypic Anchoring of Gene Expression Changes during Estrogen-Induced Uterine Growth

status: Public on Jan 28 2005

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

institute: Unilever

summary:
Immature (19/20 days of age) Alpk:APfCD-1 mice were treated with arachis oil (AO) vehicle or 0.4mg/kg 17beta-estradiol (E2), via a single subcutaneous injection, and sacrificed at 1hr, 2hr, 4hr, 8hr, 24hr, 48hr, 72hr post dose.
Keywords = estrogen
Keywords = gene expression
Keywords = microarray
Keywords = phenotypic anchoring
Keywords = uterus
Keywords: time-course

first: Jonathan

last: Moggs

first: Helen

last: Tinwell

first: Tracey

last: Spurway

last: Chang

first: Ian

last: Pate

first: David

middle: J

last: Moore

first: Anthony

last: Soames

first: Ruth

last: Stuckey

last: Currie

first: Tong

last: Zhu

last: Kimber

first: John

last: Ashby

first: George

last: Orphanides


title: Subconfluent and confluent aortic endothelial cells

status: Public on Jan 20 2005

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

summary:
Gene expression changes in subconfluent mouse aortic endothelial cells were compared with confluent endothelial cells. Compartmental analysis showed coordinater response in several endothelial-specific functions and organelles (endoplasmic reticulum, Golgi, lysosomes, peroxisomes) which were downregulated, and upregulation of the microtubular system and proliferation.
Keywords = endothelium
Keywords = confluent
Keywords = subconfluent
Keywords = organelles
Keywords: other

first: Padmavarathy

last: Krishnan

first: Mirela

last: Anghelina

first: Catalin

last: Barbacioru

first: Sumant

last: Kulkarni

first: Nicanor


title: Normal Ad Libitum

status: Public on Jan 10 2005

city: Riverside

first: Stephen

middle: R.

last: Spindler

institute: University of California, Riverside

summary:
Female Ames dwarf mouse (+/+ or +/df) with ad libitum access to water and standard pelleted food (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops.  Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted).
Keywords = Ames dwarf
Keywords = mouse
Keywords = Affymetrix
Keywords = caloric restriction
Keywords: parallel sample

first: Tomoshi

last: Tsuchiya

first: Joseph

last: Dhahbi

first: Xinping

last: Cui

first: Patricia

middle: L

last: Mote

first: Andrzej

last: Bartke

middle: R


title: caloric restriction

summary:
Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted).

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Dwarf Calorie Restricted

summary:
Female Ames dwarf mouse (df/df) with ad libitum access to water and fed 30% less of the standard pelleted diet with respect to the amount consumed by female ad libitum fed df/df mice (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops.  Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen.  Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted).
Keywords = Ames dwarf
Keywords = mouse
Keywords = Affymetrix
Keywords = caloric restriction
Keywords: parallel sample


title: Dwarf Ad libitum

summary:
Female Ames dwarf mouse (df/df) with ad libitum access to water and standard pelleted food (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops.  Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted).
Keywords = Ames dwarf
Keywords = mouse
Keywords = Affymetrix
Keywords = caloric restriction
Keywords: parallel sample


status: Public on Feb 12 2005

city: Montreal

first: Peter

last: Lee

state: QC

address: 740 Dr Penfield

department: Dept of Human Genetics

institute: McGill University

summary:
Analysis of liver, heart, spleen and lung
Keywords: other

first: Rob

last: Sladek

first: Celia

middle: MT

last: Greenwood

first: Bing

last: Ge

first: Emil

last: Skamene

first: Thomas

last: Hudson


title: ER stress time course (WT vs CHOP-/-)

status: Public on Dec 17 2004

city: New York

first: Stefan

last: Marciniak

state: NY

department: Molecular Pathogenesis

institute: Skirball

summary:
Primart mouse embryonic fibroblasts (pass 3 to 4) were treated with tunicamycin (2 micrograms/ml) for specified times - genotypes were WILDTYPE and CHOP-/-. Each time point n=4
Keywords: ordered


title: Engagement of TCR with antibodies

status: Public on Jan 01 2005

city: La Jolla

first: Nicholas

middle: Robert John

last: Gascoigne

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

summary:
Comparison of gene expression changes in CD4+CD8+ thymocytes following engagement of TCR with anti-Valpha or Vbeta antibodies
Keywords: parallel sample

first: Nathalie

last: Niederberger

first: Lukas

middle: K

last: Buehler

first: Jeanette

last: Ampudia


title: Skeletal muscle of adrenalectomized mice with and without a glucocorticoid injection 3 or 24 h previously (MG-U74Av2)

status: Public on Jan 06 2005

city: Quebec City

first: Andre

last: Boivin

state: Quebec

address: 2705 Boul. Laurier

department: SAGE Laboratory

institute: Laval University Hospital Center Research Center

summary:
Forty male C57BL6 mice 12-15 weeks old fed chow ad libitum. 30 mice underwent adrenalectomy (Adx) and 10 others a sham-Adx. Three or 24h before tissue sampling, groups of 10 mice received an I.P. injection of cortisol (0.1 mg per mice), while the remaining Adx and intact mice received an I.P. injection of the vehicle (ethanol) 24 h prior to the sacrifice. All mice were killed within a period of a few hours. Gastrocnemius muscle were dissected and pooled together for each one of the four groups. Total RNA was isolated by Trizol. Samples were processed following the labeling protocol from Affymetrix. In the MG-U74A2, each of the 12488 murine transcripts are represented by 16 probe pairs of 25mer. Images were scanned using a GeneChip scanner 3000 with autoloader, and analyzed with the MAS 5.0 software (Affymetrix). The ratio of fluorescence intensities for the 5' end and the 3' end of beta-actin and glyceraldehyde 3-phosphate dehydrogenase was less than 2. This microarray analysis was performed once.
Keywords = Skeletal muscle
Keywords = gastrocnemius
Keywords = adrenalectomy
Keywords = glucocorticoids
Keywords: other

first: A

last: Calvo

first: Mayumi

last: Yoshioka

first: Jonny

last: St-Amand


title: The role of basal immunoglobulin signaling in immature B cell development

status: Public on Feb 03 2005

city: Canberra

first: Lina

last: Tze

state: ACT

country: Australia

institute: John Curtin School of Medical Research

summary:
This series represent several subgroups of experiments designed to investigate the role of basal immunoglobulin signaling in immature B cell development.  The first subgroup of arrays (Ctrl Mhi, Cre Mhi, Cre Mlo) was done to identify the changes in gene expression in immature B cells as a consequence of inducible deletion of surface IgM expression via Cre-LoxP mediated excision of Ig heavy chain.  The second subgroup of arrays (GFPneg, GFPpos, FxE Ctrl, FxE HA) was done to identify the changes in gene expression in immature B cells as a consequence of blockade of tyrosine kinase signaling with herbimycin A treatment.  The third subgroup of arrays (FxD, FxE, B6 Mneg, HEL Mhi) was done to establish gene expression profiles of immature B, pre B and pro B cells as reference platforms for the other two subgroups.  (Tze etal. Public Library of Science Biology, 2005)

The appended supplementary tables are described as follows:

TABLE 1: Transformed array signal intensities used for statistical analysis. Listed are all probe sets excluding masked probe sets and Affymetrix hybridization control probe sets.

Results are based on the following definitions:
- Values with detection p values <0.1 were considered present.
- Signal intensities with detection = "A" or with values < 20 were set to "20".

TABLE 2: Genes differentially expressed between Ctrl Mhi and Cre Mlo cell populations and associated signal values.

Results are based on the following definitions:
- 2-fold or greater difference in means
- difference in mean expression values > 200
- P < 0.01 (by Student's T test)

TABLE 3: Probesets used for clustering in Figures 2 and 3 of publication

TABLE 4: Probesets used for clustering in Figure 7 of publication

TABLE 5: Correlation coefficients between all cell populations. Correlation coefficients were calculated as an additional method to demonstrate the relationship of the various cell populations to each other. Shown are the correlation coefficients generated using the mean expression values for each of the 101 transcripts from Figure 7 of publication.

Keywords = bone marrow B cells

first: L

last: Ramsey

first: T

middle: W

last: Behrens


title: Aging primary myoblasts

first: Marjorie

last: Beggs

address: 629 S. Elm Street

department: Geriatrics

summary:
Comparison of primary myoblasts isolated from 8- and 23-month-old DBA/2JNIA mice.
Keywords: other

first: M

first: R

last: Nagarajan

first: J

last: Taylor-Jones

first: C

middle: A

last: Peterson


title: Differentiation of NIH-3T3 cells to adipocytes by PPARg or EBF1 over-expression.

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hematopoietic stem cell biology

institute: Lund Stem Cell Center

summary:
NIH-3T3 cells transduced with either EBF1-, PPARg2- or empty vector were stimulated with hormones to initiate adipocyte differentiation. RNA extraction was done using TriZol at d0, d2, d4 and d10 after stimulation. Samples were handled according to standard affymetrix protocols.
Keywords = Adipogenesis
Keywords = adipocyte
Keywords = early B-cell factor 1 (EBF1)
Keywords = commitment
Keywords = differentiation
Keywords = NIH-3T3
Keywords = pparg
Keywords: time-course

first: Peter

last: Åkerblad

first: David

last: Liberg

first: Simonetta

last: Westerlund

first: Barbro

last: Basta

first: Ulrika

last: Lind

first: Anders

last: Thelin

first: Ramiro

last: Gisler

first: Anna

last: Lagergren

first: Krister

last: Bamberg

first: Mikael

last: Sigvardsson


title: Homeostatic Proliferation of OT-I T cells

status: Public on Dec 08 2004

first: CBDM

last: Lab

summary:
A time course of OTI CD8 T cells transferred to irradiated syngeneic hosts (or unirradiated hosts as control).
Keywords: time-course

first: Ananda

last: Goldrath

first: C. John

last: Luckey

first: Richard

last: Park

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Effect of PGE receptor EP3 subtype agonist on mouse asthma model

status: Public on Feb 18 2005

city: Kyoto

first: Eri

last: Segi-Nishida

institute: Kyoto University

summary:
We examined the effect of PGE receptor EP3 subtype on mouse OVA-induced asthma model. We treat EP3 agonist 3h after OVA challenge.  After 24 h of 3rd OVA challenge, whole lung was isolated and the gene expression change was determined.
Keywords: other

first: Tomonori

last: Kunikata

first: Toshiyuki

last: Matsuoka

first: Shuh

last: Narumiya


title: FDC-E vs FDC-D

status: Public on Mar 04 2005

city: Zürich

first: Christoph

last: Huber

institute: Neuropathology

summary:
Comparison of follicular dendritic cell-enriched versus -depleted splenocytes
Keywords: parallel sample


title: NOD.scid, NOD, BDC2.5/NOD and BDC2.5/NOD.scid mice

status: Public on Jan 26 2005

city: Cincinnati

first: Jonathan

middle: D

last: Katz

address: 3333 Burnet Avenue

department: Division of Endocrinology

institute: Cincinnati Children's Hospital Research Foundation

summary:
Total pancreatic RNA was isolated from 3 week old NOD.scid, NOD, BDC2.5/NOD and BDC2.5/NOD.scid animals by GITC method. Targets were produced using standard Affymetrix procedures from about 10ug total RNA. The data from NOD.scid, NOD, BDC2.5/NOD and BDC2.5/NOD.scid Affymetrix MGU74Av2 cel files was converted into Robust Multi Array (RMA) text file for analysis using GeneSpring 6.1
Keywords: other

first: Sankaranand

last: Vukkadapu

first: Jenine

last: Belli

first: Koji

last: Ishii

first: Anil

middle: G

last: Jegga

first: John

last: Hutton

first: Bruce

last: Aronow


title: Extraocular, hindlimb, and cardiac muscles, comparison of dko and mdx mice (Porter lab)

city: Cleveland

first: Henry

middle: J.

last: Kaminski

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

summary:
Comparison by expression profiling of tissue from dKO (utrophin/dystrophin-deficient) and MDX mice at 8 weeks of age.  Independent triplicate analyses/strain were done for  extraocular, hindlimb, and cardiac muscle.
Keywords = microarray
Keywords = extraocular
Keywords: parallel sample

last: Porter


title: Transcriptome of Ts1Cje and euploids cerebellum

status: Public on Dec 05 2004

city: Paris

first: Luce

last: Dauphinot

address: 47 boulevard de l'hôpital

department: ICM

institute: INSERM U1127-CNRS UMR7225-UPMC

summary:
Transcriptome analysis of Ts1Cje (mouse model of Down syndrome) and euploids murine cerebellum during postnatal development
Keywords = Down syndrome
Keywords = Chromosome 21
Keywords = Transcriptome
Keywords = Microarray
Keywords = Cerebellum
Keywords = Development
Keywords: other

first: Robert

last: Lyle

first: Isabelle

last: Rivals

first: Minh

last: Tran Dang

first: Randal

last: Moldrich

first: Geoffroy

last: Golfier

first: Laurence

last: Ettwiller

first: Kiyoko

last: Toyama

first: Jean

last: Rossier

first: Léon

last: Personnaz

first: Stylianos

middle: E

last: Antonarakis

first: Charles

last: Epstein

first: Pierre-Marie

last: Sinet

first: Maire-Claude

last: Potier


title: Time series of diabetes and exercise training induced expression changes in skeletal muscle of mice

status: Public on Dec 10 2004

city: Jyväskylä

first: Mika

last: Silvennoinen

address: Rautpohjankatu 8, Viveca

country: Finland

institute: LIKES - Research Center

summary:
Experiment protocol:

Experiment was performed on 10 to 15 weeks old male NMRI mice (Harlan, Holland) housed in standard conditions (temperature 22°C, humidity 60 ± 10 %, artificial light from 8.00 am to 8.00 pm, normally 5 animals per cage). Animals had free access to tap water and food pellets (R36, Labfor, Stockholm, Sweden). Animals were randomly divided into healthy and diabetic groups. The diabetic group received a single peritoneal injection of streptozotocin (STZ, Sigma-Aldrich, France, 180 mg/kg) dissolved in sodium citrate buffer solution (0.1 mol/l, pH 4.5) to induce experimental diabetes similar to type 1. The other group received injection of an equal volume of buffer. Diabetes was confirmed 72 hours after the injection by urine glucose testing (Glukotest(r), Roche, Germany), and mice were characterized diabetic when urine glucose values were greater than 200 mg/dl. Diabetic and healthy animals were randomly assigned into 12 groups (n = 5 per group), which were sedentary or trained for one, three or five weeks. Training groups performed 1 hour per day of treadmill running at 21 m/min and 2.5° incline. After one day of familiarization on a rodent treadmill, the mice ran as described above 5 days per week. Mice were sacrificed 24 hours after the last training bout (respective sedentary controls at the same time) by cervical dislocation followed by decapitation. Calf muscles were removed, dissected free of fat and connective tissue, weighed, snap frozen in liquid nitrogen and stored at -80°C for further analysis.

Total RNA extraction and sample preparation:

Total RNA was extracted from the left calf muscle complex (soleus + gastrocnemius + plantaris) with Trizol Reagent (Invitrogen, Carlsbad, CA) and further purified with RNeasy columns (Qiagen, Valencia, CA) according to the manufacturers' protocols. Concentration and purity of RNA was determined by measuring absorbances at wavelengths 260 and 280 nm. Integrity of the RNA was checked with agarose gel electrophoresis. RNA samples were pooled within each group for microarray analyses. Concentration, purity and integrity of pooled RNA samples were checked as described above.

Micro array analysis:

Pooled RNA samples were analyzed with Affymetrix Gene Chip MG U74Av2 (Affymetrix , Inc., Santa Clara, CA) representing 6000 known genes and 6000 ESTs. Microarray analyses were performed according to the instructions of Affymetrix. Briefly, 5 µg of total pooled RNA was reverse transcribed using T7-(dT)24-primers and SuperScript II RT enzyme (Invitrogen). Single stranded cDNA was turned to double stranded cDNA using T4 DNA polymerase (Invitrogen). Produced cDNA was then purified and transcribed in vitro to biotin labeled cRNA using Enzo Bioarray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics, Farmingdale, NY). RNA was purified and its quality was checked. Purity and quantity of RNA was measured with Nanodrop ND-1000 Spectrophotometer (Nanodrop Technologies, Montchanin, DE) and integrity was tested with agarose gel electrophoresis. Sample was then fragmented and hybridized to Affymetrix test chip to check the function of the hybridization cocktail and to ensure adequate representation of both 5´and 3´ends of the RNA. After testing, samples (15 µg) were hybridized to expression chips. After hybridization, chips were washed and stained in Affymetrix Fluidics Station 400. Arrays were stained first with R-Phycoerythrin Streptavidin (Molecular Probes, Eugene, OR), then with biotinylated anti-streptavidin antibody (Vector Laboratories, Burlingame, CA) and again with R-Phycoerythrin Streptavidin for signal enhancement. The chip was scanned with GeneArray Scanner G2500A (Agilent, Palo Alto, CA)

Scaling and normalization of data:

The array images were analyzed with Microarray Suite 5.0 (Affymetrix) software. All chips were scaled (global scaling) to target intensity of 50 to minimize differences between chips caused by physical differences in chips, hybridization efficiencies and manual laboratory work. The data was subjected to robust normalization that reduces the errors, which are caused by binding capacity and linearity differences between probe sets.
Keywords: time-course

first: Riikka

last: Kivelä

first: Maarit

last: Lehti

first: Anna-Maria

last: Touvras

first: Jyrki

last: Komulainen

first: Veikko

last: Vihko

first: Heikki

last: Kainulainen


title: CxVB3 infection and cardiac function

status: Public on Dec 01 2004

city: Seattle

first: John

last: Gosink

state: WA

address: 1201 Amgen Court West

institute: Amgen

summary:
Male, adolescent A/J mice (4-5 week old) were either infected (IP) with coxsackievirus B3 (CVB3; 105 pfu) or PBS. CVB3 is a cardiotropic virus which leads to cardiac inflammation and fibrosis within 9 days after IP injection. We wanted to know how the virus would impact long term cardiac function, and whether changes in cardiac function could be associated with cardiac transcriptional regulation. At days 3, 9 and 30 days post-infection, hearts were imaged with 2D echocardiography (Sonos 5500, Philips). Briefly, mice were anesthesized subcutaneously with ketamine (0.45mg/kg) and xylazine (0.03mg/kg). Mice were placed in a dorsal recumbency position and the following systolic and diastolic measurements were taken (N=5 heart beats) using an S-12 (12MHz; Sonos 5000, Philips) probe: parasternal long axis, and short axis at the level of the mitral valve and papillary muscles. Measurements were utilized for calculation of wall thickness and functional parameters. Then, heart tissues were flash frozen (N=4 mice/group except CVB3 infected 30 day samples N=2) for hybridization to Affymetrix MG U74Av2 arrays.
Keywords: time-course

first: Bobby

last: Yanagawa

first: Honglin

last: Luo

first: Theresa

last: Deisher

first: Caroline

last: Cheung

first: Ji

last: Yuan

first: Zsuzsanna

last: Hollander

first: Brian

last: Wong

first: Ann

middle: M

last: Kapounx

first: Stefanie

last: Bonigut

first: Decheng

last: Yang

first: George

middle: F

last: Schreinerx

first: Raymond

last: Ng

first: Bruce

last: McManus


title: Effect of CCL3 on target ablation-induced macrophage recruitment into the olfactory epithelium

status: Public on Nov 18 2004

city: Lexington

first: Kevin

last: Kwong

state: KY

department: Physiology

institute: University of Kentucky

summary:
The aim was to determine the identity of genes regulated at 3 d post-olfactory bulbectomy in the olfactory mucosa of carrier-injected Ccl3-/- mice compared with carrier-injected C57BL/6 mice.  Total RNA from the OE was hybridized to Affymetrix microarrays.  A number of chemokine-, cytokine-, and growth factor-related genes were significantly regulated in the Ccl3-/- mice, and were restored in CCL3 protein-injected Ccl3-/- mice.  The results illustrated that CCL3 played a key role in recruitment of macrophages to the OE and provided insight into the genomic regulation involved in OE remodeling.
Keywords: other

first: Radhika

last: Vaishnav

first: Yushu

last: Liu

first: Nishikant

last: Subhedar

first: Arnold

last: Stromberg

first: Marilyn

last: Getchell

first: Thomas

middle: V


title: Hippocampus of HuD overexpressor mice. Perrone-Bizzozero-5R01NS030255-12

status: Public on Nov 24 2004

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Post-transcriptional mechanisms play an important role in the control of gene expression. RNA-binding proteins are key players in the post-transcriptional control of many neural genes and they participate in multiple processes, from RNA splicing and mRNA transport to mRNA stability and translation. Our laboratory has developed the first mouse model overexpressing a RNA-binding protein, the ELAV-like protein HuD, in the CNS under the control of the CaMKinII alpha promoter. Initial behavioral characterization of the mice revealed that they had significant learning deficits together with abnormalities in prepulse inhibition (PPI). At the molecular level, we found that the expression of the growth-associated protein GAP-43, one of the targets of HuD, was increased in the hippocampus of HuD transgenic mice. To characterize these mice further and to evaluate the utility of these animals in understanding human diseases, we propose to use DNA microarray methods.
To test our hypothesis we propose 2 specific aims: 1)To characterize the pattern of gene expression in the hippocampus of HuD overexpressor mice 2)To compare the pattern of gene expression in our mouse model with that in the hippocampus of rats prenatally exposed to alcohol (FAS model) and in post-mortem tissues of patients with schizophrenia
Based on the behavioral and molecular properties of our HuD transgenic mice we hypothesize that these animals may be good models for the studying the basis of learning disabilities and of diseases that show deficits in PPI such as fetal alcohol syndrome and schizophrenia.
All mice are in C57BL/6 background and are male approximately 60 days old. Initial studies were performed in animals that were not subjected to any experimental manipulation. Animals were bred and sacrificed according to our approved animal protocol.  The brain was rapidly dissected on ice and we isolated the hippocampus, which has the highest expression of the transgene. After dissection both hippocampi were frozen in liquid nitrogen, pooled and stored at -80C until analysis. RNA samples were isolated using RNAeasy Qiagen columns. For our first experiment, we want to examine the pattern of gene expression in the hippocampus of 3 transgenic mice and 3 non-transgenic littermates. RNAs from the 6 hippocampi were of high quality as revealed by the integrity of the 28S and 18S rRNA. We will provide 6 samples containing 10 ug of RNA each in DEPC water at a concentration of about 0.5 ug/ul. Three of the samples (#1, #2 and # 3) are from transgenic mice and three from their non-transgenic littermates (#4, #5 and #6).
Keywords: other

first: Nora

middle: I

last: Perrone-Bizzozero


title: Disease mechanisms in peripheral neuropathies due to altered Pmp22 gene dosage or a Pmp22 point mutation

status: Public on Nov 10 2004

city: Zurich

first: Ned

last: Mantei

department: Institute for Cell Biology

institute: Swiss Federal Institute of Technology

summary:
We compared gene expression at ages P4 and P60 in sciatic nerve of wild type mice and mice with peripheral neuropathies caused by altered Pmp22 gene dosage (homozygous knockout or transgene) or a point mutation (Trembler).
Keywords: parallel sample

first: Guya

last: Giambonini-Brugnoli

first: Johanna

last: Buchstaller

first: Lukas

last: Sommer

first: Ueli

last: Suter


title: Muscle and Bone marrow SP and MP cells

status: Public on Nov 16 2004

city: Boston

first: Kalliopi

last: Liadaki

institute: Children's Hospital Boston

summary: This study identified gene expression of Side Population (SP) and Main Population (MP) cells, isolated from adult murine skeletal muscle and Bone Marrow. Five different preparations of muscle SP, muscle MP, Bone marrw SP and Bone marrow MP cells were used as replicates.


title: BPH and BPL mouse strain adrenal glands

status: Public on Nov 02 2004

first: Ryan

last: Friese

institute: University of California San Diego

summary:
We performed Affymetrix MG-U74Av2 GeneChip experiements on mRNA from the adrenal glands of the BPH hypertensive and BPL hypotensive mouse strains. All mice were aged-matched at 5 weeks. We obtained the mice from Jackson Laboratories, Bar Harbor, ME.
Keywords: other

middle: S

first: Payam

last: Mahboubi

first: Nitish

last: Mahapatra

first: Sushil

last: Mahata

first: Nicholas

middle: J

last: Schork

first: Geert

last: Schmid-Schonbein

first: Daniel

middle: T

last: O'Connor


title: mouse corneal stromal cells

status: Public on Oct 27 2004

city: Baltimore

first: Shukti

last: Chakravarti

address: 720 Rutland Ave

department: Medicine

institute: Johns Hopkins University School of Medicine

summary:
To elucidate biological processes underlying the keratocyte, fibroblast, and myofibroblast phenotypes of corneal stromal cells, the gene expression patterns of these primary cultures from mouse cornea were compared with those of the adult and 10-day postnatal mouse cornea.
Keywords = corneal stroma	maturation	keratocyte	fibroblast	myofibroblast	TGF beta 1
Keywords: other

first: Feng

last: Wu

first: Neeraj

last: Vij

first: Luke

last: Roberts

first: Sarah

last: Joyce


title: Identification of genes and quantitative trait loci (QTL) that control hematopoietic stem cell functioning

status: Public on Dec 02 2004

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
We have combined large-scale mRNA expression and gene mapping methods to identify genes and loci that control hematopoietic stem cell (HSC) functioning. mRNA expression levels were measured in purified HSC isolated from a panel of densely genotyped recombinant inbred mouse strains. Quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts were mapped. Comparison of the physical transcript position with the location of the controlling QTL identified polymorphic cis-acting stem cell genes. In addition, multiple trans-acting control loci were highlighted that modify expression of large numbers of genes. These groups of co-regulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of strong candidate genes involved with HSC turnover.  We compared expression QTLs in HSC and brain from the same animals, and document both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of co-regulated transcripts.
Keywords: other

first: Leonid

last: Bystrykh

first: Ellen

last: Weersing

first: Bert

last: Dontje

first: Sue

last: Sutton

first: Mathew

last: Pletcher

first: Tim

last: Wiltshire

first: Andrew

last: Su

first: Edo

last: Vellenga

first: Jintao

last: Wang

first: Kenneth

last: Manly

first: Lu

last: Lu

first: Elissa

last: Chesler

first: Rudi

last: Alberts

first: Ritsert

middle: C

last: Jansen

first: Robert

last: Williams

first: Michael

last: Cooke

first: Gerald

last: de Haan


title: Equivalence of biologic responses induced in the mouse uterus by E2, GEN, and DES

status: Public on Oct 14 2004

city: Sharnbrook

first: Fei Ling

last: Lim

institute: Unilever

summary:
Three independent replicates of 4 groups of immature (19/20 days of age) Alpk:APfCD-1 mice were treated with arachis oil (AO) vehicle, 2.5ug/kg 17beta-estradiol (E2), 2ug/kg diethylstilbestrol (DES), or 50mg/kg genistein (GEN), via 3 daily subcutaneous injection, and sacrificed 72hr after initial dose.
Keywords: other

first: Jonathan

last: Moggs

first: John

last: Ashby

first: Helen

last: Tinwell

first: David

last: Moore

first: Ian

last: Kimber

first: George

last: Orphanides


title: LPS induced gene expression in macrophages in the presence of Carbon monoxide

status: Public on Nov 05 2004

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary:
Murine RAW 264.7 peritoneal macrophages were treated with 250 ppm Carbon monoxide (CO) for 3 hours prior to the addition of LPS (10 ng/ml) and then for the subsequent 4 hours of the study. Air-treated cells were maintained for the same time without CO. Total RNA was harvested at 0, 15, 30, 60, 120 and 240 min after LPS addition. CRNA was produced using standard Affymetrix procedures from 10µg of total RNA. The expression values of all probe sets are scaled to a target intensity of 500 by using Affymetrix Microarray Suite 5.0
Keywords = macrophage
Keywords = inflammation
Keywords = endotoxin
Keywords = gene expression
Keywords: time-course

first: Sherrie

middle: L

last: Otterbein

first: Emeka

last: Ifedigbo

first: Keiji

last: Enjyoji

first: Anny

last: Usheva

first: Simon

last: Robson

first: Fritz

middle: H

last: Bach

first: Oswald

last: Wagner

first: Leo


title: Induction of similar multistage transcriptional responses in the mouse uterus by E2 and GEN

status: Public on Oct 06 2004

summary:
Immature (19/20 days of age) Alpk:APfCD-1 mice were treated with arachis oil (AO) vehicle, 0.4mg/kg 17beta-estradiol (E2), or 250mg/kg genistein (GEN), via a single subcutaneous injection, and sacrificed at 1hr, 2hr, 4hr, 8hr, 24hr, 48hr, 72hr post dose.
Keywords: other


title: Gene expression profiles of mouse back skin during the hair growth cycle

city: Irvine

first: Kevin

middle: K

last: Lin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

summary:
Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance. Proc. Natl. Acad. Sci. USA. (2004)
Keywords: time-course

first: Darya

last: Chudova

first: G. Wesley

last: Hatfield

first: Padhraic

last: Smyth

first: Bogi

last: Andersen


title: Na,K-ATPase alpha 1 het. heart

status: Public on Nov 19 2004

first: Amy

last: Moseley

state: OH

address: 231 Albert Sabin Way

department: Molecular Genetics

institute: University of Cincinnati

summary:
Whole hearts from wild-type and Na,K-ATPase alpha 1 het. mice.  Adult male, 8-16 weeks old on a 129/BSwiss background.
Keywords: repeat sample

first: Justin

middle: P

last: Huddleson

first: Cynthia

last: Bohanan

first: Paul

last: James

first: John

middle: N

last: Lorenz

first: Bruce

last: Aronow

first: Jerry

middle: B

last: Lingrel


title: response to HDI

status: Public on Oct 02 2004

city: Temple

first: Joni

last: Ylostalo

state: TX

address: 5701 Airport Rd., Module C

department: Institute for Regenerative Medicine

institute: Texas A&M

summary:
C57BL/6J mouse were exposed to 10 mg/m3 of aerosolic HDI-BT (hexamethylene diisocyanate biuret trimer) and followed at 6h, 18h, and 90h after exposure together with unexposed mice. Whole lungs were collected for RNA (4 mice for each group, RNA pooled).
Keywords: time-course

first: Chun-Ting

last: Lee

first: Mitchell

last: Friedman

first: Gary

middle: W

last: Hoyle


status: Public on Oct 18 2004

city: Montreal

first: Daniel

last: Leclerc

address: 4060 Ste-Catherine West

department: Medical Genetics, Room 242

institute: Montreal Children's Hospital

summary:
Transcriptional Profiling of the Transition from Normal Intestine to Adenoma in the APC(Min/+) Mouse.
Tissue was from male 91-days old APC(Min/+) mouse (an animal model for human colon cancer). RNA was purified using Trizol and labeled for hybridization to high density oligonucleotide Affymetrix MG_U74Av2 arrays, using manufacturer protocol. We measured the relative expression level of >12000 genes and ESTs.
-----------------------------------------
Samples used in analysis:
* GSM12501:  Normal intestine diet #1 sample C1_0112 Dnmt+/- Min/+
* GSM12502: Tumor diet #1 sample T1_0112 Dnmt+/- Min/+
* GSM12503:  Normal intestine diet #1 sample C2_0112 Dnmt+/+ Min/+
* GSM12504: Tumor diet #1 sample T2_0112 Dnmt+/+ Min/+
* GSM12505:  Normal intestine diet #2 sample C1_003 Dnmt+/- Min/+
* GSM12506: Tumor diet #2 sample T1_003 Dnmt+/- Min/+
* GSM12507:  Normal intestine diet #2 sample C2_003 Dnmt+/+ Min/+
* GSM12508: Tumor diet #2 sample T2_003 Dnmt+/+ Min/+
* GSM12509:  Normal intestine diet #3 sample C1_005 Dnmt+/- Min/+
* GSM12510: Tumor diet #3 sample T1_005 Dnmt+/- Min/+
* GSM12511:  Normal intestine diet #3 sample C2_005 Dnmt+/+ Min/+
* GSM12512: Tumor diet #3 sample T2_005 Dnmt+/+ Min/+
- - - - - - - - - - - - - - - - - - - - -
Comparisons were performed as described in Chen Z, Ge B, Hudson TJ and Rozen R. Gene Expression Patterns 1, 89-93, 2002. Comparing Normal intestine vs Adenoma.
- - - - - - - - - - - - - - - - - - - - -
This resulted in the identification of differentially expressed transcripts. Identified transcripts were clustered based on functional information which was publicly available at time of analysis, obtained through the NetAffx WEB portal (www.Affymetrix.com) and literature.
Keywords = Mouse
Keywords = Min
Keywords = normal
Keywords = intestine
Keywords = tumor
Keywords = tumour
Keywords = colon cancer
Keywords = gene expression
Keywords = beta-catenin
Keywords = high density oligonucleotide microarrays
Keywords = familial adenomatous polyposis
Keywords = FAP
Keywords = colorectal cancer
Keywords = Affymetrix MGU74Av2 GeneChip probe array
Keywords = mouse model
Keywords = APC
Keywords = adenomatous polyposis coli
Keywords: ordered

first: Liyuan

last: Deng

first: Jacquetta

last: Trasler

first: Rima

last: Rozen


title: F9 cells after exposure to RA or TSA

status: Public on Dec 27 2004

city: Albany

first: Niquiche

last: Sangster

department: Biology

institute: University at Albany

summary:
F9 cells were exposed to two different differentiating agents (retinoic acid or trichostatin A both dissolved in 100% ethonal) for 24 hrs.  Control cells were exposed to ethonal for 24hrs
Keywords: repeat sample

first: Li-Ming

last: Yu

first: Cheryl

last: Eifert

first: Paulette

last: McCormick


status: Public on Sep 30 2004

city: Aachen

first: Thomas

last: Hieronymus

address: Pauwelsstr. 30

department: Institute for Biomedical Engineering - Cell Biology

institute: University Medical School, RWTH Aachen

summary:
FLT3+/CD11b+ Dendritic cell (DC) progenitor was amplified in vitro from mouse bone marrow.
Keywords: repeat sample


title: HSC 5-FU time course

status: Public on Sep 28 2004

city: Houston

first: Margaret

middle: A

last: Goodell

address: One Baylor Plaza, N1030

department: Center for Cell and Gene Therapy

institute: Baylor College of Medicine

summary:
HSC (Sca+ SP) were isolated from 8-12 week C57B6 mice at various time points after treatment with 5-Fluorouracil.  RNA was isolated from 50,000-100,000 FACS sorted cells and subjected to two rounds of T7 based linear amplification using Ambion's Message Amp kit.  Two replicates from each time point were analyzed.

http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371%2Fjournal.pbio.0020301
Keywords = HSC
Keywords = proliferation
Keywords = quiescence
Keywords = 5-FU
Keywords: time-course

first: Teresa

last: Venezia

first: Akil

last: Merchant

first: Carlos

last: Ramos

first: Nathan

last: Whitehouse

first: Andrew

last: Young

first: Chad

last: Shaw


title: Effect of Neuromedin U on gene expression in murine T cells

status: Public on Sep 24 2004

city: Research Triangle Park

first: Sujoy

last: GHOSH

state: NC

institute: GLAXOSMITHKLINE

summary:
Effects of Neuromedin-U on gene expression in mouse D10.G4.1 T-cells natively expressing the GPCR Axor13
Keywords: other


status: Public on Sep 19 2004

city: Tokyo

first: Koichi

last: Matsuo

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Microbiology and Immunology

institute: School of Medicine, Keio University

summary:
Effect of c-fos expression in osteoclastogenic splenocytes.
Keywords: other

first: Chen

last: Zhao

first: Hiroyuki

last: Aburatani


title: SJL, Balb: Leg and Eye,  10/12 months

status: Public on Aug 02 2004

city: Cleveland

first: Henry

middle: J.

last: Kaminski

institute: Case Western Reserve University

summary:
SJL & Balb.  Leg and eye; 1 year, 10 months
Keywords: time-course

first: John

middle: D

last: Porter


title: 27_RA_RMA_Jan04_time_course

status: Public on Sep 07 2004

city: Cincinnati

first: Sarah

middle: S.

last: Williams

institute: Cincinnati Children's Hopital Medical Center

summary:
This series represents murine dorsal neural tube bisected along the midline with one half from each embryo used for control and the other half treated with 10-6M RA dissolved in ethanol for 6, 12, 24 or 48 h. For 6 h exposures, the explants were cultured overnight on fibronectin coated 35mm dishes (Biocoat, Becton Dickinson Labware, Bedford, MA) in DMEM with 10% horse serum in order to allow for sufficient outgrowth of neural crest cells. The RA was added the following morning; RMA Express 0.2 used to initially normalize data; GeneSpring (Silicon Genetics, Inc.) used for subsequent analysis
Samples were analyzed at 6, 12, 24, and 48 hours.
Keywords = neural crest
Keywords = microarray
Keywords = retinoic acid
Keywords = gene expression
Keywords = cell signaling
Keywords = cell proliferation
Keywords: time-course

first: Melissa

last: Colbert


title: Murine orofacial development

status: Public on Aug 03 2004

city: LOUISVILLE

first: Partha

last: Mukhopadhyay

address: 501 S PRESTON ST

department: Division of Craniofacial Development & Anomalies

institute: University of Louisville

summary:
Developmental gene expression profiling of mammalian, fetal orofacial tissue
Keywords = orofacial
Keywords = embryo
Keywords = development
Keywords: time-course

first: Robert

last: Greene

first: Wolfgang

last: Zacharias

first: Martin

last: Weinrich

first: Saurabh

last: Singh

first: William

last: Young Jr.

first: Michele

last: Pisano


title: Pioglitazone, rosiglitazone and troglitazone treatment

status: Public on Aug 01 2004

city: La Jolla

first: Albert

last: Hsiao

institute: UC San Diego

summary:
3T3-L1 cells treated 24 hours with either 0.1% DMSO, 20uM pioglitazone, 1uM rosiglitazone or 20uM troglitazone
Keywords: other

first: Dorothy

last: Worrall

first: Jerrold

middle: M

last: Olefsky

first: Shankar

last: Subramaniam


title: Gene expression in T1alpha null mutant lungs compared to wild type at dpc 18.5 and term

status: Public on Sep 15 2004

city: Boston

first: Maria

middle: Isabel

last: Ramirez

address: 72 E. Concord St. E603

institute: Boston University School of Medicine

summary:
We compared gene expression in T1alpha (-/-) lungs vs wild type at dpc 18.5 when the phenotype is moderate and at term when the phenotype is more severe. Lungs present narrow and irregular alveolar spaces, thicker mesenchyme, reduced number of attenuated type I cells, normal numbers of type II cells and secreted surfactant. At term, but not a dpc 18.5, there is increased proliferation of distal cells.

We compared gene expression of T1alpha null mutant lungs to wild type lungs at dpc 18.5. The mutant phenotype at this developmental stage is moderate but the alveolar sacs are narrower than normal.
Keywords: other

first: Guetchyn

last: Millien

first: Avrum

last: Spira

first: Anne

last: Hinds

first: Junling

last: Wang

first: Mary

middle: I


title: Embryonic Testis Developmental Time Course

city: Pullman

first: James

last: Shima

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

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


title: PS cDKO / Control, 6 months

status: Public on Jul 31 2004

first: Vassilios

last: Beglopoulos

address: 77 Avenue Louis Pasteur

department: Center for Neurologic Diseases

institute: Brigham and Women's Hospital, Harvard Medical School

summary:
Gene expression profile of presenilin conditional double knockout cerebral cortex, comparing to control.
Age of mice: 6 months
Keywords = presenilin knockout
Keywords: parallel sample

first: Richard

last: Kim

first: Jie

last: Shen


title: Embryonic Ovary Developmental Time Course

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


title: Differential expression of genes after 48 hrs, 10 d, and 3 wks of TAC

city: Palo Alto

first: Mingming

last: Zhao

department: Pediatrics

institute: Stanford University

summary:
Microarray analysis of gene expression after transverse aortic constriction in mice: comparison of TAC vs. sham group at 48 hours, 10 days, and 3 weeks.
Keywords: time-course

first: Amy

last: Chow

first: Jennifer

last: Powers

first: Giovanni

last: Fajardo

first: Daniel

last: Bernstein


title: Keratinocytes in embryos and newborns, and Notch1 expression in newborns

status: Public on Jul 22 2004

city: Epalinges

last: Dotto

state: VD

address: 153 Chemin de Bovaress

department: Biochemistry

institute: Lausanne University

summary:
Comparison between pattern of gene expression in uncultured keratinocytes derived from the epidermis of embryonic mice (E15.5) versus newborn mice and comparison between pattern of gene expression in primary keratinocytes derived from newborn mice plus/minus activated Notch1 expression.
Keywords = mouse
Keywords = keratinocyte
Keywords = skin
Keywords = embryonic development.
Keywords: other

first: R

last: Okuyama

first: B

last: Nguyen

first: C

last: Talora

first: E

last: Ogawa

first: A

last: Tommasi di Vignano

first: M

last: Lioumi

first: G

last: Chiorino

first: H

last: Tagami

last: Woo


title: Control vs. APPSw mice gene expressions

status: Public on Jul 30 2004

city: Madison

first: Thor

last: Stein

state: WI

institute: University of Wisconsin-Madison

summary: Gene expression changes in mice overexpressing amyloid precursor protein with the Swedish mutation (Tg2576; APPSw).  The gene expression levels in male 12 month-old APPSw mice (GSM26708, GSM26709) were compared to those in male nontransgenic littermate control mice (GSM26706, GSM26707).  Data were analyzed with MAS 5.0 and scaled to 2500.

first: Jeffrey

last: Johnson


title: Vehicle and sAPPalpha-treated hippocampal slice cultures

summary:
Gene expression changes induced by alpha-secretase cleaved amyloid precursor protein (sAPPalpha) in organotypic hippocampal slice cultures of male, postnatal day 15 mice (C57B6/SJL).  Hippocampal slice cultures were treated with phosphate buffered saline (GSM26700, GSM26701, GSM26702) or 1 nM sAPPalpha (GSM26703, GSM26704, GSM26705) for 24 h.  Each sample consists of total RNA isolated from 8-12 slices from 4 mice.  Data were analyzed with MAS 5.0 and scaled to 2500.  sAPPalpha induces the amyloid sequestration protein transthyretin, insulin-like growth factor 2, insulin-like growth factor binding protein 2, and other genes involved in protective pathways such as apoptosis inhibition, detoxification, and retinol transport.
Keywords = Alzheimer's disease
Keywords = neuroprotection
Keywords = sAPPalpha


title: Antigen Presenting Dendritic Cells

first: Thomas

last: Hieronymus

summary:
Assessing the gene expression repertoire of antigen presenting dendritic cells
Keywords: other

first: Ralf

last: Kirsch


title: Difference in skeletal muscle function in Males vs Females; Role of Estrogen Receptor Beta

status: Public on Jul 17 2004

city: Stockholm

first: Hui

last: Gao

institute: Karolinska institute

summary:
Male skeletal muscles are generally faster and have a higher maximum power output than female muscles. Conversely, during repeated contractions female muscles sre generally more fatigue resistant and recover faster. we hypothesized that estrogen receptor beta is involved in this gender difference. The Affymetrix micorarray were used to deteced the differently expressed genes between male BERKO and WT mice in soleus muscles. Soleus muscles from 3 individual mouse of each genotype were used to perform the experiment.
Keywords: repeat sample


title: gene activation by IFNs in wild type and Pias1 null BMMs

status: Public on Jul 16 2004

city: Los Angeles

first: Bin

last: Liu

institute: UCLA

summary:
Microarray analysis was designed to study the effect of PIAS1 on interferon (IFN) signaling pathway by comparing the gene activation profiles of wild type and Pias1 null cells in response to IFN treatments. Microarray analysis was performed essentially following the manufacturer’s instructions (Affymetrix). Briefly, bone marrow-derived macrophages (BMMs) from wile type or Pias1 null littermates were either untreated, or treated with IFN-beta (500 U/ml) or IFN-gamma (10 ng/ml) for 2h or 4h. Total RNA was prepared with RNA-STAT60 (TEL-TEST) and purified with the RNeasy kit (Qiagen). Double stranded complementary DNA was synthesized from 20 ug of total RNA according to Affymetrix methodology, and purified with Phase Lock Gels (Eppendorf). Biotin-labeled RNA was synthesized with the BioArray High Yield RNA Transcript Labeling Kit (Enzo). Samples were cleaned, fragmentated and hybridized to murine genome (MGU74Av2) Genechips (Affymetrix) as instructed. GeneChips were stained with phycoerythrin-streptavidin (Molecular Probes) and scanned with a GeneChip scanner (Affymetrix).
Keywords: parallel sample


title: Lin-c-kit+Sca1+ hematopoetic stem cells

summary:
sorted hematopoetic stem cells from bone marrow;
with two rounds of amplification
Keywords: repeat sample


title: Hepatic reductase null

status: Public on Jul 11 2004

city: Dundee

first: Wang

middle: Jun

last: Xiu

address: Ninewells Hospital

department: Biomedical Research Centre

institute: Ninewells Hospital Medical School

summary:
Microarray analysis to examine the relationship between hepatic phenotype and changes in gene expression in cytochrome P450 reductase (CPR) null mice.
Keywords: ordered

first: Xiu

last: Wang

first: Mark

last: Chamberlain

first: Olga

last: Vassieva

first: Colin

last: Henderson

first: Roland

last: Wolf


title: Preimplantation mouse embryo development U74Av2

status: Public on Jul 06 2004

city: Philadelphia

first: Richard

middle: M.

last: Schultz

state: PA

address: 415 S. University Ave.

institute: University of Pennsylvania

summary:
Preimplantation mouse embryo development study on Affymetrix U74Av2.  Zeng et al Dev Biol (2004) 272:483-496.
Keywords: other

first: Fanyi

last: Zeng

first: Don

last: Baldwin


title: Pancreatic T regulatory vs. T effector cells

status: Public on Jun 07 2004

first: CBDM

last: Lab

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
Comparison of gene expression between T regulatory and T effector cells isolated from the pancreatic lesion of 3-4 wk old BDC2.5 tg NOD mice
Keywords: cell type comparison

first: Ann

middle: E

last: Herman

first: Gordon

middle: J

last: Freeman

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Comparison of conventional and germ-free gastrointestinal tract

status: Public on Jun 24 2004

city: Lausanne

first: James

last: Holzwarth

state: Vaud

address: vers chez les blanc

department: Bioanalytical Sciences

institute: Nestle Research Center

summary:
Whole tissues corresponding to the corpus, jejunum, descending colon and rectum were dissected from each mouse, washed with ice-cold PBS, placed into 2ml of RNA-later and flash-frozen in liquid nitrogen. The corpus was defined as the part of the stomach different from the antrum (distinguished by a difference in colour). The jejunum was defined as the tissue between the first 4 cm and the last 2 cm of the small intestinal tube. The descending colon and the rectum were defined as the last 3 cm of the digestive tube, where the first 2 cm was the descending colon and the last centimetre was the rectum.
Keywords: other

first: David

last: Mutch

first: Rainer

last: Simmering

first: Dominique

last: Donnicola

first: Grigorios

last: Fotopoulos

first: Gary

last: Williamson

first: Irène

last: Corthésy-Theulaz


title: Expression profile of genes in normal and Down syndrome mouse brains

status: Public on Jun 06 2004

city: Wako-shi

first: Kazuhiro

last: Yamakawa

state: Saitama

address: 2-1 Hirosawa

institute: RIKEN Brain Science Institute

summary:
Analyses of six Ts1Cje (Down syndrome) and six normal littermate (2N) mouse brains at postnatal day 0.
Keywords: other


title: Expression profile of genes in normal and Down syndrome mouse brains MGU74A

summary:
Analyses of six Ts1Cje (Down syndrome) and six normal littermate (2N) mouse brains at postnatal day 0.
Keywords: repeat sample


title: Liver treatments Con, Veh, Dex

status: Public on Jun 30 2004

city: Cambridge

first: Akhilesh

middle: Basi

last: Reddy

address: Hills Road

department: Institute of Metabolic Science

institute: University of Cambridge

summary:
Mouse liver RNA was extracted using Trizol (Invitrogen) and Qiagen RNeasy kits. RNA was checked with an Agilent Bioanalyzer for evidence of sub-genomic DNA and degradation. Targets were produced using standard Affymetrix protocols. Each sample represents data from a single mouse liver.
Keywords: other


title: Snell Dwarf Response to 3-NPA

city: Galveston

first: John

last: Papaconstantinou

address: 301 University, Mail Route 0643

department: Dept. of Human Biological Chemistry and Genetics

institute: University of Texas Medical Branch

summary:
Comparison of Snell Dwarf and Wild Type mouse liver RNA levels in response to 3-NPA (3-nitropropionic acid).
Keywords: time-course

first: Mark

last: Madsen


title: Global analysis of genes differentially expressed in branching and non-branching regions of the mouse embryonic lung

status: Public on May 23 2004

first: Jining

last: Lu

state: MA

summary:
During development, the proximal and distal regions of respiratory tract undergo distinct processes that ultimately give rise to conducting airways and alveoli. To gain insights into the genetic pathways differentially activated in these regions when branching morphogenesis is initiating, we characterized their transcriptional profiles in murine rudiments isolated at embryonic day 11.5.
Keywords: parallel sample

first: Jun

last: Qian

first: Konstantin

last: Izvolsky

first: Wellington

middle: V

last: Cardoso


title: Mouse Kidney - Effect of Low Phosphate Diet in Normal and Hyp Mice

status: Public on May 10 2004

city: Charlotte

first: Ralph

middle: A.

last: Meyer

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

summary:
This is a study of the change in gene expression in mouse kidney after feeding control (1.0% P) or low phosphate diet (0.03% P) for 3 or 5 days to normal or Hyp (X-linked hypophosphatemic) mice at 5 weeks of age.  The mice were C57BL/6J.  Normal wild-type mice, hemizygous Hyp (Hyp/Y) male mice, or heterozygous (Hyp/+) female mice were used.  The gene is dominant, so that the two genders are equally affected with low renal retention of phosphate and severity of their bone disease.  RNA from 3 mice were pooled for each microarray.  The arrays were processed as described in the Affymetrix GeneChip Expression Analysis Technical Manual (copyright 2001, Affymetrix, Inc., Santa Clara, CA), rev. 1, Part number 701021.  The data for each array were scaled to an average signal value of 500 for all genes on the array.
Keywords = mouse
Keywords = kidney
Keywords = low phosphate diet
Keywords = Hyp
Keywords = Phex
Keywords = X-linked hypophosphatemia
Keywords: repeat sample

first: Martha

middle: H


title: RTOC thymocytes

status: Public on Jun 01 2004

first: CBDM

last: Lab

summary:
Four independent chip hybridization with RNAs from four independent RTOC cultures.
Keywords: other

first: Tetsuya

last: Yamagata

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Osteoblast differentiation experiment: BMP-2 induced osteogenesis in mouse MC3T3 cell line

city: Basel

first: Natasa

last: Zamurovic

department: Bone metabolism

institute: Novartis Institutes for BioMedical Research

summary:
MC3T3 cells clone 1b  were grown in alpha-MEM with 10% fetal calf serum (FCS, Gibco), 1% penicilin/streptomycin (Pen/Strep) and 1% L-Glutamine (L-Glu). For differentiation experiment, cells were seeded on 6 cm dishes (3x105cells/dish in 5 ml medium) and grownt to confluence for 3 days at 37C / 5% CO2. Cells were then stimulated with osteogenic stimulus (10 mM beta-glycerophosphate (GP, Sigma), 50 µM ascorbic acid (AA, Wako) and 1 mg/ml BMP-2 (Novartis)), or with 10mM GP alone for 1 or 3 days. Control cells-day 0, medium. Experiment was done in triplicate. Total RNA was extracted, treated with DNAse, and purified according to the manufacturer’s protocol (RNeasy mini kit, QIAGEN). RNA samples were analyzed on oligonucleotide microarrays Affymetrix GeneChip® Murine Genome U74Av2.
Keywords: ordered