title: Genome-wide mapping and analysis of active promoters in mouse ES cells and adult organs

status: Public on Jul 28 2007

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

type: Genome binding/occupancy profiling by genome tiling array

summary:
The analysis of several mammalian genomes has revealed between 20,000 to 30,000 genes in each genome, a number that may seem hard to reconcile with the large number of cell types and complex functions of these organisms.  The solution to this paradox partly lies in the large array of transcripts that each gene can potentially generate through usage of alternative promoters and the variable levels of transcripts that each gene produces in different tissues and cell types. Thus, in order to understand the mechanisms that control diverse patterns of gene expression in mammals, it is necessary to accurately define the active promoters and monitor their cell or tissue-dependent activity. Previous high throughput strategies for assaying tissue-specific gene expression have primarily relied on measurements of steady-state transcript levels by microarrays or tag sequencing. Here, we employ a new experimental strategy to identify and characterize tissue specific promoters by integrating genome-wide maps of RNA polymerase II (Pol II) binding, chromatin modifications and gene expression profiles.  We applied this strategy to mouse embryonic stem cells (mES), and adult brain, heart, kidney, and liver.  Our results delineated 24,363 Pol II binding sites throughout the genome, 91% of which correspond to 5’ end annotation based on known transcripts and cap-analysis of gene expression (CAGE) and can be regarded as promoters.  A majority of these experimentally defined promoters are active in all tissues, while only 4,396 can be characterized as tissue-specific using a quantitative measure of Pol II occupancy. In general, Pol II occupancy at these tissue specific promoters is correlated with the presence of active histone modification marks. However, a set of mES- specific promoters display persistent levels of H3K4me3 in non-ES tissues despite undetectable Pol II binding and transcript.  Broadly, our results expand the knowledge of tissue-specific mammalian genes and provide a resource for understanding the transcriptional programs in mammalian development and differentiation.
Keywords: ChIP-chip, expression, mouse, brain, heart, kidney, liver, ES

overall_design:
To map promoters in the mouse genome, we performed 5 genomewide (37 array set) ChIP-chip of Pol II binding in R1 ES cells and brain, heart, kidney, and liver from 10-12 week-old female BL6 mouse.

To validate genome-wide Pol II enriched regions across tissues, we filtered the genome-wide microarray set to a 4-array set which covers Pol II regions bound in any tissue.  We repeated Pol II ChIP-chip across tissues using this 4-array set.  We also performed (without replicates) ChIP-chip across tissues for H3ac and H3K4me3 using this condensed array set.

To complement our promoter mapping efforts with transcript levels, we performed expression profiling (no replicates) across tissues using Affymetrix 430 v2.0 arrays.

first: Zirong

last: Li

first: Leah

last: Barrera

first: Andrew

middle: D

last: Smith

first: Karen

last: Arden

first: Webster

last: Cavenee

first: Michael

middle: Q

last: Zhang

first: Roland

last: Green


title: Effect of chronic fluoxetine treatment on hippocampal gene expression

status: Public on Jul 04 2007

city: Jupiter

first: Mathew

middle: T

last: Pletcher

state: FL

address: 5353 Parkside Dr

country: USA

institute: Scripps Florida

summary:
Both the mechanism of action and the factors determining the behavioral response to antidepressants are unknown. It has been shown that antidepressant treatment promotes the proliferation and survival of hippocampal neurons via enhanced serotonergic signaling, but it is still unclear whether hippocampal neurogenesis is responsible for the behavioral response to antidepressants. Furthermore, a large subpopulation of patients fails to respond to antidepressant treatment due to presumed underlying genetic factors. In the present study, we have used the phenotypic and genotypic variability of inbred mouse strains to show that there is a genetic component to both the behavioral and neurogenic effects of chronic fluoxetine treatment, and that this antidepressant induces an increase in hippocampal cell proliferation only in the strains that also show a positive behavioral response to treatment. The behavioral and neurogenic responses are associated with an upregulation of genes known to promote neuronal proliferation and survival.  These results suggest that inherent genetic predisposition to increased serotonin-induced neurogenesis is a determinant of antidepressant efficacy.
Keywords: drug response

overall_design:
Male DBA/2J, age 3-5 weeks, were obtained from The Jackson Laboratory (Bar Harbor, ME) and maintained on a 12:12 light:dark cycle with lights on at 0700 hours. Following at least one week of acclimation, mice were provided with either untreated or fluoxetine-treated drinking water, available ad libitum.  Fluoxetine-HCl was obtained from Spectrum Chemicals (Gardena, CA). Differences in daily water consumption were previously determined by measuring water intake for three weeks from at least 12 mice  (6.4 mL (+/- .58 mL) per day). We also determined the average weight at 10 weeks of age (25.5 g +/- 1.4 g), and used this information to dilute fluoxetine in the water in order to provide a daily dosage of 0 or 18 mg/kg/mouse.

Mice were 8-12 weeks of age at the time of behavioral testing, which was performed during the light phase between 1300h and 1600h. Behavioral despair was measured using a mouse Tail Suspension apparatus from Med Associates (Georgia, VT).

Individual bilateral hippocampii from 21-day-treatment 0 and 18 mg/kg/day DBA/2J mice were homogenized in 500 µl TRIzol using a QIAgen Tissuelyser (15 minutes at 30 Hz, QIAgen, Chatsworth, CA). RNA was extracted by phenol-chloroform phase separation and further processed using the RNAeasy miniprep kit (QIAgen). For each treatment group of 12 animals, separate RNA pools were made using hippocampal RNA from 6 mice per pool. These biological replicates were processed separately through the entirety of the microarray procedure. Five µg of total RNA from each pool was used as a template to synthesize complementary DNA (cDNA) and biotinylated cRNA (Enzo kit, Affymetrix, Santa Clara, CA) using standard Affymetrix protocols. cRNA was hybridized to  Affymetrix GeneChip Mouse Genome 430 2.0 Array. Data were analyzed using ArrayAssist software (Stratagene, La Jolla, CA) and normalized with the GCRMA algorithm. A probeset had to obtain a minimal intensity value 100 to be considered as detecting expression above background.  Therefore, any probeset that failed to meet this cutoff was removed from the analysis.  Ratios of intensity differences were generated and genes showing at least a two-fold difference between experimental conditions were identified for further analysis.

first: Brooke

middle: H

last: Miller

first: Laura

middle: E

last: Schultz

first: Anisha

last: Gulati

last: Cameron


title: Brown versus white tissue adipose selective genes

status: Public on Jun 08 2007

city: Boston

first: Patrick

last: Seale

state: MA

address: 1 Jimmy Fund Way

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary:
The aim of this study was to identify genes expressed selectively in brown adipose tissue as compared to white adipose tissue from the same animals.  This analysis provides a gene set that is brown and white adipose selective.
Keywords: tissue comparison from mice

overall_design: Interscapular brown adipose tissue and epididymal white adipose tissue was carefully dissected from 3 male C57Bl/6 mice.  These samples were profiled independently using Affymetrix mouse 430_2 gene arrays, representing 3 biological replicates for each brown and white adipose tissues.

first: Bruce

middle: M

last: Spiegelman


title: Creatine increases health and life span in mice

status: Public on Jun 13 2007

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary:
Here we show that oral creatine (Cr) supplementation leads to increased life span in mice. Treated mice showed improved neurobehavioral performance, decreased accumulation of the aging pigment lipofuscin and upregulation of “anti-aging” genes in brain. As Cr is virtually free of adverse effects, it may be a promising food supplement for healthy aging in man.
Keywords: creatine, life span, neurobehavioural performance, microarray, oxidative stress, aging

overall_design: 6 biological replicates for creatine-treated mice, 7 biological replicates for untreated mice.

first: Thomas

last: Klopstock

first: Andreas

last: Bender

first: Sabine

last: Hölter

first: Tobias

last: Haack

first: Tanja

last: Ruthsatz

first: Daniela

last: Vogt Weisenhorn

first: Lore

last: Becker

first: Just

last: Genius

first: Dan

last: Rujescu

first: Martin

last: Irmler

first: Tomek

last: Mijalski

last: Mader

first: Leticia

last: Quintanilla-Martinez

first: Helmut

last: Fuchs

first: Valérie

last: Gailus-Durner

last: Hrabé de Angelis

first: Wolfgang

last: Wurst

first: Jörg

last: Schmidt

first: Ilka

last: Schneider


title: Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy

status: Public on Jun 01 2007

city: New York

first: antoine

last: Muchir

state: NY

address: 630W 168th street

department: Medicine

institute: columbia university

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

overall_design: Refer to individual Series


title: Striatal gene expression data from 3- and 18-month-old Q92 mice and control mice.

status: Public on Jul 01 2007

city: Bethesda

first: Alexandre

last: Kuhn

state: MD

address: 35 Convent Dr

department: NIA

institute: NIH

summary:
Achieving a mechanistic understanding of disease and initiating preclinical therapeutic trials necessitate the study of huntingtin toxicity and its remedy in model systems. To allow the engagement of appropriate experimental paradigms, Huntington’s disease (HD) models need to be validated in terms of how they recapitulate a particular aspect of human disease. In order to examine transcriptome-related effects of mutant huntingtin, we compared striatal mRNA profiles from seven genetic mouse models of disease to that of postmortem human HD caudate using microarray analysis. Transgenic models expressing short N-terminal fragments of mutant huntingtin (R6/1 and R6/2 mice) exhibited the most rapid effects on gene expression, consistent with previous studies. Although changes in the brains of knock-in models of HD took longer to appear, 15-month and 22-month CHL2Q150/Q150, 18-month HdhQ92/Q92 and 2-year-old YAC128 animals also exhibited significant HD-like mRNA signatures. When the affected genes were compared across models, a robust concordance was observed. Importantly, changes concordant across multiple lines mice were also in excellent agreement with the mRNA changes seen in human HD caudate. Although it was expected that the expression of full-length huntingtin transprotein might result in unique gene expression changes compared to those caused by expression of an N-terminal huntingtin fragment, no discernable differences between full-length and fragment models were detected. There was, however, an overall concordance between transcriptomic signature and disease stage. We thus conclude that the transcriptional changes of HD can be modelled in several available lines of transgenic mice, comprising lines expressing both N-terminal and full-length mutant huntingtin proteins. The combined analysis of mouse and human HD transcriptomes provides an important chronology of mutant huntingtin's gene expression effects.
Keywords: genetic modification

overall_design: Striatal samples from 6 Q92 mutant mice (3 3-month-old and 3 18-month-old) and 6 age-matched wild-type mice.

first: Lesley

last: Jones

first: Angela

last: Hodges

first: Stephen

last: Dunnett

first: Simon

last: Brooks

first: Polyanas

last: Cheng


title: Comprehensive Gene ExpressionProfiling of Peyer’s Patch M Cells, Villous M-like Cells, and Intestinal Epithelial Cells

city: Minato-ku

first: Kazutaka

last: Terahara

address: 4-6-1 Shirokanedai

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

summary:
Separate populations of M cells have been detected in the follicle-associated epithelium of Peyer’s patches (PPs) and the villous epithelium of the small intestine, but the traits shared by or distinguishing the two populations have not been characterized. Our separate study has demonstrated that M cells are rare but M-like cells positive for lectin Ulex europaeus agglutinin-1 and our newly developed M cell-specific mAb NKM16-2-4 are induced by oral administration of cholera toxin in the duodenal villous epithelium. Here, we determined the gene expression of PP M cells, villous M-like cells, and intestinal epithelial cells (IECs) isolated by a novel approach using FACS. Specific expression of glycoprotein 2 (GP2) and MARCKS-like protein (MLP) by PP M cells and not villous M-like cells was confirmed by additional mRNA and protein analyses. Comprehensive gene profiling also suggested that villous M-like cells share traits of both PP M cells and IECs, a finding that is supported by their unique expression of specific chemokines. The genome-wide assessment of gene expression facilitates discovery of M cell-specific molecules and enhances the molecular understanding of M cell immunobiology.
Keywords: Cell type comparison

overall_design: Epithelial cells in duodenal Peyer's patches or villi of BALB/c mice treated with or without cholera toxin were dissociated and stained with NKM16-2-4 monoclonal antibody (mAb)-FITC, lectin UEA-1-PE, and anti-CD45 mAb-APC-Cy7. Naive PP M cells (NKM16-2-4+, UEA-1+, and CD45- cells), CT-induced villous M-like cells (NKM16-2-4+, UEA-1+, and CD45- cells), and naive intestinal epithelial cells (NKM16-2-4-, UEA-1-, and CD45- cells) were isolated by FACS. Affymetrix GeneChip Mouse Genome 430 2.0 Array was used in triplicate for each cell fraction.

first: Osamu

last: Igarashi

first: Masato

last: Yoshida

first: Tomonori

last: Nochi

first: Shiho

last: Kurokawa

first: Naoko

last: Takayama

first: Yoshikazu

last: Yuki

first: Anson

middle: W

last: Lowe

first: Hiroshi

last: Kiyono


title: Osteoclastic estrogen receptor alpha mediates the osteoprotective estrogen action through Fas ligand signaling

city: Shinagawa-ku

first: KATSUHIDE

last: IGARASHI

state: Tokyo

department: Life Science Tokyo Advanced Research center (L-StaR)

institute: Hoshi University School of Pharmacy and Pharmaceutical Science

summary:
Estrogen clearly prevents osteoporotic bone loss by attenuating bone resorption. The molecular basis of how this is accomplished, however, remains elusive. Here we report a critical role of osteoclastic ERa in mediating estrogen action on bone in females. We selectively ablated ERa in differentiated osteoclasts (ERa dOc/dOc). ERa dOc/dOc females, but not males, exhibited clear trabecular bone loss, similar to the osteoporotic bone phenotype in post-menopausal women. Recovery of bone loss by estrogen treatment of the ovariectomized ERa dOc/dOc females was ineffective in the trabecular areas of the long bones and lumbar vertebral bodies. Osteoclastic apoptosis, induced by estrogen, occurred simultaneously with up-regulation of Fas ligand (FasL) expression in intact trabecular bones of ERa +/+mice, but not in ERa dOc/dOc mice.  ERa was also required for similar effects of estrogen and tamoxifen in cultured osteoclasts. These findings suggest that the osteoprotective actions of estrogen and SERMS are mediated at least in part through osteoclastic ERa in trabecular bone; and the life span of mature osteoclasts is regulated through activation of the Fas/FasL system.
Keywords: Study about estrogen response of osteoclast-specific estrogen receptor alpha mice

overall_design: Wild type and osteoclast-specific Estrogen Receptor alpha knock-out mice were ovariectomized. The number of both genotypes of mice was eight. The mice of each genotypes were divided to vehicle control and estrogen treated group. Four hours after chemical treatment, the distal 5 mm of the left femurs were harvested after sacrificing by cervical dislocation and total RNAs were purified for Affymetix GeneChip microarray analysis without pooling. Therefore, this experiment consists of four groups with four replicates per group.

first: Takashi

last: Nakamura

first: Yuuki

last: Imai

first: Takahiro

last: Matsumoto

first: Shingo

last: Sato

first: Kazusane

last: Takeuchi

first: Katsuhide

first: Yoshifumi

last: Harada

first: Yoshiaki

last: Azuma

first: Andree

last: Krust

first: Yoko

last: Yamamoto

last: Nishina

first: Shu

last: Takeda

last: Takayanagi

first: Daniele

last: Metzger

first: Jun

last: Kanno

first: Kunio

last: Takaoka

first: Thomas

middle: J

last: Martin

first: Pierre

last: Chambon

first: Shigeaki

last: Kato


title: Expression data from murine ventral prostate treated with placebo or RAD001 for 12h, 48h, 6d,9d, and 15d

city: boston

first: qing

last: xu

address: 44 binney st

department: Medical Oncology

institute: dana farber cancer institute

summary:
A mTOR depedent and a phenotype dependent sigature can be identified.
Keywords: time course

overall_design: This study aims to separate pharmacodynamic and response biomarkers in response to RAD001 treatment

first: Qing

last: Xu

first: Kenneth

last: Ross

first: William

last: Sellers

first: Todd

last: Golub


title: A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity

status: Public on May 31 2007

city: Chicago

first: Eileen

last: Dolan

state: IL

address: 5841 S. Maryland

institute: University of Chicago

summary:
Large inter-individual variance has been observed in sensitivity to drugs. To comprehensively decipher the genetic contribution to these variations in drug susceptibility, we present a genome-wide model utilizing human lymphoblastoid cell lines from the International HapMap consortium, of which extensive genotypic information is available, to identify genetic variants that contribute to chemotherapeutic agent-induced cytotoxicity. Our model integrated genotype, gene expression and sensitivity of HapMap cell lines to drugs. Cell lines derived from 30 trios of European descent (CEU) and 30 trios of African descent (YRI) were utilized. Cell growth inhibition at increasing concentrations of etoposide for 72 h was determined using alamarBlue® assay. Gene expression on 176 HapMap cell lines (87 CEU and 89 YRI) was determined using the Affymetrix GeneChip® Human Exon 1.0ST Array. We evaluated associations between genotype and cytotoxicity, genotype and gene expression and correlated gene expression of the identified candidates with cytotoxicity. The analysis identified 63 genetic variants that contribute to etoposide-induced toxicity through their effect on gene expression. These include genes that may play a role in cancer (AGPAT2, IL1B and WNT5B) and genes not yet known to be associated with sensitivity to etoposide. This unbiased method can be used to elucidate genetic variants contributing to a wide range of cellular phenotypes induced by chemotherapeutic agents.
Keywords: exon array

overall_design: Gene expression on 176 HapMap cell lines.

first: R

middle: S

last: Huang

first: Shiwei

last: Duan

first: Wasim

middle: K

last: Bleibel

first: Emily

middle: O

last: Kistner

first: Wei

last: Zhang

first: Tyson

middle: A

last: Clark

first: Tina

middle: X

last: Chen

first: Anthony

middle: C

last: Schweitzer

first: John

last: Blume

first: Nancy

last: Cox

first: M


title: Gene expression profiles in skeletal muscle after gene transfer by electroporation

status: Public on Jul 05 2007

city: Hellerup

middle: R.

last: Zibert

address: Niels Andersens Vej 65, KA-1502

department: Dep. of Dermatology

country: Denmark

institute: Copenhagen University Hospital Gentofte

summary:
Abstract
Background: Gene transfer by electroporation (electro gene transfer) to muscle results in high level long term transgenic expression, showing great promise for treatment of e.g. protein deficiency syndromes.
However little is known about the effects of electro gene transfer on muscle fibres. We have therefore investigated transcriptional changes through gene expression profile analyses, as well as morphological changes evaluated by histological analysis. Electro gene transfer was obtained using a combination of a short high voltage pulse (HV, 1000 V/cm, 100 @s) followed by a long low voltage pulse (LV, 100 V/cm, 400 ms); a pulse combination optimised for efficient and safe gene transfer. Muscles were transfected with green fluorescent protein (GFP) and excised at 4 hours, 48 hours or 3 weeks after treatment.
Results: Differentially expressed genes were investigated by microarray analysis, and descriptive statistics were performed to evaluate the effects of 1) electroporation, 2) DNA injection, and 3) time after treatment.
The biological significance of the results was assessed by gene annotation and supervised cluster analysis. Generally, electroporation caused down-regulation of structural proteins e.g. sarcospan and catalytic en-zymes such as phosphoenolpuryvate carboxykinase. Injection of DNA induced down-regulation of intracellular transport proteins e.g. sentrin. The effects on muscle fibres were transient as the expression profiles 3 weeks after treatment were closely related with the control muscles. Most interestingly, no changes in the expression of proteins involved in inflammatory responses or muscle regeneration was detected, indicating limited muscle damage and regeneration. Histological analysis revealed structural changes with loss of cell integrity and striation pattern in some fibres after DNA+HV+LV treatment, while electroporation alone caused minor loss of striation pattern but preservation of cell integrity.
Conclusion: The small and transient changes found in the gene expression profiles are of great importance, as this demonstrates that electro gene transfer is safe with minor effects on the muscle host cells. These findings are essential for introducing the electro gene transfer to muscle for clinical use. Indeed the HV+LV pulse combination used have been optimised to ensure highly efficient and safe electro gene transfer.
Keywords: Electro gene transfer, microarray, affymetrix, gene therapy, skeletal muscle, mouse, time course

overall_design:
The mice did recieve to their tibialis cranialis muscle either No tretment/control (CTRL), Electroporation only (EP), Plasmid injection only (DNA) or Plasmid DNA and in vivo Electro gene transfer (EP+DNA).
Four hrs, 48 hrs and 3 weeks after treatment the mice were euthanized and the expression profile of the treated muscles were analysed.
The following number of mice were included:
CTRL, 3 mice,
EP at 4 hrs, 1 mouse,
EP at 48 hrs, 1 mouse,
EP at 3 weeks, 1 mouse,
DNA at 4 hrs, 1 mouse,
DNA at 48 hrs, 1 mouse,
DNA at 3 weeks, 1 mouse,
EP+DNA at 4 hrs, 2 mice,
EP+DNA at 48 hrs, 1 mouse,
EP+DNA at 3 weeks, 1 mouse.
A total number of mice 13.

first: Pernille

last: Moller

middle: R

first: Jens

last: Eriksen

first: Julie

last: Gehl


title: Gene expression profiles of adult ureter isolated from SMGA (Actg2) transgenic mice. (GUDMAP Series ID: 15)

status: Public on May 25 2007

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

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

overall_design: Ureter regions from adult SMGA/EGFP animals were microdissected and total RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

first: James

last: Lessard

last: Szucsik


title: Global gene expression analysis of GMP from Icsbp (Irf-8) deficient mice

city: Berlin-Steglitz

first: Dirk

last: Carstanjen

state: Berlin

address: Krahmer Strasse 6

department: Molecular Genetics

institute: Institute for Molecular Pharmacology

summary:
In order to study the consequences of the loss of Icsbp expression in hematopoiesis Granulocyte-Monocyte Progenitors from bone marrow were isolated from Icsbp wild type and deficient mice by flow cytometry. Global gene expression was performed using Affymetrix gene chip technology.
Keywords: Gene modification, Irf-8, knock out mice

overall_design: GMP from Icsbp wild type and deficient mice were isolated as described by Terszowski et al. (Blood. 2005 Mar 1;105(5):1937-45). Wild type GMP were prepared from two independent biological replica using pooled bone marrow from alt least 10 independent mice. The first was analyzed using the Affymetrix MOE 430A and the second using MOE430_2. GMP from Icsbp deficient mice were prepared from three independent biological replica from at least 8 individual mice. The first two samples were analyzed using the Affymetrix MOE 430A and the third using MOE430_2.

first: Dido

last: Lenze

first: Jessica

last: Koenigsmann

first: Hans

last: Rodewald

first: Grzegorz

last: Terszowski


title: Comparative analysis of gene expression  WT and Nrf2-/- mice Type II cells

status: Public on May 18 2007

city: Baltimore

first: Narsa

middle: Reddy

last: Machireddy

address: 615, N Wolfe St

department: Environmental Health Sciences

institute: Bloomberg School of Public Health

summary:
We hypothesize that gene expression in the Type II cells of Nrf2+/+ and Nrf2-/- mice are divergent thus contributing the cell growth. More specifically, type II cells from Nrf2-/- mice have increased reactive oxygen species that cause the impaired cell growth.  In order to test these hypotheses at the gene expression level, we utilized microarray analysis to examine transcriptional differences between Nrf2+/+ and Nrf2-/- cells.
Keywords: comparative expression profiling

overall_design: . This study utilizes microarray analysis to test these hypotheses. Three sets of type II cells were isolated from lungs from both Nrf2+/+ and Nrf2-/- mice and grown for 5 days. RNA was isolated and used for global gene expression profiling (Affymetrix Mouse 430 2.0 array). Statistically significant gene expression was determined as a minimum 6 counts of 9 pairwise comparisons, minimum 1.5-fold change, and p < 0.05. Further, Absolute | FC - FC SEM | >= 1.5.

first: Catherine

last: Scollick

first: Steven

last: Kleeberger

first: Masayuki

last: Yamamoto

first: Thomas

last: Kensler

first: Shyam

last: Biswal

first: Sekhar

middle: P

last: Reddy


title: Gene expression in peripheral cells: effects of Foxp3 and PDE3B

city: Seattle

first: Alexander

last: Rudensky

state: WA

address: 1959 Pacific St

department: Immunology

institute: University of Washington

summary:
This data set is comprised of all peripheral (pooled lymph nodes and spleen) T cell subsets presented in this manuscript.  These include T-N, T-25, T-FN and T-R cells; T-25, T-FN and T-R cells from mice treated with IL-2; and T-R cells transduced with empty, PDE3B-expressing or PDE3B(H801A)-expressing retroviral vectors (after transfer into recipient mice).
Keywords: cell type comparison, response to growth factor, genetic modification

overall_design: Detailed methods are presented in the manuscript and in the attached Supplementary Information.  All RNA samples were derived from cells immediately after isolation from mice.  Although this data set is comprised of 2 separate experiments (cells isolated from normal mice or IL-2 treated mice and cells transduced with retroviral vectors and passaged through recipient mice), the 10 expression arrays were normalized together to allow for cross comparison.

first: Marc

last: Gavin

first: Jeffrey

last: Rasmussen

first: Jason

middle: D

last: Fontenot

first: Valeria

last: Vasta

first: Vincent

last: Manganiello

first: Joseph

last: Beavo

middle: Y


title: Gene expression in thymic CD4 T cells: effects of Foxp3

summary:
This data set is comprised of all thymic T cell subsets presented in this manuscript. These include T-N, T-25, T-FN and T-R thymocytes.
Keywords: cell type comparison, development

overall_design: Detailed methods are presented in the manuscript and in the attached Supplementary Information. All RNA samples were derived from cells immediately after isolation from mice.  Note that these samples were amplified and labeled with Affymetrix and Enzo reagents, while peripheral T cell samples were amplified and labeled with Ambion reagents.


title: Requirement for ERK MAP kinase in mouse preimplantation development

status: Public on Jun 04 2007

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary:
Preimplantation development is a crucial step for successful implantation and pregnancy. Although both compaction and blastocyst formation have been extensively studied, mechanisms regulating early cell division stages before compaction have remained unclear.  Here, we show that ERK MAP kinase function is required for early embryonic cell division and normal cell-cell adhesion before compaction.  Our analysis demonstrates that inhibition of ERK activation in the late 2-cell stage embryos leads to a reversible arrest in G2 phase in the 4-cell stage.  The G2 arrested, 4-cell stage embryos show weakened cell-cell adhesion as compared to control embryos.  Remarkably, microarray analyses show that most of the programmed changes of upregulated and downregulated gene expression during the 4- to 8-cell stages normally proceed in the 4-cell stage-arrested embryos, except for a portion of the genes whose expression profiles closely parallel the stages of embryonic development when arrested in G2 and released to resume development.  These parallel genes include the genes encoding intercellular adhesion molecules, whose expression is found to be positively regulated by the ERK pathway.  We also show that while ERK inactivation in the 8-cell stage embryos does not lead to cell division arrest, it does cause cell division arrest when cadherin-mediated cell-cell adhesion is disrupted.  These results demonstrate an essential role of ERK function in the G2/M transition and the expression of adhesion molecules during the 2-cell to 8-cell stage embryos, and suggest a loose parallelism between the gene expression programs and the developmental stages before compaction.
Keywords: preimplantation development

overall_design: We examined expression profiles of genes during early cell division stages in mouse preimplantation development.  We performed the genome-wide analysis by using Affymetrix GeneChip oligonucleotide microarrays, and examined the effect of the ERK pathway inhibitor U0126 on the expression profiles.  Two independent experiments were carried out.  We collected embryos at six points as follows; control embryos at day 1.5 (cont. 1.5, 2-cell stage), day 2.5 (cont. 2.5, 4- to 8-cell), and day 3.5 (cont. 3.5, morula to blastocyst), and the U0126-treated embryos at day 2.5 (U2.5, 4-cell arrested), embryos released from the U0126-induced arrest at day 3.5 (U3.5, 8-cell) and at day 4.5 (U4.5, morula to blastocyst).  Hybridization was carried out with the Mouse Genome 430 2.0 array following Affymetrix instructions.  Hybridized arrays were scanned using an Affymetrix GeneChip Scanner.  Expression analysis was performed using GeneChip Operating Software v. 1.2 (GCOS) and GeneSpring 7.3.

first: Momoko

last: Maekawa

first: Takuya


title: Murine Pulmonary Response to Chronic Hypoxia is Strain Specific

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

institute: Vanderbilt University

summary:
6-8 week old BL6, FVB/N and SV129 mouse strains were kept in normoxia or hypobaric hypoxia for 4 weeks and then phenotyped by echocardiogram and right ventricular heart catheterization, followed by tissue collection. In addition, Affymetrix expression analysis was conducted in a paired fashion.
Keywords: Differential response to hypoxia by strain

overall_design: This series actually includes another 12 arrays. However, the others had technical difficulties and so aren't really appropriate for general distribution.

first: Yuji

last: Tada

first: Sven

last: Laudi

first: Julie

last: Harral

first: Michelle

last: Carr

first: Charles

last: Ivester

first: Takayuki

last: Kuriyama

first: William

last: Nichols


title: Cannabinoid receptor double knockout mice (Cnr1 -/- /Cnr2 -/-) in CHS model

status: Public on Jun 11 2007

city: Bonn

first: Meliha

last: Karsak

address: Sigmund-Freud-Str. 25

department: Molecular Psychiatry

institute: University of Bonn

summary:
We evaluated cutaneous contact hypersensitivity (CHS) in Cnr1-/-/Cnr2-/- animals using the obligate contact allergen 2,4-dinitrofluorobenzene (DNFB), which generates a specific cutaneous T-cell mediated allergic response upon repeated allergen contact. Allergic contact dermatitis affects about 5% of men and 11% of women in industrialized countries and is one of the leading causes for occupational diseases. In an animal model for cutaneous contact hypersensitivity we show that mice lacking both known cannabinoid receptors display exacerbated allergic inflammation. In contrast, fatty acid amide hydrolase deficient mice, which have increased levels of the endocannabinoid anandamide, displayed reduced allergic responses in the skin. Cannabinoid receptor antagonists exacerbated whereas receptor agonists attenuated allergic inflammation. These results demonstrate a protective role of the endocannabinoid system in contact allergy in the skin, and suggest a novel target for therapeutic intervention.
Keywords: Strain (Wt versus Ko) and disease state (DNFB treated versus control).

overall_design: Three wildtype mice (Wt) and three Cnr1-/-/Cnr2-/- (Ko) mice were used. Contact hypersensitivity was determined always at the right ears, which therefore were treated with DNFB (Tr). Left ears of mice were kept untreated and served as control ears (C). A total of 12 hybridizations were performed (2 strains x 2 treatments X 3 biological replicates) in this experiment.

first: Evelyn

last: Gaffal

first: Lihua

last: Wang-Eckhardt

first: Thomas

last: Tüting

first: Andreas

last: Zimmer


title: The role of mtDNA mutations in age-related hearing loss in mice carrying a mutator DNA polymerase gamma

city: Madison

first: Shinichi

last: Someya

state: WI

address: 425 Henry Mall Dr

department: Medical Genetics

institute: University of Wisconsin-Madison

summary:
Mitochondrial DNA (mtDNA) mutations may contribute to aging and age-related disorders. Previously, we created mice expressing a proofreading-deficient version of the mtDNA polymerase gamma (Polg) which accumulate age-related mtDNA mutations and display premature aging. Here we performed microarray gene expression profiling to identify mtDNA mutation-responsive genes in the cochlea of aged mitochondrial mutator mice. Age-related accumulation of mtDNA mutations was associated with transcriptional alternations consistent with reduced inner ear function, mitochondrial dysfunction, neurodegeneration, and reduced cell structural modulation. Hearing assessment and histopathological results confirmed that aged PolgD257A/D257A (D257A) mice exhibited moderate hearing loss and severe cochlear degenerations. Age-related accumulation of mtDNA mutations also resulted in alternations in gene expression consistent with induction of apoptosis, proteolysis, stress response, and reduced DNA repair. TUNEL (Terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling) assay confirmed that the cochleae from aged D257A mice showed significantly more TUNEL positive cells compared to wild-type (WT) mice. The levels of cleaved caspase-3 were also found to increase in the cochleae of aged D257A mice. These observations provide evidence that age-related accumulation of mtDNA mutations is associated with apoptotic cell death in aged cochlea. Our results provide the first global view of molecular events associated with mtDNA mutations in postmitotic tissue, and suggest that apoptosis is the major mechanism of mtDNA mediated cell death in the development of age-related hearing disorder.
Keywords: disease state analysis

overall_design:
To determine the effects of age-related accumulation of mtDNA mutations, each WT sample (n = 5) was compared to each D257A sample (n = 5), generating a total of twenty-five pairwise comparisons. Genes with significantly altered expression levels were sorted into gene ontology biological process categories.
Gene expression change was called statistically significant when at least one gene was called present in a group, the P value was < 0.0500, FC was > 1.1, and FDR was > 30.00 for identification of mtDNA mutations-induced genes.
Affymetrix standard spike controls were used in all experiments (eukaryotic hybridization control kit). Quality control measures were not used. No replicates were done. Dye swap was not used.

first: Tatsuya

last: Yamasoba

first: Greg

last: Kujoth

first: Tom

last: Pugh

first: Richard

last: Weindruch

first: Masaru

last: Tanokura

first: Tomas

last: Prolla


title: Intestinal Phenotype of Variable Weight Cystic Fibrosis Knockout Mice

status: Public on May 21 2007

city: Montreal

first: Christina

middle: Kathleen

last: Haston

state: QC

address: 3626 St. Urbain

country: Canada

institute: McGill University

summary:
Cystic fibrosis transmembrane conductance regulator (Cftr) knockout mice present the clinical features of low body weight and intestinal disease permitting an assessment of the interrelatedness of these phenotypes in a controlled environment.  To identify intestinal alterations which affect body weight in CF mice the histological phenotypes of crypt-villus axis height, goblet cell hyperplasia, and mast cell infiltrate were measured, cardiac blood samples assessed, and gene expression profiling of the ileum was completed for 12 week old (C57BL/6xBALB) F2 Cftrtm1UNC and non-CF mice presenting a range of body weight.  Crypt-villus axis height decreased with increasing weight in CF, but not control, mice.  Goblet cell hyperplasia and mast cell infiltration in the submucosa and muscularis externa layers of the CF intestine, were identified to be independent of bodyweight.  Blood triglyceride levels were found to be significantly lower in CF mice than control mice (p = 3.02 x 10-5) but were not dependent on CF mouse body weight.  By expression profiling, genes of DNA replication and lipid metabolism were among those altered in CF mice relative to non-CF controls; and no differences in gene expression were measured between samples from CF mice in the 25th and 75th percentile for weight.  This study indicates that the absence of Cftr leads to altered morphology in the CF intestine the extent of which is correlated with body weight in CF mice while CF related changes in blood triglyceride levels and in the intestinal gene expression profile were not dependent on body weight in this model.
Keywords: disease state analysis

overall_design: B6xBALB F2 mice gene expression was collected for nine CF-/- mice and 6 controls. Differential expression was analyzed between the groups

middle: H

first: Sean

last: Cory

first: Juan

last: Carnale-Zambrano

first: Daryl

last: Humes

first: Maya

last: Poffenberger


title: mRNA expression profiles of resting and IL-15 activated murine NK cells

status: Public on May 15 2007

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

summary:
Murine NK cells were compared at rest and following 24 hours of IL-15 stimulation for their mRNA expression profiles on the Affymetrix MOE430_2 microarray platform.  Additional comparators included resting bulk splenocytes.
Keywords: mRNA, mouse, NK cell, IL-15

overall_design: Three pairs of flow sorted murine NK cells (C57Bl/6) were analzyed at rest or after 24 hours of IL-15 stimulation.  Three biological replicates of each condition (resting or IL-15) are included in this anlaysis.  In addition, bulk resting splenocytes were used (2 biological replicates with 2 chip replicates for a total of 4 replicates).

first: Todd

last: Fehniger

first: Timothy

last: Ley


title: Expression data from bone marrow hematopoietic stem cell CD34 Flt3 subfractions

status: Public on May 01 2007

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

country: Sweden

institute: Lund University

summary:
Lineage negativ Sca1+ Kit+ bone marrow cells (containing putative hematopoietic stem cells) subfractionation based on CD34 and FLT3 identifies three functionally destinc subpopulations (LSKCD34-FLT3-, LSKCD34+FLT3- & LSKCD34+FLT3+).
Keywords: cell type comparison

overall_design: Lineage negativ Kit+ Sca1+ (LSK) hematopoietic stem cell subpopulations were FACS sorted based on their CD34/FLT3 expression. Subsequently RNA was extracted, labelled and hybridized to Affymetrix microarrays. We sought to obtain expression pattern changes that might explain the difference in function between the functionally destinct LSK subpopulations.

last: Månssone

first: Sten

last: Jacobsen


title: Expression profiling of double negative thymocytes

status: Public on May 17 2007

city: Bunkyo-ku

first: Masahito

last: Kawazu

address: Hongo 7-3-1

department: Department of Hematology and Oncology

institute: University of Tokyo Hospital

summary:
In order to understand the molecular mechanisms of DN thymocyte development, it may be also of use to clarify how these developmental processes are regulated in terms of their entire gene expression, to which cell differentiation is ultimately ascribed.
In the current study, we approached this issue by investigating gene expression profiles in discrete subsets of DN thymocytes under development, in which DN2, DN3, and DN4 thymocytes were sorted and subjected to expression profiling analysis with high-density oligonucleotide microarrays.
Keywords: developmental stages

overall_design: The DN2, DN3, and DN4 populations were FACS-sorted from DN thymocytes harvested from four C57BL/6 mice and analyzed by Affymetrix® Mouse Genome 430 2.0 Array® for gene expression.  Four independent experiments were performed using 16 mice.

first: Go

last: Yamamoto

first: Mayumi

last: Yoshimi

first: Kazuki

first: Takashi

last: Asai

first: Motoshi

last: Ichikawa

first: Sachiko

last: Seo

first: Masahiro

last: Nakagawa

first: Shigeru

last: Chiba

first: Mineo

last: Kurokawa

first: Seishi

last: Ogawa


title: Gene expression analysis of male E14 genital tubercle isolated from SMAA (Acta2) transgenic mice. (GUDMAP Series ID: 16)

status: Public on May 26 2007

first: GUDMAP

last: Developers

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

overall_design: The genital tubercle region from an E14 (TS22) SMAA/EYFP males were microdissected and total RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

first: James

last: Lessard

first: Nick

middle: E

last: Maull


title: Hyperexpression of Mouse Melanotransferrin on LMTK Cell Line

status: Public on May 05 2007

city: Sydney

first: Des

middle: Raymond

last: Richardson

state: New South Wales

address: 92-94 Parramatta Rd, Sydney

department: Bosch Institute

country: Australia

institute: University of Sydney

summary:
Melanoma tumor antigen p97 or melanotransferrin (MTf) is an iron (Fe)-binding protein with high homology to serum transferrin. MTf is expressed at very low levels in normal tissues and in high amounts in melanoma cells. The over-expression of MTf in tumor cells was hypothesized to assist rapidly proliferating neoplastic cells with their increased Fe requirements. However, our recent   characterization of the MTf knockout (MTf -/-) mouse demonstrated that MTf did not have an essential role in Fe metabolism. To understand the function of MTf, we utilized whole-genome microarray analysis to examine the gene expression profile of five models after modulating MTf expression. These models included two new stably transfected MTf hyper-expression models (SK-N-MC neuroepithelioma and LMTK- fibroblasts) and one cell type (SK-Mel-28 melanoma) where MTf was down-regulated by post-transcriptional gene silencing. These findings were compared to alterations in gene expression identified using the MTf -/- mouse. In addition, the changes identified from the gene array data were also assessed in a new model of MTf down-regulation in SK-Mel-2 melanoma cells. In the cell line models, MTf hyper-expression led to increased cellular proliferation, while MTf down-regulation resulted in decreased proliferation. Across all five models of MTf down- and up-regulation, we identified three genes modulated by MTf expression. These included ATP-binding cassette sub-family B member 5 (Abcb5), whose change in expression mirrored MTf down- or up-regulation. In addition, thiamine triphosphatase (Thtpa) and transcription factor 4 (Tcf4) were inversely expressed relative to MTf levels across all five models. The products of these three genes are involved in membrane transport, thiamine phosphorylation and cell proliferation/survival, respectively. This study identifies novel molecular targets directly or indirectly regulated by MTf and potential pathways involved in its function. These molecular targets could be involved, at least in part, to the role of MTf in modulating proliferation.
Keywords: Melanotransferrin, hyperexpression cell lines, comparative genomic hybridization

overall_design: Hyper-expression constructs of the mouse MTf cDNA was generated using the pCI-neo (Promega, Madison, WI) expression vector. The inserts were sequenced and confirmed against mouse (Genbank Accession: NM_013900) using the public NCBI database. Transfections of pCI-neo transgenes/vectors into murine LMTK- fibroblasts was performed with Lipofectin® reagent (Invitrogen, Melbourne, Australia) according to the manufacturer’s protocol. Total RNA was isolated from the cells using TRIzol Reagent® (Sigma-Aldrich) according to the manufacturer’s protocol. Total RNA from the stably-transfected mouse LMTK- cell lines were prepared and hybridized onto Mouse Genome 430 2.0 Array. The mouse GeneChip® 430 2.0 consists of greater than 39,000 transcripts and variants from over 34,000 well characterized mouse genes (Affymetrix, Santa Clara, CA).

first: Yohan

last: Suryo Rahmanto


title: Identif. of oscillatory genes in somitogenesis from functional genomic analysis of C2C12 myoblast line

city: Tempe

first: Kenro

last: Kusumi

state: AZ

department: School of Life Sciences

institute: Arizona State University

summary:
During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism. To date, the periodicity and components of the human clock remain unstudied. Here we show that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression. We observed that the known cycling gene HES1 oscillated with a 5 hour period, consistent with available data on the rate of somitogenesis in humans. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 hours, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Expression patterns of these genes were disrupted in Wnt3atm1Amc mutants but not in Dll3pu mutants. Our results demonstrate that human and mouse in vitro models can recapitulate oscillatory expression observed in embryo and that a number of genes in multiple developmental pathways display dynamic expression in vitro.
Keywords: time series

overall_design: Synchronization of C2C12 myoblasts was carried out as follows: T-25 cm flasks were set up in parallel. These cells were grown to 90% confluence in DMEM supplemented with 5% FBS then incubated in DMEM with only 0.2% FBS for 24 hours, and returned to DMEM supplemented with FBS. Samples were collected every 30 min. for 8 hours.

first: Dilusha

last: William

first: Biagio

last: Saitta

first: Joshua

last: Gibson

first: Jeremy

last: Traas

first: Vladimir

last: Markov

first: Dorian

middle: M

last: Gonzalez

first: William

last: Sewell

first: Douglas

last: Anderson

first: Stephen

last: Pratt

first: Eric

middle: F

last: Rappaport


title: SYT-SSX murine synovial sarcoma model

status: Public on Apr 30 2007

city: Salt Lake City

first: Jeffrey

last: Hancock

state: UT

address: 2000 Circle of Hope Dr

department: Huntsman Cancer Institute

institute: University of Utah

summary:
The human SYT-SSX fusion protein was expressed in a developmentally dependent fashion in murine myoblasts.  Tumors harvested from mice in adolescence were compared to normal mouse skeletal muscle samples.
Keywords: tumor versus normal muscle tissue

overall_design: Murine tumors were excised from affected mice for RNA extraction and hybridization on Affymetrix microarrays. For control samples normal mouse skeletal muscle tissue was obtained and RNA extracted for hybridization to the Affymetrix arrays.

first: Malay

last: Halder

first: Cheryl

last: Coffin

last: Lessnick

first: Mario

last: Capecchi


title: Identification of oscillatory genes in somitogenesis from functional genomic analysis

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Effect of OMP on gene expression in the olfactory epithelium

city: Lexington

first: Neeraja

last: Sammeta

state: KY

address: 800 Rose Street,

department: Physiology

institute: University of Kentucky

summary:
OMP is expressed only in mature olfactory sensory neurons, arguing that its function is specially suited to the needs of OSNs. However none of the properties of OMP suggest any direct role in regulating gene expression in OSNs. Our data confirms that gene expression in the olfactory epithelium of  mice lacking OMP is indistinguishable from mice expressing OMP. We used affymerix M430v2.0 gene chips to cover as much of genome as possible and observed no statistically significant differences in mRNA abundance between the two genotypes.These results imply that OMPs ability to regulate signal transduction with in OSNs has little effect on gene expression and that its ability to promote mitosis in neighbouring cells (under culture conditions) is insufficiently active under normal laboratory housing conditions to generate detectable differences in gene expression patterns.
Keywords: genetic modification

overall_design: The overall design of the experiment is to undertand the effect of OMP (olfactory marker protein) on gene expression in the olfactory epithelium. We isolated the olfactory epithelium from homozygous and heterozygous OMP-GFP mice, extracted the RNA and hybridized on to the mouse expression set 430 2.0 Chip.

first: Tun-Tzu

last: Yu

first: Timothy

middle: S

last: McClintock


title: expression comparison of wildtype lungs and hypomorphic for nmyc

status: Public on Apr 24 2007

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

institute: University of Toronto

summary:
comparison of expression of wildtype lungs and lungs with hypomorphic expression of nmyc. the lungs were pooled from several biological samples. The hypomorphoic mutant was orignally published in Moens CB et al [PMID: 1577267]. this is part of a larger collection of data comparing nmyc misexpression in the lung (gain of fucntion) and protein expression in the hypomorphic lungs.
Keywords: expression comparison

overall_design: samples from pooled lungs were analyzed.

middle: J

first: Janet

last: Rossant

first: Dennis

last: Wigle


title: Expression data from experimental murine asthma

status: Public on Apr 23 2007

city: Abbott Park

first: Xin

last: Lu

address: 100 Abbott Park Rd

department: Cancer Research

institute: Abbott Laboratories

summary:
Experimental asthma was induced in BALB/c mice by sensitization and challenge with the allergen ovalbumin. Control groups received PBS. To investigate the innate immune component of experimental asthma, we also analyzed recombinase activating gene (RAG) deficient mice following exposure to ovalbumin and control PBS
Keywords: case control

overall_design: Each experimental group was exposed to ovalbumin or control PBS. At day 22, 1 day after completion of the allergen exposure, whole lungs were harvested, total mRNA prepared, and gene expression determined by hybridization to Affymetrix microarrays.

first: Vipul

middle: V

last: Jain

first: Patricia

middle: W

last: Finn

first: David

middle: L

last: Perkins


title: Caloric restriction suppresses apoptotic cell death in the mammalian cochlea and leads to prevention of presbycusis

first: Shinichi

last: Someya

summary:
Presbycusis is characterized by an age-related progressive decline of auditory function, and arises mainly from the degeneration of hair cells or spiral ganglion (SG) cells in the cochlea. Here we show that caloric restriction suppresses apoptotic cell death in the mouse cochlea and prevents late onset of presbycusis. Caloric restricted mice, which maintained body weight at the same level as that of young control (YC) mice, retained normal hearing and showed no cochlear degeneration. CR mice also showed significantly fewer TUNEL-positive staining cells and fewer cleaved caspase-3-positive staining cells relative to middle-age control (MC) mice. Microarray analysis revealed that CR down-regulated the expression of 28 proapoptotic genes, including Bak and Bim. Taken together, our findings suggest that loss of critical cells through apoptosis is an important mechanism of presbycusis in mammals, and that CR or staying lean can retard this process by suppressing apoptosis in the inner ear tissue.
Keywords: Effect of aging, effect of caloric restriction, time course, disease state analysis

overall_design:
To examine the effects of aging, a comparison of cochlea tissues from YC (3 samples) and MC (3 samples) mice was conducted. To examine the effects of calorie restriction (CR), a comparison of cochleae from MC (3 samples) and CR (3 samples) mice was conducted. We examined age-related changes in gene expression in the cochlea and calorie restriction-induced changes in gene expression in the cochlea. We pooled four cochleae from two mice for one sample and used three samples per group (n = 3).
Quality control measures were not used. No replicates were done. Dye swap was not used.

first: Tatsuya

last: Yamasoba

first: Richard

last: Weindruch

first: Tomas

middle: A

last: Prolla

first: Masaru

last: Tanokura


title: Foxp3-dependent programme of regulatory T-cell differentiation

first: Alexander

last: Rudensky

overall_design: Thymocyte RNA (GSE7770) was processed with Affy and Enzo reagents whereas peripheral cell RNA (GSE7280) was processed with Ambion reagents, which amplified the cRNA more robustly. As a result, the two data sets don't normalize very well to each other and shouldn't be compared directly to each other.


title: Laser capture-microarray analysis of Lim1 mutant kidney development.

status: Public on Apr 10 2007

city: Cincinnati

first: Steven

last: Potter

state: OH

address: 3333 Burnet Ave.

department: Developmental Biology

institute: Children's hospital Medical Center

summary:
The Lim1 gene has essential functions during several stages of kidney development. In particular, a tissue specific knockout in the early metanephric mesenchyme results in the formation of the earliest nephron precursor, the renal vesicle, but failure of this structure to progress to the next stage, the comma shaped body. To better understand the molecular nature of this developmental arrest we used a laser capture microdissection-microarray strategy to examine the perturbed gene expression pattern of the mutant renal vesicles. Among the genes found differently expressed were Chrdl2, an inhibitor of BMP signaling, the pro-apoptotic factor Bmf, as well as myob5, an atypical myosin which modulates chemokine and transferring signaling, and pdgfr1, which is important in epithelial folding. Of particular interest, the microarray data indicated that the Dkk1 gene, which encodes an inhibitor of Wnt signaling, was downregulated  nine fold in mutants. This was confirmed by in situ hybridizations. It is interesting to note that Lim1 and Dkk1 mutant mice have striking similarities in phenotype.  These results suggest that the Dkk1 gene might be a key downstream effector of Lim1 function.
Keywords: Lim1 mutant, kidney development, gene expression profile comparison

overall_design: We compared gene expression profiles of wild type and mutant Lim1 renal vesicles, which were isolated from E12.5 kidneys by laser capture microdissection. Nine biological independent samples were examined, with four mutant and five wild type. Each sample included approximately 30-50 renal vesicles. Detailed protocols are described at GUDMAP.org

first: Heather

last: Hartman

first: Kin

last: Kwan

middle: R

last: Behringer

first: Larry

middle: T

last: Patterson


title: The Differentiation and Stress Response Factor, XBP-1, Drives Multiple Myeloma Pathogenesis

status: Public on Apr 09 2007

city: Boston

first: Ronald

last: DePinho

state: MA

address: 44 Binney St. M417

institute: Dana Farber Cancer Institute

summary:
Multiple myeloma (MM) evolves from highly prevalent premalignant condition termed Monoclonal Gammopathy of Undetermined Significance (MGUS).  We report an MGUS-MM phenotype arising in transgenic mice with Emu-directed expression of the unfolded protein/ER stress response and plasma cell development spliced isoform factor XBP-1s.  Emu-XBP-1s elicited elevated serum Ig and IL-6 levels, skin alterations and with advancing age, a significant proportion of Emu-xbp-1s transgenic mice develop features diagnostic of human MM including bone lytic lesions. Transcriptional profiles of Emu-xbp-1s B lymphoid and MM cells show aberrant expression of genes known to be dysregulated in human MM including Cyclin D1, MAF, MAFB, and APRIL. This genetic model coupled with documented frequent XBP-1s overexpression in human MM serve to implicate chronic XBP-1s dysregulation in the development of this common and lethal malignancy.
Keywords: XBP-1, MGUS, multiple myeloma, transgenic mouse

overall_design:
In this study, we have explored the biological impact of sustained XBP-1s expression in the lymphoid system, anticipating that this genetic event would be a necessary component along with other MM-relevant oncogenes and tumor suppressor gene manipulations to generate a MM-prone mouse model.  Unexpectedly, XBP-1s overexpression alone yielded an MGUS-MM disease bearing many features classical of the human disease on the clinical, pathological and molecular levels.
We performed expression analysis of B cells derived from the spleen of 20-week old Emu-xbp-1s mice (n=5) and non-transgenic mice (n=5). Additionally, we analyzed the expression profiles from MM tumor cells arising in Emu-xbp-1s mice (n=6).

first: Daniel

last: Carrasco

first: Kumar

last: Sukhdeo

first: Marina

last: Protopopova

first: Raktim

last: Sinha

first: Miriam

last: Enos

first: Mei

last: Zheng

first: Mala

last: Mani

first: Joel

last: Henderson

first: Geraldine

last: Pinkus

first: Nikhil

last: Munshi

first: James

last: Horner

first: Elena

last: Ivanova

first: Alexei

last: Protopopov

first: Kenneth

middle: C

last: Anderson

first: Giovanni

last: Tonon


title: Expression profiling of back skin of Get1 and control mice at e18.5

status: Public on Apr 12 2007

city: Irvine

first: Kevin

middle: K

last: Lin

state: CA

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California, Irvine

summary:
Defective permeability barrier is an important feature of many skin diseases and causes mortality in premature infants. To investigate the control of barrier formation, we characterized the epidermally expressed Grainyhead-like epithelial transactivator (Get-1)/Grhl3, a conserved mammalian homologue of Grainyhead, which plays important roles in cuticle development in Drosophila. Get-1 interacts with the LIM-only protein LMO4, which is co-expressed in the developing mammalian epidermis. The epidermis of Get-1(-/-) mice showed a severe barrier function defect associated with impaired differentiation of the epidermis, including defects of the stratum corneum, extracellular lipid composition and cell adhesion in the granular layer. The Get-1 mutation affects multiple genes linked to terminal differentiation and barrier function, including most genes of the epidermal differentiation complex. Get-1 therefore directly or indirectly regulates a broad array of epidermal differentiation genes encoding structural proteins, lipid metabolizing enzymes and cell adhesion molecules. Although deletion of the LMO4 gene had no overt consequences for epidermal development, the epidermal terminal differentiation defect in mice deleted for both Get-1 and LMO4 is much more severe than in Get-1(-/-) mice with striking impairment of stratum corneum formation. These findings indicate that the Get-1 and LMO4 genes interact functionally to regulate epidermal terminal differentiation.
Keywords: knockout and wildtype mice comparison

overall_design: The same region of the mouse back skin was excised from three Get1 +/+ and three Get1 −/− mice at e18.5.

first: Zhengquan

last: Yu

first: Ambica

last: Bhandari

last: Spencer

first: Xiaoman

last: Xu

first: Ning

last: Wang

first: Zhongxian

last: Lu

first: Gordon

middle: N

last: Gill

first: Dennis

last: Roop

first: Philip

last: Wertz

first: Bogi

last: Andersen


title: Zfx controls the self-renewal of embryonic and hematopoietic stem cells

status: Public on Apr 20 2007

city: New York

first: Jose

last: Galan

state: NY

address: 701 W 168th St Room 609

institute: Columbia University Medical Center

summary:
Stem cells (SC) exhibit a unique capacity for self-renewal in an undifferentiated state. It is unclear whether the self-renewal of pluripotent embryonic SC (ESC) and of tissue-specific adult SC such as hematopoietic SC (HSC) is controlled by common mechanisms. The deletion of transcription factor Zfx impaired the self-renewal but not the differentiation capacity of murine ESC; conversely, Zfx overexpression facilitated ESC self-renewal by opposing differentiation. Furthermore, Zfx deletion abolished the maintenance of adult bone marrow HSC, but did not affect erythromyeloid progenitors or fetal HSC. In both ESC and HSC, Zfx activated a common set of direct target genes. In addition, the loss of Zfx resulted in the induction of immediate-early and/or stress-inducible genes in both SC types but not in their differentiated progeny. These studies identify the first shared transcriptional regulator of ESC and HSC, suggesting a common molecular basis of self-renewal in embryonic and adult SC.
Keywords: Global gene expression data analysis in Zfx-deficient murine ESC and HSC

overall_design:
Global gene expression analysis
For ESC, Zfxnull and control Zfxflox clones were grown on gelatin in medium with
15% Knockout SR and LIF. For HSC, BM cells were pooled from 4-6 Mx1-Cre+ Zfxflox/y CKO and control Zfxflox/y Cre- littermates 4 days after the last pI·C injection, and Lin- Sca-1+ c-Kit+ cells were flow-sorted. RNA was amplified, labeled and hybridized to Mouse Genome 430 2.0 microarrays containing probes for ~37,000 genes (Affymetrix).
Total RNA (2.5 ug) was isolated from ESC using RNeasy Mini Kit (QIAGEN) and
used for reverse transcription and antisense RNA (aRNA) amplification using
MessageAmp II system (Ambion). The resulting aRNA was labeled with Biotin-16-UTP (Roche Applied Sciences) and Biotin-11-CTP (PerkinElmer Life Sciences) in a single round of linear amplification. Labeled aRNA (average size ~1500 nucleotides) was fragmented in RNA Fragmentation Buffer (QIAGEN) prior to hybridization.
For HSC, pooled BM cells were stained with a biotinylated lineage antibody
cocktail, and Lin+ cells were depleted using streptavidin-conjugated magnetic beads and LS selection columns (Miltenyi Biotech). Enriched cells were stained for lineage, c-Kit and Sca-1, and 5 x 104 LSK cells were sorted directly into Trizol Reagent (Invitrogen). Total RNA was isolated and quantified using the Quant-IT RNA Assay Kit (Invitrogen), and 100 ng of each RNA sample were used for reverse transcription and two-round linear aRNA amplification. The aRNA was amplified without labeling in the first round, and then labeled with Biotin-16-UTP/Biotin-11-CTP in the second round. Labeled aRNA (average size ~800 nucleotides) was fragmented as above.
Labeled RNA samples (10 ug/array) were hybridized to Mouse Genome 430 2.0
arrays (Affymetrix) at the Columbia University Microarray Project core facility according to the manufacturer's instructions. Samples were hybridized in duplicates, with the correlation between duplicate samples calculated at 0.995-0.997. Quality control and normalization were performed using positive and negative hybridization controls (Affymetrix) spiked into the RNA prior to labeling. Linear amplification of RNA was confirmed for every sample. Array scanning and raw data processing were done using GCOS 1.4 software (Affymetrix).

last: Galan-Caridad

first: Sivan

last: Harel

first: Teresita

last: Arenzana

first: Esther

middle: Z

last: Hou

first: Fiona

last: Doetsch

first: Leonid

last: Mirny

first: Boris

last: Reizis


title: A high fat, ketogenic diet induces a unique metabolic state in mice.

status: Public on May 04 2007

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary:
Analysis of liver gene transcription during feeding of a ketogenic diet.  Ketogenic diets may alter physiologic and metabolic profiles in a direction that favors weight loss. C57BL/6J mice were maintained for six weeks on either chow or ketogenic diet. Mice eating KD had lower weights, 90% reduction in insulin levels and increased energy expenditure compared to animals fed chow. Despite consumpiton of a very high fat diet serum lipids remained normal.  Here we show that consumption of KD shifted liver metabolism to drastically increased fatty acid oxidation. Concurrently, expression of genes involved in fatty acid synthesis were markedly suppressed.
Keywords: Hepatic profile

overall_design: Eight week old C57BL/6 mice were fed either chow (Labdiet 5008, Pharmserv) or KD (F3666, Bio-Serv) for six weeks. Livers were harvested in the morning in ad lib fed animals. Total RNA from 2-3 animals in each group was used for Affymetrix analysis.

first: A

last: Kennedy

first: P

last: Pissios

first: H

last: Otu

first: B

last: Xue

first: K

last: Asakura

first: N

last: Furukawa

first: F

middle: E

last: Marino

last: Liu

middle: B

last: Kahn

first: T

last: Liberman

first: M

last: Badman

first: E

last: Maratos-Flier


title: Investigate the role of Wnt/beta-catenin signaling in development of the exocrine pancreas

status: Public on Apr 04 2007

first: Bruce

last: Aronow

institute: Cincinnati Children's Hospital Medical Center

summary:
beta-catenin is an essential mediator of canonical Wnt signaling and a central component of the cadherin-catenin epithelial adhesion complex. Dysregulation of beta-catenin expression has been described in pancreatic neoplasia. Newly published studies have suggested that beta-catenin is critical for normal pancreatic development although these reports reached somewhat different conclusions. In addition, the molecular mechanisms by which loss of beta-catenin affects pancreas development are not well understood. The goals of this study then were; 1] to further investigate the role of beta-catenin in pancreatic development using a conditional knockout approach and 2] to identify possible mechanisms by which loss of beta-catenin disrupts pancreatic development. A Pdx1-cre mouse line was used to delete a floxed beta-catenin allele specifically in the developing pancreas, and embryonic pancreata were studied by immunohistochemistry and microarray analysis.

Keywords: Time course

overall_design:
Parameter: embryonic pancreas from wild type and Pdx1Cre/+; beta-cateninflox/flox
Sample type: RNA
Source name: Embryonic day 14.6 and 16.5 pancreas
Organism: Mus Musculus
Strain: Derived from an intercross of Pdx1Cre/+ ; beta-cateninflox/+ mice.
Extracted molecule:	Total RNA
In the study, we hybridized RNA from Embryonic day 14.6 and 16.5 pancreas of wild type (WT) control and Pdx1Cre/+; beta-cateninflox/flox beta-catenin null in the pancreas) embryonic pancreas to Affymetrix MOE430 2.0 GeneChipÂ® arrays containing 45,101 well characterized mouse genes/ESTs.

first: James

middle: M

last: Wells


title: Mouse model of Endometrioid Ovarian Adenocarcinomas by conditional inactivation of PTEN and APC genes

city: Ann Arbor

first: Rork

last: Kuick

state: MI

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

institute: University of Michigan

summary:
Fifty million plaque-forming units of AdCre was injected into the right ovarian bursal cavity of 56- 70 day old female mice.  Mice were euthanized 63 days later to obtain ovary tumors and normal ovary tissue.  Seven individual ovarian tumors and 4 individual normal ovary samples were each assayed on an Affymetrix Mouse Genome 430 2.0 array.
Keywords: Tumor vs normal comparisons

overall_design: 7 individual ovarian tumors and 4 individual normal ovary samples.  RNA expression was analyzed using one Affymetrix Mouse Genome 430 2.0 array per sample.

first: Rong

last: Wu

first: Neali

last: Hendrix

first: David

last: Misek

first: Samir

last: Hanash

first: Yali

last: Zhai

first: Donald

last: Schwartz

first: Aytekin

last: Akyol

first: Hidetaka

last: Katabuchi

first: Bart

middle: O

last: Williams

first: Eric

last: Fearon

first: Kathleen

last: Cho


title: Regulation of Gene Expression by Sirt1 in the heart

status: Public on Mar 31 2007

city: Newark

first: Bin

last: Tian

state: NJ

address: 185 South Orange Ave.

department: Biochemistry and Molecular Biology

institute: UMDNJ-New Jersey Medical School

summary:
We harvested the heart from transgenic mice with cardiac specific overexpression of Sirt1 (Tg-Sirt1) and non-transgenic (NTg) control littermate at 3 months of age and then microarray analyses were conducted.
Keywords: Gene expression comparison

overall_design: Two transgenic mice and two wild type mice were used.

first: Ralph

last: Alcendor

first: Shumin

last: Gao

first: Peiyong

first: Daniela

last: Zablocki

last: Holle

first: Xianzhong

last: Yu

first: Thomoas

last: Wagner

first: Stephen

middle: F

last: Vatner

first: Junichi

last: Sadoshima


title: miR-1-2 knockout versus wild-type hearts

status: Public on Mar 29 2007

city: San Francisco

first: Yong

last: Zhao

address: 1650 owens street

department: Gladstone Institute of Cardiovascular Disease

institute: The J. David Gladstone Institutes

summary:
microarray was done on Heart tissue from ko and wt
MicroRNAs (miRNAs) are genomically encoded small RNAs used by organisms to regulate the dosage of proteins generated from messenger RNA transcripts. The in vivo requirement of specific miRNAs in mammals is unknown, and reliable prediction of mRNA targets remains problematic. Here, we show that miRNA biogenesis in the mouse heart is essential for cardiogenesis. Furthermore, targeted deletion of the muscle-specific miRNA, miR-1-2, revealed numerous functions in the heart, including regulation of cardiac morphogenesis, electrical conduction, and cell cycle control. Analyses of miR-1 complementary sequences in mRNAs upregulated upon miR-1-2 deletion revealed an enrichment of miR-1 "seed matches" and a strong tendency for potential miR-1 binding sites to be located in physically accessible regions. These findings indicate that subtle alteration of miRNA dosage can have profound consequences in mammals and demonstrate the utility of mammalian loss-of-function models in revealing physiologic miRNA targets.
Keywords: miRNA

overall_design: Heart tissues from 3 wild type and 3 miR-1-2 knockout mice at postnatal days 10 were used and total RNA was extracted by Trizol. Expression level was compared between wild type and miR-1-2 knockout mice.  The affy package from R/Bioconductor was used to generate RMA values.

first: Deepak

last: Srivastava


title: response to IL-1b of WT and IRAK4 kinase dead mouse embryonic fibroblasts

status: Public on Mar 30 2007

city: Basel

first: Anton

last: Glück

country: Switzerland

institute: Novartis Institutes for BioMedical Research

summary:
IRAK-4 is an essential component of the signal transduction complex downstream of the IL-1- and Toll-like receptors. Though regarded as the first kinase in the signaling cascade, the role of IRAK-4 kinase activity versus its scaffold function is still controversial. In order to investigate the role of IRAK-4 kinase function in vivo, ‘knock-in’ mice were generated by replacing the wild type IRAK-4 gene with a mutant gene encoding kinase deficient IRAK-4 protein (IRAK-4 KD). Analysis of embryonic fibroblasts and macrophages obtained from IRAK-4 KD mice with a number of experimental techniques demonstrated that they greatly lack responsiveness to stimulation with IL-1b or a Toll-like receptor 7 (TLR7) agonist. One of the techniques used, microarray analysis, identified IRAK-4 kinase-dependent IL-1b response genes in mouse embryonic fibroblasts and revealed that the induction of IL-1b-responsive mRNAs was largely ablated in IRAK-4 KD cells. In summary, our results suggest that IRAK-4 kinase activity plays a critical role in IL-1R/TLR7-mediated induction of inflammatory responses.
Keywords: genetic modification, strain comparison, cell stimulation, time course, inflammatory response

overall_design: The response of mouse embryonic fibroblasts from WT and IRAK4 kinase dead animals to stimulation with IL-1b at two time points was determined. There were 12 samples in total, 6 from WT and 6 from IRAK4 kinase dead cells; for each strain there were 3 conditions: growth for 4 hours without stimulation (the strain-specific control), growth for 1 hour with stimulation, and growth for 4 hours with stimulation; for each condition there were two biological replicates.

first: Magdalena

last: Koziczak-Holbro

first: Hermann

last: Gram

first: Bernd

last: Kinzel

last: Glueck

first: Nicole

last: Hartmann

first: Martin

last: Letzkus


title: Expression data from p38 knock out versus wild type fetal liver

status: Public on Mar 23 2007

city: Vienna

first: Norbert

last: Schweifer

address: Dr. Boehringer Gasse 5-11

country: Austria

institute: Boehringer Ingelheim Austria

summary:
The mitogen-activated protein kinase (MAPK) p38alpha controls inflammatory responses and cell proliferation. Using mice carrying conditional p38alpha alleles, we investigated its function in postnatal development and tumorigenesis. When p38alpha is specifically deleted in the mouse embryo, fetuses develop to term but die shortly after birth, likely due to lung dysfunction. Fetal hematopoietic cells and embryonic fibroblasts deficient in p38alpha display increased proliferation, resulting from sustained activation of the c-Jun N-terminal kinase (JNK)/c-Jun pathway. Importantly, in chemical-induced liver cancer development, mice with liver-specific deletion of p38alpha show enhanced hepatocyte proliferation and tumor development that also correlates with JNK/c-Jun upregulation. Furthermore, increased proliferation of p38alpha-deficient hepatocytes and tumor cells is suppressed by inactivation of JNK or c-Jun.  These results reveal a novel mechanism whereby p38alpha negatively regulates cell proliferation through antagonizing the JNK/c-Jun pathway in multiple cell types and in liver cancer development.
We used microarrays to identifiy differental regulated genes by p38alpha in fetal liver cells
Keywords: time course

overall_design: Wild type and p38 deficient fetal liver cell were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Lijian

last: Hui

first: Christian

last: Haslinger

first: Erwin


title: Comparison of Longitudinal Leukocyte Gene Expression after Burn Injury or Trauma Hemorrhage in Mice

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

summary: We report here the genes that are sequentially expressed in white blood cells from blood and spleen at 2 hours, 2 day,3 days, and 7 days after burn and sham injury or trauma-hemorrhage (T-H) and sham T-H. Includes WBC treated with LPS for 2 hours and 1 day.

overall_design: White blood cells (WBC) and splenocytes were harvested from individual mice and RNA was extracted, labeled and hybridized to Affymetrix Mouse Genome 430 2.0  GeneChips™. The results were analyzed by dCHIP and BRB Array Tools software. Ingenuity Pathway Analysis (IPA) was applied to identify molecular networks significantly affected by the injuries.

first: James

last: Lederer

first: Buddy

middle: H

last: Brownstein

first: M

last: Lopez

first: Sandra

last: MacMillan

first: Adam

last: Delisle

first: Malcolm

last: MacConmara

first: Mashkoor

last: Chaudhry

first: Wenzhong

last: Xiao

first: Steven

last: Lekousi

first: J

middle: P

last: Cobb

first: Henry

last: Baker

first: John

last: Mannick

first: Irshad

last: Chaudry


title: Neocortical and cerebellar astrocytes

status: Public on Mar 14 2007

city: Saint Louis

first: Mukesh

last: Sharma

address: 4566 Scott Avenue, room 306

department: Neurology

institute: Washington University School of Medicine in Saint Louis

summary:
Affymetrix Mouse Genome 430 2.0 GeneChip microarrays were used to analyze murine neocortical and cerbellar astrocytes generated from postnatal (PN) day 1 wild-type (ICR) pups.
Keywords: neocortical astrocyte, cerebellar astrocyte, murine, postnatal day 1

overall_design: Three samples each of murine neocortical and cerebellar astrocytes were analyzed.

first: David

last: Mansur

first: Guido

last: Reifenberger

first: Arie

last: Perry

first: Jeffrey

last: Leonard

first: Kenneth

middle: D

last: Aldape

first: Meredith

middle: G

last: Albin

first: Ryan

middle: J

last: Emnett

first: Simon

last: Loeser

first: Mark

last: Watson

first: Rakesh

last: Nagarajan

last: Gutmann


title: day3 brown fat from wt compared to day3 from Gyk ko

status: Public on Mar 11 2007

city: Los Angeles

first: Lola

last: Rahib

address: 695 Charles E young Drive south Gonda 5335

department: Human Genetics

institute: UCLA

summary:
Glycerol kinase (GK) is at the interface of fat and carbohydrate metabolism and has been implicated in insulin resistance and type 2 diabetes mellitus (T2DM). To define GK’s role in insulin resistance, we examined gene expression in brown adipose tissue in a glycerol kinase (Gyk) knockout (KO) mouse model using microarray analysis. Global gene expression profiles of KO mice were distinct from wild type (WT) with 668 genes that were differentially expressed. These included genes involved in lipid metabolism, carbohydrate metabolism, insulin signaling, and insulin resistance. Real-Time (RT) PCR analysis confirmed the differential expression of selected genes involved in lipid and carbohydrate metabolism. PathwayAssist analysis confirmed direct and indirect connections between GK and genes in lipid metabolism, carbohydrate metabolism, insulin signaling, and insulin resistance. Network Component Analysis (NCA) showed that the transcription factors, peroxisome proliferator-activated receptor gamma (PPAR-γ), sterol regulatory element binding factor 1 (SREBP-1), SREBP-2, signal transducer and activator of transcription 3 (STAT3), STAT5, trans-acting transcription factor 1 (SP1),  CCAAT/enhancer binding protein alpha (CEBP-α), cAMP responsive element binding protein 1 (CREB), glucocorticoid receptor (GR), and PPAR-α have altered activity in the KO mice.  NCA also revealed the individual contribution of these transcription factors on the expression of genes altered in the microarray data. This study elucidates the transcription network of Gyk and further confirms a role for Gyk, a simple Mendelian disorder, in insulin resistance and T2DM, a common complex genetic disorder.
Keywords: genotype state analysis

overall_design: 7 samples are analyzed; 3 wildtype and 4 KO. the WT samples are used as control and KO samples are used as the experimental group.


title: FOG-1-independent transcripition by GATA-1(V205G) in G1E cells

status: Public on Mar 05 2007

city: Madison

first: Kirby

middle: Dean

last: Johnson

address: 1300 University Avenue

department: Pharmacology

institute: University of Wisconsin-Madison

summary:
Identification of genes regulated by GATA-1 independent of the cofactor FOG-1.
Keywords: cell treatment comparison

overall_design: A conditionally activated FOG-1-binding defective mutant of GATA-1, ER-GATA-1(V205G), was expressed in GATA-1-null G1E cells.  Transcipt levels were compared in cells untreated or treated with estradiol to activate the GATA-1 mutant.

first: Emery

last: Bresnick


title: The molecular consequences of Nix ablation on apoptosis and erythropoiesis

status: Public on Feb 14 2007

first: Bruce

last: Aronow

summary:
Normal erythropoiesis requires a critical balance between proapoptotic and antipaoptotic pathways. Bcl-xl, an antiapoptotic protein is induced at end-stages of differentiation of erythroid precursors in response to erythropoietin. The details of the proapoptotic pathway and the critical proapoptotic proteins inhibited by Bcl-xl in erythropoiesis are not well understood. We employed gene targeting to ablate Nix, a proapoptotic BH3-domain only Bcl2 family protein, which is known to be transcriptionally induced during erythropoiesis. Nix null mice exhibited reticulocytosis and thrombocytosis in the peripheral blood; and profound splenomegaly with erythroblastosis in the spleen and bone marrow despite normal erythropoietin levels and blood oxygen tension. In vivo apoptosis was diminished in erythroblast precursors from Nix null spleens. To define the molecular consequences of Nix ablation on apoptosis and erythropoiesis, we conducted a detailed comparative analysis of gene expression in spleens from 8 week old Nix null mice and wild type controls. Of 45,101 genes analyzed, 514 were significantly upregulated and 386 down-regulated in Nix-/- splenocytes. Functional cluster analysis delineated the ten most highly regulated gene sets, revealing increased levels of cell cycle and erythroid genes, with decreased levels of cell death and B-cell genes.
Keywords: strain comparison

overall_design: In the study, we hybridized RNA from 8 week old spleens of wild type (WT) control and Nix null mice (Nix-/-) to Affymetrix MOE430A GeneChip® arrays containing 45,101 well characterized mouse genes/ESTs.


title: Global gene expression across a range of tissues

status: Public on Feb 23 2007

city: St. Louis

middle: Martin

last: Murphy

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary:
The aim of this study is to survey global gene expression across a range of mouse tissues. Biotinylated cRNA was synthesized from total RNA, then fragmented and hybridized to Affymetrix Mouse Genome 430 2.0 GeneChip arrays at the Siteman Cancer Center Gene Chip Core Facility (Washington University, St Louis, Missouri) according to manufacturer's protocols. Image files were generated using MicroArray Suite 5.0 (Affymetrix).
Keywords: other

first: R

last: Lindsley

first: K


title: Mouse small intestine epithelium vs. mesenchyme

status: Public on Mar 12 2007

first: Xing

last: Li

address: 109 Zina Pitcher Place,045 BSRB

department: Bioinformatics Program & CDB

institute: Universtiy of Michigan

summary:
During organogenesis of the intestine, reciprocal crosstalk between the endodermally-derived epithelium and the underlying mesenchyme is required for regional patterning and proper differentiation.  Though both of these tissue layers participate in patterning, the mesenchyme is thought to play a prominant role in the determination of epithelial phenotype during development and in adult life.  However, the molecular basis of this instructional dominance is unclear. In fact, surprisingly little is known about the cellular origins of many of the critical signaling molecules and the gene transcriptional events that they impact.  Here, we profile genes that are expressed in separated mesenchymal and epithelial compartments of the perinatal mouse intestine. The data indicate that the vast majority of soluble modulators of signaling pathways such as Hedgehog, Bmp, Wnt, Fgf and Igf are expressed predominantly or exclusively by the mesenchyme, accounting for its ability to dominate instructional crosstalk. We also catalog the most highly enriched transcription factors in both compartments and find evidence for a major role for Hnf4alpha and Hnf4 gamma in the regulation of epithelial genes. Finally, we find that while epithelially enriched genes tend to be highly tissue-restricted in their expression, mesenchymally-enriched genes tend to be broadly expressed in multiple tissues. Thus, the unique tissue-specific signature that characterizes the intestinal epithelium is instructed and supported by a mesenchyme that itself expresses genes that are largely non-tissue specific.
Keywords: comparative genomic hybridization: epithelium vs. mesenchyme

overall_design: Mouse small intestine (E18.5) is separated to epithelium and mesenchyme. Total RNA is extracted from epithelium and mesenchyme. There are 6 samples in this microarray experiment: 3 for epithelium and 3 for mesenchyme.  Samples are hybridized the affymetrix Mouse Genome 430 2.0 Array. We compare the gene expression between epithelium and mesenchyme to study the gene expression profiles in these two compartments.

first: Blair

last: Madison

first: Deborah

middle: L

last: Gumucio


title: Divergent and Convergent Effects on Gene Expression and Function in Acute versus Chronic Endothelial Activation

status: Public on Mar 21 2007

city: Indianapolis

first: Matthew

last: Grow

state: IN

institute: Indiana University

summary:
Activation of the vascular endothelium with cytokines such as TNF is widely used to study the role of the vasculature in proinflammatory disease. To gain insight into mechanisms of prolonged vascular endothelial activation we compared changes in gene expression induced by continuous activation in stable tmTNFalpha expressing cells with changes due to acute TNFalpha challenge in vitro. Affymetrix Genechip® analysis was performed on RNA from control, acute and continuous TNFalpha-activated endothelial cells. Only 36% of the significant changes in gene expression were convergent between the acute and continuously activated endothelial cells in comparison to the control.  From the divergently regulated genes, for example the cytokine ENA-78 was specifically induced in chronically activated cells, while E-Selectin, a cell adhesion molecule, was upregulated only in acutely activated endothelial cells. Antioxidant SOD gene induction was noted in acute activation while NADPH oxidase was selectively upregulated in continuous activated endothelium in accordance with significant ROS induction occurred only in these cells. In addition, the anti-angiogenic genes PAI-1 and thrombospondin were upregulated only in acutely activated endothelium, consistent with reduced angiogenic activity observed in acute versus chronically activated endothelial cells in vitro. These data suggest that continuous activation of endothelial cells leads to specific expression and functional changes, consistent with alterations observed in dysfunctional endothelium exposed to or involved in chronic inflammation.
Keywords: Expression profiling

overall_design: This experiment compares the response of endothelial cells from newborn mice that were either stably transfected with a non-cleavable transmembrane mutant form of murine TNFalpha, or treated with soluble TNFalpha (20ng/ml) for 4 hours.  Each treatment was compared to mock-transfected control cells. Four replicates for each condition were used.  Five micrograms of total RNA was assayed per Genechip using standard Affymetrix protocols.

first: Gangaraju

last: Rajashekhar

first: Antje

last: Willuweit

first: Carolyn

last: Patterson

first: Matthias

last: Clauss


title: Expression time course data HEY2 KO and WT MASMC treated with PDGF

status: Public on Mar 01 2007

city: Seattle

first: Michael

middle: T

last: Chin

state: WA

address: 815 Mercer Street

department: Medicine

institute: University of Washington

summary:
The cardiovascular restricted transcription factor CHF1/Hey2 has been previously shown to regulate the smooth muscle response to growth factors. To determine how CHF1/Hey2 affects the smooth muscle response to growth factors, we performed a genomic screen for transcripts that are differentially expressed in wild type and knockout smooth muscle cells after stimulation with platelet derived growth factor.
We screened 45101 probes representing more than 39,000 transcripts derived from at least 34,000 genes, at eight different time points. We analyzed the expression data utilizing an algorithm based on Bayesian statistics to derive the best polynomial clustering model to fit the expression data. We found that in a total of 9827 transcripts the normalized ratio of knockout to wild type expression diverged more than 3 fold from baseline in at least one time point, and these transcripts separated into 17 distinct clusters. Further analysis of each cluster revealed distinct alterations in gene expression patterns for immediate early genes, transcription factors, matrix metalloproteinases, signaling molecules and other molecules important in vascular biology.
Keywords: time course

overall_design: WT and Hey2 knockout mouse aortic smooth muscle cells were treated in parallel with PDGF and harvested at successive time points for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify differentially expressed transcripts through Bayesian statistical methods that would explain the differential response to PDGF observed in vitro.

first: Shervin

last: Shirvani

first: Linette

last: Mookanamparambil

first: Marco

last: Ramoni


title: Mouse brain region gene expression (430 2.0 Array)

city: La Jolla

first: Carrolee

last: Barlow

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

summary:
Gene expression patterns were determined from five brain regions (bed nucleus of the stria terminalis, hippocampus, hypothalamus, periaqueductal gray, and pituitary gland) in six mouse strains (129S6/SvEvTac, A/J, C57BL/6J, C3H/HeJ, DBA/2J, and FVB/NJ). At least two replicate samples per brain region/strain were analyzed using Affymetrix Mouse Genome 430 2.0 arrays.
Keywords: mouse strain and brain region comparison

overall_design: six mouse strains and five brain regions were analyzed

first: Iiris

last: Hovatta

first: David

last: Lockhart


title: Expression profiling of developmental and regenerating liver in mice

status: Public on Feb 09 2007

first: Hasan

middle: Huseyin

last: Otu

address: 4 Blackfan Circle Rm. 238

institute: Harvard Medical School

summary:
Normal adult liver is uniquely capable of renewal
and repair after injury. Whether this response
represents simple hyperplasia of various liver elements
or requires recapitulation of the genetic program of
the developing liver is not known. To study these possibilities,
we examined transcriptional programs of
adult liver after partial hepatectomy and contrasted
these with developing embryonic liver. Principal component
analysis demonstrated that the time series of
gene expression during liver regeneration does not segregate
according to developmental transcription patterns.
Gene ontology analysis revealed that liver restoration
after hepatectomy and liver development differ
dramatically with regard to transcription factors
and chromatin structure modification. In contrast, the
tissues are similar with regard to proliferationassociated
genes. Consistent with these findings, realtime
polymerase chain reaction showed transcription
factors known to be important in liver development
are not induced during liver regeneration. These three
lines of evidence suggest that at a transcriptional level,
restoration of liver mass after injury is best described
as hepatocyte hyperplasia and not true regeneration.
We speculate this novel pattern of gene expression may
underlie the unique capacity of the liver to repair itself
after injury.
Keywords: time course

overall_design:
In order to elucidate the molecular similarities between regenerating and developing liver, we performed high-density microarray analysis using Affymetrix MG 430 2.0 chips for targets at 0, 1, 2, 6, 12, 18, 24, 30, 48, and 72 hours after partial hepatectomy and at 10.5, 11.5, 12.5, 13.5, 14.5, and 16.5 days post conception (dpc).

Each experimental time point is represented by two separate samples, each consisting of at least 3 pooled tissues from different animals. For example, 6 hepatectomies were performed for the 1 hour post-hepatectomy time point. Time 0 is used as control.

first: Kamila

last: Naxerova

first: Karen

last: Ho

first: Handan

last: Can

first: Nicole

last: Nesbitt

first: Towia

middle: A

last: Libermanna

first: Seth

last: Karp


title: Diabetic mice fat- niacin bound chromium

city: Columbus

first: Sashwati

last: Roy

department: Surgery

institute: Ohio State University

summary:
To study effect of niacin bound chromium in changing genetic profile of subcutaneous fat from diabetic mice
Keywords: nutritional supplemetation, obesity

overall_design: Two groups (n=4 each group) of mice were supplemented (oral gavage) with: i) niacin bound chromium (10 mg/kg body wt) in water for 10 wks (5d/wk) or ii) matching volume of water. After 10 wks of supplementation the subcutaneous fat was harvested and gene expression profile was studied using Affymetrix mouse genome 430 v 2.0 chips.

first: Chandan

middle: K

last: Sen

first: Cameron

last: Rink


title: Intragraft gene expression profile associated with the induction of tolerance

status: Public on Apr 03 2007

first: Tomoko

last: Doki

address: 4661 Sunset Blvd.

department: Cardiothoracic Surgery Research

institute: Childrens Hospital Los Angeles

summary:
Xenotransplantation holds the promise of providing an unlimited supply of donor organs for terminal patients with organ failure. The gal carbohydrate results in rejection of wild type pig grafts, however, chimerism established by expression of the GalT gene prior to transplantation in GalT knockout mice results in tolerance to Gal+ heart grafts.
We used microarrays in order to further understand the early events that occur within grafts that demonstrate tolerance.
Keywords: transplntation tolerance

overall_design: The GalT BMT recipient is a GalT knockout mouse which recieved GalT gene transduced allo-bone marrow cells transplantation after sublethal irradiation. A heart of wild type C57BL/6 was heterotopically transplanted into the recipient after GalT BMT. Syngeneic Control recipient is a wild type C57BL/6 transplanted a heart of wild C57BL/6.

first: Mary

last: Kearns-Jonker


title: The Retinoblastoma Binding Protein RBP2 is an H3K4 demethylase

status: Public on Feb 22 2007

city: New Haven

first: Qin

last: Yan

state: CT

address: Department of Pathology, PO Box 208023

institute: Yale School of Medicine

summary:
The roles of histone demethylase RBP2 in gene expression were assessed using gene expression profiling experiments with wild type and RBP2-/- primary MEFs. Several cytokine genes including SDF1 and Kit ligand were upregulated upon inactivation of RBP2.
Keywords: mouse embryonic fibroblasts, gene expression profiling, microarray, Affymetrix Mouse Genome 430 2.0, cell type comparison

overall_design: Total RNA were extracted from two independent lines of wild type and RBP2 primary MEFs at passage 3 and analyzed for gene expression profiles using Affymetrix platform.

first: Robert

last: Klose

first: Zuzana

last: Tothova

first: Kenichi

last: Yamane

first: Hediye

last: Erdjument-Bromage

first: Paul

last: Tempst

first: Dwight

last: Gilliland

first: Yi

last: Zhang

first: William

last: Kaelin