title: Ovarian Transcript Expression in Newborn Mouse

first: Aleksandar

last: Rajkovic

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
Microarray analysis of normal newborn ovarian transcript levels, for use in comparison to array based studies of differential expression in mouse knockout models.
Keywords: Genetic Modification

overall_design: Newborn ovaries were pooled separately from wild type  animals and total RNA isolated using RNeasy mini kit (Qiagen, CA). Newborn ovaries were collected within 12 hours of delivery. Animal experimentation was approved by the Institutional Animal Care and Use Committee of Baylor College of Medicine. Three independently pooled RNA samples from wild type used to generate biotinylated cRNA. Biotinylated cRNA was hybridized to GeneChip Mouse Expression Set 430 2.0 (Affymetrix, Inc.). Since three independent experiments were performed from three independent pools of wild type RNA, signal intensities for particular genes were averaged between the three chips.

first: Youngsok

last: Choi

first: Yingying

last: Qin

last: Ballow

first: Stephanie

last: Pangas


title: Identifying gene expression changes in adipose tissue of lipodystrophic mice

status: Public on Sep 22 2007

city: Bar Harbor

first: Yaacov

last: Barak

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

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

overall_design: Refer to individual Series

first: Kathy

middle: J

last: Snow


title: Expression changes in intestinal crypts upon deletion of beta-catenin

status: Public on Sep 24 2007

city: Epalinges

first: Joerg

last: Huelsken

address: Ch. des Boveresses 155

country: Switzerland

institute: ISREC

summary:
The Wnt signaling pathway is deregulated in over 90% of human colorectal cancers. β Catenin, the central signal transducer of the Wnt pathway, can directly modulate gene expression by interacting with transcription factors of the TCF/LEF-family. In the present study we investigate the role of Wnt signaling in the homeostasis of intestinal epithelium using tissue-specific, inducible beta-catenin gene ablation in adult mice. Block of Wnt/beta-catenin signaling resulted in rapid loss of transient-amplifying cells and crypt structures. Importantly, intestinal stem cells were induced to terminally differentiate upon deletion of beta-catenin resulting in a complete block of intestinal homeostasis and fatal loss of intestinal function. Transcriptional profiling of mutant crypt mRNA isolated by laser capture micro dissection confirmed those observations and allowed to identify genes potentially responsible for the functional preservation of intestinal stem cells.
Keywords: genetic modification

overall_design: laser capture microdissection of intestinal crypts, control vs. beta-catenin mutant (2days after induction of deletion by tamoxifen), two rounds of amplification of mRNA

first: Tea

last: Fevr

first: Fabio

last: Parisi

first: Felix

last: Naef


title: Pparg<ldi/+> white Adipose Tissue expression differentials

summary:
Identifying gene expression changes in adipose tissue of lipodystrophic Pparg<ldi/+> targeted mice
Keywords: Genetic modification

overall_design: RNA from epididymal white adipose pads of three 10-week-old Pparg<ldi/+> males and three litter-matched WT controls was analyzed by MOE430v2.0 GeneChip™ arrays, one mouse per array.


title: HOXB4 target genes in ES cell-derived embryoid bodies (EBs)

status: Public on Sep 19 2007

city: Oeiras

first: Moises

last: Mallo

address: Rua da Quinta Grande 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

summary:
To unravel the molecular mechanism by which HOXB4 promotes the expansion of early hematopoietic progenitors within differentiating ES cells, we analzed the gene expression profiles of embryoid bodies (EBs) in which transcription of HOXB4 had been induced or not induced. A substantial number of the identified HOXB4 target genes are involved in signaling pathways important for controlling self-renewal, maintenance and differentiation of stem cells. Furthermore, we demonstrate that HOXB4 activity and FGF-signaling are intertwined. HOXB4-mediated expansion of ES cell-derived early progenitors was enhanced by specific and complete inhibition of FGF-receptors. In contrast, the expanding activity of HOXB4 on hematopoietic progenitors in day4-6 embryoid bodies was blunted in the presence of basic FGF (FGF2) indicating a dominant negative effect of FGF-signaling on the earliest hematopoietic cells. Taken together, we show that modulation of FGF signaling is an essential feature of HOXB4 activity in the context of embryonic hematopoiesis.
Keywords: plus/minus induction of HOXB4 gene expression by treatment with doxycycline (Dox)

overall_design:
The Hoxb4i ES cell line (Kyba et al. 2002, Cell 109:29-37) contains an integrated “tet-on” cassette that allows induction of HOXB4 expression upon treatment with doxycycline. These ES cells can be used to produce hematopoietic cells through the formation of embryoid bodies (EBs). Hematopoiesis starts in these EBs at day 4 and the differentiation into hematopoietic fates can be quantified by colony assays on methyl-cellulose using cells dissociated from EBs at day 6 of incubation. The induction of HOXB4 by incubation with doxycycline increases the production of hematopoietic progenitors within EBs by day 6. Using this specific ES cell line, we compared the transcriptome between embryoid bodies (EBs) in which transcription of HOXB4 had been induced or not induced from day 4 to day 6 (48hours).
Biological replicates: 3

first: Ana-Cristina

last: Santos

first: Ana

last: Ribeiro


title: Evaluation of murine mast cells derived exosomal RNA versus their parental cells MC/9.

status: Public on Sep 05 2007

city: Gothenburg

first: Hadi

last: Valadi

address: Guldhedsgatan 10A

department: Dept. of Rheumatology and Inflammation Research

country: Sweden

institute: University of Gothenburg

summary:
Exosomes are vesicles of endocytic origin released by many types of cells into the extracellular environment. In an attempt to further examine the exosome-mediated cellular communication, we show that exosomes from a mouse mast cell line (MC/9), exosomes from primary bone marrow derived mast cells, and exosomes from a human mast cell line (HMC-1) contain RNA but not DNA.
Microarray assessments of exosome-derived RNA revealed that these vesicles contain mRNA from approximately 1200 genes, many of which are unique and not present in the cytoplasmic RNA pool in the donor cell.
Keywords: Exosomal RNA versus their parental cells, MC/9

overall_design: Exosomes were prepared from the supernatant of MC/9 cells by differential centrifugations and filtration. RNA was isolated from the exosomes and their parental cells using Trizo. The microarray experiments were performed by SweGene (www.swegene.org/) according to Affymetrix microarray DNA chip analysis. The experiment was performed in quadruple samples. ExoRNA1, ExoRNA2, ExoRNA3, and ExoRNA4 for the exosomes samples and Mast_cells1, Mast_cells2, Mast_cells3, and Mast_cells4 for the MC/9 cells.

first: Jan

last: Lötvall


title: Age-related transcriptional changes and the effect of dietary supplementation of vitamin E in the mouse brain

status: Public on Aug 31 2007

city: Boulder

first: Sang-Kyu

last: Park

state: CO

department: IBG

institute: University of Colorado at Boulder

summary:
We established the transcriptional profile of brain aging and examine the global effects of vitamin E supplementation on age-related alterations in expression in the aged mouse brain.
Keywords: expression profiling

overall_design: Gene expression profiles were obtained from the neocortex tissues of 5-month-old controls, 30-month-old controls and 30-month old B6C3F1 mice with middle age-onset supplementation of α-tocopherol or a mixture of α- and γ-tocopherol (500mg/kg of each tocopherol).

first: Grier

middle: P

last: Page

first: Kyoungmi

last: Kim

first: David

middle: B

last: Allison

first: Mohsen

last: Meydani

first: Richard

last: Weindruch

first: Tomas

middle: A

last: Prolla


title: Expression data from hAT1R transgenic and non-transgenic C57BL/6 mouse heart tissue

status: Public on Sep 15 2007

city: Cleveland

first: Venkata Suresh Kumar

last: surampudi

state: OH

address: 9500 Euclid Avenue

department: Molecular Cardiology

institute: Lerner Research Institute

summary:
Excessive Ang II signaling through AT1R is shown to cause pathological hypertrophy. Underlying molecular mechanisms are not yet known and expression studies are not available so far.
To understand hAT1R signaling, cardiac tissue, from C57BL/6 mouse over expressing hAT1R signaling, is subjected to genomic microarray studies. This data compared with the data from healthy, non transgenic C57BL/6 mouse.
Keywords: disease state analysis

overall_design: Mouse heart tissues are collected from age matched and gender matched samples. RNA is isolated using commercial kits as per the manufacturer's instructions and subjected to quality checks before experiments. cRNA preparation, pre hybridization, hybridization and post hybridization were carried out Genomics core facility, Case western reserve university. 3 chips for each category were  taken for present analysis.

first: Venkata

middle: S

last: Kumar

first: Yasser

last: Saad

first: Sadashiva

last: Karnik


title: Cardiac differentiation of embryonic stem cells recapitulates embryonic cardiac development.

status: Public on Aug 30 2007

city: Baltimore

first: Nicolas

last: Christoforou

state: MD

address: 733 North Broadway

department: ICE/ OBGYN

institute: Johns Hopkins Medical Institutions

summary:
Mouse embryonic stem cells can differentiate in vitro into spontaneously contracting cardiomyocytes. The main objective of this study was to investigate cardiogenesis in cultures of differentiating embryonic stem cells (ESCs) and to determine how closely it mimics in vivo cardiac development. We identified and isolated a population of cardiac progenitor cells (CPCs) through the use of a reporter DNA construct that allowed the expression of a selectable marker under the control of the Nkx2.5 enhancer. We proceeded to characterize these CPCs by examining their capacity to differentiate into cardiomyocytes and to proliferate. We then performed a large-scale temporal microarray expression analysis in order to identify genes that are uniquely upregulated or downregulated in the CPC population. We determined that the transcriptional profile of the mESC derived CPCs was consistent with pathways known to be active during embryonic cardiac development. We conclude that in vitro differentiation of mESCs recapitulates the early steps of mouse cardiac development.
Keywords: embryonic stem cell, differentiation, cardiac progenitor, cardiogenesis

overall_design:
Cell culture and cell differentiation
Mouse embryonic stem cells (mESCs) were maintained undifferentiated by culturing on a feeder layer of mitomycin C pretreated primary mouse embryonic fibroblasts (PMEFs, Specialty Media, cat.# PMEF-H) at 37oC, 90% humidity and 5% CO2. The cell line used was the mESC D3 (passage #12-18). The basic culture medium was comprised of DMEM (Invitrogen, cat.# 11965-092), heat inactivated (56oC for 30 minutes) fetal bovine serum (Hyclone, cat#. S11550, 15%), Glutamax (Invitrogen, cat.# 35050-065, 1%), non-essential amino acids (Invitrogen, cat.# 11140-050, 1%), sodium pyruvate (Invitrogen, cat.# 11360-070, 1%), ?-mercaptoethanol (Sigma, cat.# M7522, 0.1mM), gentamicin (Cambrex, cat.# 17-518, 25?g/ml) and ESGRO leukemia inhibitory factor (Chemicon, cat.# ESG1106, 1000units/ml). Prior to initiation of differentiation The PMEF feeder layer was subtracted and the mESCs were maintained on a 0.01% gelatin pretreated plate for 24-48 hours. Differentiation through embryoid body (EB) formation was initiated by dissociating the mESCs using trypsin (Invitrogen, cat#. 25300-054, 0.05%) and resuspending them in basic culture medium (without the leukemia inhibitory factor) at a final concentration of 5x104 cells/ml. The hanging droplet (HD) technique was used for EB formation. HDs were plated on the lid of H2O containing tissue culture dishes at a volume of 20?L/droplet (approximately 1000 cells/ droplet). Two days post initiation of differentiation the EBs were transferred in suspension on poly-HEMA (Sigma, cat#. P3932) treated tissue culture dishes. The plates were pretreated with poly-HEMA in order to avoid any cell attachment on the plastic. Basic culture medium was supplemented with ascorbic acid(Takahashi et al., 2003) (Sigma, cat#. A4403, 0.1mg/ml) and it was exchanged with fresh medium every 2 days during differentiation.
Transfection of mouse embryonic stem cells
	The mouse Nkx2.5 enhancer fragment #5(Lien et al., 1999) and the hsp68 minimal promoter was excised from the provided vector (XhoI/ NcoI) and inserted in front of the EGFP gene in the Bluescript vector. A vector containing the hygromycin resistance gene (hygromycin phosphotransferase) under the control of the mouse polymerase II promoter was also used in order to select for the transfected mESCs. Prior to transfection the two vectors were linearized. Undifferentiated mESCs were grown to confluency on a layer of primary embryonic fibroblasts and dissociated with trypsin. The cells were combined with the linearized DNA and electroporated (Biorad Gene Pulser Xcell, 240V/ 500?F). The cells were then replated on a fresh layer of PMEFs. Hygromycin B (Invitrogen, cat.# 10687-010, 50?g/ml) was used for 7 days after transfection for selection. Resistant colonies were picked and grown on layers of PMEFs in the presence of antibiotic. Once sufficient cells were present the clones were differentiated in order to check for the correct expression of the GFP in the cardiac areas (spontaneously contracting) of the differentiating cultures. Successful clones were further amplified and used for characterization of the GFP expressing cardiac progenitor cells.
	In order to select mESC derived cardiomyocytes for the microarray analysis experiment, a stable transgenic clone of mESCs was made that allowed the expression of the neomycin resistance gene under the control of the alpha myosin heavy chain promoter (U71441) as described by Klug et al., (Klug et al., 1996). The transgenic clone was prepared as described above.
FACS Analysis
	For determination of the CPC yield in the differentiating cells, EBs were harvested at the indicated timepoints (between days 6 and 10 of differentiation). Each sample contained approximately 100 hanging droplets on day 0 of differentiation. The EBs were washed in PBS and resuspended in 0.05% trypsin at 4oC (1/2 hour) and 37oC (10 minutes). The percentage of GFP+ cells was determined in a BD FACS Calibur (Cell Quest Pro software). Age matched EBs from untransfected mESCs were used as negative controls. Cells from the same samples were also counted.
FACS sorting
	The BD Biosciences FACSAria Cell sorting system was used to sort the GFP+ and GFP- cells between days 5 and 10 of differentiation. EBs were harvested and dissociated as described above. The cells were suspended in sorting medium (96% DMEM without phenol red, 1% fetal bovine serum, 1% Glutamax, 1% non essential amino acids, 1% sodium pyruvate, 25?g/ml gentamicin) and kept at 4oC. The cells were sorted into a fetal bovine serum rich medium (20%) in order to increase their survival. For further culture the cells were resuspended in mESC culture medium at a concentration of 5x105 cells/ml and cultured in suspension for 48 hours. The cells were then transferred on tissue culture plates for another 48 hours. For RNA isolation the cells were spun down and washed in PBS before the RNA isolation procedure.
	To assay their proliferation capacity, GFP+ CPCs were FACS sorted on day 5 of differentiation. Cells were reaggregated in suspension (5x105 cells/ ml) in the presence of mouse recombinant Igf1 (Chemicon, Cat.# GF121, 100ng/ml) for 14 days. Cell aggregates were fixed and stained for the colocalization of the antigens: Nkx2-5 and Ki67 or Pcna. The same ICC reagents were used as described above.
GeneChip microarray hybridization
	Total RNA for the microarray expression analysis was isolated from FACS sorted cells (GFP+ and GFP-) on days 5, 6, 7, and 8 of differentiation as described above. Two separate differentiation batches were prepared for the sake of data reproducibility. Total RNA was also isolated from terminally differentiated mESC derived genetically selected cardiomyocytes 3 weeks post initiation of differentiation. The GeneChip® two cycle target labeling kit (Affymetrix, cat.# 900494) was used to convert 100ng of total RNA to biotinylated labeled cRNA. This was then hybridized to the Affymetrix murine MOE430 2.0 genome GeneChip® array (Affymetrix, cat.# 900496). Fluorescence was detected using the Affymetrix GS3000 GeneArray scanner and image analysis for each chip was done through the GeneChip® operating system software from Affymetrix (GCOS1.3) using the standard default settings.
Microarray data analysis
To estimate the gene expression signals, data analysis was conducted on the chips’ CEL file probe signal values at the Affymetrix probe pair (perfect match (PM) probe and mismatch (MM) probe) level, using the statistical technique RMA (Robust Multiarray Analysis) (Irizarry et al., 2003) with the bioconductor package Affy. The data normalization procedure utilized the quantile normalization method (Bolstad et al., 2003) to reduce the obscuring variation between microarrays, which might be introduced during the processes of sample preparation, manufacture, fluorescence labeling, hybridization and/or scanning.
The Spotfire DecisionSite software package was used for the identification of uniquely upregulated or downregulated (at least 1.5 times increase or decrease in the expression value) probe sets in the CPC population when compared to the rest of the cells in the differentiating EBs. Probe sets that were considered unique for the CPC population were found to be commonly upregulated or downregulated during all four days of analysis. Probe sets that exhibited an increasing or decreasing pattern of expression with at least 1.5 times increase or decrease in the expression values of day 5 CPCs and day 8 CPCs were also reported. Probe sets of the CPC population that exhibited upregulation or downregulation by at least 1.5 times when compared to the mESC derived cardiomyocytes were also reported. The final analysis included probe sets that exhibited a different temporal pattern of expression in the CPC population when compared to the rest of the cells along the four days of differentiation. Specifically in order to identify these probe sets gene expression curve over time was modeled flexibly

first: Christine

middle: M

last: Hill

first: Chunfa

last: Jie

first: John

middle: D

last: Gearhart


title: Age-related transcriptional changes and the effect of dietary supplementation of vitamin E in the mouse heart and brain


title: Differential gene expression in placentae (E10.5) from adra2bKO and adra2bWT mice

city: Freiburg

first: Ralf

last: Gilsbach

address: Albertstr. 25

country: Germany

institute: Institute of Pharmacology

summary:
alpha2-adrenoceptors are essential presynaptic regulators of norepinephrine release from sympathetic nerves. Previous studies in mice with targeted deletions in the three alpha2-adrenoceptor genes have indicated that these receptors are essential for embryonic development. In the present study, we searched for the alpha2-adrenoceptor subtype(s) involved in placental development and its molecular mechanism using mice carrying targeted deletions in alpha2-adrenoceptor genes.
Congenic alpha2B-adrenoceptor-deficient mice (Adra2b-/-) developed a defect in fetal and maternal vessel formation in the placenta labyrinth at embryonic day E10.5. This defect was accompanied by reduced endothelial cell proliferation and decreased ERK1/2 phosphorylation levels in Adra2b-/- as compared with Adra2b+/+ placenta. Microarray analysis of wild-type and mutant placentae (maternal genotype Adra2b+/-) revealed 179 genes which were significantly up- or downregulated >1.5-fold in alpha2B-deficient placenta. The type 1 receptor for vascular endothelial growth factor (Flt1), which is coexpressed with alpha2B-adrenoceptors in spongiotrophoblast and giant cells of the placenta, was found to be 2.3-fold upregulated in alpha2B-deficient placenta. Neutralization of Flt1 and its soluble splice variant sFlt1 by a specific antibody in vivo prevented the vascular defect in alpha2B-deficient placenta at E10.5. Thus, alpha2B-adrenoceptors are essential to suppress antiangiogenic (s)Flt1 in spongiotrophoblasts to control the coordinated formation of a vascular labyrinth of fetal and maternal blood vessels in the murine placenta during development.
Keywords: Comparative expression profiling

overall_design: Comparative transcriptome analysis was determined using the GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA, USA). Six microarrays from three wild-type and three adra2b deficient mice were performed.

first: Verena

last: Muthig

first: Tomi

last: Ivacevic

first: Lutz

last: Hein


title: Transcriptional profiling of growth plate chondrocyte differentiation yields insight into endochondral ossification

status: Public on Sep 01 2007

city: London

first: Claudine

last: James

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

state: Ontario

address: 1151 Richmond Street, Suite 2

department: Physiology and Pharmacology

country: Canada

institute: University of Western Ontario

summary:
A variety of cell cultures models and in vivo approaches have been used to study gene expression during chondrocyte differentiation.   The extent to which the in vitro models reflect bona fide gene regulation in the growth plate has not been quantified.  In addition, studies that evaluate global gene expression changes among different growth plate zones are limited. To address these issues, we completed a microarray screen of three growth plate zones derived from manually segmented embryonic mouse tibiae.  Classification of genes differentially expressed between each respective growth plate zone, functional categorization as well as characterization of gene expression patterns, cytogenetic loci, signaling pathways and functional motifs confirmed documented data and pointed to novel aspects of chondrocyte differentiation.  Parallel comparisons of the microdissected tibiae data set to our previously completed micromass culture screen further corroborated the suitability of micromass cultures for modeling gene expression in chondrocyte development. The micromass culture system demonstrated striking similarities to the in vivo microdissected tibiae screen; however, the micromass system was unable to accurately distinguish gene expression differences in the hypertrophic and mineralized zones of the growth plate.  These studies will allow us to better understand zone-specific gene expression patterns in the growth plate.  Ultimately, this work will help define both the genomic context in which genes are expressed in the long bones and the extent to which the micromass culture system is able to recapitulate chondrocyte development in endochondral ossification.
Keywords: Growth plate microdissection

overall_design:
Tibiae from 15.5 day old mouse embryos were isolated and partitioned into three distinct zones.  Total RNA was isolated from each segment and the individual segments pooled within a litter.
Samples were hybridized to Affymetrix MOE 430 2.0 mouse chips for analysis.  Four independent trials were executed for each zone.

Number of time points: 1
Number of treatments: 0
Number of Samples: 4 replicates per zone
Affymetrix chip: MOE 430 2.0
Tissue or origin: Tibiae
Species E15.5 mice
Samples: Total RNA

first: Lee-Anne

last: Stanton

first: Hanga

last: Agoston

middle: G

first: T

last: Underhill

first: Frank

last: Beier


title: aP2-nSREBP1c_white_Adipose_Tissue_expression_differentials

first: Yaacov

last: Barak

summary:
Identifying gene expression changes in adipose tissue of lipodystrophic aP2-nSREBP1c trangenic mice
Keywords: Genetic modification

overall_design: RNA from epididymal white adipose pads of three 10-week-old aP2-nSREBP1c transgenic males and three litter-matched WT controls was analyzed by MOE430v2.0 GeneChip™ arrays, one mouse per array.

first: Kathy

last: Snow


title: transcription factor PlagL2 regulates steps in chylomicron metabolism

city: boston

first: zhao

last: chen

state: MA

address: 1 jimmy fund way

institute: Dana Farber Cancer Institute

summary:
Enterocytes assemble dietary lipids into chylomicron particles that are taken up by intestinal lacteal vessels and peripheral tissues. Although chylomicrons are known to assemble in part within membrane secretory pathways, the modifications required for efficient vascular uptake are unknown. We report that the transcription factor Pleomorphic adenoma gene-like 2 (PLAGL2) is essential for this aspect of dietary lipid metabolism. PlagL2-/- mice die from post-natal wasting owing to failure of fat absorption. Lipids modified in the absence of PlagL2 exit from enterocytes but fail to enter interstitial lacteal vessels. Dysregulation of enterocyte genes closely linked to intracellular membrane transport identified candidate regulators of critical steps in chylomicron assembly. PlagL2 thus regulates essential and poorly understood aspects of dietary lipid absorption and its deficiency represents an authentic animal model with implications for amelioration of obesity or the metabolic syndrome.
Keywords: gene expression profiling analysis

overall_design: Total RNA was extracted from 4 knockout and 4 wild-type mouse small intestines at 18.5 dpc using the Macherey-Nagel Nucleospin kit. cRNA synthesis and labeling, hybridization to Affymetrix (Santa Clara, CA) MOE430 2.0 expression arrays, and data acquisition occurred on the Affymetrix GeneChip Instrument System.

first: Frederik

last: Van Dyck

first: Caroline

middle: V

last: Braem

first: Zhao

last: Chen

first: Jeron

last: Declercq

first: Rob

last: Deckers

first: Byeong-Moo

last: Kim

first: Susumu

last: Ito

first: Michele

middle: K

last: Wu

first: David

middle: E

last: Cohen

first: Mieke

last: Dewerchin

first: Rita

last: Derua

first: Etienne

last: Waelkens

first: Laurence

last: Fiette

first: Anton

last: Roebroek

first: Frans

last: Schuit

first: Wim

last: Van de Ven

first: Ramesh

last: Shivdasani


title: Comparative analysis of gene expression in C57BL/6J and DBA/2J aging lungs.

first: vikas

last: misra

address: 615 N. Wolfe street, E6609

department: Environmental health sciences

institute: Johns Hopkins University School of public health

summary:
We hypothesize that gene expression in the aging lungs of these two strains of mice are divergent thus contributing to the disparity in the phenotypes. More specifically, (1) Aging DBA/2J mice compared to aging C57BL/6  mice are known to be accelerated in their lung physiology and morphometry; (2) C57BL/6J are known to have longer natural longevity than DBA/2J mice. In order to test these hypotheses at the gene expression level, we utilized microarray analysis to examine transcriptional differences between aging lungs of both strains of mice.
Keywords: comparative expression profiling

overall_design: This study utilizes microarray analysis to test these hypotheses. Three sets of lungs were harvested from both strains at each time point (C57BL/6J: 2, 18, AND 26 mos; DBA/2J: 2 and 18 mos).  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: Vikas

last: Misra

first: Hannah

last: Lee

first: Anju

last: Singh

first: Kewu

last: Huang

first: Rajesh

last: Thimmulappa

first: Wayne

last: Mitzner

first: Shyam

last: Biswal

first: Clarke

last: Tankersley


title: Expression of the human Cathepsin L inhibitor hurpin in mice: skin alterations and increased carcinogenesis.

status: Public on Aug 18 2007

city: Duesseldorf

first: Birgit

last: Andree

address: Moorenstr. 5

institute: BMFZ

summary:
Aim of this study was to identify gene expression differences in the skin of hurpin (=headpin=serpinB13) transgenic mice in comparison to wildtype mice.
Keywords: genetic modification

overall_design:
Comparison of 4 transgenic mice with 3 wildtype mice. One wildtye sample was used two times.
Age: 8 month.
Gender: mixed (male and female)

first: Markus

last: Walz


title: Gene Expression and Biological Processes Influenced By Deletion of Stat3 in pulmonary Alveolar Type II Cells

status: Public on Aug 24 2007

city: Cincinnati

first: Yan

last: Xu

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary:
Deletion of Stat3 induced genes influencing protein metabolism, transport, chemotaxis and apoptosis and decreased the expression of genes mediating lipid synthesis and metabolism. Srebf1 and 2, key regulators of fatty acid and steroid biosynthesis, were decreased in Stat3D/D mice. Stat3 influenced both pro- and anti-apoptotic pathways, regulating and maintaining the balance between a subset of pro- and anti-apoptotic genes that determine cell death or survival. Akt, a known target of Stat3, participates in many Stat3 mediated pathways including Jak-Stat signaling, apoptosis, the MAPK signaling, cholesterol and fatty acid biosynthesis. Deletion of Stat3 from type II epithelial cells altered the expression of genes regulating diverse cellular processes, including cell growth and apoptosis, lipid biosynthesis and metabolism. Stat3 regulates cell formation through a complex regulatory network that likely enhances alveolar epithelial cell survival and surfactant/lipid synthesis, necessary for the protection of the lung during injury.
Keywords: genotype comparison

overall_design: To better understand the roles and molecular mechanisms by which Stat3 influences gene expression in lung, the effect of cell-selective deletion of Stat3 (Stat3D/D) on genome wide mRNA expression profiles was determined in murine type II alveolar epithelial cells.  Differentially expressed genes were identified from Affymetrix Murine GeneChips analysis and subjected to gene ontology classification promoter analysis, pathway mapping and literature mining.

first: Machiko

last: Ikegami

first: Yanhua

last: Wang

first: Yohei

last: Matsuzaki

first: Jeffrey

last: Whitsett


title: Heritability of alternative splicing in the human genome

status: Public on Aug 08 2007

city: Montreal

first: Tony

last: Kwan

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

summary:
Alternative pre-mRNA splicing increases proteomic diversity and provides a potential mechanism underlying both phenotypic diversity and susceptibility to genetic disorders in human populations. To investigate the variation in splicing among humans on a genomewide scale, we use a comprehensive exon-targeted microarray to examine alternative splicing in lymphoblasts derived from the CEPH HapMap population. We show the identification of transcripts containing annotated and novel sequence verified exon skipping, intron retention, and cryptic splice site usage that are specific between individuals.
Using family-based linkage analysis, we demonstrate Mendelian inheritance and segregation of specific splice isoforms with regulatory haplotypes for three genes. Allelic association was further used to identify individual SNPs or regulatory haplotype blocks linked to the alternative splicing event, taking advantage of the high-resolution genotype information from the CEPH HapMap population.
Keywords: Comparative genomic hybridiation within a 3 generation pedigree

overall_design: We used 14 individuals from the 3 generation CEPH/UTAH 1444 pedigree for our analysis of looking at heritability of differentially spliced exons within the family. 3 biological growths of individuals NA12739, NA12740, NA12750, and NA12751 were used and a single biological growth for the remaining 10 individuals.

first: Jacek

last: Majewski


title: Expression data from wild type and Taf7l mutant testes

status: Public on Aug 09 2007

city: Philadelphia

first: Jeremy

state: PA

address: 3800 Spruce Street

department: Animal Biology

institute: University of Pennsylvania

summary:
TFIID is a general transcription factor required for transcription of most protein-coding genes by RNA polymerase II. TAF7L is an X-linked germ cell-specific paralogue of TAF7, which is a generally expressed component of TFIID. Here we report the generation of Taf7l mutant mice by homologous recombination in embryonic stem cells using the Cre-loxP strategy. While spermatogenesis is completed in Taf7l mutant mice, the weight of Taf7l mutant testis is decreased and the amount of sperm in the epididymis is sharply reduced. Mutant epididymal sperm exhibit abnormal morphology including folded tails. Sperm motility is significantly reduced, and Taf7l mutant males are fertile with reduced litter size. Microarray profiling reveals that the abundance of six gene transcripts (including Fscn1) in Taf7l mutant testis decreases by > 2-fold. In particular, FSCN1 is an F-action-bundling protein and thus may be critical for normal sperm morphology and sperm motility. Although deficiency of Taf7l may be compensated in part by Taf7, Taf7l has apparently evolved new specialized functions in the gene-selective transcription in male germ-cell differentiation. Our mouse studies suggest that mutations in human TAF7L gene might be implicated in X-linked oligozoospermia in men.
Keywords: genetic modification

overall_design: Mice on C57BL/6J strain background were selected. Testes from Taf7l mutant and wild type littermates at 8-weeks old were dissected.

first: Yong

last: Cheng

first: Mariano

last: Buffone

first: Martin

last: Kouadio

first: Mary

last: Goodheart

first: David

middle: C

last: Page

first: George

middle: L

last: Gerton

first: Irwin

last: Davidson


title: Transcriptional Profiling of the Megabladder Mouse - A Unique Model of Bladder Dysmorphogenesis

city: Columbus

first: Kirk

last: McHugh

address: 700 Children's Drive

department: Cell & Developmental Biology

institute: Columbus Children's Hospital

summary:
Recent studies in our lab have identified a mutant mouse model of obstructive nephropathy designated mgb for megabladder. Homozygotic mgb mice (mgb-/-) develop lower urinary tract obstruction in utero due to a lack of bladder smooth muscle differentiation. This defect is the result of a random transgene insertion into chromosome 16 followed by a translocation of this fragment into chromosome 11. In an effort to identify potential gene targets affected in mgb mice, we performed transcriptional profiling on embryonic day 15 (E15) mgb-/- bladders using both a Chromosome 11/16 Custom GeneChip Array and the Affymetrix Mouse Genome 430 2.0 GeneChip. This analysis identified no definitive mis-expressed gene targets on chromosome 11. In contrast, mgb-/- mice significantly over-expressed a cluster of gene products located on the translocated fragment of chromosome 16 including urotensin II-related peptide (Urp), which was shown to be preferentially over-expressed in developing mgb-/- bladders. Immunohistochemical studies indicated that the spatial distribution of Urp was altered in mgb-/- bladders, while biochemical studies suggested a potential role for Urp in modifying smooth muscle cell phenotype in vitro. Pathway analysis of mgb microarray data showed dysregulation of at least 60 gene products associated with the differentiation of smooth muscle. In conclusion, the results of this study indicate that the molecular pathways controlling normal smooth muscle development are severely altered in mgb-/- bladders, and provide the first evidence that Urp may play a critical role in bladder smooth muscle development.
Keywords: mgb mutant bladders

overall_design: Gene expression profiling was performed on two separate study groups. First, total cellular RNA was isolated from wildtype (n=2; 1 female/1 male), mgb+/- (n=2; 1 female/1 male), and mgb-/- (n=2; 1 female/1 male) E15 whole embryos. Second, total cellular RNA was isolated from the bladders of E15 wildtype (n=7; 3 female/4 male), mgb+/- mice (n=7; 3 female/4 male), and mgb-/- mice (n=11; 7 females/4 males).

first: Sunita

last: Singh

first: Melissa

last: Robinson

first: Ihab

last: Ismail

first: Monalee

last: Saha

first: Herbert

last: Auer

first: Karl

last: Kornacher

first: Michael

first: Carlton

last: Bates


title: Gene expression in Wip1+/+ or -/- MEFs after gamma radiation

city: Houston

first: Ou

last: Ma

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

summary:
Assessment of p53 targets by gene expression array analysis in irradiated and nonirradiated Wip1+/+ and Wip1-/- MEFs.
Keywords: response to gamma radiation

overall_design:
mRNA from each set of cells harvested four hours after IR (5 Gy) was
used for gene expression microarray analysis of p53 target genes using the Affymetrix Mouse Genome 430 2.0 Chips.

first: Xiongbin

last: Lu

first: Lawrence

last: Donehower


title: Gene expression data from sorted IL-7Rhi/lo effector CD8 T cells on day 6/7 after LCMV armstrong infection

status: Public on Aug 23 2007

city: New Haven

first: Susan

last: Kaech

state: CT

address: 300 Cedar St, TAC S641B

institute: Yale University

summary:
At the peak of the CD8 T cell response to acture viral and bacterial infections, expression of the Interleukin-7 Receptor (IL-7R) marks Memory Precursor Effector CD8 T Cells (MPECs) from other Short-Lived Effector CD8 T cells (SLECs), which are IL-7Rlo. This study was designed to determine the gene expression differences between these two subsets of effector CD8 T cells.
Keywords: expression comparison

overall_design: This study compared IL-7Rhi and IL-7Rlo LCMV-specific P14 Transgenic CD8 T cells, sorted from LCMV armstrong infected recipient mice 6/7 days after infection. Data includes 3 independent replicates for the IL-7Rhi and IL-7Rlo groups.

first: Nikhil

last: Joshi


title: The MicroRNA miR-124 Promotes Neuronal Differentiation by Triggering Brain-Specific Alternative Pre-mRNA Splicing

status: Public on Aug 04 2007

city: Cambridge

first: Jiangwen

last: Zhang

address: 7 Divinity Ave

department: FAS Center for Systems Biology

institute: Harvard University

summary:
Both microRNAs and alternative pre-mRNA splicing have been implicated in the development of the nervous system (NS), but functional interactions between these two pathways are poorly understood. We demonstrate that the neuron-specific microRNA miR-124a directly targets PTBP1/PTB/hnRNPI mRNA, which encodes a global repressor of alternative pre-mRNA splicing in non-neuronal cells. Among the targets of PTBP1 is a critical cassette exon in the pre-mRNA of PTBP2/nPTB/brPTB, an NS-enriched PTBP1 homolog. When this exon is skipped, PTBP2 mRNA is subject to nonsense-mediated decay. During neuronal differentiation, miR-124a reduces PTBP1 levels leading to the accumulation of correctly spliced PTBP2 mRNA and a dramatic increase in PTBP2 protein. These events culminate in the transition from non-NS to NS-specific alternative splicing patterns. We also present evidence that miR-124a plays a key role in the differentiation of progenitor cells to mature neurons. Thus, miR-124a promotes NS development at least in part by regulating an intricate network of NS-specific alternative splicing.
We used microarrays to detail the global programme of gene expression of CAD cells over-expressing miR-124a-2.
Keywords: treatment versus control

overall_design: Expression data from CAD cells transfected with plasmid expressing miR-124a-2.

first: Eugene

last: Makeyev

first: Monica

last: Carrasco

first: Tom

last: Maniatis


title: Systematic discovery and classification of ovarian fertility factors.

status: Public on Aug 02 2007

city: Dallas

first: Diego

middle: H

last: Castrillon

address: 6000 Harry Hines Blvd. NB6.126

department: Pathology

institute: U.T. Southwestern Medical Center

summary:
Female infertility syndromes are among the most prevalent chronic health disorders in women, but their molecular basis remains unknown because of the complexity of oogenesis and uncertainty regarding the number and identity of ovarian factors controlling the assembly, preservation, and maturation of ovarian follicles. To systematically discover such ovarian fertility factors en masse, we employed a mouse model (Foxo3), where follicles are assembled normally but are then synchronously activated. Gene expression profiling of mutant and normal ovaries led to the identification a surprisingly large set of ovarian factors. The set included the vast majority of known ovarian factors, many of which when mutated produce female sterility phenotypes, but most were novel. Subsequent analyses revealed novel classes of ovarian factors and significant overrpresentation on the X chromosome, among other insights into the general properties of oogenesis genes and their patterns of expression.
Keywords: time course, ovarian fertility factors, Foxo3 mutant

overall_design: Total ovarian RNA from +/+ and -/- ovaries at PND1, 3, 7, and 14 (n=3 replicates per timepoint and genotype, a total of 24 microarrays) was subjected to linear RNA amplification and hybridized to Affymetrix 430 2.0 mouse whole-genome microarrays, which interrogate >39K transcripts including the vast majority of protein-coding genes. We also profiled 14 somatic tissues. Additionally, to provide more refined views of gene expression, we profiled adult ovaries, adult testis, KitlSl/KitlSl-d testis (devoid of germ cells except for rare spermatogonia) (Shinohara et al., 2000), ES cells, laser-capture microdissected (LCM) primary oocytes, LCM somatic cells (granulosa cells + surrounding stroma), superovulated unfertilized eggs, cumulus granulosa cells, and E11 Foxo3 +/+ and -/- embryos. Each array data set was independently normalized by global median scaling, and the signal strengths were averaged for those samples for which replicates were available (PND1-14).

first: Teresa

last: Gallardo

first: George

last: John

first: Lane

last: Shirley

first: Cristina

last: Contreras

first: Esra

last: Akbay

first: Marshall

last: Haynie

first: Samuel

last: Ward

first: Meredith

last: Schidler


title: Expression data from high-fat diet feeded WT and LIGHT Tg mice

status: Public on Aug 03 2007

city: Chicago

first: Yugang

last: Wang

state: IL

address: 5841 S. Maryland

institute: University of Chicago

summary:
effect of over-expression LIGHT on T cells for the liver gene expression
We used microarrays to detail the global programme of gene expression underlying WT and LIGHT Tg liver
Keywords: genetic difference

overall_design: mice were selected at 4-8 wks old after 2 weeks HFD feeding for RNA extraction and hybridization on Affymetrix microarrays. The total liver were used.

first: Yang

middle: X

last: Fu

first: Jame

last: Lo

first: Alexei

last: Tumannov


title: Response of murine splenocytes to infection with wild type or virB mutant Brucella strains

city: Davis

first: Renee

last: Tsolis

state: CA

address: One Shields Avenue

department: Medical Microbiology & Immunology

institute: University of California at Davis

summary:
The virB operon, encoding a Type IV secretion system (T4SS), is essential for intracellular survival and persistent infection of Brucella spp. To better understand the role of the T4SS in evading host defense mechanisms and establishing chronic infection, we compared transcriptional profiles of the host response to infection with wild type Brucella strains and strains that fail to express the virB genes. Analysis of host gene expression profiles three days after inoculation with wild type Brucella strains revealed an inflammatory response dominated by interferon-induced genes. This analysis found that not only the type II but also type I interferon pathway was elicited by Brucella infection. Real time RT-PCR showed that a group of genes from these pathways was induced by day 3 post-infection and declined to baseline levels by day 7. In contrast, neither of the two virB mutant strains elicited expression of interferon-induced genes, demonstrating that the T4SS was required to trigger an inflammatory response early during infection.
Keywords: analysis of transcriptional responses induced by infection

overall_design: We performed microarray-based expression analyses of splenocytes from mice infected with two virulent strains (B. abortus 2308 and B. melitensis 16M), and two different B. abortus virB mutants, whose virB operon was either disrupted (BA41) or completely deleted (ADH4.2), to better understand the contribution of the T4SS in establishing infection of the reticuloendothelial system. 3 days after infection of mice, spleens were excised for RNA extraction. For each bacterial strain, RNA from 5 mice was pooled and reverse transcribed for hybridization to an array. Each experiment was performed in duplicate.

first: Christelle

last: Roux


title: Transcriptional regulation by Errb (Nr3b2) in stria vascularis

status: Public on Aug 01 2007

city: Stanford

first: Jichao

last: Chen

address: 279 Campus Drive, B461

institute: Stanford University

summary:
Transcriptional profiles were compared in microdissected lateral walls of the inner ears from Errb mutant mice and wild type littermate controls.  The goal is to identify transcriptional targets of Errb and candidate genes for inner ear diseases.
Keywords: genetic mutant analysis

overall_design: Errb mutant mice were generated by conditional knock-out strategy.  Inner ears from 10 mice were pooled for each sample and 3 replicates of wild type and mutant samples were analyzed.

first: Jeremy

last: Nathans


title: Offsprings of crosses between hypercholesterolemic and normocholesterolemic parents LUMC-HKG-ApoE-Atherosclerosis

city: Leiden

first: Anja

last: Schiel

address: Einthovenweg 20

department: Human Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

summary:
Enhanced prenatal fatty streak formation in human fetuses has been associated with maternal hypercholesterolemia. However, the possible roles of maternal genetic background and in utero environment on development of atherosclerosis in adult life have not been unraveled. We generated genetically identical heterozygous apoE-deficient mice offspring with a different maternal background to study the intrauterine effect of maternal genotype and associated hypercholesterolemia on the developing vascular system. As read out for increased atherosclerosis development in adult life, a constrictive collar was placed around the carotid artery to induce lesion formation. A significant increase in endothelial cell activation and damage was detected in the carotid arteries of heterozygous apoE-deficient fetuses with apoE-deficient mothers compared with offspring from wild type mothers, but no fatty streak formation was observed. Postnatally, all carotid arteries revealed normal morphology. In adult offspring with maternal apoE-deficiency, the constrictive collar resulted in severe lesion (9/10) development compared with no to only minor lesions (2/10) in offspring of wild type mothers. Microarray analysis showed no effect of maternal apoE-deficiency on gene expression in adult offspring. We conclude that maternal apoE-deficiency not only affects fetal arteries, but also increases the susceptibility for development of collar-induced atherosclerosis in adult life.
Keywords: Atheroslcersosis development

overall_design: Crossing of hypercholesterolemic female with normocholesterolemic male and vice versa, determination of susceptabilioty to atherosclerosis in offspring

first: Fanneke

last: Alkemade

first: Adriana

last: Gittenberg-de Groot

first: Conny

last: vanMunsteren

first: Louis

last: Havekes

first: Ko

last: Willems van Dijk

first: Marco

last: de Ruiter


title: E14 ES cells and Embryoid bodies

city: Berkeley

first: Alex

last: Nord

address: 1 Cyclotron Road, Mail Stop 84-171

department: Genomics Divsion

institute: Lawrence Berkeley National Laboratory

summary:
Gene expression in murine ES cells
Using the association of gene length and gene expression with gene-trap likelihood, we constructed spline-based regression models that characterize which genes are susceptible and which genes are resistant to gene-trapping techniques.
Keywords: mouse E14 embryonic stem cells

overall_design: We used E14 murine ES celss to determine genomewide expression characteristics

first: Bruce

last: Conklin


title: Identification of novel genes expressed during mouse molar tooth development by microarray gene expression analysis

status: Public on Jul 31 2007

city: Ann Arbor

first: Trevor

last: Pemberton

state: MI

address: 100 Washtenaw Ave

institute: University of Michigan

summary:
To identify genes heretofore undiscovered as critical players in the biogenesis of teeth, we have used microarray gene expression analysis of the developing mouse molar tooth (DMT) between 1 and 10 days postnatal to identify genes differentially expressed when compared to 16 control tissues (GEO accession # GSE1986).  Of the top 100 genes exhibiting increased expression in the DMT, 29 were found to have been previously associated with tooth development. Differential expression of the remaining 71 genes not previously associated with tooth development was confirmed by qRT-PCR analysis. Further analysis of seven of the latter genes by mRNA in situ hybridization found that five were specific to the developing tooth in the craniofacial region (Rspo4, Papln, Amtn, Gja1, Maf). Of the remaining two, one was found to be more widely expressed (Sp7) and the other was found to be specific to the nasal serous gland, which is close to, but distinct from, the developing tooth (Vrm).
Keywords: tooth development

overall_design: mRNA from molar teeth extracted from Swiss Webster mouse pups between 1 and 10 days post-natal was pooled, labeled, and hybridized in quadruplicate  to Affymetrix Mouse Genome Expression 430 2.0 microarrays.  This data was compared to that of 16 control tissues (GEO accession # GSE1986) to identify genes differentially expressed in the DMT mRNA.

first: Gustavo

last: Mendoza-Fandino

first: Ya-Hsuan

last: Hsu

first: Malcolm

last: Snead

first: Ruty

last: Mehrian-Shai

first: Pragna

middle: I

last: Patel


title: CD4+ T cells gene-transduced with AML1, wild type Foxp3, and a Foxp3 mutant defective in binding to AML1

city: London

first: Masahiro

last: Ono

address: 30 Guilford Street

department: Immunobiology Unit

country: United Kingdom

institute: Institute of Child Health

summary:
To clarify how Foxp3 regulates its target genes, we performed co-immunoprecipitation experiments and found that Foxp3 physically bound to AML1/Runx1 (Ono, M. et al, Nature, 2007). In this series of study, we compared gene regulations by AML1, wild type Foxp3, and a Foxp3 mutant with defective binding to AML1.
Keywords: Retroviral gene-transduction into primary CD4+ T cells

overall_design: CD4+ naive T cells were activated and retrovirally gene-transduced with either empty vector (pMCsIg), or AML1-, wild type Foxp3-, or an AML1-non binding mutant Foxp3-encoding vectors. Sixty hours after transfection, 5 x 10^6 GFP-expressing cells were sorted and total RNA was extracted. One cycle target labelling protocol was used for labelling RNA with biotin.

first: Hiroko

last: Yaguchi

first: Naganari

last: Ohkura

first: Issay

last: Kitabayashi

first: Yuko

last: Nagamura

first: Takashi

last: Nomura

first: Yoshiki

last: Miyachi

first: Toshihiko

last: Tsukada

first: Shimon

last: Sakaguchi


title: Effects of JNK on TGF-beta responses of mouse B lymphoma derived A20 cells

city: Kyoto

first: shin

last: yonehara

address: Yoshida Konoe-cho, Sakyo-ku

country: Japan

institute: Graduate School of Biostudies, Kyoto University

summary:
TGF-beta plays multiple functions in a board range of cellular responses such as proliferation, differentiation, motility and survival by activating several cellular signaling pathways, including Smads and MAP kinases (Erk, JNK and p38). In particular, TGF-beta can activate pro- or anti-apoptotic signals depending on the target cells. We found that blockage of JNK activation sensitized mouse B lymphoma derived A20 cells to TGF-beta-induced apoptosis. These results suggest that TGF-beta activate JNK to inhibit the activation of death signal that is simultaneously activated by TGF-beta.
We used microarrays to gain insight into the effects of JNK inhibition on gene expression in TGF-b-stimulated A20 cells and identified JNK-dependent TGF-beta inducible genes.
Keywords: time course

overall_design: The following six samples were prepared: untreated A20 cells (non-stimulated, DMSO): A20 cells cultured with SP600125 for 24 h (non-stimulated, SP600125):  A20 cells stimulated with TGF-beta for 12 h (TGF-beta 12 h, DMSO) and 24 h (TGF-beta 24 h, DMSO): and A20 cells stimulated with TGF-beta in the presence of SP600125 for 12 h (TGF-beta 12 h, SP600125) and 24 h (TGF-beta 24 h, SP600125), respectively. Total RNA was prepared and hybridized to the Affymetrix Mouse Genome 430 2.0 array. Genes whose expression was increased by more than 2-fold at either 12 or 24 h after TGF-beta stimulation were identified as TGF-beta inducible genes. Amongst them, we identified genes whose induction levels were reduced by more than 75% by co-treatment with the JNK inhibitor SP600125.

first: Masatoshi

last: Ohgushi

first: Takuya

last: Yamamoto

first: Eisuke

last: Nishida

first: Shin

last: Yonehara


title: R6/1 brain hemisphere time series gene expression

city: Cardiff

first: Lesley

last: Jones

address: Heath Park

department: Psychological Medicine

institute: Cardiff University School of Medicine

summary:
HD R6/1 transgenic mouse line brain hemispheres dissected.  RNA targets were created for transgenics and wildtypes at time points 18, 22 and 27 weeks.  Profiles and data analysis performed using the Bioconductor software and linear model contrasts using LIMMA on RMA probeset summarys.
Keywords: timecourse

overall_design: 18 samples extracted, 3 transgenic plus 3 littermate controls analysed at each timepoint.


title: Elucidation of the phenotypic, functional and molecular topography of a myeloerythroid progenitor cell hierarchy

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

institute: Lund University

summary:
The major myeloid blood cell lineages, including erythrocytes, platelets, granulocytes and macrophages, are generated from hematopoietic stem cells (HSC) by differentiation through a series of increasingly more committed progenitor cells. Precise phenotypic identification and functional characterization of such intermediate progenitors has important consequences for understanding fundamental differentiation processes and is clinically relevant since such events become dysregulated in various disease settings, including leukemia. While previous studies have suggested a hierarchy for myeloid differentiation involving a common progenitor through which all myeloid lineages are derived, several recent studies have suggested that such a developmental intermediate might not be an absolute requirement. Here, we evaluated the functional in vitro and in vivo potentials of a range of prospectively isolated myeloid precursors with differential expression of CD150, Endoglin and CD41. Our studies reveal a complex hierarchy of myeloerythroid progenitors with distinct and developmentally restricted lineage potentials. Global gene expression signatures of these cellular subsets revealed expression patterns consistent with their functional capacities, while hierarchical clustering analysis provides details on their lineage relationships. These data challenge existing models of hematopoietic differentiation, by suggesting that progenitors of the innate and adaptive immune system in the adult separate late, and to a large extent, following the divergence of megakaryocytic/erythroid potential.
Keywords: global gene expression profiling of prospectively isolated murine bone marrow progenitor subset by usage of affymetrix

overall_design: RNA was extracted from purified adult BM subsets using RNeasy mRNA purification kit (Qiagen). Subsequent handling was performed at the SweGene Affymetrix unit at Lund University (http://www.swegene.org/microarray). Briefly, RNA (arrays in triplicate for all progenitor fractions except for pre MegE for which 5 arrays were produced) was labeled and amplified according to AffymetrixTM; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using AffymetrixTM GeneChipTM Expression 3’amplification kit. Hybridization and washing was performed according to AffymetrixTM GeneChipTM Expression analysis technical manual. Chips were scanned using an AffymetrixTM GeneChipTM Scanner 3000 and scaled to a median intensity of 100. For subsequent analysis, probe level expression values were extracted using RMA (Irizarry et al., 2003) and subsequent analyses was performed using dChip software (http://biosun1.harvard.edu/complab/dchip/) following filtering (0.5<SD/mean<1,000).

first: Cornelis

last: Pronk

first: Derrick

last: Rossi

first: Joanne

last: Attema

first: Gudmundur

last: Logi Norddahl

first: Charles

last: Kwok Fai Chan

first: Mikael

last: Sigvardsson

first: David

last: Bryder


title: Expression data from adult laboratory mouse brain hemispheres

status: Public on Jul 30 2007

city: Orangeburg

first: Csaba

last: Vadasz

state: NY

address: 140 Old Orangeburg Road

department: Center for Neurobehavior Genetics

institute: New York University NKI

summary:
Inbred congenic strain B6.C6.132.54/Vad was created using C57BL/6ByJ background and BALB/cJ donor strains. Flanking background markers at chr. 6: 75.9 Mb (rs4226008, NCBI Mouse Build 36 / dbSNP Build 126) and 122.3 Mb (rs3023093), and limiting donor markers at 81.9 Mb (rs4226024) and at 91.8 Mb (rs3712161) defined the introgressed region. We concluded the segment size must be between 9.9 Mb and 46.4 Mb. In a Quantitative Trait Gene identification study we compared brain (without cerebellum) gene expression between progenitors and congenics. Such comparisons can facilitate identification of cis-regulated genes and to establish genetic control of a complex phenotype whose expression is associated with the introgressed chromosome segment.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
Keywords: strain comparison

overall_design: Experiments were carried out in three batches. In each batch 10 animals per strain were used. After processing each hemisphere separately, 10 hemispheres were pooled for one high-density oligonucleotide microarray (Mouse Genome 430 2.0, Affymetrix, Santa Clara, CA). For each strain 3 oligonucleotide microarrays were used (n=3). We used adult, untreated, male mice (n=30, 90 mice in toto).

first: Mariko

last: Saito


title: Folate deficiency enhances arsenic effects on ODC mouse skin gene expression

status: Public on Aug 10 2007

city: Research Triangle Park

first: Gail

last: Nelson

state: NC

address: 109 TW Alexander Dr.

institute: U.S. Environmental Protection Agency

summary:
We demonstrate that expression of key markers of keratinocyte differentiation is suppressed by exposure to sodium arsenite.  Folate deficiency exacerbates this effect.  In addition, cancer-related cell movement genes, and growth and proliferation genes are altered.  Several redox-sensitive transcription factors are implicated in mediating these gene expression changes due to arsenic treatment and folate deficiency.
Keywords: gene expression/microarray

overall_design: K6/ODC mice were maintained on either a folate deficient or folate sufficient diet and exposed to 0, 1, or 10 ppm sodium arsenite in the drinking water for 30 days.  Total RNA was isolated from skin samples and gene expression analyzed using Affymetrix Mouse 430 2.0 GeneChips.  Data from 24 samples, with four mice in each of the six treatment groups, were analyzed.

first: Gene

last: Ahlborn

first: Don

last: Delker

first: Kirk

middle: T

last: Kitchin

first: Thomas

last: O'Brien

first: Yan

last: Chen

first: Michael

last: Kohan

first: Barbara

last: Roop

first: William

middle: O

last: Ward

first: James

middle: W

last: Allen


title: Comprehensive analysis of PPARα-dependent regulation of hepatic lipid metabolism by expression profiling - 3

status: Public on Jul 24 2007

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary:
PPARα is a ligand-activated transcription factor involved in the regulation of nutrient metabolism and inflammation. Although much is already known about the function of PPARα in hepatic lipid metabolism, many PPARα-dependent pathways and genes have yet to be discovered.  In order to obtain an overview of PPARα-regulated genes relevant to lipid metabolism, and to probe for novel candidate PPARα target genes, livers from several animal studies in which PPARα was activated and/or disabled were analyzed by Affymetrix GeneChips. Numerous novel PPARα-regulated genes relevant to lipid metabolism were identified. Out of this set of genes, eight genes were singled out for study of PPARα-dependent regulation in mouse liver and in mouse, rat, and human primary hepatocytes, including thioredoxin interacting protein (Txnip), electron-transferring-flavoprotein β polypeptide (Etfb), electron-transferring-flavoprotein dehydrogenase (Etfdh), phosphatidylcholine transfer protein (Pctp), endothelial lipase (EL, Lipg), adipose triglyceride lipase (Pnpla2), hormone-sensitive lipase (Lipe), and monoglyceride lipase (Mgll). Using an in silico screening approach, one or more PPAR response elements (PPREs) were identified in each of these genes.  Since Pnpla2, Lipe, and Mgll contribute to hepatic triglyceride hydrolysis, gene regulation was studied under conditions of elevated hepatic lipids. In wild-type mice fed a high fat diet, the decrease in hepatic lipids following treatment with the PPARα agonist Wy14643 was paralleled by significant up-regulation of Pnpla2, Lipe, and Mgll, suggesting that induction of triglyceride hydrolysis may contribute to the anti-steatotic role of PPARα. Our study illustrates the power of transcriptional profiling to uncover novel PPARα-regulated genes and pathways in liver.
Keywords: identification of target genes

overall_design:
3-5 months old male pure bred wild-type (129S1/SvImJ) and PPARα-null (129S4/SvJae) mice were used.
Wild-type and PPARα-null mice fasted for 4 hours received a single dose of WY14643 (400 μl of 10 mg/ml WY14643) or vehicle and were killed 6 hours later (n=3-5 per group). Liver total RNA from biological replicates was hybridized onto Affymetrix mouse genome 430 2.0 GeneChip arrays.
Five microgram total RNA was labelled according to the ENZO-protocol, fragmented and hybridized according to Affymetrix's protocols.

first: Maryam

last: Rakhshandehroo

first: Linda

last: Sanderson

first: Merja

last: Matilainen

first: Rinke

last: Stienstra

first: Carsten

last: Carlberg

first: Philip

middle: J

last: de Groot

last: Muller

first: Sander

last: Kersten


title: Differential transcription of ip Chlamydia infected C57BL6J and DBA2J mice

status: Public on Jul 15 2007

city: Memphis

first: Lorne

middle: A

last: Rose

state: TN

address: 854 Madision Ave

department: Molecular Sciences

institute: University of Tennessee

summary:
C57BL/6J mice were 105-fold more resistant to Chlamydia psittaci infection than DBA/2J mice by LD100 determinations. Linkage analysis using BXD recombinant inbred strains revealed a single effector locus at a 1.5 Mbp region on chromosome 11 encoding a cluster of three p47GTPases (Irgb10, Igtp, and Iigp2). Western blots of infected tissue showed that Irgb10 was elevated in resistant mice and one of the two possible Iigp2 protein isoforms was preferentially expressed in susceptible mice. The BXD39 strain, susceptible at Irgb10 and resistant at Iigp2, had an intermediate phenotype, implicating the non-redundant role of these p47GTPases. C57BL/6J and DBA/2J exhibited a difference in IFNg dependent chlamydial control, which was reversible by Iigp2 siRNA knockdown. Microarrays of infected peritoneal lavage revealed >10 fold up regulation of neutrophil recruiting chemokines in susceptible mice and >100 fold increase in macrophage differentiation genes in resistant mice, indicating that susceptibility pattern involves stimulation of different inflammatory cell recruiting pathways. Massive neutrophil recruitment was seen in susceptible mice by histology and flow cytometry, and neutrophil chemokine receptor (CXCR2) knockout mice on a susceptible background survived lethal challenge confirming that neutrophil recruitment was required for susceptibility. Congenic Igtp knockout mice also susceptible at Irgb10 and Iigp2 on a resistant background recruited neutrophils and succumbed to infection. We conclude that Irgb10 and Iigp2 act together to confer differential susceptibility against murine chlamydial infection. Results indicate that these p47GTPases have cell autonomous effects, which results in vastly different inflammatory stimulation leading to either recovery or death.
Keywords: Comparative disease state analysis

overall_design: C57BL/6J and DBA2J mice (4 mice each) were infected I.p. with 10E4 IFU of Chlamydia psittaci then peritoneal lavage was collected on day 3 post infection. Cells were centrifuged then treated with Trizol for total RNA extraction.

first: Isao

last: Miyairi

first: Gerald

last: Byrne

first: Robert

last: Belland

first: Lu

last: Lu

last: Williams

first: Yanhua

last: Qu


title: Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers.

status: Public on Jul 19 2007

city: Houston

first: Scott

middle: Andrew

last: Ochsner

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Genome-wide analysis of Phgdh inactivation in murine embryonic head

status: Public on Jul 25 2007

city: Fukuoka

first: Shigeki

last: Furuya

state: Fukuoka

address: 6-10-1 Hakozaki, Higashiku

department: Bio-Architecture Center

institute: Kyushu University

summary:
D-3-Phosphoglycerate dehydrogenase (Phgdh; EC 1.1.1.95) is a necessary enzyme for de novo L-serine biosynthesis via the phosphorylated pathway. We demonstrated previously that Phgdh is expressed exclusively by neuroepithelium and radial glia in developing mouse brain and later mainly by astrocytes. Mutations in the human PHGDH gene cause serine deficiency disorders (SDD) associated with severe neurological symptoms such as congenital microcephaly, psychomotor retardation, and intractable seizures. We recently demonstrated that genetically engineered mice, in which the gene for Phgdh has been disrupted, have significantly decreased levels of serine and glycine, and exhibit malformation of brain such as microcephaly. The Phgdh null (KO) embryos exhibit lethal phenotype after gestational day 14, indicating that the phosphorylated pathway is essential for embryogenesis, especially for brain development. It is worth noting that the Phgdh knockout (KO) embryos primarily displayed microcephaly, which is the most conspicuous phenotype of patients with SDD.  Thus, Phgdh KO mice are a useful animal model for studying the effect of diminished L-serine levels on development of the central nervous system and other organs. To better understand the mechanism underlying the molecular pathogenesis of SDD, we sought to examine whether gene expression is altered in the Phgdh KO mouse model. We identify genes that have altered expression in the head of the Phgdh KO embryos using the GeneChip array. Some of the genes identified by this method belong in functional categories that are relevant to the biochemical and morphological aberrations of the Phgdh deletion.
Keywords: genetic modification

overall_design:
Total RNA samples were prepared from head tissues from 2 embryos of Phgdh knockout and littermate wild-type controls.
RNA of 4 biological replicates was hybridized to Affymetrix Mouse Genome 430 2.0 arrays. Five microgram total RNA was labelled according to the ENZO-protocol, fragmented and hybridized according to Affymetrix's protocols.

first: Kazuyuki

last: Yoshida

first: Yoshio

last: Hirabayashi


title: Uterus_Gravid_d18_WT vs. Cox-1 KO

city: Indianapolis

first: Kathleen

last: Bethin

state: IN

address: 702 Barnhill Dr.

department: Pediatrics

institute: Indiana University

summary:
Background:  Preterm birth is the leading cause of all infant mortality.  In 2004, 12.5% of all births were preterm.  In order to understand preterm labor, we must first understand normal labor.  Since many of the myometrial changes that occur during pregnancy are similar in mice and humans and mouse gestation is short, we have studied the uterine genes that change in the mouse during pregnancy.  Here, we used microarray analysis to identify uterine genes in the gravid mouse that are differentially regulated in the cyclooxygenase-1 knockout mouse model of delayed parturition.
Methods:  Gestational d18.0 uteri (n=4) were collected from pregnant wild-type and cyclooxygenase-1 knockout mice.  Part of the uterus was used for frozen sections and RNA was isolated from the remainder.  Microarray analysis was performed at the Indiana University School of Medicine Genomic Core and analyzed using the Microarray Data Portal.  Northern analysis was performed to confirm microarray data and the genes localized in the gravid uterus by in situ hybridization.
Results:  We identified 277 genes that are abnormally expressed in the gravid d18.0 cyclooxygenase-1 knockout mouse.  Nine of these genes are also regulated in the normal murine uterus during the last half of gestation.  Many of these genes are involved in the immune response, consistent with an important role of the immune system in parturition.  Expression of 4 of these genes; arginase I, IgJ, Tnfrsf9 and troponin; was confirmed by Northern analysis to be mis-regulated during pregnancy in the knockout mouse.  In situ hybridization of these genes demonstrated a similar location in the gravid wild-type and Cox-1 knockout mouse uteri.
Conclusions:  To our knowledge, this is the first work to demonstrate the uterine location of these 4 genes in the mouse during late pregnancy.  There are several putative transcription factor binding sites that are shared by many of the 9 genes identified here including; estrogen and progesterone response elements and Ets binding sites.  In summary, this work identifies 9 uterine murine genes that may play a role in parturition.  The function of these genes is consistent with an important role of the immune system in parturition.
Keywords: Comparative genomic hybridization of gravid wild-type and Cox-1 KO mouse uterus

overall_design: Gestational d18.0 uteri (n=4) were collected from pregnant wild-type and cyclooxygenase-1 knockout mice.  Part of the uterus was used for frozen sections and RNA was isolated from the remainder.  Microarray analysis (affymetrix 430 2.0) was performed at the Indiana University School of Medicine Genomic Core and analyzed using the Microarray Data Portal.  In order to reduce the number of candidate parturition-related genes identified we compared the genes identified as abnormally expressed in the Cox-1 KO uterus to the genes that we had previously identified as changing from gestational d13.5 to d19.0 in the wild-type mouse uterus.  Northern analysis was performed to confirm microarray data and the genes localized in the gravid uterus by in situ hybridization.

first: Baohui

last: Zhao

first: Deanna

last: Koon

first: Allyson

last: Curtis

first: Jessica

last: Soper


title: Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers (430)

state: TX

summary:
The ability to purify to homogeneity a population of hepatic progenitor cells from adult liver is critical for their characterization prior to any therapeutic application.  As a step in this direction, we have utilized gene profiling of a bipotential liver cell line from dpc 14 mouse embryonic liver to catalog genes expressed by liver progenitor cells.  These cells, known as Bipotential Mouse Embryonic Liver (BMEL) cells, proliferate in an undifferentiated state and are capable of differentiating into hepatocyte-like and cholangiocyte-like cells in vitro.  Upon transplantation, BMEL cells are capable of differentiating into hepatocytes and cholangiocytes in vivo.  Microarray analysis of gene expression in the 9A1 and 14B3 BMEL cell lines grown under proliferating and differentiating conditions was used to identify cell surface markers preferentially expressed in the bipotential undifferentiated state.  This analysis revealed that proliferating BMEL cells express many genes involved in cell cycle regulation whereas differentiation of BMEL cells by cell aggregation causes a switch in gene expression to functions characteristic of mature hepatocytes.  In addition, microarray data and protein analysis indicated that the Notch signaling pathway could be involved in maintaining BMEL cells in an undifferentiated stem cell state.  Using GO annotation, a list of cell surface markers preferentially expressed on undifferentiated BMEL cells was generated.  One marker, Cd24a, is specifically expressed on progenitor oval cells in livers of DDC treated animals.  We therefore consider Cd24a expression a candidate molecule for purification of hepatic progenitor cells.
Keywords: cell type comparison

overall_design: RNA was extracted from two independently isolated BMEL cell lines (9A1 and 14B3) after culture under three conditions (basal, aggregate 1 day, and aggregate 5 days).  Duplicate biological replicates were collected for each cell line:culture condition combination for a total of 12 samples.  Samples were biotin-labeled, hybridized to mouse 430 2.0 chips, and scanned according to established Affymetrix protocols.

first: S

first: H

last: Strick-Marchand

last: Venable

first: A

last: Dean

first: M

last: Wilde

last: Weiss

first: G

last: Darlington


title: Microarray of Dexamethasone-treated primary chondrocytes identifies downstream targets of glucocorticoid signalling

status: Public on Jul 04 2007

first: Claudine

last: James

address: 1151 Richmond Street, Suite 2

department: Physiology and Pharmacology

institute: University of Western Ontario

summary:
Background: Glucocorticoids (GCs) are widely used anti-inflammatory drugs. While useful in clinical practice, patients taking GCs often suffer from skeletal side effects including growth retardation and decreased bone quality in adults. On a physiological level, GCs have been implicated in the regulation of chondrogenesis and osteoblast differentiation, as well as maintaining homeostasis in cartilage and bone. We identified the glucocorticoid receptor (GR) as a potential regulator of chondrocyte hypertrophy in a microarray screen of primary limb bud mesenchyme micromass cultures.  Some targets of GC regulation in chondrogenesis are known, but the global effects of pharmacological GC doses on chondrocyte gene expression have not been comprehensively evaluated.
Results:  This study systematically identifies a spectrum of GC target genes in embryonic growth plate chondrocytes treated with synthetic GR agonist, dexamethasone (DEX), at 6 and 24 hrs. Conventional analysis of this data set and gene set enrichment analysis (GSEA) was performed. Transcripts associated with metabolism were enriched in the DEX condition along with extracellular matrix genes. In contrast, a subset of growth factors and cytokines were negatively correlated with DEX treatment. Comparing DEX-induced gene expression data to developmental changes in gene expression in micromass cultures revealed an additional layer of complexity in which DEX maintains the expression of certain chondrocyte marker genes while inhibiting factors that promote vascularization and ultimately ossification of the cartilaginous template.
Conclusions: Together, these results provide insight into the mechanisms and major molecular classes functioning downstream of DEX in primary chondrocytes monolayers. In addition, comparison of our data with microarray studies of DEX treatment in other cell types demonstrated that the majority of DEX effects are tissue-specific. This study provides novel insights into the effects of pharmacological GC on chondrocyte gene transcription and establishes the basis for subsequent functional studies.
Keywords: Time course and pharmacological treatment

overall_design:
Primary chondrocytes isolated from the tibiae, humeri and femurs of 15.5 day old mice are treated with 10EXP-7M DEX or an equal volume of the DMSO vehicle for 24 hrs.  Total RNA is isolated after 6 hrs and 24 hrs of treatment.  Samples from three independent experiments independent time courses were hybridized to Affymetrix MOE 430 2.0 mouse chips.

Number of time points: 2 (6hr and 24 hr)
Number of treatments: 2 (DEX and the vehicle control)
Number of Samples: 3 replicates per time point per treatment
Affymetrix chip: MOE 430 2.0
Cell type: Primary chondrocyte
Tissue or origin: Tibiae, humerus, femur
Species E15.5 mice
Samples: Total RNA

first: Veronica

last: Ulici

first: Jan

last: Tuckermann

first: T

middle: M

last: Underhill

first: Frank

last: Beier


title: Gene expression profiles of E15.5 cortical collecting duct and anlage of loop of Henle isolated from developing kidney using LCM. (GUDMAP Series ID: 18)

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

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

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

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Inflammatory response to titanium dioxide particles exposure is enhanced during pregnancy

status: Public on Jun 30 2007

city: Boston

first: Alexey

last: Fedulov

address: 75 Francis St.

department: Brigham and Women's Hospital

institute: Harvard Medical School

summary:
Rationale: Maternal immune responses can promote allergy development in offspring. Pilot data show that neonates of mother mice exposed during pregnancy to air pollution particles have increased allergic susceptibility. Objective: We investigated whether inflammatory response to titanium dioxide (TiO2) particles earlier considered immunologically ‘inert’ is enhanced during pregnancy. Methods: Pregnant BALB/c mice (or non-pregnant controls) received particle suspensions intranasally at day 14 of pregnancy. Lung inflammatory responses were evaluated 19 and 48 h after exposure. Results: Pregnant mice showed robust and persistent acute inflammatory responses after exposure to TiO2, while non-pregnant females had the expected minimal responses. Genomic profiling identified genes differentially expressed in pregnant lungs exposed to TiO2. Neonates of mothers exposed to TiO2 (but not PBS) developed increased susceptibility to allergens. Conclusion: Pregnancy enhances lung inflammatory responses to otherwise relatively innocuous inert particles.
Keywords: Particles exposure, pregnancy vs normal

overall_design:
To test whether pregnancy alters the normally minimal inflammatory response to ‘inert’ particles, we have administered TiO2 and DEP suspensions (50 ug/mouse) or PBS solution by intranasal insufflation to normal or pregnant E14 mice (see Figure 1B). The mice were subjected to pathologic analysis 19 or 48 hrs later.
Respirable-size TiO2 particles were generously provided by Dr. Ian Gilmour (US EPA). Particle samples were baked at 165 0C for 3 h to eliminate endotoxin, aliquoted and stored frozen at – 80 0C. Particle suspensions (50 ug in 50 uL) or PBS solution (vehicle) were administered by single intranasal insufflation of pregnant or normal Balb/c mice under light halothane anesthesia
Total lung RNA extraction and isolation was performed 19 hrs after exposure using a Qiagen RNAeasy Mini kit according to manufacturer’s instructions (Qiagen, Valencia, CA). RNA purity and quality were analyzed by Agilent Bioanalyzer 2100 scan. The hybridization was carried out at the Harvard Partners Genomic Center Microarray facility (Cambridge, MA) using the Affymetrix GeneChip ® platform and Affymetrix mouse 430 2.0 chips (Affymetrix, Santa Clara, CA).
4 samples were analyzed in each of 4 groups: Normal PBS, Normal TiO2, Pregnant PBS and Pregnant TiO2, for a total of 16 samples.

first: Zhiping

last: Yang

first: Thomas

last: Mariani

first: Lester

last: Kobzik


title: Dlx homeodomain transcription factor mutants (ruben-affy-mouse-313340)

status: Public on Jun 27 2007

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
The Dlx homeodomain transcription factors are implicated in regulating the function of inhibitory GABAergic interneurons; therefore understanding their functions will provide insights into disorders such as epilepsy, mental retardation and autism.
Identifying genes that are downstream of Dlx1/2 function and are relevant for the differentiation and survival of GABAergic interneurons.
During embryonic development, cortical GABAergic interneurons are generated in the proliferative zone of the medial ganglionic eminence (MGE), from where they migrate to reach their final positions in the cortex. The differentiation of these interneuron precursors is dependent on Dlx genes, as shown by Dlx1/Dlx2 double mutants, which have a block in GABAergic cell differentiation and in cell migration. When interneuron progenitors are isolated from the mutant MGE and growth in culture, they are able to proceed along their differentiation program. However, mutant cells growth in vitro show defects in cell morphogenesis and increased cell apoptosis. We hypothesize that Dlx transcription factors regulate important aspects of GABAergic neuron differentiation such as the formation and growth of axon and dendrites, and the formation of inhibitory synapses.
We generated E15.5 mouse embryos that are Dlx1/2 -/- or Dlx1/2 +/?. Genotype was confirmed by PCR. A total of 8 litters were used. For each experiment, we pooled tissue from at least 6 different embryos of the same genotype. We dissected the ventricular and subventricular zones of the MGE (rostral part). This area contains ~1 million of progenitor cells per embryo. We isolated total RNA using the Stratagene RNA Miniprep kit (these samples are called MGE+/ and MGE-/- in our proposal). In addition, we used the same area (ventricular and subventricular zones of the rostral MGE) to perform primary neuronal cultures. Cells were maintained 3 days in vitro. After that, we isolated total RNA using the Stratagene RNA Miniprep kit (samples called primary cells+/ and primary cells-/- in our proposal). We would like to perform gene expression comparison between: 1) MGE+/ and MGE-/-, and 2) primary cells+/ and primary cells-/-.
Keywords: Dlx mutants, medial ganglionic eminence, neuronal cultures

first: John

last: Rubenstein


title: Gene expression profiles of E15.5 peripheral blastema isolated from Meis1-EGFP transgenic mice using FACS. (GUDMAP Series ID: 17)

status: Public on Jun 25 2007

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

overall_design: At specific developmental time points we isolate discrete elements of the kidney by using fluorescent  activated cell sorting (FACS) and then define their gene expression  profiles with microarrays.


title: Murine ES cells, neural precursor cells and embryonic fibroblasts

city: Cambridge

first: Tarjei

middle: S

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

summary:
Expression profiles for isogenic (129SvJae x C57BL/6) murine embryonic stem (ES) cells, neural precursors (NPC) obtained through in vitro differentiation of the ES cells, and embryonic fibroblasts (MEF) obtained at day 13.5.
Keywords: cell type comparison

overall_design: 3 replicates of wt ES cells, 3 replicates of wt NPCs obtained by in vitro differentiation, 2 replicated of primary MEFs

first: Alex

last: Meissner

first: Marius

last: Wernig

first: Rudolf

last: Jaenisch

last: Lander

first: Bradley

last: Bernstein


title: Morphine effects on striatal transcriptome in four inbred mouse strains

status: Public on Jun 14 2007

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

summary:
Chronic opiate use produces molecular and cellular adaptations in the nervous system, leading to tolerance, physical dependence and addiction. Genome-wide comparison of morphine-induced changes in brain transcription of mouse strains with different opioid-related phenotypes provides an opportunity to discover the relationship between gene expression and behavioral response to the drug.
Keywords: Drug response

overall_design: Microarray experiment was designed to determine the impact of genetic background on the transcriptional effects of morphine in the striatum. The effects of single (20 mg/kg, s.c.) and repeated morphine administration (10-40 mg/kg, 3 times daily for 5 days) were analyzed in four inbred mouse strains (129P3/J. DBA/2J, C57BL/6J, SWR/J). Twelve experimental groups were compared. Control animals received injections of saline. Three independent biological replicates of the microarray were prepared for each experimental group. For each array, independent pools of total RNA from three animals were prepared.

first: Michal

last: Korostynski

first: Ryszard

last: Przewlocki


title: Role of thrombospondin-1 in T cell response to ocular pigment epithelial cells.

status: Public on Jun 22 2007

city: Tokyo

first: Yuri

last: Futagami

address: 1-5-45 Yushima Bunkyoku

department: Ophthalmology

institute: Tokyo Medical and Dental University

summary:
Ocular pigment epithelium (PE) cells promote the generation of T regulators (PE-induced Treg cells). Moreover, T cells exposed to PE acquire the capacity to suppress the activation of bystander T cells via TGFbeta. Membrane-bound TGFbeta on iris PE cells interacts with TGFbeta receptors on T cells, leading to the conversion of T cells to CD8(+) Treg cells via a cell contact-dependent mechanism. Conversely, soluble forms of TGFbeta produced by retinal PE cells can convert CD4(+) T cells into Treg cells in a manner that is independent of cell contact. In this study, we looked at the expression of immunoregulatory factors (TGFbeta, thrombospondins, CD59, IL-1 receptor antagonist, etc.) in PE cells as identified via an oligonucleotide microarray. Several thrombospondin-binding molecules were detected, and thus we focused subsequent analyses on thrombospondins. Via the conversion of latent TGFbeta to an active form that appears to be mediated by thrombospondin 1 (TSP-1), cultured iris PE and retinal PE cells induce a PE-induced Treg cell fate. After conversion, both ocular PE and PE-induced Treg cells express TSP-1. Regulatory T cell generation was amplified when the T cells also expressed TSP-1. In addition, PE-induced Treg cells significantly suppressed activation of bystander T cells via TSP-1. These results strongly suggest that the ability of ocular PE and PE-induced Treg cells to suppress bystander T cells depends on their capacity to produce TSP-1. Thus, intraocular TSP-1 produced by both ocular parenchymal cells and regulatory T cells is essential for immune regulation in the eye.
Keywords: Comparison

overall_design:
Comparison of gene expression pattern in Mouse Primary Cultured Cell Lines (RPE, IPE, CBPE).
Adult (6- to 8-week-old) C57BL/6 purchased from CLEA Japan Inc. (Tokyo, Japan) were used as donors ocular pigment epithelium (PE). To cultivate iris PE (IPE) and ciliary body PE (CBPE), iris and ciliary body tissues in the eyes were dissected out, and then incubated in 1 mg/ml Dispase and 0.05 mg/ml DNase I (both from Boehringer-Mannheim, Mannheim, Germany) for 1 hr. To cultivate retinal PE (RPE) Eyes were cut into two parts along a circumferential line posterior to the ciliary process, creating a ciliary body-deficient posterior eyecup.  The eyecup was then incubated in 0.2% trypsin (Biowhitaker) for 1 hr.  These tissues were triturated to make a single cell suspension, and then re-suspended in the medium.

first: Sunao

last: Sugita

first: Jose

last: Vega

first: Kazuhiro

last: Ishida

first: Hiroyuki

last: Aburatani

first: Manabu

last: Mochizuki


title: A dominant negative form of cJun affects genes that have opposing effects on lipid homeostasis in mice

status: Public on Jun 15 2007

city: Athens

first: Despina

last: Sanoudou

address: Soranou Efesiou 4

department: Molecular Biology

country: Greece

institute: Foundation for Biomedical Research, Academy of Athens

summary:
cJun is a transcription factor activated by phosphorylation by SAPK/JNK MAP kinase pathway that has been linked to atherosclerosis. Adenovirus mediated gene transfer of a dominant negative form of cJun in C57BL/6 mice increased greatly the apolipoprotein E (ApoE) mRNA and plasma apoE levels and induced dyslipidmia, characterized by increased plasma cholesterol, triglyceride and VLDL levels and accumulation of discoidal HDL particles. Unexpectedly, infection of ApoE-/- mice with adenovirus expressing dn-cJun reduced by 50% plasma cholesterol, suggesting that the dn-cJun affected other genes that control plamsa cholesterol. To determine the molecular pathways implicated in this process we performed whole genome expression profiling using total RNA from the liver of infected ApoE-/- mice.
Keywords: disease

overall_design: We extracted total RNA from 5 ApoE-/- mice infected with an adenovirus expressing dominant negative cJun and 5 ApoE-/- mice infected with a control adenovirus expressing GFP. Each RNA sample was hybridized to a different Affymetrix 430 2.0 array.

first: Konstantinos

last: Drosatos

first: Kyriakos

last: Kypreos

first: Dimitris

last: Kardassis

first: Vassilis

last: Zannis


title: Gene expression during early postnatal development of the small intestine

status: Public on Jun 12 2007

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary:
It was the purpose to analyse the changes in gene expression which occur in the mouse small intestine from the pre-weaning to the post-weaning stage. The gene expression was accordingly followed from postnatal day 4 to postnatal day 32.
Keywords: Time-course

overall_design: 6 time-points were defined corresponding to postnatal day 4, 7, 9, 11, 24 and 32. Ileal samples were taken from individual mice at each time-point. All layers of the small intestine were included in the sample. Three samples from individual mice were analysed by hybridization to Affymetrix GeneChips.

first: Jørgen

first: Jesper

last: Troelsen


title: E18.5 Estrogen-related Receptor gamma Knockout Mouse Heart

status: Public on Jul 10 2007

city: La Jolla

first: Ronald

last: Evans

address: 10010 North Torrey Pines

department: Howard Hughes Medical Institute

institute: The Salk Institute for Biological Studies

summary:
3 ventricles from E18.5 male mice were pooled for each array. Three arrays per genotype.

Title: ERRγ Directs and Maintains the Transition to Oxidative Metabolism in the Post-Natal Heart

Abstract: At birth the heart undergoes a critical metabolic switch to transition from a predominant dependence on carbohydrates during fetal life to a greater dependence on postnatal oxidative metabolism. This remains the principle metabolic state throughout life; although pathologic conditions such as heart failure and cardiac hypertrophy reactivate components of the fetal genetic program to increase carbohydrate utilization. Disruption of the ERRγ gene, which is expressed at high levels in the fetal and postnatal mouse heart, blocks this switch resulting in lactatemia, electrocardiographic (ECG) abnormalities and death during the first week of life. Genomic ChIP-on-chip and expression analysis at E18.5 clearly identifies ERRγ as both a direct and indirect regulator of a nuclear-encoded mitochondrial genetic network that coordinates the postnatal metabolic transition. These findings reveal an unexpected and essential molecular genetic component of the oxidative metabolic gene program in the heart and highlight ERRγ in the study of cardiac hypertrophy and failure.
Keywords: ChIP-on-chip, electrocardiography, fetal gene program, OXPHOS, PGC-1a, sodium current, Single time point (E18.5) to compare genotype differences

overall_design: Fetal mice were collected by caesarean secation. Hearts were stored in RNALater (Qiagen)

first: William

last: Alaynick


title: Huntington's disease: Gene expression changes caused by Hdh CAG mutation or 3-nitropropionic acid in striatal cells

status: Public on Jun 20 2007

first: Marcy

last: MacDonald

address: 185 Cambridge Street

department: Center for Human Genetic Research

institute: Mass General Hospital

summary:
Affymetrix MG430 2.0 expression levels of wild-type (STHdhQ7/Q7), 3NP-treated wild-type (STHdhQ7/Q7+3-NP), and mutant (STHdhQ111/Q111) striatal cells
Keywords: Pharmacological and genetic HD cell culture models

overall_design: Investigation of HD disease mechanism by gene expression profiling of two HD model systems

first: Jong-Min

last: Lee