title: Molecular pathways involved in neuronal degeneration of polyglutamine mouse models

city: ILLKIRCH

first: Gretta

last: ABOU-SLEYMANE

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary:
To elucidate the pathways involved in the SCA7 retinal degeneration, we used DNA GeneChips and compared the gene expression profiles of the mutant mice (R7E) and the control ones (R7N). We performed these experiments at the onset stage of the disease (3w) as well as on the moderate one (9w) in order to correlate the transcriptional deregulations with the phenotype progression.
We also compared the R6/2 mice vs wild type (wt) ones to identify between the deregulated transcripts the ones that were also differentially expressed in the R7E vs R7N mice. These common changes are likely caused by polyQ expansion independently of the protein context.
Keywords: Polyglutamine disorders, Spinocerebellar ataxia type 7 (SCA7), Huntington’s disease (HD), Neuronal dysfunction, Retinal degeneration

overall_design: Retina RNA was prepared from 4-6 animals from each mouse line. Each RNA sample was independently hybridized on a different Genehip.


title: Twelve weeks expression data of the antipsychotics Clozapine and Haloperidol in the mouse brain (Affymetrix, GCRMA).

status: Public on Dec 13 2006

city: London

first: Mie

middle: A

last: Rizig

address: Windeyer Institute of Medical Sciences,46 Cleveland Street

department: Mental Health Sciences

country: United Kingdom

institute: University Collage London

summary:
Atypical antipsychotic Clozapine has a superior antipsychotic and antimanic effects compared to other antisphicotics. Its widespread use was limited by the side effects of agranulocytosis, cardiomyopathy and metabolic anomalies such as weight gain, and diabetes. Very little is known about mechanisms by which Clozapine works. The aim of this experiment is to compare the chronic gene expression profile of the atypical antipsychotic Clozapine to the typical antipsychotic drug Haloperidol using gene expression Microarray in order to understand the intercellular mechanism behind the therapeutic and the toxic effects of Clozapine.
Keywords: drug response

overall_design: The study was designed to compare the chronic therapeutic and toxic expression profile of Clozapine to Haloperidol in the mouse brain. All experiments were performed in male C57BL mice at four weeks of age (Biological services, University Collage London). Several theoretical and practical considerations influenced the final experimental design. To avoid the effect of injections on genes’ expression and to simulate the clinical scenario in human, both drugs were applied to the animals’ drinking water using the maximum human therapeutic dose (i.e. 1.6mg/kg/day for Haloperidol and 12mg/kg/day for Clozapine). Thirty animals were divided equally between three treatment groups and received either Haloperidol (10 animals), Clozapine (10 animals) or no treatment (10 animals) for 12 weeks. After twelve weeks, the total RNA from the right forebrains were extracted and hybridized to the Affymetrix MOE430A array. In all the Microarray experiments we have avoided pooling and each RNA sample was an independent biological replicate. The total numbers of used arrays were 30 Affymetrix MOE430A arrays.

first: Hugh

middle: M

last: Gurling


title: Gene expression profiling: breast cancer formation in WAP-SVT/t transgenic animals

status: Public on Nov 10 2006

city: Berlin

first: Andreas

last: Klein

address: Charitéplatz 1

department: Institute of Biochemistry

country: Germany

institute: Charité (CCO)

summary:
Microarray studies revealed that as a first hit, SV40 T/t-antigen causes deregulation of 462 genes in mammary gland cells (ME-cells) of WAP-SVT/t transgenic animals. The majority of deregulated genes are cell-proliferation specific and Rb-E2F dependent, causing ME-cell proliferation and gland hyperplasia but not breast cancer formation. In the breast tumor cells, a further 207 genes are differentially expressed, most of them belonging to the cell communication category. In tissue culture, breast tumor cells frequently switch off WAP-SVT/t transgene expression and regain the morphology and growth characteristics of normal-ME-cells, although the tumor-revertant cells are aneuploid and only 114 genes regain the expression level of normal-ME-cells. The profile of retransformants shows that only 38 deregulated genes appear to be tumor-relevant and that none of them is considered to be a typical breast cancer gene.
Keywords: Tumorigenesis, Breast cancer, SV40 T/t antigen

overall_design: We have analyzed nine mammary gland tissue segments from three normal NMRI, three WAP-SVT/t mice on the first day of lactation and from three WAP-SVT/t breast cancers (583-tumor 1, 585-tumor 2, 597-tumor 3) as well as three distinct breast cancer derived cell lines (ME-A cells, revertant-ME-B cells and ME-B-T/t cells).

first: Eva

last: Guhl

first: Raphael

last: Zollinger

first: Yin-Jeh

last: Tzeng

first: Ralf

last: Wessel

first: Michael

last: Hummel

first: Monika

last: Graessmann

first: Adolf


title: Clozapine and Haloperidol effect on the mouse brain

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

overall_design: Refer to individual Series


title: Gene expression series from murine liver samples comparing ABCA1 over-expression in LDL receptor -/- genetic background

status: Public on Aug 10 2006

city: Bethesda

first: Eric

last: Billings

state: MD

address: 10 Center Drive

country: USA

institute: NHLBI

summary:
Changes in the transcript profile due to ABCA1 expression in murine liver samples was evaluated in LDL receptor -/- genetic backgrounds.
Keywords: Genetic modification to analyze transgenic overexpression of ABCA1 in a knock-out LDLr genetic backgrounds.

overall_design: Case (ABCA1-transgenic) versus control (wild-type) design with 4 biological replicates per condition

first: E

last: Wagner

first: S

last: Santamarina-Fojo

first: C

middle: W

last: Joyce


title: lipin 1beta overexpression in mouse liver

status: Public on Aug 16 2006

city: St. Louis

first: Brian

last: Finck

state: MO

address: 660 S. Euclid Ave

institute: Washington University

summary:
Mutations in the gene encoding lipin 1 cause hepatic steatosis in fld mice, a genetic model of lipodystrophy. Lipin 1 appears to be highly involved in the control of fatty acid metabolism. Lipin 1 is most often located in the nucleus, but other studies suggest that lipin also has effects in the cytoplasm. However, the molecular function of lipin 1 is unclear. To evaluate the effects of activation of the lipin 1 system in liver, lipin 1beta was overexpressed in mouse liver using an adenoviral vector. We found that lipin 1 overexpression increased the expression of many genes involved in mitochondrial fatty acid oxidation while repressing expression of genes involved in lipogenesis. We believe that lipin is a transcriptional coactivator of the peroxisome proliferator-activated receptor (PPAR) complex. However, the many molecular aspects of its function remain unclear.

Abstract of published manuscript follows:
Lipin 1 is an inducible amplifier of the hepatic PGC-1alpha/PPARalpha regulatory pathway.Finck BN, Gropler MC, Chen Z, Leone TC, Croce MA, Harris TE, Lawrence JC Jr, Kelly DP.
Center for Cardiovascular Research and Washington University School of Medicine, St. Louis, Missouri 63110; Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110.

Perturbations in hepatic lipid homeostasis are linked to the development of obesity-related steatohepatitis. Mutations in the gene encoding lipin 1 cause hepatic steatosis in fld mice, a genetic model of lipodystrophy. However, the molecular function of lipin 1 is unclear. Herein, we demonstrate that the expression of lipin 1 is induced by peroxisome proliferator-activated receptor gamma (PPARgamma) coactivator 1alpha (PGC-1alpha), a transcriptional coactivator controlling several key hepatic metabolic pathways. Gain-of-function and loss-of-function strategies demonstrated that lipin selectively activates a subset of PGC-1alpha target pathways, including fatty acid oxidation and mitochondrial oxidative phosphorylation, while suppressing the lipogenic program and lowering circulating lipid levels. Lipin activates mitochondrial fatty acid oxidative metabolism by inducing expression of the nuclear receptor PPARalpha, a known PGC-1alpha target, and via direct physical interactions with PPARalpha and PGC-1alpha. These results identify lipin 1 as a selective physiological amplifier of the PGC-1alpha/PPARalpha-mediated control of hepatic lipid metabolism.

Keywords: response to lipin 1 activation

overall_design: Adult male C57BL6 mice were injected with adenovirus driving expression of mouse lipin 1beta or green fluorescent protein (GFP). Mice were recovered and sacrificed 6 days after injection. Total RNA was isolated and analyzed using Affymetrix microarray.

middle: N

first: Daniel

middle: P

last: Kelly


title: Antenatal steroid (AS) adversely affects placental function: A study of molecular effects using micro-array analysis

status: Public on Sep 02 2006

city: Augusta

first: Beth

last: Baisden

state: GA

institute: Medical College of Georgia

summary:
Antenatal steroids (AS) are used to augment fetal lung maturity and there is a major concern that they impair fetal growth. If delivery is delayed after using AS, placental function and hence fetal growth may be compromised even further. We treated three pairs of pregnant C57/BL mice with AS and studied changes in placental gene expression by microarray analysis, these results were later confirmed by semi quantitative RT-PCR, in situ hybridization and Oligo ApopTaq assay. AS treated placentas were hydropic, friable and pale. Placental weight was decreased (78.8±16.7 mg compared to 81.3±17 mg, p<0.05) and so was fetal weight (914 38 mg compared to 1160 85 mg, p<0.05). There was more than 99% similarity between the three gene chip data sets. AS led to down-regulation of 1212 genes and up-regulation of 1382 genes. AS led to decrease in expression of genes involved in cell division like cyclin A2, B1, D2, CDK2, CDK4 and M phase protein kinase along with growth promoting genes like BMP4 and IGF-BP4. Tryptophan hydroxylase gene a key regulator of serotonin production was upegulated by >15 fold. AS treatment caused deleterious effects on placenta by decreasing expression of growth related genes and increased apoptosis of trophoblast cells.
Keywords: comparitive gene expression

overall_design: 3 sets of pregnant C57/BL mice were treated with dexamethasone (0.5 mg/kg) on gestational day 15, 16, 17. 3 sets of pregant mice were injected with saline and served as controls.

first: Srinivas

last: Sonne

first: Ratanmani

last: Joshi

first: Vadivel

last: Ganapathy

first: Prem

middle: S

last: Shekhawat


title: MLL-AF9 transforms committed progenitors to leukemia stem cells by activation of a stem cell program (expt 1)

status: Public on Dec 02 2006

city: Boston

first: Scott

middle: A.

last: Armstrong

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Children's Hospital

summary:
Leukemias and other cancers possess a rare population of cells capable of self-renewal, and eradication of these cancer stem cells is likely necessary for long-term cancer-free survival. Given that both normal and cancer stem cells are capable of self-renewal the extent to which cancer stem cells resemble normal tissue stem cells is a critical issue if targeted therapies are to be developed.  We introduced the MLL-AF9 fusion protein encoded by the t(9;11)(p22;q23) found in human acute myelogenous leukemia (AML) into murine committed granulocyte-macrophage progenitors (GMP). The resultant leukemias contained cells with an immunophenotype similar to normal GMP that were highly enriched for leukemia stem cells (LSC). Detailed gene expression comparisons between normal hematopoietic stem cells (HSC), committed progenitors, and the LSC population demonstrated the LSC were globally more similar to the normal GMP than any other population. However, a subset of genes highly expressed in normal stem cells was re-activated in the LSC. These data demonstrate LSC can be generated from committed progenitors without widespread reprogramming of gene expression, and a leukemia self-renewal associated signature is activated in the process. Our findings define progression from normal hematopoietic progenitor to leukemia stem cell, and suggest that targeting a self-renewal program expressed in an abnormal context may be possible.
Keywords: MLL, stem cells, leukemia stem cells

overall_design: isolated granulocyte macrophage progenitors were incubated with a retrovirus that expressed either GFP or MLL-AF9 and GFP. Forty hours later, the GFP positive cells were isolated and RNA was hybrided to Affymetrix microarrays. The experiment was repeated three times.


title: Expression data from skeletal muscle of young, old and old calorie restricted mice

status: Public on Dec 01 2006

city: Aurora

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

summary:
We investigated age-related changes in the transcriptional profile of skeletal muscle in 5 month old (young) and 25 month old (old) C57BL/6NHsd mice using high density oligonucleotide arrays (22,690 transcripts probed).  We identified 712 transcripts that are differentially expressed in young (5 month old) and old (25-month old) mouse skeletal muscle.  Caloric restriction (CR) completely or partially reversed 87% of the changes in expression. Examination of individual genes revealed a transcriptional profile indicative of increased p53 activity in the older muscle.  To determine whether the increase in p53 activity is associated with transcriptional activation of apoptotic targets, we performed RT-PCR on four well known mediators of p53-induced apoptosis: puma, noxa, tnfrsf10b and bok.  Expression levels for these proapoptotic genes increased significantly with age (P<0.05), while CR significantly lowered expression levels for these genes as compared to control fed old mice (P<0.05). Age-related induction of p53-related genes was observed in multiple tissues, but was not observed in SOD2+/- and GPX4+/- mice, suggesting that oxidative stress does not mediate the observed age-related increase in expression. Western blot analysis confirmed that protein levels for both p21 and GADD45a, two established transcriptional targets of p53, were higher in the older muscle tissue. These observations support a role for p53-mediated apoptotic activity in mammalian aging.
Keywords: aging, calorie restriction, muscle, p53

overall_design: Animals were killed by cervical dislocation.  Five different animals were used for each experimental group.  All collected gastrocnemius tissue was then dissected, placed in a microcentrifuge tube, flash-frozen in liquid nitrogen, and stored at -80°C until processed for microarrays.

middle: G

first: Rozalyn

last: Anderson

first: Ming

last: Yuan

first: Christina

last: Kendziorski

first: Richard

last: Weindruch

first: Tomas

last: Prolla


title: Effect of Hyp, low phosphate diet and sex on mRNA gene expression in the mouse kidney

status: Public on Jan 01 2007

city: Charlotte

first: Ralph

last: Meyer

state: NC

department: Orthopaedic Research Laboratory

institute: Carolinas Medical Center

summary:
The renal adaptation to changing dietary phosphate levels is not well understood.  The dominant Hyp mutation of the Phex gene in mice causes X-linked hypophosphatemia with low renal retention of phosphate and blocks physiologic adaptation to low phosphate diets.   At P < 0.01, there were 1,711 transcripts significantly affected by genotype, 1,428 by diet and 5,601 by sex.  Many renal transporters other than phosphate, as well as many novel transcripts of unknown function, were affected by the Hyp mutation.  Some genes for fat metabolism and inflammation were up-regulated in Hyp kidneys.  Of the genes affected by genotype and diet, only 378 were affected by both.  In summary, the Hyp mutation induced changes in mRNA levels for numerous transcripts exceeding that required to alter phosphate retention.  The data suggest broader physiological roles for the Phex gene unrelated to phosphate conservation.

Keyword = Phex
Keyword = Hyp
Keyword = mouse
Keyword = kidney
Keyword = sex
Keyword = mRNA
Keyword = microarray
Keyword = low phosphorus diet
Keywords: disease state analysis

overall_design: A 2x2x2 factorial design, balanced for genotype (normal vs. Hyp), diet (control vs. low phosphate), and sex (male vs. female) was employed.  Control or low phosphate diets were fed for three days to 10-week-old mice.  A total of 24 samples of renal RNA were collected from 72 mice (3/array), processed to biotin-labeled cRNA, and hybridized to Affymetrix mouse MOE 430A and 430B for measurement of expression of over 45,000 transcripts.

first: Martha

middle: H


title: Islet microarray on 2 days PERK wild type and knockout mice

status: Public on Oct 30 2006

city: University Park

first: YULIN

last: LI

state: PA

address: 113 life sciences building

institute: Penn State

summary:
to study the proliferation of PERK knockout mice islets.

The major changes are the proliferation genes
Keywords: cDNA microarray on genetically modified mouse islets

overall_design:
2days after birth,
Collagenase P digestion
cRNA label with Ambion kit
Hybridization with Affymetrix mouse 430A chip

first: Yulin

last: Li


title: Hoxb1 mutant mRNA levels  in rhombomere 4 at E10.5

status: Public on Aug 28 2006

city: Salt Lake City

first: Petr

last: Tvrdik

state: UT

department: Human Genetics

institute: University of Utah

summary:
Hoxb1 is required for proper specification of rhombomere 4 and the facial motor neurons. This study analyzed gene expression in the corresponding hindbrain segment of E10.5 mutant embryos. Several genetic pathways were found altered, including transcription factors such as Phox2b, Gata3, Nkx2-2 and Nkx6-1.
Keywords: hindbrain development, rhombomere 4, Hoxb1

overall_design: Each of the three mutant and control samples was an independent biological replicate. Pools of r4 segments from multiple embryos were snap frozen on dry ice and stored at -80ºC. Total RNA was isolated, processed with standard Affymetrix protocols and hybridized to GeneChip Mouse Expression Sets 430A.

first: Benjamin

middle: R

last: Arenkiel

first: Gary

middle: O

last: Gaufo

first: Robert

middle: B

last: Weiss

first: Mario

last: Capecchi


title: nmyc misexpression in lung (gain of function)

status: Public on Oct 27 2006

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

summary:
Understanding how lung progenitor cells balance
proliferation against differentiation is relevant to clinical
disorders such as bronchopulmonary dysplasia of
premature babies and lung cancer. Previous studies have
established that lung development is severely disrupted in
mouse mutants with reduced levels of the proto-oncogene
Nmyc, but the precise mechanisms involved have not been
explored. We show here that Nmyc expression in the
embryonic lung is normally restricted to a distal population
of undifferentiated epithelial cells, a high proportion of
which are in the S phase of the cell cycle. Overexpression
of NmycEGFP in the epithelium under the control of
surfactant protein C (Sftpc) regulatory elements expands
the domain of S phase cells and upregulates numerous
genes associated with growth and metabolism, as shown by
transcriptional microarray. In addition, there is marked
inhibition of differentiation, coupled with an expanded
domain of expression of Sox9 protein, which is also
normally restricted to the distal epithelial compartment. By
contrast, conditional deletion of Nmyc leads to reduced
proliferation, epithelial differentiation and high levels
of apoptosis in both epithelium and mesenchyme.
Unexpectedly, about 50% of embryos in which only one
copy of Nmyc is deleted die perinatally, with similarly
abnormal lungs. We propose a model in which Nmyc is
essential in the developing lung for maintaining a distal
population of undifferentiated, proliferating progenitor
cells.
Keywords: genetic modification: mutant vs control

overall_design:
To generate Nmyc1EGF fusion protein, mouse Nmyc1 cDNA was
inserted into the SmaI site of pEGFP (BectonDickinson), excised by
SalI and EcoRI, and inserted into a vector containing a 3.7 kb
promoter/enhancer of the human SFTPC gene (Wert et al., 1993).
Transfection of 293 cells shows that the fusion protein localizes to
the nucleus (see Fig. S1 in supplementary material). Four transgenic
embryos were generated by pronuclear injection into
(C57BL/6J and DBA/2J) F2 fertilized eggs. They were collected at
E18.5, so it is not known if they would have survived postnatally.

Duplicate samples are biological replicates.

first: Tadashi

last: Okubo

first: Paul

last: Knoepfler

last: Eisenman

first: Brigid

last: Hogan


title: MLL-AF9 transforms committted progenitors to leukemia stem cells

status: Public on Jun 20 2006

first: Scott

last: Armstrong

summary:
Leukemias and other cancers possess a rare population of cells capable of self-renewal, and eradication of these cancer stem cells is likely necessary for long-term cancer-free survival. Given that both normal and cancer stem cells are capable of self-renewal the extent to which cancer stem cells resemble normal tissue stem cells is a critical issue if targeted therapies are to be developed.  We introduced the MLL-AF9 fusion protein encoded by the t(9;11)(p22;q23) found in human acute myelogenous leukemia (AML) into murine committed granulocyte-macrophage progenitors (GMP). The resultant leukemias contained cells with an immunophenotype similar to normal GMP that were highly enriched for leukemia stem cells (LSC). Detailed gene expression comparisons between normal hematopoietic stem cells (HSC), committed progenitors, and the LSC population demonstrated the LSC were globally more similar to the normal GMP than any other population. However, a subset of genes highly expressed in normal stem cells was re-activated in the LSC. These data demonstrate LSC can be generated from committed progenitors without widespread reprogramming of gene expression, and a leukemia self-renewal associated signature is activated in the process. Our findings define progression from normal hematopoietic progenitor to leukemia stem cell, and suggest that targeting a self-renewal program expressed in an abnormal context may be possible.
Keywords: cell type comparison

overall_design: RNA from normal GMP, GMP-like cells isolated from leukemic bone marrow (LGMP) and cells derived from the in vitro propagation of LGMP were hybridized to affymetrix microarrays.


title: Microarray skeletal muscle PPARalpha overexpressing mice

status: Public on Sep 08 2006

last: Finck

summary:
This experiment was conducted to identify target genes of the peroxisome proliferator-activated receptor alpha (PPARa) in skeletal muscle of transgenic mice that overexpressed PPARa. The following abstract from the published manuscript describes the major findings of this work.

A potential link between muscle peroxisome proliferator- activated receptor-alpha signaling and obesity-related diabetes.Finck BN, Bernal-Mizrachi C, Han DH, Coleman T, Sambandam N, LaRiviere LL, Holloszy JO, Semenkovich CF, Kelly DP.

The role of the peroxisome proliferator-activated receptor-alpha (PPARalpha) in the development of insulin-resistant diabetes was evaluated using gain- and loss-of-function approaches. Transgenic mice overexpressing PPARalpha in muscle (MCK-PPARalpha mice) developed glucose intolerance despite being protected from diet-induced obesity. Conversely, PPARalpha null mice were protected from diet-induced insulin resistance in the context of obesity. In skeletal muscle, MCK-PPARalpha mice exhibited increased fatty acid oxidation rates, diminished AMP-activated protein kinase activity, and reduced insulin-stimulated glucose uptake without alterations in the phosphorylation status of key insulin-signaling proteins. These effects on muscle glucose uptake involved transcriptional repression of the GLUT4 gene. Pharmacologic inhibition of fatty acid oxidation or mitochondrial respiratory coupling prevented the effects of PPARalpha on GLUT4 expression and glucose homeostasis. These results identify PPARalpha-driven alterations in muscle fatty acid oxidation and energetics as a potential link between obesity and the development of glucose intolerance and insulin resistance.
Keywords: genetic modification

overall_design: RNA from two wild-type (non-transgenic (NTG)) and two PPARalpha overexpressing (MCK-PPARa) mice was analyzed. Two replicates of each are provided.

first: Daniel

last: Kelly


title: shRNAi induced differentiation time courses in mouse embrionic stem cells.

status: Public on May 31 2006

city: Princeton

first: Ihor

last: Lemischka

state: NJ

address: Washington Rd

institute: Princeton University

summary:
We present an integrated approach to identify genetic mechanisms that control self-renewal in mouse embryonic stem (ES) cells.  Short hairpin RNA (shRNA) techniques are employed to down regulate a set of gene-products whose expression patterns suggest self-renewal regulatory functions.  We focus on transcriptional regulators and identify seven molecules whose shRNA-mediated depletion induces differentiation, including four whose roles in self-renewal had not been demonstrated.
We analyze the expression profiles of embryonic stems (ES) cells transduced with individual shRNA vectors, maintained in the presence of LIF.
Keywords: time course

overall_design: We analyze transcriptome dynamics after down-regulating each of the 8 self-renewal regulators identified in the current studies.  These are Nanog, Oct4, Sox2, Esrrb, Tbx3, Tcl1, Mm.343880 and Dppa4. Gene specific shRNA transduced GFP+ cells were FACS purified daily during a seven day interval and used to interrogate Affymetrix microarrays.  Empty H1P vector served as a reference.

first: Natalia

last: Ivanova

first: Radu

last: Dobrin

first: Rong

last: Lu

first: Iulia

last: Kotenko

first: John

last: Levorse

first: Christina

last: DeCoste

first: Xenia

last: Schafer


title: Expression data from T65H translocation mice

status: Public on Jul 28 2006

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

summary:
Tissue-specific comparison of gene expression levels in T65H translocation mice, either with or without uniparental duplications of Chrs 7 & 11. Identification of highly differentially expressed transcripts.
Keywords: genetic modification

overall_design: Pairwise array comparative analyses were performed using MAS5/GCOS where sample age and tissue were matched, while the sample genotype varied between the compared arrays: matUpDp Chr 7 prox T65H vs either patUpDp Chr 7 prox T65H or normal (T65H translocation mouse w/o uniparental duplications), and matUpDp Chr 7 dist T65H vs normal.

first: Trevelyan

last: Menheniott

first: Kathryn

last: Woodfine

first: Andrew

middle: J

last: Wood

first: Jonathan

middle: D

last: Choi

first: Rebecca

last: Oakey


title: Expression data from alveolar type II epithelial cells

status: Public on Aug 01 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
The importance of alveolar type II epithelial cells (AEC II) in all aspects of the induction and regulation of respiratory immune responses has become increasing appreciated. We determined the genome-wide profile of gene expression in response to immune mediated airway inflammation. Overall, our results provide detailed description of specific AEC II gene expression under disease conditions. Differentially expressed genes of diverse molecular functions have been identified that may be critical for numerous physiologic activities, some of which may be currently unappreciated. Data obtained by such analysis will help to understand the function of these important immune cells in the respiratory system and may point out strategies for intervention in the progression of inflammatory diseases.
We used microarrays to detail changes in the gene expression profile in alveolar type II epithelial cells during interstitial airway inflammation and identified a wide variety of differentially expressed genes during this process.
Keywords: comparison healthy versus diseased

overall_design: Alveolar type II epithelial cells from the lung of healthy SPC-HA and diseased SPC-HAxTCR-HA mice were isolated by enzymatic tissue desintegration followed by one step negative selection using a MoFlow cell sorter. RNA was extracted and hybridization on Affymetrix microarrays was performed.

first: Gereke

last: Marcus

first: Gröbe

last: Lothar

first: Prettin

last: Silvia

first: Kasper

last: Michael

first: Enelow

last: Richard I.

first: Buer

last: Jan

first: Bruder

last: Dunja

first: Geffers

last: Robert


title: MLL-AF9 transforms committed progenitors to leukemia stem cells by activation of a stem cell program

first: Scott

last: Armstrong

overall_design:
This reference series is composed of two noncomparable experiments (RNA was amplified on different days):

GSE3721
GSE3722


title: Expression data from primitive and maturing hematopoietic stem cells

status: Public on Jul 11 2006

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
Gene expression studies from hematopoietic stem cell (HSC) populations purified to variable degrees have defined a set of stemness genes. The present study describes the construction and comparative molecular analysis of l-phage cDNA libraries from highly purified primitive HSCs (PHSCs) which retained their long term repopulating activities (LTRAs), and from maturing HSCs (MHSCs) which were largely depleted of LTRAs. Library inserts were amplified and tagged by a T7 RNA polymerase promoter and used to generate biotinylated cRNA for Microarray hybridization. Microarray analysis of the libraries confirmed previous results but also revealed an unforseen preferential expression of translation and metabolism associated genes in the PHSCs. Therefore these data indicate that HSCs are quiescent only in regard of proliferative activities, but are in a state of readiness to provide the metabolic and translational activities required following induction of proliferation by factors which induce differentiation and exit from the HSC pool.
We used microarrays to detail the global programme of gene expression distinguishing primitive and maturing hematopoietic stem cells from mouse bone marrow and identified distinct classes of up- and down-regulated genes.
Keywords: Adult hematopoietic stem cell populations

overall_design: To compare the transcriptosomes of primitive and maturing hematopoietic stem cells from mouse bone marrow, cDNA libraries were generated from RNA isolated from highly purified stem cell populations and used to generate biotinylated cRNA for Affymetrix microarray analysis.

first: Andreas

last: Huettmann

first: Ulrich

last: Duehrsen

first: Katja

last: Heydarian

first: Alexander

last: Carpinteiro

first: Tanja

last: Boes

first: W

last: Boyd

first: Chung

middle: L

last: Li


title: Developmental changes in RNP and Polysome associated mRNAs in Mouse testes

status: Public on May 15 2006

city: Philadelphia

first: Norman

last: Hecht

address: 421 Curie Blvd

institute: University of Pennsylvania

summary:
Gametes rely heavily on post-transcriptional control mechanisms to regulate their differentiation. In eggs, the storage and selective temporal activation of maternal mRNAs is essential for normal development. In the male, transcription ceases during spermiogenesis necessitating the post-transcriptional regulation of many paternal mRNAs required for spermatid differentiation and spermatozoan function. Messenger RNAs that are being actively translated form polysomes. whereas translationally inactive mRNAs are often sequestered in ribonucleoproteins (RNPs). Here we combine polysome display and microarray analyses of RNP and polysome fractions of testes from prepuberal and adult mice to characterize the translation state of individual mRNAs as spermatogenesis proceeds.. Consistent with published reports, many post-meiotic mRNAs known to be translationally delayed shift from the RNPs into the polysomes, confirming the validity of this approach.  In addition, based upon the criterion of movement from RNPs to polysomes, we detect another 742 mouse testicular genes showing dramatic shifts between RNPs and polysomes. One sub-group of 35 genes including the known translationally delayed Pgk2, are initially transcribed and translationally repressed in meiotic spermatocytes, and translated post-meiotically. This high-through-put approach defines the changing translation patterns of a large number of genes as male germ cells differentiate and identifies a new group of post-transcriptionally regulated meiotic transcripts for future study.
Keywords: time course

overall_design: Mouse testes from animals of 3 different ages were fractionated on a sucrose gradient and transcripts were quantified in the RNP and Polysome fractions. Transcripts were identified that changed their RNP/Polysome representation at the diffent developmental time points.

first: Naoko

last: Iguchi

first: John

last: Tobias


title: Erbb2 regulates inflammation and proliferation in the skin after ultraviolet irradiation.

status: Public on Jul 01 2006

city: Omaha

first: Laura

last: Hansen

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University School of Medicine

summary:
Exposure to ultraviolet (UV) irradiation is the major cause of nonmelanoma skin cancer, the most common form of cancer in the United States. UV irradiation has a variety of effects on the skin associated with carcinogenesis, including DNA damage and effects on signal transduction. The alterations in signaling caused by UV regulate inflammation, cell proliferation, and apoptosis. UV also activates the orphan receptor tyrosine kinase and proto-oncogene Erbb2 (HER2/neu). In this study, we demonstrate that the UV-induced activation of Erbb2 regulates the response of the skin to UV. Inhibition or knockdown of Erbb2 before UV irradiation suppressed cell proliferation, cell survival, and inflammation after UV. In addition, Erbb2 was necessary for the UV-induced expression of numerous proinflammatory genes that are regulated by the transcription factors nuclear factor-kappaB and Comp1, including interleukin-1beta, prostaglandin-endoperoxidase synthase 2 (Cyclooxygenase-2), and multiple chemokines. These results reveal the influence of Erbb2 on the UV response and suggest a role for Erbb2 in UV-induced pathologies such as skin cancer.
Keywords: time course, ultraviolet irradiation, UV, erbB2, mouse skin

overall_design: The dorsal skin of adult female CD-1 mice was clipped one day before treatment and shaved on the day of treatment.  DMSO or 4 mg AG825 dissolved in DMSO was applied topically to the shaved back of the mice 2 h prior to exposure to 10 kJ/m^2 UV or sham irradiation.  The UV dose was approximately 30% UVA, 70% UVB and <1% UVC, with a total output of 470 μW/cm^2.  Flash frozen skin was removed and total RNA expracted with TRIzol reagent (Invitrogen) and further purified with an RNeasy kit (Qiagen).  Amplification, reverse-transcription, biotinylation, and hybridization were all carried out under standard conditions and procedures recommended by the manufacturer.

first: Justin

last: Madson


title: Genes in nonpermissive temperature-induced cell differentiation of testicular Sertoli TTE3 cells

status: Public on Feb 23 2007

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

summary:
We performed global scale microarray analysis to identify detailed mechanisms by which nonpermissive temperature induces cell differentiation in testicular Sertoli TTE3 cells harboring temperature-sensitive SV40 large T-antigen by using an Affymetrix GeneChip system. Testicular Sertoli TTE3 cells used in the present study were derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen. In the TTE3 cells, inactivation of the T-antigen by a nonpermissive temperature at 39˚C led to cell differentiation accompanying elevation of transferrin and cyclin-dependent kinase inhibitor CDKN1A. Of the 22, 690 probe sets analyzed, nonpermissive temperature up-regulated 729 probe sets and down-regulated 471 probe sets by >2.0-fold.
Keywords: Sertoli cell; differentiation; temperature-sensitive SV40 large T-antigen; nonpermissive temperature

overall_design: TTE3 cells were cultured at 39˚C for 0, 6, 12, and 24 h. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with the Mouse Expression Array 430A which was spotted with 22,690 probe sets. Sample preparation for array hybridization was carried out as described in the manufacture’s instructions.

first: Ichiro

last: Takasaki

first: Atsumi

last: Suto


title: Expression data from C57BL/6 and MRL/MpJ heart left ventrical with LAD ligation

status: Public on Apr 24 2006

city: Minneapolis

first: Daniel

last: Garry

state: MN

department: Cancer & Cardiovascular Research Center

institute: LILLEHEI HEART INSTITUTE

summary:
Previous studies have suggested that the heart may be capable of limited repair and regeneration in response to a focal injury while other studies indicate that the mammalian heart has no regenerative capacity.  To further explore this issue, we performed a series of superficial and transmural myocardial injuries in C57BL/6 and MRL/MpJ adult mice.  At defined time intervals following the respective injury (Days 3, 14, 30 and 60) we examined cardiac function using echocardiography, morphology, FACS cell sorting for BrdU positive cells and molecular signature using microarray analysis.  We observed complete restoration of myocardial function in the superficial MRL cryoinjured heart and significantly less scar formation as compared to the injured hearts of C57BL/6 mice.  Following a severe transmural myocardial injury, the MRL mouse has increased survival and decreased ventricular remodeling compared to the C57BL/6 mouse but without evidence of significant regeneration.  The cytoprotective program observed in the severely injured MRL heart is in part due to increased vasculogenesis and decreased apoptosis that limits the extension of the injury.  We conclude that C57BL/6 and MRL injured hearts have evidence of limited myocardial regeneration, in response to superficial injury, but the improved function and survival observed in the MRL mouse heart following severe injury is not due to significant regenerative processes.
Keywords: time course

overall_design: Mouse hearts from C57BL/6 and MRL/MpJ strains were injured with LAD ligation and harvested at 3, 30 and 60 days after treatement.

first: Jane

last: Doe

first: R

last: Naseem

first: Annette

last: Meeson

first: J

last: DiMaio

first: Michael

last: White

last: Kallhoff

first: Caroline

last: Humphries

first: Sean

middle: C

last: Goetsch

first: Leon

last: De Windt

first: Maurice

last: Williams

first: Mary


title: Microarray analysis of gene expression during early stages of mild and severe cardiac hypertrophy

status: Public on Apr 18 2006

city: Cincinnati

first: David

middle: F

last: Wieczorek

state: OH

address: 231 Albert Sabin Way

department: Molecular Genetics, Biochemistry and Microbiology

institute: University of Cincinnati

summary:
Familial hypertrophic cardiomyopathy (FHC) is a disease characterized by ventricular hypertrophy, fibrosis, and aberrant systolic and/or diastolic function.  We previously developed two transgenic mouse models that carry FHC associated mutations in  alpha-tropomyosin (TM):  FHC  alpha-TM175 mice show patchy areas of mild ventricular disorganization and limited hypertrophy; whereas FHC  alpha-TM180 mice exhibit severe hypertrophy and fibrosis and die within 6 months.  To obtain a better understanding of the molecular mechanisms associated with the early onset of cardiac hypertrophy, we conducted a detailed comparative analysis of gene expression in 2.5-month-old control and FHC  alpha-TM175 and  alpha-TM180 ventricular tissue.  Results show that 754 genes (from a total of 22,600) were differentially expressed between the NTG and the FHC hearts.  There are 178 differentially regulated genes between NTG and the FHC  alpha-TM175 hearts, 388 genes are differentially expressed between NTG and FHC  alpha-TM180 hearts, and 266 genes are differentially expressed between FHC  alpha-TM175 and FHC  alpha-TM180 hearts.  Genes that exhibit the largest increase in expression belong to the "secreted/extracellular matrix" category, and those with the most significant decrease in expression are associated with "metabolic enzymes."
Keywords: Cardiac hypertrophy, Tropomyosin, Mutation, Transgenic mouse, Microarray

overall_design: Samples used for hybridization consisted of pooled (P) and non-pooled (NP) RNA extracts from the three groups namely NTG,  alpha-TM175 and  alpha-TM180. Ten hybridization experiments were performed in which each genotypic group was represented by two or more non-pooled (NP) individual RNA extracts and one pooled (P) sample that resulted from combining 20 individual heart extracts

first: Sudarsan

last: Rajan

first: Sarah

first: Bruce

last: Aronow


title: Cross-regulation between Notch and p63 in keratinocyte commitment to differentiation

status: Public on Jul 08 2006

city: Epalinges

last: Dotto

state: VD

address: 153 Chemin de Bovaress

department: Biochemistry

country: Switzerland

institute: Lausanne University

summary:
Notch signaling promotes commitment of keratinocytes to differentiation and suppresses tumorigenesis. p63, a p53 family member, has been implicated in establishment of the keratinocyte cell fate and/or maintenance of epithelial self-renewal. Here we show that p63 expression is suppressed by Notch1 activation in both mouse and human keratinocytes through a mechanism independent of cell cycle withdrawal and requiring down-modulation of selected interferon-responsive genes, including IRF7 and/or IRF3. In turn, elevated p63 expression counteracts the ability of Notch1 to restrict growth and promote differentiation. p63 functions as a selective modulator of Notch1-dependent transcription and function, with the Hes-1 gene as one of its direct negative targets. Thus, a complex cross-talk between Notch and p63 is involved in the balance between keratinocyte self-renewal and differentiation.
Keywords: Notch1, p63, keratinocyte differentiation, gene expression profiling

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: PolyA+ mRNA (2-5 ug) from cells infected with the Ad GFP and Ad-NotchIC viruses was used as template for double stranded cDNA preparations with a T7-(dT)24 oligonucleotide primers for the first strand reaction.  The resulting cDNA was used for preparation of biotin-labeled antisense cRNA and further used for hybridization to Affymetrix U74A or U95A “gene chips” according to the manufacturer’s recommendation.

first: Bach

last: Nguyen

first: Jian

last: Wang

first: Vikram

last: Devgan

first: Karine

last: Lefort

first: Cristina

last: Buck

first: Dario

last: Antonini

first: Jan

last: Kitajewski

first: Giovanna

last: Chiorino

first: Caterina

last: Missero

first: Gian


title: Complete embryonic metanephric kidney analysis of wild type and Hoxa11, Hoxd11 null targeted mice

status: Public on May 01 2006

first: Kristopher

middle: Robert

last: Schwab

address: 3333 Burnett Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital Research Foundation

summary:
Complete (whole) embryonic kidneys were dissected from wild type and Hoxa11, Hoxd11 compound null embryons throughout development.  Targets from two biological replicates of each were generated and the expression profiles were determined using Affymetrix MOE430A and MOE430B arrays.  Comparisons between normal and mutant and comparisons of development samples identified global patterns of gene regulation in kidney development
Keywords: embryonic metanephric kidney, kidney development, Hoxa11, Hoxd11, compound null targeted mice

overall_design: Embryonic metanephric kidney samples throughout development were analyzed based on normalization to adult kidney samples.  In addition, Hoxa11, Hoxd11 compound null embronic kidneys were normalized to wild type embryonic controls.  All developmental and adult stages were represented in biological (seperate embryo/animal replicate)

first: Steven

last: Potter


title: IL-18 and Pressure Overload-induced Cardiac Hypertrophy

status: Public on Jul 04 2006

city: San Antonio

first: James

middle: T.

last: Colston

state: TX

address: 7703 Floyd Curl Drive

department: Medicine

institute: UTHSCSA

summary:
Pressure overload-induced cardiac hypertrophy was examined in IL-18 knockout and littermate control mice.
Keywords: genetic modification / disease model

overall_design: 4 groups with RNA pooled from 5-6 per group.  Role of IL-18 on gene expression in cardiac hypertrophy induced by pressure overload (transaortic constriction)

middle: T

first: William

last: Boylston

first: Marc

last: Feldman

first: Chris

last: Jenkinson

first: Sam

last: de la Rosa

first: Gregory

last: Freeman

first: Bysani

last: Chandrasekar


title: Sex Differences in Response to Plasmodium chabaudi Infection: Involvement of Gonadal Steroids

status: Public on Jun 01 2006

city: Baltimore

first: Sabra

middle: Lynn

last: Klein

address: 615 North Wolfe Street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins Bloomberg School of Public Health

summary:
The goal of this study was to examine whether immune responses to Plasmodium chabaudi infection differ between the sexes and are altered by the presence of gonadal steroids.  Gonadally-intact males were more likely than intact females to die following P. chabaudi infection, exhibit slower recovery from infection-associated weight loss, hypothermia, and anemia, have reduced IFNγ-associated gene expression and IFNγ production during peak parasitemia, and produce less antibody during the recovery phase of infection.  Gonadectomy of male and female mice altered these sex-associated differences, suggesting that sex steroid hormone, in particular androgens and estrogens, may modulate immune responses to infection.
Keywords: Time Course

overall_design: Intact and gonadectomized (gdx) male and female C57BL/6 mice were inoculated with 106 P. chabaudi AS-infected erythrocytes and responses to infection were monitored.  For microarray analyses, RNA was isolated from 5 x 106 white blood cells (WBCs) that were isolated from spleens 0, 3, 7, or 14 days after inoculation with P. chabaudi.  Equivalent aliquots of RNA from 3 animals/treatment group were pooled and 3 separate pools were processed on separate Affymetrix GeneChips (n = 3 GeneChips/time point/treatment group).

first: Amy

last: Cernetich

first: Lindsey

last: Garver

first: Anne

middle: E

last: Jedlicka

first: Pamela

middle: W

first: Nirbhay

last: Kumar

first: Alan

last: Scott


title: Expression profiling of Treg cell versus their controls in human and mouse

first: Robert

last: Geffers

summary:
We applied Affymetrix GeneChip technology for expression profiling of CD4+CD25+ (Treg) T cells versus their naive CD4+CD25- controls to obtain more information about the underlying molecular mechanisms involved in Treg specific immune suppression
Keywords: cell type comparison

overall_design:
Expression profiles from:

[1] human Treg cells obtained from peripheral blood by cell sorting were compared to their naive controls.  RNAs were prepared from pools of ten individual healthy donors, labeled in two independend labeling reactions and hybridized onto two GeneChips of the same lot.

[2] mouse Treg cells obtained from spleen by cell sorting of Balb/c mice were compared to their naive controls.  RNAs were prepared from pools of three individual Balb/c mice, labeled in three independend labeling reactions and hybridized onto three GeneChips of the same lot.

The differences in gene expression were used to unravel molecular mechanisms that help to explain the suppressive and anergic phenotypes of Treg cells after antigen activation.

first: W

last: Hansen

first: M

last: Probst-Kepper

first: J

last: Buer


title: Accurate and precise transcriptional profiles from 50 pg of total RNA or 100 flow-sorted primary lymphocytes

status: Public on Jun 23 2006

city: Boston

first: Jeff

last: Shearstone

address: 70 Fargo Street

department: Biology

institute: Acetylon Pharmaceuticals

summary:
We have developed a total RNA amplification and labeling strategy for use with Affymetrix GeneChips. Our protocol, which we denote BIIB, employs two rounds of linear T7 amplification followed by Klenow labeling to generate a biotinylated cDNA. In benchmarking studies using a titration of mouse universal total RNA, BIIB outperformed commercially available kits in terms of sensitivity, accuracy, and amplified target length, while providing equivalent results for technical reproducibility. BIIB maintained 50 and 44% present calls from 100 and 50 pg of total RNA, respectively. Inter- and intrasample precision studies indicated that BIIB produces an unbiased and complete expression profile within a range of 5 ng to 50 pg of starting total RNA. From a panel of spiked exogenous transcripts, we established the BIIB linear detection limit to be 20 absolute copies. Additionally, we demonstrate that BIIB is sensitive enough to detect the stochastic events inherent in a highly diluted sample. Using RNA isolated from whole tissues, we further validated BIIB accuracy and precision by comparison of 224 expression ratios generated by quantitative real-time PCR. The utility of our method is ultimately illustrated by the detection of biologically expected trends in a T cell/B cell titration of 100 primary cells flow sorted from a healthy mouse spleen.
Keywords: Development and validation of an amplification and labeling protocol for transcriptional profiling on Affymetrix GeneChips, cDNA target on Affymetrix Genechip, small or limiting total RNA samples

overall_design: Various experimental designs were used as part of the validation process for this total RNA amplification and labeling protocol.  103 samples were analyzed on Affymetrix GeneChips as part of this GEO series.  Details of the BIIB protocol and supporting experiments are published in Genomics. 2006 Jul;88(1):111-21

first: Jeffrey

first: Normand

last: Allaire

first: Juanita

last: Campos-Rivera

first: Sambasiva

last: Rao

first: Steven

last: Perrin


title: PKCa -/- vs wt small intestine

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

institute: University of Lübeck

summary:
Members of the PKC family of serine / threonine kinases play key regulatory roles in numerous cellular processes including differentiation and proliferation. Of the eleven mammalian PKC isoforms known several have been implicated in tumor development and progression. However, in most cases isotype specificity is poorly defined and even contrary functions for a single PKC have been reported, mostly because appropriate molecular and genetic tools were missing to specifically assess the contribution of single PKC isoforms in vivo.
In this report we therefore used PKC genetic targeting to study the role of PKCa and PKCz in colorectal cancer. Both isoforms were found to be strongly down-regulated in intestinal tumors of ApcMin/+ mice. A deletion of PKCz did not affect tumorigenesis in this animal model. In contrast, PKCa deficient ApcMin/+ mice developed more aggressive tumors and died significantly earlier than their PKCa proficient littermates. Even without an additional Apc mutation PKCa knock out mice showed an elevated tendency to develop spontaneous intestinal tumors. Transcriptional profiling revealed a role for this kinase in regulating EGFR signaling and proposed a synergistic mechanism for EGFR / AP-1 and WNT / APC pathways in mediating intestinal tumor development.
Keywords: genetic modification

overall_design:
Adult male animals (PKCa -/- and congenic wt controls; 50-60 days old) were sacrificed by cervical dislocation. Small intestines were dissected and total RNA (~5µg per sample) was extracted using the QIAGEN RNeasy kit.
Sample processing (performed at the RZPD, Deutsches Ressourcenzentrum für Genomforschung GmbH, Heubnerweg 6, 14059 Berlin) included cRNA generation and labeling with biotin. cRNA samples were hybridized to the GeneChips and chips stained with a streptavidine-phycoerythrine conjugate,
washed and scanned. Hybridization images were analyzed using
GCOS™ 1.1.

first: Michael

last: Leitges


title: NF639 cells original population vs EGCG-resistant population

first: Gail

last: Sonenshein

address: 715 Albany Street

institute: Boston University Medical School

summary:
Overexpression of the epidermal growth factor receptor family member Her-2/neu in breast cancer leads to autophosphorylation of the receptor, and induction of multiple downstream signaling pathways including Akt kinase to NF-kappaB cascade that is associated with poor prognosis. Previously, we demonstrated green tea polyhenol epigallocatechin 3-gallate (EGCG) inhibits growth of NF639 Her-2/neu-driven breast cancer cells via reducing receptor autophosphorylation, and downstream Akt and NF-kappaB activities (Pianetti et al., 2002). Interestingly, we noted that upon prolonged culture in the presence of EGCG some cells developed resistance to the polyphenol. Here we report that resistant cells have lost tyrosine phosphorylation on the Her-2/neu receptor. Surprisingly, they displayed elevated NF-kappaB activity, and inhibition of this activity sensitized cells to EGCG. Data from microarray analysis of the original and resistant NF639 populations of cells were subjected to Gene Set Enrichment Analysis (GSEA) pathway analysis, which revealed that the mitogen activated protein kinase (MAPK) pathway was activated in the resistant cells. Treatment of the resistant cells with a combination of EGCG and the MAPK inhibitor U0216 dramatically reduced colony growth and mesenchymal phenotype. Thus, activation of the MAPK pathway mediates resistance to EGCG. Our studies suggest that gene expression profiling of drug resistant cells may provide a mechanism of determining effective systemic therapies for treatment of these advanced cancers.
Keywords: Drug resistance

overall_design: Total RNA from original NF639 cells and EGCG resistant NF639 cells were harvested using the UltraspecII RNA isolation kit (Biotecx), following the manufacturer’s instruction. The RNA samples were submitted to Boston University Microarray Resource for microarray hybridization using Affymetrix Mouse 430A 2.0 chips. RNAs from two independent experiments were analyzed and data pooled for computational analysis.

first: Shangqin

last: Guo

first: Jun

last: Lu

first: Aravind

last: Subramanian


title: Adaptive mechanisms in the Mdr2-knockout mouse HCC model

status: Public on Apr 23 2006

city: Ramat-Gan

first: Mark

last: Katzenellenbogen

address: Ramat-Gan 52900, Israel

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

country: Israel

institute: Bar Ilan University

summary:
We studied the molecular mechanisms of hepatocellular carcinoma (HCC) initiation and promotion using the Mdr2-knockout (Mdr2-KO) mice at pre-cancerous stages of liver disease. These mice lack the liver-specific P-glycoprotein responsible for phosphatidylcholine transport across the canalicular membrane. Portal inflammation ensues at an early age followed by the development of HCC between the ages of 12 and 15 months. Liver tissue samples of Mdr2-KO and control Mdr2-heterozygotes mice aged 3 and 12 months, were subjected to histological, biochemical and gene expression profiling analysis using Affymetrix Mouse Genome Array.
Keywords: HCC, murine model, precancerous stages, chronic liver desease

overall_design: The RNA samples from Mdr2-KO and control heterozygous mice aged 3 and 12M (3 males in each experimental group) were subjected to genome scale gene expression profiling with Affymetrix Mouse Array. The gene expression values were extracted with the help of MAS 5.0 software, and analyzed by cluster analysis, and by fold change filtering

first: Orit

last: Pappo

first: Hila

last: Barash

first: Naama

last: Klopstock

first: Lina

last: Mizrahi

first: Devorah

last: Olam

first: Jasmine

last: Jacob-Hirsch

first: Ninette

last: Amariglio

first: Gidi

last: Rechavi

first: Leslie-Ann

last: Mitchell

first: Ron

last: Kohen

first: Eytan

last: Domany

first: Eithan

last: Galun

first: Daniel

last: Goldenberg


title: Genes responsive to bisphenol A in testicular Sertoli cells

status: Public on Apr 13 2006

first: Yoshiaki

last: Tabuchi

summary:
We performed global scale microarray analysis to identify detailed mechanisms by which bisphenol A (BPA) induce cell death by using an Affymetrix GeneChip system. Testicular Sertoli TTE3 cells used in the present study were derived from transgenic mice harboring a temperature-sensitive simian virus 40 large T-antigen. Cell death accompanying endoplasmic reticulum stress was observed in the cells treated with 0.2 mM BPA. Of the 22,690 probe sets analyzed, approximately 1,300 genes were down- and up-regulated by a factor of 2.0 or greater in the cells treated with BPA.
Keywords: bisphenol A, gene expression, testicular Sertoli cell

overall_design: TTE3 cells were treated with BPA for 0, 3, 6, and 12 h. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with the Mouse Expression Array 430A which was spotted with 22,690 probe sets. Sample preparation for array hybridization was carried out as described in the manufacture’s instructions.

first: Ichiro

last: Takasaki


title: AireKO vs Black6

status: Public on Apr 11 2006

city: Augusta

first: Ratanmani

last: Joshi

address: Laney Walker Blvd

department: Genomics

institute: Center for Biotechnology and Genomic Medicine

summary:
TEC (B6 vs Aire KO). Thymic epithelial cells from B6 strain and AIRE KO are compared.
Keywords: repeat sample


status: Public on Apr 21 2006

city: xi an

first: ping

last: zhang

state: shaanxi

address: changleroad 17

country: China

institute: fmmu

summary:
Immature B cells in spleens of mouse and human differentiate into at least two subsets of mature B cells, the follicular (FO) B cells and the marginal zone (MZ) B cells, but functions, maturation and other properties of these cells are largely unknown. To solve these questions, in this study, we performed transcriptome analyses of FO and MZ B cells sorted from spleens of normal unimmunized mice using gene chips. By comparison of gene expression profiles between FO and MZ B cells, we identified 1226 genes that are expressed higher in FO B cells than in MZ B cells. On the other hand, 1734 genes were found to be expressed higher in MZ B cells than in FO B cells. We noticed that some of differentially expressed genes have been reportedly characterized in FO and MZ B cells, suggesting the reliability of the analysis. By using FACS analyses, we confirmed that CD36, CD68, and CD49e are expressed on MZ B-cells but not on FO B-cells. These results revealed new phenotypic and functional properties of FO and MZ B cells, and set a molecular basis for further studying differentiation and functions of these mature B cells.
Keywords: Comparison of gene expression profiles between mouse follicular and marginal zone B-cells

overall_design: one follicular B cells replicate and one marginal zone B cells  replicate were analyzed.

first: jishu

last: wang

first: wei

last: li

first: lihong

last: hou

first: yaochun

first: yingmin

last: liang

first: hua

last: han


title: Analysis of Akt1 activation in transgenic mouse hearts show expression profiles associated with hypertrophy and failure

status: Public on Aug 25 2006

first: Stephan

last: Schiekofer

address: 700 Albany Street, W611

department: Molecular Cardiology

institute: Boston University School of Medicine

summary:
To investigate molecular mechanisms involved in the development of cardiac hypertrophy and heart failure, a tetracycline-regulated transgenic system to conditionally switch a constitutively-active form of the Akt1 protein kinase on or off in the adult heart was developed. Short-term activation (2 weeks) of Akt1 resulted in completely reversible hypertrophy with maintained contractility. In contrast, chronic Akt1 activation (6 weeks) induced extensive cardiac hypertrophy, severe contractile dysfunction, and massive interstitial fibrosis. The focus of this study was to create a transcript expression profile of the heart as it undergoes reversible Akt1-mediated hypertrophy and during the transition from compensated hypertrophy to heart failure. Heart tissue was analyzed before transgene induction, 2 weeks after transgene induction, 2 weeks of transgene induction followed by 2 days of repression, 6 weeks after transgene induction and 6 weeks of transgene induction followed by 2 weeks of repression. Acute over expression of Akt1 (2 weeks) leads to changes in the expression of 826 transcripts relative to non-induced hearts, whereas chronic induction (6 weeks) led to changes in the expression of 1611, of which 65% represented transcripts that were regulated during the pathological phase of heart growth. Another set of genes identified were uniquely regulated during heart regression but not growth, indicating that non-overlapping transcription programs participate in the processes of cardiac hypertrophy and atrophy. These data define the gene regulatory programs downstream of Akt that control heart size and contribute to the transition from compensatory hypertrophy to heart failure.
Keywords: transgenic mice, Akt1, time course, cardiac hypertrophy and contractile dysfunction, DNA microarrays

overall_design: Gene expression data from DTG-positive mouse hearts were examined before the induction of the transgene Akt1 (time point 1), 2 weeks after the induction of the transgene Akt1(time point 2), 2 weeks after the induction of the transgene Akt1 and 2 days after the repression of the transgene Akt1 (time point 3), 6 weeks after the induction of the transgene Akt1(time point 4) and 6 weeks after the induction of the transgene Akt1 and 2 weeks after the repression of the transgene Akt1 (time point 5). N = 3 to 4 sets of independent hybridizations from individual mice were performed for each time point.

last: Shiojima

first: Kaori

last: Sato

first: Benjamin

last: Kraus

first: Gennaro

last: Galasso

first: Kenneth

last: Walsh


title: normal human CFTR overexpression in mouse lung

status: Public on Mar 24 2006

first: Yan

last: Xu

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary:
Identification of Genes Responsive to the Expression of Normal Human CFTR
Keywords: genotype comparison

overall_design: To discern the effects of increased expression of normal human CFTR, lung mRNA levels were assessed in mice expressing the normal human CFTR cDNA under control of the Sftpc gene promoter in respiratory epithelial cells of adult mice. Triplicate samples from SP-C-hCFTRtg/tg, SP-C-hCFTRtg/-, and wild type mice were compared.


title: Genes responsive to sodium butyrate in colonic epithelial cells

status: Public on Mar 10 2006

summary:
We performed global scale microarray analysis to identify detailed mechanisms by which sodium butyrate (SB) induce cell growth arrest and differentiation of colonic epithelial cells by using an Affymetrix GeneChip system. Colonic epithelial MCE301 cells used in this study were derived from transgenic mice harboring a tsSV40 large T-antigen. Arrested cell growth and a differentiated phenotype accompanying elevations of alkaline phosphatase activity and histone acetylation were observed in the cells treated with 2 mM SB. Of the 22,690 probe sets analyzed, approximately 2,000 genes were down- and up-regulated by a factor of 2.0 or greater in the cells treated with SB.
Keywords: sodium butyrate, gene expression, colonic epithelial cell

overall_design: MCE301 cells were treated with SB for 0, 6, 12 and 24 h. Total RNA samples were prepared from the cells. Gene expression was analyzed by a GeneChip® system with the Mouse Expression Array 430A which was spotted with 22,690 probe sets. Sample preparation for array hybridization was carried out as described in the manufacture’s instructions.


title: Microarray Analysis of the Developing Murine Prefrontal Cortex

status: Public on May 15 2006

city: Toronto

first: Paul

last: Boutros

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
Abnormal development of the prefrontal cortex (PFC) is associated with a number of neuropsychiatric disorders that have an onset in childhood or adolescence. Although the basic laminar structure of the PFC is established in utero, extensive remodeling continues into adolescence. To map the overall pattern of changes in cortical gene transcripts during post-natal development, we made serial measurements of mRNA levels in mouse PFC using oligonucleotide microarrays. We observed changes in mRNA transcripts consistent with known post-natal morphological and biochemical events. Overall, most transcripts that changed significantly showed a progressive decrease in abundance after birth, with the majority of change between post-natal weeks 2 and 4. Genes with cell proliferative, cytoskeletal, extracellular matrix, plasma membrane lipid / transport, protein folding, and regulatory functions had decreases in mRNA levels. Quantitative PCR verified the microarray results for six selected genes: DNA methyltransferase 3A (Dnmt3a), procollagen, type III, alpha 1 (Col3a1), solute carrier family 16 (monocarboxylic acid transporters), member 1 (Slc16a1), MARCKS-like 1 (Marcksl1), nidogen 1 (Nid1) and 3-hydroxybutyrate dehydrogenase (heart, mitochondrial) (Bdh).
Keywords: time course, development, mRNA expression

overall_design: Single-channel affymetrix arrays were used to profile mRNA expression in the prefrontal cortex (PFC) of male mice at different time-points after birth (post-natal).  Each array is an independent animal.

first: Mawahib

last: Semeralul

first: Olga

last: Likhodi

first: Allan

last: Okey

first: Hubert

last: Van Tol

first: Albert

last: Wong


title: Clenbuterol administration in mouse muscle

status: Public on Mar 18 2006

city: Ames

first: Diane

middle: Moody

last: Spurlock

state: IA

address: 239 Kildee Hall

department: Animal Science

institute: Iowa State University

summary:
Background: Beta-adrenergic receptor agonists (BA) induce skeletal muscle hypertrophy, yet specific mechanisms that lead to this effect are not well understood.  The objective of this research was to identify novel genes and physiological pathways that potentially facilitate BA induced skeletal muscle growth.  We chose to evaluate global changes in gene expression by utilizing the Affymetrix platform to identify gene expression changes in mouse skeletal muscle.  Changes in gene expression were evaluated 24 h (1D) and 10 days (10D) after administration of the BA clenbuterol.
Results: Administration of clenbuterol stimulated anabolic activity, as indicated by decreased blood urea nitrogen (BUN; P < 0.01) and increased body weight gain (P < 0.05) 24 h or 10 d, respectively, after initiation of clenbuterol treatment.  A total of 22,787 probesets were evaluated with 113 probesets defined as differentially expressed based on a false discovery rate of 10%.  Differential mRNA abundance of four of these genes was validated in an independent experiment by quantitative PCR.  Patterns of gene expression change observed from the microarray data suggested more genes are differentially regulated after 24 h than 10 d of BA administration.  Functional characterization of differentially expressed genes revealed several categories that participate in biological processes important to skeletal muscle growth, including regulators of transcription and translation, mediators of cell-signaling pathways, and genes involved in polyamine metabolism.  Included within these lists were several genes previously associated with myogenic differentiation, along with multiple genes known to promote a general up-regulation of translation.
Conclusions:  Global evaluation of gene expression after administration of clenbuterol identified changes gene expression and overrepresented functional categories of genes that may regulate BA-induced muscle hypertrophy.  Changes in the mRNA abundance of multiple genes associated with myogenic differentiation may indicate an important effect of BA on the proliferation, differentiation, and/or recruitment of satellite cells into muscle fibers to promote muscle hypertrophy.  Additionally, increased mRNA abundance of genes involved in the initiation of translation suggests that increased levels of protein synthesis often associated with BA administration may result from a general up-regulation of translational initiators, rather than a sustained up-regulation of gene expression at the transcriptional level.  Additionally, numerous other genes and physiological pathways were identified that will be important targets for further investigations of the hypertrophic effect of BA on skeletal muscle.
Keywords: Compound administration, time course

overall_design: A total of 27 mice were used to represent three treatments.  Hybridizations were done using RNA pools from 3 mice, with 3 pools (replicates) per treatment.  Treatments included control, 1 day of clenbuterol administration, and 10 days of clenbuterol administration.  Data represent skeletal muscle gene expression.

middle: M

first: Tara

middle: G

last: McDaneld

first: Lauren

last: McIntyre


title: Laminin-deficient muscular dystrophy, dy/dy diaphragm

status: Public on Mar 16 2006

city: Cleveland

first: Erik

last: van Lunteren

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

summary:
Laminin (merosin) deficient muscular dystrophy in dy/dy mouse diaphragm muscle, 8 weeks old
Keywords: muscle, muscular dystrophy, laminin, merosin, diaphragm, mouse

overall_design:
4 normal samples
4 dystrophic samples

Each sample consists of muscle pooled from 3 mice, thus a total of 12 normal and 12 dystrophic mice were studied

first: Michelle

last: Moyer

first: Patrick

last: Leahy


title: Dexamethasone responses in BRC-Abl (p210) transformed murine B-cells

status: Public on Feb 25 2006

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

institute: Institut fuer Zellbiologie

summary:
For generation of pre-B cell lines, bone marrow from tibias and femurs of 4 to 8 week old C56Bl/6 mice (wt and vav-Gfi1b transgene) was infected with retroviral stocks of different BCR-Abl constructs (MSCV-GFP-IRESp210 or pSRa-p210-tkneo) and plated at a density of 5E+06 per 6 cm dish. All pre-B cells were fed twice a week and analyzed after they became stroma independent. Cells received 1E-08 M dexamethasone or vehicle for 12 hours prior to RNA extraction using TRIzol. mRNAs were converted into doublestranded cDNA using a T7-promoter tagged oligodT primer and transcribed by T7 RNA polymerase in the presence of biotinylated NTPs. Targets were hybridized to Affymetrix MOE430A arrays, washed, stained and scanned (GeneChip scanner 2500) as recommended by the manufacturer. Images were processed either by MAS5.0 (global scaling, TGT=1000) or RMAExpress (quantile normalization and background substraction) software tools.
By comparing the gene expression profiles of dexamethasone and non-induced cells, dexamethasone target genes were identified
Keywords: ordered

first: Lothar

last: Vassen

first: Katharina

last: Fiolka

first: Stefan

last: Mahlmann

first: Tarik

last: Möröy


title: AMPK gamma3 knock-out and mutant (R225Q) transgenic mice compared to corresponding wild type littermates

status: Public on Feb 15 2006

city: Göteborg

first: Elisabeth

last: Nilsson

address: Arvid Wallgrens Backe 20

country: Sweden

institute: Arexis AB

summary:
Note: GSE4063 and GSE4065 are not directly comparable.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Liver transcriptional response to quercetin in WT and POR-null mice

status: Public on Mar 01 2006

city: Guelph

first: David

last: Mutch

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

institute: University of Guelph

summary:
Using mice deficient in hepatic cytochrome-P450 oxidoreductase (POR), which disables the liver cytochrome P450 system, the metabolism and biological response of the anti-carcinogenic flavonoid, quercetin, was examined. Profiling circulating metabolites revealed similar profiles over 72 h in wild type (WT) and POR-null (KO) mice, showing that hepatic P450 and reduced biliary secretion do not affect quercetin metabolism. Transcriptional profiling at 24 h revealed that 2-3 fold more genes responded significantly to quercetin in WT compared to KO in the jejunum, ileum, colon, and liver, suggesting that hepatic P450s mediate many of the biological effects of quercetin, such as immune function, estrogen receptor signaling and lipid, glutathione, purine, and amino acid metabolism, even though quercetin metabolism is not modified. The functional interpretation of expression data in response to quercetin (single dose of 7 mg/animal) revealed a molecular relationship between the liver and jejunum. In WT animals, amino acid and sterol metabolism were predominantly modulated in the liver, fatty acid metabolism response was shared between the liver and jejunum, and glutathione metabolism was modulated in the small intestine. In contrast, KO animals do not regulate amino acid metabolism in the liver or small intestine, they share the control of fatty acid metabolism between the liver and jejunum, and regulation of sterol metabolism is shifted from the liver to the jejunum and that of glutathione metabolism from the jejunum to the liver.  This demonstrates that the quercetin-mediated regulation of these biological functions in extrahepatic tissues is dependent on the functionality of the liver POR. In conclusion, using a systems biology approach to explore the contribution of hepatic phase I detoxification on quercetin metabolism demonstrated the resiliency and adaptive capacity of a biological organism in dealing with a bioactive nutrient when faced with a tissue-specific molecular dysfunction.
Keywords: nutritional intervention, comparative genomic response, genotype variation

overall_design:
All animals were adapted to the RM3 (E) 801710 Soya-free powdered diet (B. S & S. [Scotland] Ltd, UK) over a period of 14 days. Quercetin was added separately to the semi-purified diets at a concentration of 6200 ppm (0.62 %; 6.2 g per kg). 65 male cytochrome P450 reductase null (KO) mice and 65 wild type (WT) C57BL/6 mice were reared, all aged between 6-8 weeks. Animals were housed 3 per cage, where both temperature and relative humidity were maintained within a range of 19-23oC and 40-70%, respectively. Twelve-hour periods of light were cycled with twelve-hour periods of darkness.

For each strain of mouse, the following experimental design was used: a control group (25 mice) receiving powdered RM3 diet ad libitum and a group (25 mice) receiving a ‘high dose’ of quercetin (7 mg / mouse). The experimental diet was administered on day 15, following a 14-day adaptation period to the RM3 diet. Animals were sacrificed after 24 h.

RNA samples destined for microarray analysis were only accepted and pooled into three groups if no aberrant signs of degradation (e.g. multiple peaks) were observed. The comprehensive gene expression profiles of the liver, jejunum, ileum, and colon were analyzed. In all cases, except those listed, RNA from 3 mice was pooled to form sample 1, another 3 mice to form sample 2, etc. Thus, 9 mice were used for the four experimental groups: wild-type, wild-type+quercetin, POR-null, POR-null+quercetin.

first: Vanessa

last: Crespy

first: Jennifer

last: Clough

first: Colin

last: Henderson

first: Sofiane

last: Lariani

first: Robert

last: Mansourian

first: Julie

last: Moulin

first: C

middle: R

last: Wolf

first: Gary

last: Williamson


title: Gene expression in skeletal muscle in AMPK gamma3 knock-out mice and wild type littermates

summary:
Analysis of AMPK gamma3-dependent transcriptional responses by analyzing global gene expression in the white portion of the gastrocnemius muscle in AMPK gamma3 knock-out mice and corresponding wild type littermates.
Keywords: Genetic modification

overall_design:
Mice were maintained in a 12-h light-dark cycle.
Gene expression profiles were characterized in 14 weeks male mice fasted over-night.
6 biological replicates.


title: Jejunum transcriptional response to quercetin in WT and POR-null mice


title: Colon transcriptional response to quercetin in WT and POR-null mice


title: effect of types of olive oil on hepatic gene expression

status: Public on Feb 09 2006

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

summary:
Two isocaloric, isonitrogenous diets containing 10% (w/w) olive oil or unsaponifiable-enriched olive oil have been provided to male apo E knockout mice for 11 weeks. Then RNA was isolated and  hepatic gene expression analyzed.
Keywords: other

first: Sergio

last: Acín

first: Javier

middle: S

last: Perona

first: María

middle: A

last: Navarro

first: Alfonso

last: Sarría

first: Jose

last: Arbonés-Mainar

first: Carmen

last: Arnal

first: Joaquín

last: Surra

first: Ricardo

last: Carnicer

first: Jesús

first: Valentina

last: Ruiz-Gutiérrez


title: Ileum transcriptional response to quercetin in WT and POR-null mice

first: David

last: Mutch

first: Vanessa

last: Crespy

first: Jennifer

last: Clough

first: Colin

middle: J


title: Gene expression in skeletal muscle in AMPK gamma3 mutant (R225Q) transgenic mice and wild type littermates.

first: Elisabeth

last: Nilsson

summary:
Analysis of AMPK gamma3-dependent transcriptional responses by analyzing global gene expression in the white portion of the gastrocnemius muscle in AMPK gamma3 mutant (R225Q) transgenic mice and corresponding wild type littermates.
Keywords: Genetic modification

overall_design:
Mice were maintained in a 12-h light-dark cycle.
Gene expression profiles were characterized in 17-18 weeks male mice fasted over-night.
6 biological replicates.


title: Gene inductions in response to B-DNA transfection in Tbk1 and/or Ikbke-deficient embryonic fibroblasts

status: Public on Feb 04 2006

city: Suita

first: Shizuo

last: Akira

state: Osaka

address: 3-1 Yamada-oka

department: Department of Host Defense

institute: Reserch Institute for Microbial Diseases, Osaka University

summary:
B-DNA-induced gene expression profile in wild-type, TBK1, IKKi(Ikbke), or TBK1 IKKi doubly deficient embryonic fibroblats; to elucidate how TBK1 and/or IKKi mediates B-DNA-mediated innate immune responses.
Keywords: ordered

overall_design: Total RNA was extracted from embryonic fibroblats transfected for 4 h with or without poly(dA-dT)-poly(dT-dA), after which cRNA was synthesized. Preparation of cRNA, hybridization and scanning of the microarray were done according to the manufacturer's instructions (Affymetrix). A microarray (MG U74A version 2; Affymetrix) was used with Microarray Suite software (version 5.0; Affymetrix) and GeneSpring software (Silicon Genetics).

first: Ken

last: Ishii


title: Cell Culture A and B chips on EOM and leg

status: Public on Mar 14 2006

first: Henry

middle: J.

last: Kaminski

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

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


title: Transcriptional responses to quercetin in WT and POR-null mice


title: Comparison of transcripts from the anterior tibialis, gastrocnemius, and liver of glycogen synthase WT, GSL30 or KO mice

status: Public on Jan 27 2006

city: Indianapolis

first: Peter

last: Roach

state: IN

institute: IU School of Medicine

summary:
Anterior tibialis removed from 3-month old muscle glycogen synthase WT or knockout mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. GSM40057-GSM40063 AND GSM40956.

Liver removed from 3-month old muscle glycogen synthase WT or knockout mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA. GSM40064-GSM40071.

Medial gastrocnemius removed from 3-month old muscle glycogen synthase WT or knockout mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. GSM40072-GSM40079.

Medial gastrocnemius removed from 8-month old muscle glycogen synthase WT or overexpressing mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA.  GSM40080-GSM40089
Keywords: other

first: Bartholomew

last: Pederson

first: Gretchen

last: Parker

first: Jill

last: Schroeder


title: Pac1+/+ versus Pac1-/- BMMCs_IgE-DNP 2 h

status: Public on Jan 10 2006

city: Darlinghurst

first: Charles

middle: Reay

last: Mackay

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute for Medical Research

summary:
Bone marrow-derived mast cells were differentiated over 4-6 weeks using bone marrow from Pac-1+/+ and Pac1-/- littermate mice. Cell purity was 99% c-kit and Fc epsilon receptor positive as assessed by flow cytometry. Cells were stimulated by Fc epsilon receptor crosslinking using IgE-DNP/HSA for sensitization for 18 hours and DNP-HSA antigen for crosslinking for 2 hours. Gene transcript abundance was determined and scaled to 150 using alogorithms in MicroArray Analysis Suite Software 5.0 (Affymetrix).
Keywords: Cpmparison of Pac-1+/+ and Pac-1-/- activated BMMCs

overall_design: Two genechips on independent mBMMC cultures was performed.  The signal data of the .CEL files for the four Affymetrix 430A chips (2 Pac1+/+ and 2 Pac1–/–) were normalised using the RMA method 49. The ebayes function implemented in the version 1.3.12 of the Limma package (2003) of Bioconductor was used to analyse the data and P-values were adjusted for multiple testing. After conversion from logged values to the original intensities, the data was filtered to remove probe sets with mean, non-logged, intensities below 100.  Transcripts with p-values less than 0.05 were considered different from Pac1+/+.

first: Kate

middle: L

last: Jeffrey


title: The Effect of Cell Aggregation on Gene Expression of Pluripotent Embryonal Carcinoma Cells

status: Public on Jan 24 2006

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
Investigation of very early events required for initiating differentiation of pluripotent embryonal carcinoma cells - the effect of cell aggregation on gene expression.
Keywords: cell aggregation

overall_design: this experiment include 4 samples and 24 replicates


title: Neuronal Differentiation of Primary Myoblast Sphere Cultures

summary:
Adult mouse muscle was enzymatically dissociated. Muscle derived stem cells proliferate unattached, in spheres, in the proliferation medium. Cells from spheres were also incubated in a differentiation medium. They differentiated into neurons after 7 days in culture.
Keywords: neuronal differentiation

overall_design: this experiment include 2 samples and 12 replicates


title: Comparison of HNF4 null to control colons

status: Public on Jan 01 2006

city: Charleston

first: Stephen

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

summary:
Background and Aims: HNF4a is a nuclear hormone receptor transcription factor that has been shown to be required for hepatocyte differentiation and development of the liver.  It has also been implicated in regulating expression of genes that act in the epithelium of the lower gastrointestinal tract.  This implied that HNF4a might be required for development of the gut.  Methods:  We generated mouse embryos in which HNF4a was ablated in the epithelial cells of the fetal colon using Cre-loxP technology.  Embryos were examined using a combination of histology, immunohistochemistry, gene array and RT-PCR, and chromatin immunoprecipitation analyses to define the consequence of loss of HNF4a on colon development.  Results: Embryos could be generated until E18.5 that lacked HNF4a in their colon.  Although, early stages of colonic development occurred, HNF4a null colons failed to form normal crypts.  In addition, goblet cell maturation was perturbed and expression of an array of genes that encode proteins with diverse roles in colon function was disrupted.  Several genes whose expression in the colon was dependent on HNF4a contained HNF4a–binding sites sequences within putative transcriptional regulatory regions and a subset of these sites were occupied by HNF4a in vivo.  Conclusion:  HNF4a is a transcription factor that is essential for development of the mammalian colon, regulates goblet cell maturation and is required for expression of genes that control normal colon function and epithelial cell differentiation.
Keywords: E18.5 FETAL HNF4 NULL COLONS

overall_design: COMPARISON OF 3 MUTANT TO 2 CONTROL COLONS.


title: HNF4 small intestine knockout

status: Public on Dec 31 2005

summary:
To define changes in gene expression resulting from loss of hnf4 in the small intestine.
Keywords: genetic modification

overall_design: hnf4 null intestines were generated by breeding hnf4loxp mice to vill-cre mice.  Animals appeared to be healthy.  Gene arrays were performed on two null and two control intestines.


title: D4 and C2 assessed for chimerism and germline transmission

summary:
Two independent ES cell lines (D4 and C2) were assessed for chimerism and germline transmission. Although these lines were able to produce chimerism at early passage, no germ line transmission was seen. After passaging in a proprietary medium and subcloning by detaching loosely connected cells and culturing in the recommended medium, both lines experienced an increase in potential as evidenced by an enhanced ability to go germ line. Analysis of early passage, and late passage detached and attached cells will allow the determination of genes that may be implicated in the increase of potential seen in these cells.
Note: additional replicates may be added at a later date.
Keywords: embryonic stem cells, chimerism, germline transmission

overall_design: this experiment include 6 samples and 34 replicates


title: To compare expression profiles of CD4 cells isolated from an ENU induced mouse mutant Sanroque to wildtype

city: Oxford

first: Teresa

last: Lambe

institute: Oxford University

summary:
Male C57BL/6 mice were treated with ENU to generate single base substitutions,  the variant genome sequences were breed to homozygosity in inbreeding pedigrees, and screened for antinuclear autoantibodies (ANA). The sanroque pedigree contained multiple progeny with ANA of mixed homogeneous nuclear and cytoplasmic immunofluorescence pattern by 12 weeks of age, due to an autosomal recessive gene variant. Comparison of the gene expression profile of CD4 cells from  Sanroque to wild type was performed.
Keywords: repeat sample

first: Carola

last: Vinuesa


title: strain dependent pulmonary bleomycin response

status: Public on Dec 29 2005

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

institute: McGill University

summary:
right lung gene expression of C57BL/6J, A/J and C3H/HeJ mice following bleomcyin exposure
Keywords: other

middle: K

first: Anne-Marie

last: Lemay

first: Michael

last: Hallett

first: Tomasz

last: Tomko


title: training induced gene expression in arrhythmogenic plakogloin (+/-) mice

status: Public on Feb 01 2006

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

institute: Max Planck Institute for Molecular Genetics

summary:
Endurance training accelerated development of right ventricular dysfunction and arrhythmias in plakoglobin+/- mice. Histology and electron microscopy did not identify right ventricular abnormalities. To identify differences in the transcriptional response to training gene expression profiling was performed.
Keywords: expression response of plakoglobin (+/-) to training

overall_design: Gene expressson analyses were performed in 5 pairs of plakoglobin (+/-) mice and their wildtype littermates. Four pairs of trained mice and one pair of old untrained mice were studied. Training induced expression of several hypertrophy associated genes such as ANP but no differences between the trained plakoglobin (+/-) mice and wt mice was seen.

first: Ute

last: Ungethuem

first: Paulus

last: Kirchhof

first: Larissa

last: Fabritz

first: Melanie

last: Zwiener

first: Patrizia

last: Ruiz


title: Mouse BMDM Yersinia infection

status: Public on Dec 21 2005

city: Munich

first: Reinhard

last: Hoffmann

address: Trogerstr. 30

institute: Institute for medical microbiology

summary:
BMDM from BAL/c and C57BL/6 BMDM were stimlated with IFN-g overnight and infected with different Yersinia strains for 3 hrs.
Keywords: repeat

overall_design: 3-4 biological replicates were analyzed from each condition

first: John

middle: H

last: Smith


title: Control of LPS-response by DUSP1

status: Public on Dec 15 2005

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary:
Activation of the Mitogen activated protein kinase (MAPK) cascade following Toll-like receptor (TLR) stimulation enables innate immune cells to rapidly activate cytokine gene expression. A balanced response to signals of infectious danger requires that cellular activation is transient. Here, we identify the MAPK phosphatase Dual specificity phosphatase-1 (DUSP1) as an essential endogenous regulator of the inflammatory response to LPS. DUSP1-deficient (DUSP1-/-) bone marrow derived macrophages showed selectively prolonged activation of p38 MAPK and increased cytokine production. Intraperitoneal challenge of DUSP1-/- mice with LPS caused increased lethality and overshooting production of IL-6 and TNF?. Transcriptional profiling revealed that DUSP1 controls a significant fraction of LPS-induced genes, that includes IL-6 and IL-10 as well as the chemokines CCL3, CCL4 and CXCL2. In contrast, the expression of  the important mediators of endotoxin lethality, IFN? and IL-12,  was not  significantly altered by the absence of DUSP1. These data together demonstrate a specific regulatory role of DUSP1 in controlling a subset of LPS-induced genes that determines the outcome of endotoxin shock.
Keywords: in vivo analysis of splenic mRNA expression

overall_design: Mice were injected intraperitoneally with E. coli LPS (10µg/g bodyweight) and sacrificed 6h later. Total spleen RNA (5 µg) was prepared, labeled and hybridized to Affymetrix MOE430A 2.0 GeneChips according to the manufacturer’s instructions. Three biological replicates per condition were analysed. CEL Files were processed for global normalization and generation of expression values using the rma algorithm in the R affy package (www.bioconductor.org).

last: Hammer

first: Jörg

last: Mages

first: Harald

last: Dietrich

first: Angela

last: Servatius

first: Norma

last: Howells

first: Andrew

last: Cato


title: Transplantation of ALDHhiSSClo Neural Stem Cells in nmd Mice, an Animal Model of SMARD1

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

country: Italy

institute: University of Milan

summary:
SMARD1 is an infantile autosomal recessive motor neuron (MN) disease, caused by mutations in the Immunoglobulin mu binding protein 2 (IGHMBP2).
We investigated the potential of a spinal cord neural stem cell population isolated on the basis of aldehyde dehydrogenase activity (ALDH) to modify disease progression of nmd mice, an animal model of SMARD1.
ALDHhiSSClo stem cells are self-renewing and multipotent and when intratechally transplanted in nmd mice generate motor neurons properly localized in the spinal cord ventral horns.
Transplanted nmd animals presented delayed disease progression, sparing of motor neurons and ventral root axons and increased life-span.
To further investigate the molecular events responsible for these differences, microarray and Real time RT-PCR analysis of wild-type, mutated and transplanted nmd spinal cord were undertaken.
We demonstrated a down-regulation of genes involved in excitatory amino acid toxicity and oxidative stress handling, as well as an up-regulation of genes related to the chromatin organization in nmd compared to wild-type mice, suggesting that they may play a role in SMARD1 pathogenesis. Spinal cord of nmd transplanted mice expressed high transcript levels for genes related to neurogenesis such as Doublecortin (DCX), LIS1 and drebrin. The presence of DCX-expressing cells in adult nmd spinal cord suggests that both exogenous and endogenous neurogenesis may contribute to the observed nmd phenotype amelioration.
Keywords: disease analysis, Cell Transplantation response

overall_design:
We intratechally transplanted a spinal cord neural stem cell population isolated on the basis of aldehyde dehydrogenase activity (ALDH) in nmd mice, an animal model of SMARD1.
We analyzed the lumbar spinal cord tract of transplanted nmd mice (n=3), untransplanted nmd mice (n=3) and wild-type mice (n=3) (all mice are of male gender). The latter groups underwent surgical procedure with vehicle. The surgical procedure and cell transplantation were done at P1 and the animals were sacrificed at 6 weeks of age.

first: Federica

last: Locatelli

first: Dimitra

last: Papadimitriou

first: Chiara

last: Donadoni

first: Roberto

last: Del Bo

first: Marco

last: Crimi

first: Andreina

last: Bordoni

first: Francesco

last: Fortunato

first: Sandra

last: Strazzer

first: Giorgia

last: Menozzi

first: Sabrina

last: Salani

first: Nereo

last: Bresolin

first: Giacomo

middle: P

last: Comi


title: Cell type specific expression profiles of mouse forebrain neurons

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

summary:
The mammalian forebrain is a tissue of stunning complexity comprised of numerous regions each containing many distinct cell types that differ in their intrinsic and synaptic physiology, morphology and connectivity. These differences are likely conferred by  differential gene expression, but the extent and nature of cell type specific gene expression is largely unknown. Here, we carried out microarray analysis of twelve major classes of fluorescently labelled neurons within the forebrain and provide the first comprehensive view of gene expression differences. The results demonstrate a profound molecular heterogeneity among neuronal subtypes, represented disproportionately by gene paralogs, and begin to reveal the genetic programs underlying the fundamental divisions between neuronal classes including that between glutamatergic and GABAergic neurons.
Keywords: cell type comparison

overall_design: Total of 36 samples from 12 different cell types were anlyzed. Three biological replicates (each sample from different animal(s)) were analyzed for each cell type.

first: Chris

last: Hempel

first: Sacha

middle: B

last: Nelson