title: Expression data from wildtype and alb/cre liver-conditional Pdss2 knockout mutant mice

status: Public on Apr 30 2008

city: Philadelphia

first: Eric

middle: F.

last: Rappaport

address: 3516 Civinc Center Blvd

department: Abramson Research Center

institute: Children's Hospital of Philadelphia

summary:
Utilizing M. musculus as a model of mitochondrial dysfunction provides insight into cellular adaptations which occur as a consequence of genetic alterations causative of human disease.  We characterized genome-wide expression profiles of liver-conditional knockout mice for Pdss2 compared with loxP controls.
Our goal was to detect concordant changes among clusters of genes that comprise defined metabolic pathways utilizing gene set enrichment analysis.
Keywords: Wildtype vs mutant comparison as a method for studying contributors to disease processes.

overall_design: Liver from three biological replicates each of wildtype and coenzyme Q biosynthetic mutant M. musculus were used as sources of total RNA for hybridization to Affymetrix whole-genome microarrays.  Comparison of the data was intended to reveal metabolic pathway alterations downstream of the mutation.

first: Falk

last: Marni

first: Zhang

last: Zhe


title: Control of hematopoietic stem cell quiescence by the E3 Ubiquitin Ligase Fbw7

status: Public on Apr 15 2008

city: New York

first: Iannis

last: Aifantis

state: NY

address: 550 First Ave

department: Pathology

country: USA

institute: NYU Sch of Medicine

summary:
Ubiquitination is a post-translational mechanism of control of diverse cellular processes. We focus here on the ubiquitin ligase Fbw7, a recently identified hematopoietic tumor suppressor that can target for degradation several important oncogenes including Notch1, c-Myc and cyclin E. We have generated conditional Fbw7 knock-out animals and inactivated the gene in hematopoietic stem cells (HSC) and their differentiated progeny. Deletion of Fbw7 specifically and rapidly affects the HSC compartment in a cell-autonomous manner. Fbw7-/- HSCs show defective maintenance of quiescence, leading to impaired self-renewal and a severe loss of competitive repopulating capacity. Furthermore, Fbw7-/- HSC  are unable to colonize the thymus leading to a profound depletion of T cell progenitors. Deletion of Fbw7 in bone marrow stem cells and progenitors leads to the stabilization of c-Myc, a transcription factor previously implicated in HSC self-renewal. On the other hand, neither Notch1 nor cyclin E are stabilized in the bone marrow of Fbw7 deficient mice. Genome-wide transcriptome studies of Fbw7-/- HSC and hematopoietic progenitors indicate that Fbw7 controls, through the regulation of HSC cell cycle entry, the global transcriptional “signature” that is associated with the quiescent, self-renewing HSC phenotype.
Transcriptional consequences of inactivating Fbw7 in LKS cells.
Keywords: cell type comparison

overall_design: Four samples were analyzed: wild-type (WT) control and Fbw7-deficient (FBW7) Lin-ckit+Sca1+ (LSK) cells, as well as Lin-ckit+Sca1- myeloid progenitor (MP) cells, which served as a control for LSK-enriched/specific genes.  Total bone marrow cells were pooled from three WT and three FBW7 mice before sorting LSK and MP populations.

first: Benjamin

middle: J

last: Thompson

first: Vladimir

last: Jankovic

first: Jie

last: Gao

first: Silvia

last: Buonamici

first: Jiri

last: Zavadil

first: Jennifer

middle: M

last: Lee

first: Alan

last: Vest

first: Stephen

last: Nimer


title: Maternal versus paternal uniparental disomy of Chr12 and Chr18: whole embryo and placenta

status: Public on Apr 14 2008

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

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

overall_design: Refer to individual Series


title: Dnmt3l-/+ (maternal methylation-deficient) vs normal 8.5dpc embryos

summary:
During oogenesis, DNA methyltransferase 3-like (Dnmt3l) is required for the establishment of the maternal germline DNA methylation imprints that in the offspring, govern the parent-of-origin-specific expression of most known imprinted genes (Science 2001, 294:2536-9). Dnmt3l-deficient dams were crossed with wildtype sires to obtain Dnmt3l-/+ embryos that lack maternal methylation imprints. Gene expression was measured in Dnmt3l-/+ and wildtype embryos and is expected to differ for imprinted genes that are under the control of a maternal methylation mark.
Keywords: genetic modification, DNA methylation

overall_design: 1 normal control sample/array. 2 biologically replicate Dnmt3l-/+ samples/arrays.

first: Kathryn

last: Woodfine

first: Trevelyan

last: Menheniott

first: Deborah

last: Bourc'his

first: Timothy

last: Bestor

first: Rebecca

last: Oakey


title: The effect of embryo biopsy on global patterns of gene expression in the mouse blastocyst

status: Public on Apr 22 2008

first: Francesca

middle: Elizabeth

last: Duncan

state: PA

address: 433 South University Avenue/ 205 Lynch Laboratories

department: Biology

institute: University of Pennsylvania

summary:
Preimplantation Genetic Testing (PGT), which encompasses both Preimplantation Genetic Diagnosis (PGD) and Preimplantation Genetic Screening (PGS), is a form of prenatal screening done on embryos conceived through assisted reproduction techniques (ART) prior to the initiation of pregnancy to ensure that only select embryos are used for transfer.  PGT is typically performed on 8-cell embryos derived from either in vitro fertilization or intracytoplasmic sperm injection (ICSI) followed by extended culture.  PGT requires a highly invasive embryo biopsy procedure that involves 1) incubating embryos in divalent-cation-deficient medium to disrupt cell adhesion, 2) breaching the protective zona pellucida with acid Tyrode’s, laser drilling, or mechanical force and 3) aspirating one or two blastomeres.  In this study we developed a mouse model of the embryo biopsy procedure inherent to PGT to determine the effect of various aspects of the procedure (incubation in Ca2+/Mg2+-free medium (CMF), acid Tyrode’s treatment, blastomere aspiration), performed individually or in combination, on global patterns of gene expression in the resulting blastocysts.
Keywords: embryo biopsy, preimplantation genetic diagnosis, blastocyst

overall_design:
The comprehensive embryo biopsy procedure was done as outlined below and was modified according to the specific experimental treatment being performed.
Eight-cell embryos with rounded blastomeres and no fragmentation were initially incubated in CMF-Chatot-Ziomek-Brinster medium for 5 min at 37oC in a humidified atmosphere of 5% CO2 in air to loosen cell-cell contacts and then transferred to CMF-Dulbecco’s Phosphate-Buffered Saline.  The biopsies were done on the stage of a Nikon Eclipse TE2000 microscope equipped with Hoffman optics and motorized Eppendorf micromanipulators. No more than three embryos were manipulated outside of the incubator at any time.  Embryos were held in place by gentle suction on an Eppendorf Sterile VacuTip holding pipette (15 μm diameter), and a dual-holder system was used to control the pipette containing acid Tyrode’s (6 μm diameter) and the biopsy pipette (15 μm diameter).  The zona pellucida was breached by gentle expulsion of a steady stream of acid Tyrode’s solution (pH 1.6), and a single blastomere with a clear nucleus was removed by aspiration.  Following each respective treatment, embryos were cultured individually in 10 μl drops of Potassium Simplex Optimization Medium supplemented with amino acids at 37oC in a humidified atmosphere of 5% CO2 in air until 96 h post-hCG injection.  Four replicates of these five experimental groups, each containing 20 embryos, were generated for a total of 20 samples and 400 embryos.
To determine the effect of the various aspects of the embryo biopsy procedure on global patterns of gene expression, total RNA was extracted from each set of 20 embryos in each treatment group at 96 h post-hCG injection.  This total RNA was then used to prepare target cRNA by linear two-round amplification as described previously.   The final yield of biotinylated cRNA/20 embryos ranged from 34 μg -78 μg, of which 20 μg was fragmented and submitted to the University of Pennsylvania Microarray Facility where the samples were serially hybridized to the MOE430v2 GeneChip.  Quality control parameters for all samples were within the following ranges: scale factor:  0.27-0.47, percent of genes detected: 44-51%, actin 3’/5’ signal ratio: 1.5-4.2, and GAPDH 3’/5’ signal ratio: 3.1-4.3.   The GC-RMA algorithm was used to quantify and normalize microarray signals using Stratagene Array Assist Lite, Version 3.4.  The resulting .chp files were imported to GeneSpring (v7.31, Agilent Technologies) where probe sets were filtered to retain those that were flagged as P (present) in at least 3 of the 20 samples.  The data was log2-transformed and subjected to analysis using Partek Genomics Suite (v6.3, Partek, Inc).

middle: E

first: Paula

last: Stein

first: Richard

last: Schultz


title: Genes regulated by GATA6 in the lung

first: Edward

last: Morrisey

address: 941 Curie Blvd.

department: Medicine and Cell and Developmental Biology

summary:
Epithelial organs including the lung are known to possess regenerative abilities through activation of endogenous stem cell populations but the molecular pathways regulating stem cell expansion and regeneration are not well understood.  Here we show that Gata6 regulates the temporal appearance and number of bronchioalveolar stem cells (BASCs) in the lung leading to the precocious appearance of BASCs and concurrent loss in epithelial differentiation in Gata6 null lung epithelium.  This expansion of BASCs is the result of a dramatic increase in canonical Wnt signaling in lung epithelium upon loss of Gata6. Expression of the non-canonical Wnt receptor Fzd2 is down-regulated in Gata6 mutants and increased Fzd2 or decreased β-catenin expression rescues, in part, the lung epithelial defects in Gata6 mutants.  During lung epithelial regeneration, we show that canonical Wnt signaling is activated in the niche containing BASCs and forced activation of Wnt signaling leads to a dramatic increase in BASC numbers.  Moreover, Gata6 is required for proper lung epithelial regeneration and postnatal loss of Gata6 leads to increased BASC expansion and decreased differentiation.  Together, these data demonstrate that Gata6 regulated Wnt signaling controls the balance between stem/progenitor expansion and epithelial differentiation required for both lung development and regeneration.
Keywords: gene targets in knockout mouse model

overall_design: 3 replicates of each condition-wild-type and GATA6 null tissue.  6 total samples.


title: Polytopic protease downregulation effect on the brain (rogae-affy-arabi-492460)

status: Public on Apr 12 2008

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Regulation of AD-related genes. Presenilins are intramembrane polytopic proteases. These proteases are critical proteins in pathogenesis of Alzheimer's disease. The function of other polytopic proteases expressed in brains is unknown.  Proteins that may potentially interact with PS pathway are of interest to elucidate.
In this project we will determine gene expression patterns in the brains of  mice with altered expression of polytopic protease.
We hypothesize that  family of polytopic proteases expressed in brain may potentially interact with presenilin pathway.
We will examine 4 RNA samples isolated from brains of  mice with significant downregulation of polytopic protease and control animals.
Total RNA was extracted, purified according to the manufacturer's  protocol and stored at -80C.

Keywords: polytopic protease, brain

first: Evgeny

middle: I

last: Rogaev


title: Hippocampus of HuD overexpressor mice (perro-affy-mouse-309741)

summary:
Post-transcriptional mechanisms play an important role in the control of gene expression. RNA-binding proteins are key players in the post-transcriptional control of many neural genes and they participate in multiple processes, from RNA splicing and mRNA transport to mRNA stability and translation. Our laboratory has developed the first mouse model overexpressing a RNA-binding protein, the ELAV-like protein HuD, in the CNS under the control of the CaMKinII alpha promoter. Initial behavioral characterization of the mice revealed that they had significant learning deficits together with abnormalities in prepulse inhibition (PPI). At the molecular level, we found that the expression of the growth-associated protein GAP-43, one of the targets of HuD, was increased in the hippocampus of HuD transgenic mice. To characterize these mice further and to evaluate the utility of these animals in understanding human diseases, we propose to use DNA microarray methods.
To characterize the pattern of gene expression in the hippocampus of HuD overexpressor mice
Based on the behavioral and molecular properties of our HuD transgenic mice we hypothesize that these animals may be good models for the studying the basis of learning disabilities and of diseases that show deficits in PPI such as fetal alcohol syndrome and schizophrenia.
All mice are in C57BL/6 background and are male approximately 30 days old. Animals are bred and sacrificed according to our approved animal protocol.  Brains will be rapidly dissected on ice, quickly frozen and stored at -80C until analysis. Frozen brains will be embedded in OCT and shipped to the DNA microarray facility at Duke University where LCM was performed. Dentate granule cells from control and HuD transgenic mice will be isolated by Susan Su, who will also perform RNA isolation and the first round of RNA amplification. For our first experiment, we want to examine the pattern of gene expression in the hippocampus of 2 transgenic mice and 2 non-transgenic littermates.
Keywords: HuD, hippocampus

first: Nora

last: Perrone-Bizzozero


title: Effects of NgR overexpression on the developing and mature forebrain (backm-affy-mouse-433094)

summary:
The lack of axonal growth after injury in the adult central nervous system (CNS) is partly due to the presence of growth-inhibitory molecules associated with myelin and the intrinsic growth-state of the injured neurons. To date, three inhibitors have been identified in myelin: Myelin- Associated Glycoprotein (MAG), Nogo A, and Oligodendrocyte-Myelin glycoprotein (OMgp). These three proteins all appear to be located in the periaxonal surface of the myelin membrane placing them in an optimal location to mediate axon-glial interaction.  In addition, the three proteins have been shown to bind the same neuronal receptor, known as the Nogo-66 receptor (NgR).  It has been hypothesized that inhibition of NgR may be a strategy to increase regeneration, plasticity and functional recovery of the lesioned central nervous system. Strong NgR mRNA expression is observed in the hippocampal pyramidal cell layers (CA1-3) and the granular layer of the dentate gyrus.  It has been shown that animals exposed to entorhinal lesions show a biphasic regulation of NgR in the hippocampus, suggesting a tightly regulated mechanism mediated by this receptor.  We have access to a transgenic model to over-express NgR in forebrain hippocampal neurons. Preliminary results have shown a phenotypic response in behavior and some molecular markers, as result of NgR overexpression.  Knowledge of what genes are reacting in this novel transgenic model may provide insights into what pathways are affected by NgR to control synaptic plasticity in normal animals and during injury.
We have access to a bitrasgenic conditional mouse model to everexpress the NgR receptor in forebrain neurons, through the CamKII promoter.  This conditional model uses the tetracycline transactivator (tTA), which is expressed through the CamKII promoter. Upon removal of doxycycline, the TetOp target gene becomes active and over-expression of NgR in cells with an active CaMKII promoter is achieved.

We will determine gene expression patterns in the dentate gyrus of transgenic animals engineered to over-express NgR through the CamKII promoter (present in several forebrain areas), and upon removal of doxyxycline.
We hypothesize that over-expression of NgR in the hippocampus inhibits synaptic plasticity, thereby suppressing the formation of new synapses necessary for the formation of memory.
EXPERIMENT 1
- Effects of NgR overexpression in the mature forebrain -
1)  Experimental group: Bitrasgenic + water: Overexpresses NgR in forebrain neurons. In this group, doxyxycline was removed from the drinking water in adult animals. All the control groups were aged matched.
2)  Control group: Bitransgenic + doxy: Should control for leakage by the TetOp target gene, or for any effects mediated by doxycycline, as compared to other control groups.
3)  Control group: Monotransgenic + water:  Should control for any leakage mediated by the TetOp target gene, as compared to other control groups.
4) Control group: Monotrangenic + water: Should control for leakage by the TetOp target gene, or for any effects mediated by doxycycline, as compared to other control groups.

EXPERIMENT 2
- Effects of NgR overexpression in the developing forebrain  -
We will also analyze the effects of NgR overexpression in bitransgenic animals raised on water.  In these animals, the NgR transgene is expressed in the forebrain upon activation of the CamKII promoter.  Since neuronal differentiation and neuronal pathways are being formed during development, we anticipate that NgR overexpression (de)effects in these animals will be markedly different to those observed in adult animals.
1) Bitransgenic +  water (through entire lifespan): The animals in this group were never treated with doxycycline, and therefore expressed the NgR transgene upon activity of the CamKII promoter.
2) Monotransgenic + water: This control group will control for leakage by the Tet Op gene, or for effects of the tTA expression.

Keywords: NgR, forebrain, development

first: Cristina

last: Backman


title: Wildtype, Fah and Fah, p21 ON and OFF NTBC

status: Public on Apr 09 2008

city: San Francisco

first: Holger

last: Willenbring

state: CA

address: 35 Medical Center Way

institute: UCSF

summary:
Fumarylacetoacetate hydrolase (Fah), the last enzyme of the tyrosine degradation pathway, is specifically expressed in hepatocytes in the liver. Loss of Fah leads to liver failure in mice within 6-8 weeks. This can be prevented by blocking tyrosine degradation upstream of Fah with 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione (NTBC). Here, we investigate the impact of p21 on global gene expression in Fah deficiency.
Keywords: treatment, genotype

overall_design: Livers from adult wildtype, Fah or Fah, p21 knockout mice were analyzed either after continuous treatment (ON) with NTBC or after NTBC withdrawal for 14 days (OFF).

first: Markus

last: Grompe


title: Role of Endothelin in SCG axon pathfinding

city: Baltimore

first: David

middle: D

last: Ginty

state: MD

address: 725 N. Wolf ST

department: Neuroscience

institute: HHMI/Johns Hopkins Univ

summary:
Sympathetic neurons of SCG (Superior Cervical Ganglia) send axonal projections either along the external carotid arteries to innervate the salivary glands, or along the internal carotid arteries to the lacrimal and pineal glands, the eye, blood vessels and skin of the head, and the mucosa of the oral and nasal cavities. Previous studies using Wnt1Cre and R26R have defined the neural crest and mesodermal origins of vascular smooth muscle in the heart outflow tract and great vessels, although not specifically of the segments that are relevant for the projections of the SCG neurons.  The third pharyngeal arch arteries are lined by neural crest-derived smooth muscle, and consequently, their derivatives, including the entirety of the external carotid arteries and only the base of the internal carotid arteries, also have a neural crest origin.  In contrast, the dorsal aortae are lined by smooth muscle that is mesodermal in origin, and as a result, the internal carotid arteries from just above their origination from the common carotid arteries have a mesoderm-derived smooth muscle layer. To address the possibility that guidance cues for SCG neurons are selectively expressed by the external carotid vs. the internal carotid arteries, we isolated these segments of the vasculature from mouse embryos at E13.5 and extracted RNA to screen microarrays for differentially expressed genes.
Keywords: differential expression in genes expressed in two different vascular segments.

overall_design:
Vascular segments were isolated from 22 embryos at E13.5, pooled and extracted RNA for microarray screen.  Total RNA samples from the internal or the external carotid arteries were subjected for two-round amplification to synthesize cRNA to probe microarray. Neither experimental nor technical replicate was made for this experiment.
Vascular segments were isolated from 22 embryos at E13.5, pooled and extracted RNA for microarray screen.  Total RNA samples from the internal or the external carotid arteries were subjected for two-round amplification to synthesize cRNA to probe microarray. Neither experimental nor technical replicate was made for this experiment.

first: Takako

last: Makita

first: Henry

last: Sucov

first: Cheryl

last: Gariepy

first: Masashi

last: Yanagisawa


title: MIA overexpression

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary:
In experiments using tissue recombinants and mesenchyme-free culture, we have demonstrated that the entire embryonic respiratory tract epithelium, from the trachea to the distal lung tips, exhibits substantial plasticity in its eventual phenotype that is dependent on the inductive cues it receives from its associated mesenchyme.  This observation led us to speculate that the differences between embryonic trachea and lung are defined by limited subset of genes, and that the molecular comparison of these two tissues might provide new information on genes that are important for both lung and trachea development.  Microarray experiments designed to identify genes differentially expressed in the E11.5 lung and trachea showed that melanoma inhibitory activity (Mia1) was expressed only in the lung.  Mia1 was abundantly expressed during early lung development, but was virtually absent by the end of gestation.  Bitransgenic mice expressing MIA under the control of the SFTPC promoter after E16.5, the age when Mia1 is normally silenced, died from respiratory failure at birth with morphologically immature lungs associated with reduced levels of saturated phosphatidylcholine and mature SP-B.  Microarray analysis showed significant reductions expression of Sftpa, Sftpb, Abca3, Aqp5, Lzp-s, Scd2, and Aytl2 in lungs misexpressing MIA.
Keywords: genotype comparison

overall_design:
To identify genes differentially expressed in the embryonic lung and trachea, we used microarray analysis to compare RNA from day E11.5 mouse lung and trachea.
To assess the effect of misexpressing MIA on overall lung gene expression, we analyzed RNA from day E18.5 lungs of bitransgenic and control littermates by microarray (Affymetrix MOE430 chip).

first: Sui

last: Lin

first: Machiko

last: Ikegami

first: Anja-Katrin

last: Bosserhoff

first: Alvin

last: Malkinson

first: John

last: Shannon


title: mKIAA1583 (Tmem132a) siRNA interference

city: Kisarazu

first: Kazuhide

last: Imai

state: Chiba

address: 2-6-7 Kazusa-Kamatari

country: Japan

institute: Chiba Industry Advancement Center

summary:
Gene expression profiling comparisons of Neuro2a transfected with either mKIAA1583 (Tmem132a) siRNA or control (non-specific) siRNA.
Keywords: siRNA, gene expression

overall_design: Genes were selected using fold change and ABS-call from MAS5-calculated signal intensity.

first: Kentaro

last: Ohashi

first: Hisashi

last: Koga


title: Gene profile data from Df(16)A/+ and wild type littermates

status: Public on Apr 10 2008

first: Joseph

last: Gogos

department: Physiology

institute: Columbia University

summary:
This represents an unbiased evaluation of the transcriptional response in the prefrontal cortex and hippocampus areas in the Df(16)A/+ mice, a mouse model of human 22q11 microdeletion syndrome. These mice were generated by chromosomal engineering and carry a microdeltion of ~1.3Mb in the mouse locus syntenic to the human 22q11.1
The reasoning behind this expression profiling is that alterations in transcriptional programs reflect either downstream (immediate or remote) effects of the deficiency or reactive (compensatory) changes, and can thus point to affected biological processes and molecular functions.
Keywords: disease state analysis, genetic modification

overall_design: A total of 20 PFC and 20 HPC from 10 Df(16)A/+ mutants and 10 WT control mice was used for RNA extraction and hybridization on Affymetrix microarrays. All mice were male littermates 8 weeks of age.

first: Kimberly

middle: L

last: Stark

first: Bin

first: Maria

last: Karayiorgou

middle: A


title: Strain-specific differences in lactation performance of mice

status: Public on Apr 03 2008

city: Camperdown

first: Peter

last: Williamson

state: NSW

address: RMC Gunn Building, B19

department: Faculty of Veterinary Science

country: Australia

institute: University of Sydney

summary:
The QSi5 inbred strain of mice was established from an outbred Quackenbush-Swiss strain by full-sib inbreeding and selection on the basis of increased litter size and shortened inter-litter interval in the Department of Veterinary Physiology (later REPROGEN) , University of Sydney (Holt et al., 2004). The strain has an average litter size of more than 13 pups, and females commonly nurse up to 18 pups with greater than 90% survival to weaning. Along with an increased body weight (BW), these traits are clearly indicative of enhanced lactation performance (Knight et al., 1986). Indeed lactation performance, assessed by a weigh-suckle-weigh method, was 3-fold greater in QSi5 mice than the CBA strain (Riley et al., 2006). In this study, we utilize the divergent phenotypes of QSi5 and CBA/CaH mice to identify genes associated with enhanced mammary gland capacity.
Keywords: Strain differences

overall_design: Five replicates from each of the two strains CBA and QSi5 were used for gene expression profiling. Mice were force weaned after 9 days of first lactation and the fourth inguinal mammary glands were collected.

first: Palaniappan

last: Ramanathan

first: Ian

last: Martin

first: Margaret

last: Gardiner-Garden

last: Thomson

first: Rosanne

last: Taylor

first: Chris

last: Moran


title: Comparison of the transcriptional profiles of the retinal pigmental epithelium/choroid from young and old mice

status: Public on Mar 29 2008

city: Chicago

first: Huiyi

last: Chen

state: IL

address: 303 E Chicago Ave, Tarry 13-752

department: Ophthalmology

institute: Northwestern University School of Medicine

summary:
To characterize underlying changes in the retinal pigment epithelium (RPE)/choroid with age, we produced gene expression profiles for the RPE/choroid and compared the transcriptional profiles of the RPE/choroid from young and old mice. The changes in the aged RPE/choroid suggest that the tissue has become immunologically active. Such phenotypic changes in the normal aged RPE/choroid may provide a background for the development of age-related macular degeneration.
Keywords: age-related change

overall_design: We compared the gene expression of retinal pigmental epithelium/choroid from young and old animals. There were 4 samples from young mice and 4 samples from old mice. Each sample contained 4 retinal pigmental epithelium/choroid from 2 animals

first: Arthur

middle: H

last: Neufeld

last: Liu

first: Thomas

last: Lukas


title: Comparison of normal and beta catenin deficient kidney gene expression profiles at E12.5

status: Public on Mar 25 2008

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

country: Canada

institute: University of Toronto

summary:
We generated a murine genetic model of beta-catenin deficiency targeted to the ureteric bud cell lineage to study the role of beta-catenin mediated Wnt signaling during ureteric morphogenesis.
Keywords: mutation

overall_design: A comparison was made between triplicate samples of E12.5 kidneys from either normal mice or mice with a b-catenin allele containing LoxP sites flanking exons 2 through 6 crossed to Hoxb7-Cre:Gfp mice

first: Darren

last: Bridgewater

first: Jason

last: Cain

first: Agnes

last: Lau

first: Valerie

last: Athaide

first: Paul

last: Gill

first: Satu

last: Kuure

first: Kirsi

last: Sainio

first: Norman

last: Rosenblum


title: Gene expression profiles of neonatal bladder samples. (GUDMAP Series ID: 19)

status: Public on Apr 17 2008

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 bladder. The central thesis is straightforward. The combination of microdissected tissues and FACS sorted cells plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of FACS sorted newborn bladder cells and compares two distinct cell populations of smooth muscle cells since both of these populations contain EGFP from a SMGA (Actg2) promoter shown to be expressed only in smooth muscle cells.
Gene expression comparison from developing regions of the mouse postnatal day 2 urogenital system.

overall_design: Bladder cells were FACS sorted from newborn double transgenic mice expressing EGFP under the control of a SMGA promoter and EYFP under the control of a SMAA promoter. Total RNA was isolated and underwent 2-round amplification (Epicentre® Biotechnologies) for gene expression analysis using the Affymetrix MOE430 microarray chip.

first: James

last: Lessard

first: Nick

last: Maull


title: Irradiation response in PKBalpha MEF

status: Public on Apr 04 2008

city: Basel

first: Lana

last: Bozulic

address: Maulbeerstr 66

country: Switzerland

institute: FMI

summary:
MEF proficient or deficient in PKBalpha, or PKBalpha knockout MEF where PKBalpha expression was reconstituted by stable transfection were subjected to 10Gy gamma-IR treatment. 4 or 24 hours after treatment, gene expression changes were analyzed.
Keywords: genotype0-specific stress response in PKBalpha MEF

overall_design: three biological replicates were included in the experiment for each condition analyzed. overall, 27 samples were included in the study. the reference samples were untreated MEF of each respective genotype.


title: Transcriptional Adaptation to Clcn5 Knockout in Proximal Tubules of the Mouse Kidney

first: Jerry

middle: M.

last: Wright

address: 725 N. Wolfe St

institute: Johns Hopkins Medical Institutions

summary:
Dent disease has multiple defects attributed to proximal tubule malfunction including low molecular weight proteinuria, aminoaciduria, phosphaturia and glycosuria. In order to understand the changes in kidney function of the Clc5 transporter gene knockout mouse model of Dent disease, we examined gene expression profiles from proximal tubules of mouse kidneys.
Overall 720 genes are expressed differentially in the proximal tubules of the Dent Clcn5 knockout mouse model compared to those of control wild type mice. The fingerprint of these gene changes may help us to understand the phenotype of Dent disease.
Keywords: gene knockout, mouse, Clcn5, Dent's disease

overall_design:
Renal proximal tubules were dissected from wild type and Clcn5 knockout mice. Mice were anesthetized with halothane, the abdominal aorta of each animal was accessed and the left kidney was perfused with an ice-cold salt.  Proximal tubule dissection was performed in an ice-cold salt solution. After dissection of approximately 80-100 segments of 2 mm in length per kidney, the RNA for 3-4 mice was combined to have enough RNA per chip.
3 microarrays each of wild type and knockout mouse proximal tubule were processed

first: Sandra

last: Guggino

first: Marcelo

last: Morales

first: Jackson

last: Sousa-Menzes

first: Debora

last: Ornellas

first: Jennifer

last: Sipes


title: Profiling of CD4+ T cells responding to transient or persistent antigen presented by dendritic cells in vivo

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
These experiments were done to compare the gene expression profiles in CD4+ T cells responding to antigen presented by dendritic cells transiently or persistently. Some treatments include the activation of the dendritic cells by CD40 engagement.
Keywords: immune response

overall_design: 2-4x106 lymph node cells from AND TCR-transgenic animals that expressed the congenic marker CD90.1 were transferred into double-transgenic (Ii-rTA/TIM) recipient animals that expressed the corresponding peptide from moth cytochrome c under a doxycycline-controllable promoter and were FACS-sorted 60 hours later. Recipients expressed the antigen not at all (“ctrl”), transiently (“short”) or throughout the experiment (“long”) due to different doxycycline treatment protocols. A second variable tested was the activation status of the dendritic cells: recipients were either injected by the stimulatory antibody FGK45.5 targeting CD40 (“FGK”) or PBS (“PBS”).

first: Reinhard

last: Obst

first: Hisse-Martien

last: van Santen

first: Rachel

last: Melamed

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Microarray platform comparison study of hippocampal gene expression in DCLK1 transgenic and wild-type mice

city: Leiden

first: Peter

last: 't Hoen

address: PO Box 9600

department: Center for Human and Clinical Genetics

country: Netherlands

institute: Leiden University Medical Center

summary:
The aim of the present study was to compare, on a statistical basis, the performance of different microarray platforms to detect differences in gene expression in a realistic and challenging biological setting. Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina and home-spotted oligonucleotide arrays. We observed considerable overlap between the different platforms, the overlap being better detectable with significance level-based ranking than with a p-value based cut-off. Confirming the qualitative agreement between platforms, Pathway analysis consistently demonstrated aberrances in GABA-ergic signalling in the transgenic mice, even though pathways were represented by only partially overlapping genes on the different platforms.
Keywords: microarray platform comparison

overall_design:
5 biological replicates for each experimental group were analyzed on each of the five platforms. For two-color arrays a dye swap was performed.

ABI_raw_data.csv contains the raw data for GSM206638 to GSM206647.
Illumina_raw_data.csv contains the raw data for GSM206887 to GSM206896.  In these files, the sample identifiers are included in the column headers.

first: P

last: Pedotti


title: Gene expression profiling in BCR/ABL expressing HSCs

status: Public on Mar 22 2008

city: Bar Harbor

first: Shaoguang

last: Li

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary:
The BCR-ABL oncogene,  generated by Philadelphia chromosome, is present in about 95% human Chronic myeloid leukemia (CML) and 20~30% acute lymphoblastic leukemia (ALL). One of BCR-ABL isoforms, P210, is more often detected in CML and ALL patients. Although BCR-ABL kinase inhibitors are effective in controlling the diseases, they do not provide cure due to the development of drug resistance and the insensitivity of leukemia stem cells to these drugs. Identification of new therapeutic targets is critical. To identify potential target against leukemia stem cells, we studied gene expression in leukemia stem cells, which were identified in mice in our lab (Hu Y, Swerdlow S, Duffy TM, Weinmann R, Lee FY, Li S.  2006. Targeting multiple kinase pathways in leukemic progenitors and stem cells is essential for improved treatment of Ph+ leukemia. Proc Natl Acad Sci USA 103(45):16870-16875.). The sorted leukemia stem cells that expressed BCR-ABL were used for isolation of RNA, followed by the analysis of gene expression using the DNA microarray.  The same lineage of non-BCR-ABL-expressing normal hematopoietic stem cells was used as control. We have identified some interesting genes that are up- or down-regulated by BCR-ABL in these leukemia stem cells. We are currently studying the functions of these identified genes.
Keywords: Genetic modification

overall_design:
Identification of genes that are regulated by BCR/ABL in HSCs.
Bone marrow cells are isolated from the long bones of CML mice that are untreated or treated with imatinib. BCR-ABL-expressing or non-BCR-ABL-expressing (transduced with the empty GFP vector) hematopoietic stem cells (GFP+Lin-c-Kit+Sca-1+) are stored by FACS directly into RNAlater (Ambion, Austin, TX) and are homogenized in RLT Buffer (RNeasy Micro Kit (Qiagen, Valencia, CA)). Total RNA is isolated by following the protocol for the RNeasy Micro Kit, and quality is assessed using a 2100 Bioanalyzer instrument and RNA 6000 Pico LabChip assay (Agilent Technologies, Palo Alto, CA). Utilizing the GeneChip Whole Transcript Sense Target Labeling Assay kit (Affymetrix, Santa Clara, CA.) between 100-300ng of total RNA undergoes reverse transcription with random hexamers tagged with T7 sequence.  The double stranded cDNA that is generated is then amplified by T7 RNA polymerase to produce cRNA.  Second cycle first strand cDNA synthesis then takes place incorporating dUTP which is later used as sites where fragmentation occurs by utilizing an uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 enzyme mix.  The fragmented cDNA is then labeled by terminal transferase attaching a biotin molecule using Affymetrix proprietary DNA labeling Reagent.  Approximately 2.0µg of fragmented and biotin-labeled cDNA is then hybridized onto a Mouse Gene ST 1.0 Array (Affymetrix, Santa Clara, CA.) for 16 hours at 45°C.  Post-hybridization staining and washing are performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix). Finally, the arrays are scanned with a GeneChip? Scanner 3000.  Images are acquired and cel files generated which are then used for analysis.

first: Yaoyu

last: Chen

first: Yiguo

last: Hu

first: Haojian

last: Zhang


title: Bmp2 Is Critical for the Murine Decidual Response

status: Public on Mar 21 2008

city: Houston

first: Michael

last: Large

state: TX

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicine

summary:
The role of bone morphogenetic protein 2 (Bmp2)in regulating the transformation of the uterine stroma during embryo implantation in the mouse was investigated by the conditional ablation of Bmp2 in the uterus using the (PR-cre) mouse.
Keywords: Genetic modification

overall_design: Bmp2 gene ablation was confirmed by real-time PCR analysis in the PR-cre; Bmp2fl/fl (termed Bmp2d/d) uterus. While littermate controls average 0.9 litter of 6.2 ± 0.7 pups per month, Bmp2d/d females are completely infertile. Analysis of the infertility indicates that whereas embryo attachment is normal in the Bmp2d/d as in control mice, the uterine stroma is incapable of undergoing the decidual reaction to support further embryonic development. Recombinant human BMP2 can partially rescue the decidual response, suggesting that the observed phenotypes are not due to a developmental consequence of Bmp2 ablation. Microarray analysis demonstrates that ablation of Bmp2 leads to specific gene changes, including disruption of the Wnt signaling pathway, Progesterone receptor (PR) signaling, and the induction of prostaglandin synthase 2 (Ptgs2). Taken together, these data demonstrate that Bmp2 is a critical regulator of gene expression and function in the murine uterus.

first: Kevin

middle: Y

last: Lee

first: Jae-Wook

last: Jeong

first: Jinrong

last: Wang

first: Lijiang

last: Ma

first: James

middle: F

last: Martin

first: Sophia

last: Tsai

first: John

middle: P

last: Lydon

first: Francesco

last: DeMayo


title: Foxj3 KO myoblast transcriptome data

status: Public on Mar 31 2008

city: Birmingham

first: Matthew

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

summary:
Myoblasts harvested from a postnatal day 2 WT and Foxj3 KO litter.
We used Affymetrix microarrays to identify dysregulated transcripts in Foxj3 mutant myoblasts.
Keywords: mutant analysis, skeletal myoblasts

overall_design: Myoblasts were passaged 3 times prior to harvest

first: Daniel

last: Garry

last: Jiang


title: Expression data from UPD18 mice

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

institute: King's College London

summary:
Comparison of gene expression levels between matUPD18 and patUPD18 8.5 dpc whole embryo samples (maternal versus paternal uniparental disomy of Chr 18). Identification of highly differentially expressed transcripts.
Keywords: genetic modification

overall_design: Pairwise array comparative analyses were performed using MAS5/GCOS where sample age and tissue were matched, while the sample genotype varied between the compared arrays: matUPD18 vs patUPD18.

first: Kathryn

last: Woodfine

first: Rebecca

last: Oakey


title: Comparison of parental vs tumor-derived imortalized mouse kidney epithelial cell (iBMK) lines

city: Piscataway

first: Cristina

last: Karp

state: NJ

address: 679 Hoes lane

institute: Rutgers University

summary:
Most tumors are epithelial-derived, and although disruption of polarity and aberrant cellular junction formation is a poor prognosticator in human cancer, the role of polarity determinants in oncogenesis is poorly understood. Using in vivo selection, we identified a mammalian orthologue of the Drosophila polarity regulator crumbs as a gene whose loss of expression promotes tumor progression. Immortal baby mouse kidney epithelial (iBMK) cells selected in vivo to acquire tumorigenicity displayed dramatic repression of crumbs3 (crb3) expression associated with disruption of tight junction formation, apicobasal polarity, and contact-inhibited growth.  Restoration of crb3 expression restored junctions, polarity and contact inhibition, while suppressing migration and metastasis. These findings suggest a role for mammalian polarity determinants in suppressing tumorigenesis that may be analogous to the well-studied polarity tumor suppressor mechanisms in Drosophila.
Keywords: Crumbs, crb3, tight junctions, polarity, metastasis, cancer

overall_design: Gene Expression analysis was carried out using the Affymetrix Mouse 430 A 2.0 chips representing about 22,629 full-length genes and ESTs.  Initial scaling was done using the Affymetrix  Microarray Suite Expression Software version 5.0 and subsequent analysis was done using GeneSpring Software version 6.1 ( Silicon Genetics).     (Tumor derived cell lines) /in vivo selected cell lines were compared to the parental cell lines from which they were derived.  We had two parental cell  line samples which were defined as replicates and treated as a single sample and 4 cell lines namely TD A, B, C and D derived from the parents.      Three different filtering conditions were applied.  First, we applied Expression Percentage Restriction retaining only those genes  which had a raw expression value of 80.0 or more in at least 1 out of the 5 samples being compared.  This enabled us to filter out the low-intensity values while retaining genes that may have a very low expression level in one sample but may be switched on in another sample.  The cut-off value of 80.00 was determined by analyzing the raw data of each of the chips being compared and estimating the average background expression value.  Of the 22,629 genes represented on the chips, 11,418 genes were retained.    Secondly, we filtered on data quality selecting for genes with a Flag value of Present (P) in all the samples being compared.  10,126 genes were retained after applying this filter.    We then carried out a pair-wise fold-change analysis comparing each tumor derived cell line to the parental cell-line.  We retained genes that underwent at least 2 folds or more up-regulation or down-regulation in the tumor derived cell l  ines, compared to the parentals.  1,010 genes were retained after this step.    In order to identify genes that underwent statistically significant changes in gene expression in the tumor derived cell-lines when compared to the parentals we applied a statistical filter analysis and performed the Student’s-t-test with a p value cut-off of 0.05.  Multiple testing correction was turned off.  We found 123 genes that were over-expressed and 5 that were underexpressed.    We carried out two-way hierarchical clustering using the GeneSpring Software 6.1 using standard correlation as similarity metric.  We also analyzed our data using Venn Diagrams in order to identify the statistically significant genes that were common to all 4 tumor derived cell-lines. We obtained 55 that were up-regulated while there were 5 which were down-regulated and common to all four cell-lines.

first: Chandreyee

last: Mukherjee


title: Analysis of RNA distribution between pseudopodia and cell bodies in response to LPA stimulation or fibronectin

status: Public on Mar 18 2008

city: Charlottesville

first: Stavroula

last: Mili

state: VA

address: 1400 Jefferson Park Avenue

department: Microbiology

institute: University of Virginia

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

overall_design: Refer to individual Series


title: Analysis of RNA distribution between pseudopodia and cell bodies in response to Fibronectin

summary:
The goal of the study was to identify on a genome-wide scale RNAs that are enriched at the leading edge of migrating cells. For this, we employed a fractionation method in which cells are plated on a microporous filter whose bottom side only is coated with fibronectin. The cells thus polarize and extend pseudopodial protrusions towards the bottom surface. These protruding pseudopodia can then be physically isolated from the bottom surface of the filter and their contents compared with the remaining cell bodies, which are isolated from the upper surface of the filter.
Keywords: comparative RNA distribution

overall_design: We analyzed 2 independent pseudopodia samples (samples 06-23_PS_A and 06-23_PS_B) and 2 independent cell body samples (samples 06-23_CB_A and 06-23_CB_B)

first: Ian

middle: G

last: Macara


title: Expression data from Hfe-deficient liver and duodenum in mouse strains with differing susceptibilities to iron loading

city: Toulouse

first: Marie-Paule

last: Roth

address: Chu Purpan

country: France

institute: Inserm

summary:
Hfe disruption in the mouse leads to experimental hemochromatosis by a mechanism which remains elusive. Evidence for at least five modifier genes has been obtained. These account for the higher iron load of Hfe-deficient D2 mice compared to B6 mice. Gene expression profling was used to clarify the mechanism of Hfe action and to identify potential modifier genes.
Keywords: response to genetic modification

overall_design: Liver and duodenum were obtained from wild-type and Hfe-deficient B6 and D2 mice (three mice per strain/genotype combination).

first: Helene

last: Coppin


title: Analysis of RNA distribution between pseudopodia and cell bodies in response to LPA stimulation

summary:
The goal of the study was to identify on a genome-wide scale RNAs that are enriched at the leading edge of migrating cells. For this, we employed a fractionation method in which serum-starved cells are first plated and allowed to spread on a microporous filter. Addition of LPA at the bottom side of the filter induces the cells to polarize and extend pseudopodial protrusions. These protruding pseudopodia can then be physically isolated from the bottom surface of the filter and their contents compared with the remaining cell bodies, which are isolated from the upper surface of the filter.
Keywords: comparative RNA distribution

overall_design: We analyzed two independent pseudopodia samples (05-61_PS_A and 06-04_PS_A) and two independent cell body samples (05-61_CB_A and 06-04_CB_A)


title: Expression data from  the colon of wild-type and Slc9a3 (NHE3)-deficient mice

status: Public on Mar 06 2008

city: Tucson

first: Pawel

middle: R.

last: Kiela

address: 1501 N. Campbell Ave.

institute: University of Arizona

summary:
Na+/H+ exchanger 3 (NHE3) provides a major route for intestinal Na+ absorption. It has been considered as a target of proinflammatory cytokines and enteropathogenic bacteria and impaired NHE3 expression and/or activity may be responsible for inflammation-associated diarrhea.
We used microarray analysis to detail the global programme of colonic gene expression in the absence of functional NHE3.
Keywords: knockout effect

overall_design: Whole colon was dissected from 6-8 week old NHE3-deficient mice and their wild-type littermates and total RNA isolated for microarray analysis using Affymetrix murine MOE430 2.0 arrays

middle: R

first: Fayez

middle: K

last: Ghishan


title: NIK/NF-kappaB2 regulated gene products.

status: Public on Mar 05 2008

city: Portland

first: Evan

middle: F.

last: Lind

state: OR

address: Mail Code L220, 3181 SW Sam Jackson Park Road

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

summary:
This study aims at identifying genes that are NIK/NF-kappaB2 responsive in murine dendritic cells matured in vivo.
Keywords: NIK/NF-kappaB2 responsive genes in dendritic cells after TLR/CD40 signaling

overall_design: This study isolated dendritic cells from the spleens of Alymphoplasia or heterozygeous littlermates (wild type).  Mice were eiter not treated as a reference or treated I.P. with 25 micrograms of LPS and 100 micrograms of agonistic anti-CD40 antibody.  DCs were isolated 6 hours after treatment allowing in vivo maturation via both TLR and CD40 signals.  DCs from 3 mice per group were pooled.  Experiment was performed in triplicate.

first: Randolph

middle: J

last: Noelle


title: Predominance of interferon-related responses in the brain during murine malaria as identified by microarray analysis.

status: Public on Mar 14 2008

city: Sydney

first: Jenny

last: Miu

address: 92-94 Parramatta Rd

department: Department of Pathology

institute: University of Sydney

summary:
Cerebral malaria (CM) can be a fatal manifestation of Plasmodium falciparum infection. We examined global gene expression patterns by microarray during fatal murine CM (FMCM) and non-cerebral malaria (NCM). There was differential expression of a number of genes, including some not yet characterized in the pathogenesis of FMCM. Some gene induction was observed during Plasmodium infection regardless of the development of CM and there was a predominance of genes linked to IFN responses, even in NCM. However, upon real-time PCR validation and quantitation, these genes were much more highly expressed in FMCM than in NCM. The observed changes included genes belonging to pathways such as interferon (IFN) signaling, MHC processing and presentation, apoptosis, immunomodulatory and anti-microbial processes. We further characterized differentially expressed genes by examining the cellular source of their expression as well as their temporal expression patterns during the course of malaria infection. These data identify a number of novel genes that represent interesting candidates for further investigation in FMCM.
Keywords: disease state analysis

overall_design: 5 individual mouse brains were collected for each group (Uninfected control, PbA(6), PbK(6), PbK(14). RNA was extracted from these mice and then pooled to create a single sample for hybridisation. Comparisons were made between the experimental groups (PbA(6), PbK(6), PbK(14)) and the reference group (Uninfected control).

first: Nicholas

last: Hunt

first: Helen

last: Ball


title: AFFYMETRIX ANALYSIS OF E9.5 RFC MOUSE KO EMBRYOS REVEALS ALTERED EXPR’N OF GENES IN THE CUBILIN-MEGALIN COMPLEX

status: Public on Mar 17 2008

city: Omaha

first: Janee

last: Gelineau-van Waes

state: NE

address: 985455 Nebraska Medical Center

department: Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

summary:
The reduced folate carrier (RFC1) is an integral membrane protein and facilitative anion exchanger that mediates delivery of 5-methyltetrahydrofolate into mammalian cells.  Adequate maternal-fetal transport of folate is necessary for normal embryogenesis.  Targeted inactivation of the murine RFC1 gene results in post-implantation embryo lethality, but daily folic acid supplementation of pregnant dams prolongs survival of homozygous embryos until mid-gestation.  At E10.5 RFC1-/- embryos are developmentally delayed relative to wildtype littermates, have multiple malformations, including neural tube defects, and die due to failure of chorioallantoic fusion.  The mesoderm is sparse and disorganized, and there is a marked absence of erythrocytes in yolk sac blood islands.  Affymetrix microarray analysis and quantitative RT-PCR validation of the relative gene expression profiles in E9.5 RFC1-/- vs. RFC1+/+ embryos indicates a dramatic downregulation of multiple genes involved in erythropoiesis, and upregulation of several genes that form the cubilin-megalin multiligand endocytic receptor complex.  Megalin protein expression disappears from the visceral yolk sac of RFC1-/- embryos, and cubilin protein is widely misexpressed.  Inactivation of RFC1 impacts the expression of several ligands and interacting proteins in the cubilin-amnionless-megalin complex that are involved in the maternal-fetal transport of folate, vitamin B12, and other nutrients, lipids and morphogens required for normal embryogenesis.
Comparison of RFC KO, wildtype normal embryos vs. RFC KO, nullizygous affected embryos
Keywords: reduced folate carrier knockout, folate receptor, cubilin, megalin, embryos, gene expression, neural tube defect, chorioallantoic fusion

overall_design: 6 samples RFC KO mouse embryos, E9.5, folic acid treated: 3 Control, Wildtype, normal; 3 Affected, Nullizygous, CR/chorioallantoic defect; as paired-littermates with one normal and one affected embryo per set from each of three separate litters for RNA extraction and hybridization on Affymetrix microarrays.

first: J

last: Maddox

first: L

last: Smith

first: M

last: van Waes

last: Wilberding

last: Eudy

last: Bauer

first: R

last: Finnell


title: Identification of MCIP1 as an ATF6-inducible ER Stress Response Gene in the Heart by Gene Expression Profiling

city: San Diego

first: Peter

last: Belmont

address: 10724 Science Center Drive

institute: Pfizer

summary:
We recently found that the endoplasmic reticulum (ER) stress response (ERSR) is activated in surviving cardiac myocytes in a mouse model of in vivo myocardial infarction.  ATF6 is an ER stress-activated transcription factor that induces ERSR genes, some of which encode proteins that may protect against ischemic damage.  However, few ERSR genes have been identified in the heart, and there have been no gene expression profiling studies of ATF6-inducible genes, in vivo.  We previously generated transgenic (TG) mice that express tamoxifen-activated ATF6, ATF6-MER, in the heart; ATF6-MER conferred tamoxifen-dependent ATF6 activation and protection from ischemic damage.  To understand of the mechanism of ATF6-mediated cardioprotection, gene expression profiling of ATF6-MER TG mouse hearts was performed.  Activated ATF6 changed expression levels of 1,162 genes in the heart; of the 775 ATF6-inducible genes, only 23 are known ERSR genes.  One of the genes not expected to be induced by ATF6 is modulatory calcinuerin-interacting protein-1 (MCIP1).  MCIP1 is induced in a calcineurin/NFAT-dependent manner during myocardial hypertrophy and it can feedback inhibit cardiomyocyte growth.  We found that MCIP1 expression in cultured cardiomyocytes was increased by the prototypical ER stresser, tunicamycin (TM), or by simulated ischemia.  Moreover, infecting cardiomyocytes with adenovirus encoding activated ATF6 induced MCIP1 expression and inhibited myocyte growth in response to the alpha 1-adrenergic agonist, phenylephrine.  These results suggest that MCIP1 can be induced in the heart by ER stresses, such as ischemia.  Moreover, b integrating hypertrophy and ER stress, MCIP-modulated myocyte growth may help rejuvenate nascent ER protein folding, which could contribute to protection from ischemic damage.
Keywords: Gene expression analysis of the effect of activating ATF6 in the hearts of transgenic mice upon treatment with tamoxifen.

overall_design: 12 mice were analyzed in this study. Four treatment groups were included in this study: transgenic ATF6-MER mice treated with tamoxifen, transgenic ATF6-MER mice treated with vehicle, nontransgenic littermates treated with tamoxifen, and nontransgenic littermates treated with vehicle. Each treatment group included 3 separate biological replicate samples. Each mouse sampled was male, C57/BL6, ~30 weeks old. Each mouse was treated, then the mouse was sacrificed, the heart was extracted, and left ventricle was isolated. Total RNA was isolated from the left ventricle, and used for hybridization onto an Affymetrix mus 430 2.0 full-genome chip. Each heart was hybridized onto its own chip.

first: Archana

last: Tadimalla

first: Wenqiong

last: Chen

first: Joshua

last: Martindale

first: Donna

last: Thuerauf

first: Natalie

last: Gude

first: Mark

last: Sussman

first: Christopher

middle: C

last: Glembotski


title: Differential expression of genes in pancreatic islets from high fat fed AKR/J and C57Bl/6J

status: Public on Feb 28 2008

city: Norfolk

first: yumi

last: imai

address: 799W Olney Road, LH 2156

institute: Eastern Virginia Medical School

summary:
Increased fat intake is associated with obesity and insulin resistance. In some individuals, a failure of pancreatic b-cells to increase insulin production in response to the high demands of obesity leads to diabetes. We sought to determine whether the impaired b- cell adaptation in obesity is associated with differential expression of genes involved in b-cell expansion and intermediary metabolism. Two strains of inbred mice prone to obesity, C57Bl/6J and AKR/J, were fed regular rodent chow or high-fat diet, after which islet morphology, secretory function and gene expression were assessed. AKR/J had lower blood glucose and higher insulin levels compared with C57Bl/6J mice on regular rodent chow or high fat diet. Insulin secretion was 3.2 fold higher in AKR/J than C57Bl/6J mice following intraperitoneal glucose injection. Likewise, glucose-stimulated insulin secretion from isolated islets was higher in AKR/J. Additionally, islet mass was 1.4 fold greater in AKR/J compared with C57Bl/6J. To elucidate the factors associated with the differences in insulin, we analyzed the gene expression profiles in pancreatic islets in AKR/J and C57Bl/6J mice. Of 14,000 genes examined, 220 were up-regulated and 286 were down-regulated in islets from diet-induced obese AKR/J mice compared with C57Bl/6J mice. Key genes involved in islet signaling and metabolism, e.g. glucagon like peptide-1 receptor, sterol Co-A desaturase 1 & 2 and fatty acid desaturase 2 were upregulated in obese AKR/J mice. The expression of multiple extracellular matrix proteins was also increased in AKR/J mice, suggesting a role in modulation of islet mass. Functional analyses of differentially regulated genes hold promise for elucidating factors linking obesity to alterations in islet function.
Keywords: response to high fat diet

overall_design: Microarray analyses were performed on quadruplicate RNA samples of pancreatic islets from AKR and Bl6 mice placed on high-fat diet for 3 months. Pancreases from two mice were combined to yield one sample of islet RNA. All protocols were conducted as described in the Affymetrix GeneChips Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA) using 5 μg total RNA and GeneChip Mouse Expression Arrays MOE 430 (Affymetrix).

first: Yumi

last: Imai

first: Rexford

last: Ahima


title: Investigating genes regulated by mir-155 in a mouse macrophage cell line

status: Public on Mar 24 2008

city: Pasadena

first: David

last: Baltimore

address: 1200 E California Blvd

institute: Caltech

summary:
Mammalian microRNAs (miRNAs) are emerging as key regulators of the development and function of the immune system. Here, we report a strong but transient induction of miR-155 in mouse bone marrow after injection of bacterial lipopolysaccharide (LPS) correlated with granulocyte/monocyte (GM) expansion. Demonstrating the sufficiency of miR-155 to drive GM expansion, enforced expression in mouse bone marrow cells caused GM proliferation in a manner reminiscent of LPS treatment. However, the mir-155-induced GM populations displayed pathological features characteristic of myeloid neoplasia. Extending possible relevance to human disease, miR-155 was overexpressed in the bone marrow of patients with acute myeloid leukemia (AML). Furthermore, miR-155 repressed a subset of genes implicated in hematopoietic development and disease. These data implicate miR-155 as a contributor to physiological GM expansion during inflammation and to certain pathological features associated with AML, emphasizing the importance of proper miR-155 regulation in developing myeloid cells during times of inflammatory stress.
Keywords: genetic modification

overall_design: Construct stable RAW264.7 mouse macrophage cell lines expressing mir-155 or empty vector. RNA is extracted and global gene expression analysis performed to identify mir-155 regulated mRNAs.

first: Ryan

middle: M

last: O'Connell

first: Dinesh

last: Rao

first: Aadel

last: Chaudhuri

last: Boldin

first: Konstantin

middle: D

last: Taganov

first: John

last: Nicoll

first: Ronald

last: Paquette


title: Traf2 and Traf3 B cell knockout mice and Baff tg mice - gene expression in lymph node B cells

city: Darlinghurst

first: Sandra

last: Gardam

address: 384 Victoria St

department: Autoimmunity Unit

institute: Garvan Institute of Medical Research

summary:
Tumor necrosis factor-associated factors 2 and 3 (TRAF2 and TRAF3) were shown to function in a co-operative and non-redundant manner to suppress nuclear factor-κB2 (NF-κB2) activation, gene expression and survival in mature B cells. In the absence of this suppressive activity, B cells developed independently of the obligatory B cell survival factor, BAFF (B cell activating factor of the tumor necrosis factor family).  This constitutive, lineage-specific suppression of B cell survival by TRAF2 and TRAF3 determines the requirement for BAFF to sustain B cell development in vivo.  We wished to investigate the effect on gene expression in B cells which lacked the negative regulators TRAF2 and TRAF3, and hence had hyperactive NF-kB2 signalling.  As Baff-tg mice display a similar phenotype, and have a genetic modification which acts in the same pathway, yet further up, than TRAF2 and TRAF3, we wished to compare and contrast Baff-tg B cells with TRAF2 and TRAF3 deficient B cells.  This analysis should identify genes that are important in B cell survival.
Keywords: Genetic modification

overall_design: Lymph node B cells were purified from Traf2 B cell knockout mice, Traf3 B cell knockout mice, Baff-tg mice and respective controls.  RNA was extracted and hybridised to Affymetrix 430 2.0 Mouse Genome Arrays.  Samples were processed and hence analysed on three spearate days.  Day 1 two control mice: Traf2lox/lox pool and CD19-cretg were compared to two knockout mice: Traf2DB 80 and Traf3DB 94.  On Day 2 three control mice: Traf2lox/lox 77, Traf2lox/lox 79 and Traf3lox/lox 97 were compared to two knockout mice: Traf2DB 76 and Traf3DB 01.  On Day 3 three control mice: WT33, WT34, WT35 were compared to three Baff-tg mice: Baff-tg 99, Baff-tg 100, Baff-tg 101.

first: Robert

last: Brink


title: Gene expression of mouse ES cells, Eed KO

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

summary:
The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2).  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC1. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.
Keywords: genetic modification

overall_design:
Eed is a protein included in PRC2 (Polycomb repressor complex).
We generated constitutive Eed KO mouse ES cells and observed gene expression using Affymetrix MOE430.2 microarray.
These results were compared with other KO cells of PRC1 proteins (Ring1A, Ring1B) and other proteins in our study.

first: Mitsuhiro

last: Endoh

middle: A

first: Yuichi

last: Fujimura

first: Osamu

last: Ohara

first: Tetsuro

last: Toyoda

first: Arie

last: Otte

first: Masaki

last: Okano

first: Hitoshi

last: Niwa

first: Neil

last: Brockdorff

first: Miguel

last: Vidal

first: Haruhiko

last: Koseki


title: Mouse Salmonella Study

status: Public on Feb 22 2008

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
Salmonella enterica serotype Typhimurium causes an acute inflammatory reaction in the cecum of streptomycin pre-treated mice. We determined global changes in gene expression elicited by serotype Typhimurium in the cecal mucosa. The gene expression profile was dominated by T cell derived cytokines and genes whose expression is known to be induced by these cytokines. Markedly increased mRNA levels of interferon (IFN-gamma), interleukin-22 (IL-22) and IL-17 were detected by quantitative real-time PCR. Furthermore, mRNA levels of genes whose expression is induced by IFN-gamma, IL-22 or IL-17, including macrophage inflammatory protein 2 (MIP-2), inducible nitric oxide synthase (Nos2), lipocalin-2, MIP-1alpha, MIP-1beta, and keratinocyte-derived cytokine (KC), were also markedly increased. To assess the importance of T cells in orchestrating this pro-inflammatory gene expression profile, we depleted T cells using a monoclonal antibody prior to investigating cecal inflammation caused by serotype Typhimurium in streptomycin pre-treated mice. Depletion of CD3+ T cells resulted in a dramatic reduction in gross pathology, a significantly reduced recruitment of neutrophils and a marked reduction in mRNA levels of IFN-gamma, IL-22, IL-17, iNOS, lipocalin-2 and KC. Our results suggest that T cells play an important role in amplifying inflammatory responses induced by serotype Typhimurium in the cecal mucosa.
Keywords: Disease state analysis

overall_design: Determine global changes in gene expression elicited by serotype Typhimurium in the cecal mucosa. For each condition, control and infected, total cecal RNA from 4 mice was pooled


title: F9 Embryonal Carcinoma cell line

status: Public on Feb 27 2008

city: New York

first: Lisa

last: Dailey

state: NY

address: 550 1st Avenue

institute: NYU School of Medicine

summary:
Expression profile for undifferentiated F9 Embryonal Carcinoma cell line
Keywords: expression profile

overall_design: 3 replicates of RNA derived from undifferentiated F9 cells

first: Mahesh

last: Yaragatti

first: Claudio

last: Basilico


title: Expression data from mouse germline stem (GS), multipotent germline stem (mGS), and embryonic stem (ES) cells.

status: Public on Feb 23 2008

city: kyoto

first: jiyoung

last: lee

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Molecular Genetics

institute: kyoto university

summary:
A single spermatogonial stem cell can aquire pluripotentiality but that conversion into a pluripotent cell type is accompanied by loss of spermatogenic potential.
We used microarrays to compare the expression profiles among the different stem cell types.
Keywords: cell type comparison

overall_design: GS, mGS and ES cells were cultured for RNA extraction and hybridization on Affymetrix microarrays. We examined the gene expression profiles of GS and mGS cells to find candidate molecules that are involved in the conversion process of GS into mGS cells.

first: Takashi

last: Shinohara


title: Retinal transcripts level alteration in the prCAD -/- mouse, a model for retinal degeneration

status: Public on Feb 21 2008

city: Baltimore

first: Amir

last: Rattner

address: 725 North Wolfe St., PCTB Room 805

department: Molecular Biology and Genetics

institute: Johns Hopkins University

summary:
This experiment was designed to identify transcripts that exhibit changes in abundance in the context of retinal degeneration by comparing transcript levels in  adult wild type and prCAD -/-  mouse retinas.
Keywords: genetic mutant analysis

overall_design: Retinas were dissected from ~4 weeks old mice. Retinas from 3 prCAD knockout mice or wild type 129 mice were pooled for each sample and 3 replicate of wild type and mutant samples were analysed.

first: Jeremy

last: Nathans


title: Gene expression of mouse ES cells in Gata6 overexpression experiments

first: Takaho

last: Endo

summary:
The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2)1.  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC1. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.
Keywords: genetic modification

overall_design:
ES cells were genetically modified to overexpress Gata6 responding to dex.
Gata6 overexpression induces differentiation of ES cells.
Repressed and derepressed genes in these cells were compared with other experiments and we analyzed how these expression patterns were similar or not similar.

first: Mitsuhiro

last: Endoh

first: Yuichi

last: Fujimura


title: Gene expression of mouse ES cells, Dnmt1 KO

summary:
The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2)1-5. PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC13-7. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8. PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4. We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.
Keywords: genetic modification

overall_design:
Gene expression in Dnmt1-KO cells were observed using Affymetrix chip: MOE 430 2.0.
These experiments were performed to obtain control of KO cells for other experiments that affect stem cell differentiation.

first: Osamu

last: Ohara

first: Tetsuro

last: Toyoda

first: Arie

last: Otte


title: Mll-AF9 induced changes in gene expression in various hematopoietic cells

status: Public on Feb 25 2008

city: Minneapolis

first: Ashish

last: Kumar

state: MN

address: 425 East River Road

institute: University of Minnesota

summary:
The pathways by which oncogenes, such as MLL-AF9, initiate transformation and leukemia in  humans and mice are incompletely defined. In a study of target cells and oncogene dosage, we found that  Mll-AF9, when under endogenous regulatory control, efficiently transformed LSK (Lin- Sca1+ c-kit+) stem  cells while committed granulocyte-monocyte progenitors (GMPs) were transformation-resistant and did not  cause leukemia. Mll-AF9 was expressed at higher levels in hematopoietic stem (HSC) than GMP cells. Mll-  AF9 gene dosage effects were directly shown in experiments where GMPs were efficiently transformed by  the high dosage of Mll-AF9 resulting from retroviral transduction. Mll-AF9 up-regulated expression of 196  genes in both LSK and progenitor cells, but to higher levels in LSKs than in committed myeloid progenitors.
Keywords: mutant hematopoietic cells

overall_design: Comparison of gene expression profiles among four types of hematopoietic cells (GMP, CMP, CLP and HSC), FACS sorted from wild type and Mll-AF9 knock-in mice. The goal was to identify genes differentially expressed in each Mll-AF9 cell type compared to the corresponding wild type cells.

first: Weili

last: Chen

first: Thien

middle: N

last: Sam

first: Baolin

last: Wu

first: Rodney

last: Staggs

first: Wendy

last: Hudson

first: Erik

last: Lund

first: Quanzhi

last: Li

first: John

middle: H

last: Kersey


title: Medulloblastomas derived from Cxcr6 mutant mice respond to treatment with a Smoothened inhibitor

status: Public on Mar 01 2008

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary:
Study of mouse medulloblastoma in response to inhibitor of Smoothened.
Keywords: gene modification

overall_design: Several signal array comparisons are used to supplement other forms of data.  There are insufficent replicates for a statistical treatment.

first: Ken

last: Sasai

first: Justyna

middle: T

last: Romer

first: Hiromichi

last: Kimura

first: Derek

middle: E

last: Eberhart

first: Dennis

last: Rice

first: Tom

last: Curran


title: BAF 250 ko ES cells series

city: Berkeley

first: Ping

last: Hu

state: CA

address: Hearst & Oxford

department: MCB

institute: University of California, Berkeley

summary:
To study the function of BAF250 during ES cell self renewal and differentiation
Keywords: gene expression comparison between heterozygous,homozygoous and wild type ES cells

overall_design: wild type,BAF250 heterozygous, and BAF250 homozygous ES cells were analyzed

first: Xiaolin

last: Gao

first: Peri

last: Tate

first: Robert

last: Tjian

first: William

last: Skarnes

first: Zhong

last: Wang


title: Gene expression of mouse ES cells, Ring1A/B double KO

first: Takaho

last: Endo

summary:
The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2)1-5.  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC13-7. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog9. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.
Keywords: genetic modification

overall_design:
We observed gene expression of Ring1B single and Ring1A/B double KO cells using Affymetrix chip: MOE 430 2.0.
Because constitutive Ring1A/B-dKO cells can not be maintained we generated conditional KO cells with OHT.

first: Mitsuhiro

last: Endoh

first: Yuichi

last: Fujimura

first: Osamu

last: Ohara

first: Tetsuro

last: Toyoda

first: Arie

last: Otte

first: Masaki

last: Okano

first: Hitoshi

last: Niwa

first: Neil

last: Brockdorff

first: Miguel

last: Vidal

first: Haruhiko

last: Koseki


title: Gene expression of mouse ES cell, conditional Pou5f1 KO

overall_design: These experiments were designed to investigate how gene expression would be affected in the absence of Oct3/4 in mouse ES cells. Because constitutive Oct3/4 KO cells are not maintained, we generated conditional KO cells.


title: Expression data from Helicobacter pylori-infected mouse gastric epithelial progenitor and non-progenitor cells.

city: Saint Louis

first: Marios

last: Giannakis

state: MO

address: 4444 Forest Park Blvd.

department: Developmental Biology

institute: Washington University in Saint Louis

summary:
Helicobacter pylori clinical isolates can establish themselves in gastric epithelial stem cells and this interaction may have implications for gastric tumorigenesis. Mouse gastric epithelial progenitor cells (mGEPs) and non-progenitor gastric epithelial cells (npGECs) were infected for 24hrs with Helicobacter pylori clinical isolates Kx1 and Kx2. Kx1 was isolated from a patient with chronic atrophic gastritis (ChAG) and Kx2 from the same patient 4 years later, when he progressed to gastric adenocarcinoma.
Keywords: RNA Expression Array

overall_design: mGEPs and npGECs were seeded and grown to 70% confluency in RPMI1640 medium supplemented with 10% FBS before being infected with H. pylori strains Kx1 or Kx2 that had been grown to log phase. After 24h, media and non-attached bacteria were washed off and the cells harvested by trypsinization. RNA was prepared from triplicate cultures of mGEP cells infected with Kx1 or Kx2, npGECs infected with Kx1 or Kx2 and uninfected mGEPs and npGECs that served as controls.

first: Jeffrey

middle: I

last: Gordon


title: Expression data of bronchoalveolar lavage cells from control or urethane treated  AJ mice

status: Public on Feb 20 2008

city: Denver

middle: S

last: Stearman

state: CO

address: 4200 E Ninth Ave

department: Medicine/Pulmonary

institute: UCHSC

summary:
AJ mouse is susceptible to lung carcinogenesis from urethane treatment and is a good model for human adenocarcinoma.  We completed a study using microarray analysis of bronchoalveolar lavage cells from control or urethane treated mice. A unique macrophage expression signature in the lung tumor microenvironment was able to correctly classify the lavage samples.
Keywords: AJ mouse control and urethane treatment carcinogenesis protocol

overall_design: RNA from bronchoalveolar lavage cells of age matched untreated AJ mice controls (C) or from urethane treated (T) AJ mice was prepared. Datasets were accurately classified using a unique macrophage gene expression signature derived from the tumor microenvironment.

first: Lori

last: Nield

first: Michael

last: Grady

first: Alvin

last: Malkinson

first: Mark

middle: W

last: Geraci


title: Intestinal gene expression in ENU mutagenesis mouse strains with missense mutations in Muc2 mucin and ER stress

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

institute: Queensland Facility for Advanced Bioinformatics

summary:
Background
MUC2 mucin produced by intestinal goblet cells is the major component of the intestinal mucus barrier.  MUC2 homo-oligomerizes intracellularly into large secreted polymers which give mucus its viscous properties. The inflammatory bowel disease (IBD) ulcerative colitis is characterized by depleted goblet cells and a reduced mucus layer, whereas goblet cells and the mucus layer are increased in the other major inflammatory bowel disease, Crohn’s disease.

Methods and Findings
By murine N-ethyl-N-nitrosourea-mutagenesis we identified two distinct non-complementing missense mutations in Muc2 exons encoding N- and C-terminal homo-oligomerization domains causing an ulcerative colitis-like phenotype.  Both strains developed mild spontaneous distal intestinal inflammation, chronic diarrhea, rectal bleeding and prolapse, increased susceptibility to acute and chronic colitis induced by a luminal toxin, aberrant Muc2 biosynthesis, smaller goblet cell thecae (less stored mucin) and a diminished mucus barrier. Enhanced local production of IL-1beta, TNF-alpha and IFN-gamma was seen in the distal colon.  The number of leukocytes within mesenteric lymph nodes was increased five-fold and leukocytes cultured in vitro produced both Th1 and Th2 cytokines (IFN-gamma, TNF-alpha and IL-13). Intestinal permeability was increased and the luminal bacterial flora were more heavily coated with immunoglobulin as occurs in IBD. This pathology was accompanied by accumulation of the Muc2 precursor and ultrastructural and biochemical evidence of endoplasmic reticulum (ER) stress in goblet cells, activation of the unfolded protein response, and altered intestinal expression of genes involved in ER stress, inflammation, apoptosis and wound repair. Expression of mutated Muc2 oligomerization domains in vitro demonstrated that aberrant Muc2 oligomerization underlies the ER stress. These models show that mutations in Muc2 oligomerization domains can lead to aberrant assembly of the Muc2 complex leading to ER stress, a depleted mucus barrier and intestinal inflammation.  In ulcerative colitis we demonstrate similar accumulation of non-glycosylated MUC2 precursor in goblet cells together with ultrastructural and biochemical evidence of ER stress even in non-inflamed intestinal tissue.
Conclusions
The observations that mucin misfolding and ER stress lead directly to intestinal inflammation and that ER stress and goblet cell pathology occur in ulcerative colitis suggest that ER stress-related mucin depletion could be a fundamental component of the pathogenesis of colitis.
Keywords: Single gene, multiple mutant comparison

overall_design: 3 individual mice from the Eeyore, Winnie or Wild-type strains were compared as groups. An Affymetrix ID was compared between groups if the ID was Present within two of the three mice within each grouping. IDs were compared by calculating the log2 of Group One average signal divided by Group 2 average signal.

first: Chad

last: Heazlewood

first: Matthew

last: Cook

first: Rajaraman

last: Eri

first: Douglas

last: Taupin

first: David

last: Thornton

first: Chin-Wen

last: Png

first: Tanya

middle: L

last: Crockford

first: Richard

last: Cornall

first: Masato

last: Kato

first: Keats

last: Nelms

first: Nancy

last: Hong

first: Timothy

last: Florin

first: Christopher

last: Goodnow

last: McGuckin


title: The genomic response to retinal disease and injury: evidence for endothelin signaling from photoreceptors to glia.

first: Amir

last: Rattner

state: MD

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

overall_design: Refer to individual Series


title: IL-9/mast cell-mediated intestinal permeability predispose to oral antigen hypersensitivity

city: Cincinnati

first: Simon

last: Hogan

state: OH

address: 3333 burnet avenue

department: Allergy and Immunology

institute: Cincinnati Children's Hospital

summary:
Small intestine of a pool of three Wt mice and a pool of 3 IL-9tg mice in a balb/c backround.
We demonstrated that intestinal IL-9 over expression predispose to oral antigen sensitization
Keywords: TG vs WT

overall_design: In the study, we hybridized RNA from 6-8 week old small intestine of wild type (WT) control and Interleukin 9 (IL-9Tg) to Affymetrix MOE430 2 GeneChip® arrays. Each sample is a pool of three mice.

first: Elizabeth

last: Forbes

first: Katherine

last: 'Groschwitz

first: J

middle: P

last: Abonia

first: Eric

middle: B

last: Brandt

last: Cohen

first: Carine

last: Blanchard

last: Ahrens

first: Luqman

last: Seidu

first: Andrew

last: McKenzie

last: Strait

first: Fred

last: Finkelman

first: Paul

last: Foster

first: Klaus

last: Matthaei

first: Marc

last: Rothenberg


title: The retinal transcriptional response to light damage

status: Public on Feb 15 2008

summary:
Transcriptional profiles were compared between dark adapted and light damaged BALBc (albino) mouse retinas.
Keywords: stress response

overall_design: BALBc mice were dark adapted for one week. To produce light damage a subset of the mice were then exposed to 6,000 lux white fluorescent light for 6 hours. Retinas were collected for RNA extraction 24 hours after light damage.

first: Jeremy

last: Nathans


title: Superseries_Endoh2008_PcG_Pou5f1

first: Takaho

last: Endo

type: Genome binding/occupancy profiling by genome tiling array

summary:
The Polycomb group (PcG) gene products mediate heritable silencing of developmental regulators in metazoans, participating in one of two distinct multimeric protein complexes, the Polycomb repressive complexes-1 (PRC1) and -2 (PRC2).  PRC2 catalyses trimethylation of histone H3 at lysine 27 (H3K27) which in turn is thought to provide a recruitment site for PRC1. Recent studies demonstrate that mono-ubiquitylation of histone H2A at lysine 119 is important in PcG mediated silencing with the core PRC1 component Ring1A/B functioning as the E3 ligase8.  PRC2 has been shown to share target genes with the core transcription network to maintain embryonic stem (ES) cells including Oct4 and Nanog. Here we identify an essential role for PRC1 in repressing developmental regulators in ES cells, and thereby in maintaining ES cell pluripotency. A significant proportion of the PRC1 target genes are also repressed by Oct4.  We demonstrate that engagement of PRC1 and PRC2 at target genes is Oct4-dependent and moreover that Ring1B interacts with Oct4. Collectively these results show that PcG complexes are instrumental in Oct4-dependent repression required to maintain pluripotency of ES cells. This study provides a first functional link between a core ES cell regulator and global epigenetic regulation of the genome.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
This study is designed to investigate a functional link between a core ES cell regulator and global epigenetic regulation.
ChIP-chip experiments (GSM266076 and GSM266077) revealed the Ring1B-binding sites in promoter regions in ES cells. Microarray experiments were also performed (GSM265040 and GSM265041 for Ring1B KO, GSM265042 and GSM265043 for Ring1A and Ring1B double KO, and GSM265044, GSM265045 and GSM266115 for Oct3/4 KO).
Our study focused how these genes interplay in the regulation of gene expression in ES cells.

first: Mitsuhiro

last: Endoh

first: Yuichi

last: Fujimura

first: Osamu

last: Ohara

first: Tetsuro

last: Toyoda

first: Arie

last: Otte

first: Masaki

last: Okano

first: Hitoshi

last: Niwa

first: Neil

last: Brockdorff

first: Miguel

last: Vidal

first: Haruhiko

last: Koseki


title: AKT regulates de novo induction of Foxp3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
The CD4+Foxp3+ regulatory T cells play an essential role in maintaining tolerance via their suppressive function on conventional T cells.  The intracellular signaling pathways that regulate Foxp3 expression are largely unknown.  In this study we describe a novel inhibitory role for AKT in regulating de novo induction of Foxp3 both in vivo and in vitro.  A constitutively active allele of AKT significantly diminished TGF-â induced Foxp3 induction via a rapamycin-sensitive pathway, establishing a role for the AKT-mTOR axis in Treg cells. Moreover, the observed impairment in Foxp3 induction was paralleled by a selective downmodulation of the imparted Treg transcriptional signature highlighting the importance of the balance of intracellular signals in Treg differentiation .  Our results provide a basis for further elucidation of molecular mechanisms that regulate Foxp3 induction and identify AKT as an important negative regulator of this process.
Keywords: Cell population comparison

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled for sorting, and three replicates were generated for all groups. RNA from 0.5-2.5 x 105 cells was amplified, labeled, and hybridized to Affymetrix M430v2 microarrays. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

first: Sokol

last: Haxhinasto

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Rb Intrinsically Promotes Erythropoiesis by Coupling Cell Cycle Exit with Mitochondrial Biogenesis

status: Public on Feb 14 2008

first: Vijay

middle: G.

last: Sankaran

address: 300 Longwood Avenue

department: Department of Medicine

institute: Children's Hospital Boston

summary:
Regulation of the cell cycle is intimately linked to erythroid differentiation, yet how these processes are coupled is not well understood. To gain insight into this coordinate regulation, we examined the role that the retinoblastoma protein (Rb), a central regulator of the cell cycle, plays in erythropoiesis. We found that Rb serves a cell-intrinsic role and its absence causes ineffective erythropoiesis, with a differentiation block at the transition from early to late erythroblasts. Unexpectedly, in addition to a failure to properly exit the cell cycle, mitochondrial biogenesis fails to be upregulated concomitantly, contributing to this differentiation block. The link between erythropoiesis and mitochondrial function was validated by inhibition of mitochondrial biogenesis. Erythropoiesis in the absence of Rb resembles the human myelodysplastic syndromes, where defects in cell cycle regulation and mitochondrial function frequently occur. Our work demonstrates how these seemingly disparate pathways play a role in coordinately regulating cellular differentiation.
Keywords: disease state analysis

overall_design: Microarray expression analysis from sorted CD71+/Ter-119+ bone marrow erythroid progenitors of Rb-null animals and controls.  The Rb-null genotype was EpoR-GFPcre/+; Rb fl/fl and the control genotype was EpoR-GFPcre/+; Rb fl/+.  We have analyzed 3 Rb-null datasets and 3 control datasets.

middle: G


title: Microarray based comparison of gene expression in stria vascularis of 129S6 mice lacking slc26a4 and wildtype controls

city: Manhattan

first: Philine

last: Wangemann

state: KS

address: 1600 Dension Avenue

department: Anatomy and Physiology

institute: Kansas State University

summary:
To see for differential expression of genes in the stria vascularis of wild type and pendrin knockout mice
Keywords: Knockout vs Control

overall_design: Six samples in total of stria vascularis RNA were analyzed. Triplicates from wild type and pendrin knockout mice were run and analyzed.

first: Ruchira

last: Singh

first: Rajanikanth

middle: J

last: Maganti

first: Sairam

middle: V

last: Jabba


title: Identification of genes controlled by LMX1B in the developing mouse hindlimb bud

city: Montreal

first: dayana

last: krawchuk

state: QC

address: 110 Ave. des Pins O.

institute: IRCM

summary:
A control vs. genetic knockout experiment aimed at determining what RNAs are upregulated or downregulated in e11.5 mouse proximal limb tissue lacking the Lmx1b gene.  Because Lmx1b is required for dorsal-ventral patterning of the limb, this screen gives insight into what putative downstream targets of Lmx1b contribute to dorsal-ventral patterning.
Keywords: Genetic allele comparison

overall_design: The proximal portion of e11.5 hindlimb buds (~500um) was used for RNA extraction.  Each array was hybridized with pooled cRNAs from both hindlimb buds of three embryos (6 hindlimbs/sample).

first: Dayana

last: Krawchuk

first: Artur

last: Kania


title: Gene regulation profile of Medroxyprogesterone acetate (MPA)-treated late pregnant cervix

status: Public on Feb 06 2008

city: philadelphia

first: Hua

last: Xu

state: PA

address: 421 Curie Blvd

department: OB/GYN

institute: University of Pennsylvania

summary:
Noval and traditional signaling pathways involved in cervical ripening that were regulated by MPA were identified.
Keywords: Mouse, translational research

overall_design: MPA treatment on E15 pregnant cervix (n=6) vs Vehicle group (n=6)

first: Michal

last: Elovtiz


city: Kuopio

first: Markus

last: Storvik

address: University of Eastern Finland

department: Pharmacology

country: Finland

institute: University of Eastern Finland

summary:
The effect of dietary calcium and dairy proteins on adipose tissue gene expression profile in diet induced obesity
Keywords: disease state analysis

overall_design: 9-week-old C57Bl/6J-mice were divided into two groups (n=10/group). The control diet was a standard high-fat diet (60% of energy) low in calcium (0.4%). The whey protein diet was a high-calcium (1.8%) high-fat diet with whey protein isolate. After the 21-week treatment, the adipose tissue transcript profiling (2 mice/group) was carried out using Affymetrix Mouse Genome 430 2.0 array.

first: Taru

middle: K

last: Pilvi

first: Marjut

last: Louhelainen

first: Riitta

last: Korpela

first: Eero

middle: M

last: Mervaala


title: Transcriptional response to PFOA in wild-type and PPARalpha-null mice

status: Public on Feb 04 2008

city: RTP

first: Hongzu

last: Ren

state: NC

address: 109 TW Alexander Dr

institute: US Environmental Protection Agency

summary:
Toxicogenomic Dissection of the Perfluorooctanoic Acid (PFOA) Transcript Profile in Mouse Liver: Evidence for the Involvement of Nuclear Receptors PPARalpha and CAR
We performed a toxicogenomics dissection of the transcript profiles in the mouse liver after exposure to PFOA.  We uncovered classes of genes that were regulated independently of PPARalpha.  Some of these genes, including those involved in lipid metabolism, may be regulated by PPARbeta/delta or PPARgamma, whereas others, such as those involved in xenobiotic metabolism are likely regulated through CAR.
Keywords: toxicogenomic analysis

overall_design: 129S1/SvlmJ wild-type and PPARalpha-null mice were exposed to 3 mg/kg/day PFOA or water for 7 days.  Total RNA was isolated from liver samples and gene expression analyzed using Affymetrix Mouse 430 2.0 GeneChips.  Data from 16 samples, with four mice in each of the 4 treatment groups, were analyzed.

first: Mitchell

last: Rosen

first: Janice

last: Lee

first: Beena

last: Vallanat

first: Jie

last: Liu

first: Michael

last: Waalkes

first: Barbara

middle: D

last: Abbott

first: Christopher

last: Lau

first: J

middle: C

last: Corton


title: AJ mouse lung carcinogenesis study

first: Robert

last: Stearman


title: Emx2 knock-out urogenital epithelium

status: Public on Jan 30 2008

city: Okazaki

first: Ken-ichirou

last: Morohashi

state: Aichi

address: 5-1 Higashiyama, Myodaiji

department: Developmental biology

institute: National institute for basic biology

summary:
Series of samples studying effect of knock out Emx2 in urogenital epithelium of mouse embryos at E10.5.
Keywords: repeated sample

overall_design: The epithelial cells of the gonadal primordium were obtained by Laser Microdissection System. The specimens prepared from three individuals were mixed as one pool. There are three experimental replicates in each genotype, 3-pools of wild-type and 3-pools of Emx2 KO mouse.