title: T cell-expressed proprotein convertase furin is essential for maintenance of peripheral tolerance

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

summary: Furin is a proprotein convertase induced in activated T cells, reported to processes the anti-inflammatory cytokine TGFb-1.  Herein, we show that conditional deletion of furin in T cells allowed for normal T cell development but impaired the function of regulatory T cells and effector cells, which produced less TGFb-1.  Furin-deficient Treg cells, were less protective in a T cell transfer colitis model and failed to induce Foxp3 in normal T cells. Furin-deficient effector cells were inherently overly active and were resistant to suppressive activity of wild-type Tregs. Thus, our results indicate that furin is indispensable in maintaining peripheral tolerance, which is due, at least in part, to its nonredundant, essential function in regulating TGFb-1 production.  Targeting furin has emerged as a strategy in malignant and infectious disease.  The current work suggests that inhibiting furin might activate immune responses, but may result in a breakdown in peripheral tolerance.

overall_design: Naive CD4+ CD62L+ CD44- T cells were isolated from Fur flox/flox and CD4 cre Fur flox/flox mice. Replicated samples were achieved for wild type and knockout conditions.

first: Marko

last: Pesu

first: Wendy

last: Watford

first: Lili

last: Xu

first: Ivan

last: Fuss

first: Warren

last: Strober

first: John

last: Anderson

first: Ethan

last: Shevach

first: Martha

last: Quezado

first: Nicolas

last: Bouladoux

first: Anton

last: Roebroek

first: Yasmine

last: Belkaid

last: Creemers

last: O'Shea


title: PPARdelta ligand GW1516, AMPK agonist AICAR, and exercise training

status: Public on Jun 18 2008

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

country: USA

institute: Salk Institute

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

overall_design: Refer to individual Series


title: Selective miRNA disruption in Tregs leads to uncontrolled autoimmunity

status: Public on Jun 20 2008

city: San Francisco

first: Xuyu

last: Zhou

address: 513 Parnassus Ave

department: Diabetes Center

institute: UCSF

summary: A new Treg-specific, FoxP3-GFP-hCre BAC transgenic was crossed to a conditional Dicer knock-out mouse strain to analyze the role of microRNAs (miRNA) in the development and function of regulatory T cells (Tregs). Although thymic Tregs developed normally in this setting, the cells showed evidence of altered differentiation and dysfunction in the periphery. Dicer-deficient Treg lineage cells failed to remain stable as a subset of cells down-regulated the Treg-specific transcription factor, FoxP3, while the majority expressed altered levels of multiple genes and proteins (including Neuropilin 1, GITR and CTLA-4) associated with the Treg fingerprint. In fact, a significant percentage of the Treg lineage cells took on a Th memory phenotype including increased levels of CD127, IL-4, and interferon-g. Importantly, Dicer-deficient Tregs lost suppression activity in vivo; the mice rapidly developed fatal systemic autoimmune disease resembling the FoxP3 knockout phenotype. These results support a central role for miRNAs in maintaining the stability of differentiated Treg function in vivo and homeostasis of the adaptive immune system.

overall_design: Lymph node CD4+YFP+ T cells from FoxP3-GFP-hCre x ROSA26R-YFP Dicerwt/lox (Het) and FoxP3-GFP-hCre x ROSA26R-YFP Dicerlox/lox (KO) mice were isolated by flow cytometry. Triplicate GeneChips were used for each T cell population.

first: Lukas

last: Jeker

first: Brian

last: Fife

first: Shirley

last: Zhu

first: Mark

first: Michael

last: McManus

first: Jeffrey

middle: A

last: Bluestone


title: Gene expression profiles of E15.5 endothelial cells in the developing kidney isolated from TIE2-GFP transgenic mice using FACS. (GUDMAP Series ID: 21)

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

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

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

first: Steve

last: Potter

first: Eric

last: Brunskill


title: Effect of v-erbA on RA-responsive genes in AML12 hepatocytes

status: Public on Jun 15 2008

city: Jackson

first: Tereza

last: Ventura-Holman

state: MS

address: 2500 North State St.

institute: University of Mississippi Medical Center

summary: The v-erbA oncogene belongs to a superfamily of transcription factors called nuclear receptors, which includes the retinoic acid receptors (RARs) responsible for mediating the effects of retinoic acid (RA). Nuclear receptors bind to specific DNA sequences in the promoter region of target genes and v-erbA is known to exert a dominant negative effect on the activity of the RARs. The repressor activity of v-erbA has been linked to the development of hepatocellular carcinoma (HCC) in a mouse model. We have used microarray analysis to identify genes differentially expressed in hepatocytes in culture (AML12 cells) stably transfected with v-erbA and exposed to RA.  We have found that v-erbA can affect expression of RA-responsive genes. We have also identified a number of v-erbA-responsive genes that are known to be involved in carcinogenesis and which may play a role in the development of HCC.

overall_design: AML12 control cells and v-erbA-transfected AML12 cells were exposed to 1 µM RA for 3h or 24h. Using microarray analysis, we compared gene expression in the presence and absence of v-erbA and identified RA-regulated genes differentially expressed in the presence of v-erbA.

first: Abulkhair

last: Mamoon

first: Jose

middle: S

last: Subauste


title: Smad1/5/8 mutant granulosa cell tumor gene expression

city: Houston

first: Martin

last: Matzuk

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
The objective of this study was to understand the gene expression changes during granulosa cell tumor development in Smad1/5/8 mutant ovaries.
Keywords: Microarray analysis, gene expression

overall_design: Three independent mouse mutant granulosa cell tumors were compared to three wild type granulosa cells samples.

first: Stephanie

last: Pangas

middle: M


title: Transcriptional repression of c-Myb and GATA-2 is involved in the effects of C/EBPα in p210 BCR/ABL-expressing cells

status: Public on Jun 13 2008

city: Cambridge

first: Robert

middle: Vincent

last: Martinez

state: MA

address: 35 Cambridgepark Drive

department: Biological Technologies

institute: Wyeth Research

summary: Levels of C/EBPα are low in myeloid blast crisis (BC) of chronic myelogenous leukemia (CML) and its expression in p210BCR/ABL-expressing hematopoietic cells induces granulocytic differentiation, inhibits proliferation and suppresses leukemogenesis.  To assess the mechanisms involved in these effects, C/EBPα targets were identified  by microarray analyses.  Upon C/EBPα activation, expression of c-Myb and GATA-2 was  repressed in 32D-BCR/ABL, K562 and CML-BC primary cells but only c-Myb levels decreased slightly   in CD34+ normal progenitors. The role of these two genes for the biological effects of C/EBPα was assessed by perturbing their expression in K562 cells. Expression of c-Myb blocked the proliferation inhibition and differentiation-inducing effects of C/EBPα while c-Myb siRNA treatment enhanced C/EBPα-mediated proliferation inhibition and induced changes in gene expression indicative of monocytic  differentiation. GATA-2 expression suppressed the proliferation inhibitory effect of C/EBPα but blocked in part the effect on differentiation; GATA-2 siRNA treatment had no effects on C/EBPα induction of differentiation but inhibited proliferation of K562 cells, alone or upon C/EBPα activation. In summary, the effects of C/EBPα in p210BCR/ABL -expressing cells depend, in part, on transcriptional repression of c-Myb and GATA-2.  Since perturbation of c-Myb and GATA-2 expression has non identical consequences for proliferation and differentiation of K562 cells, the effects of C/EBPα appear to involve different transcription-regulated targets.

overall_design: 48 samples total. 4-HT-treated 32D-BCR/ABL cells transduced with the MigRI empty vector, MigRI WT C/EBPα-ER , MigRI K298E C/EBPα-ER  (a DNA binding-deficient mutant) or MigRI-delta(177-191) C/EBPα-ER  (a mutant deficient in CDK2/CDK4 interaction). Total RNA was extracted at 0, 6, 9 and 12h post-4-HT treatment in triplicate and hybridized onto the Affymetrix MOE430 _2 array.


title: Microarray data of mouse fetal liver

first: Bing Mei

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

summary:
Iron is essential for all cells but is toxic in excess, so iron absorption and distribution are tightly regulated.  Serum iron is bound to transferrin and primarily enters erythroid cells via receptor-mediated endocytosis of the transferrin receptor (Tfr1).  Tfr1 is essential for developing erythrocytes and reduced Tfr1 expression is associated with anemia.  The transcription factors STAT5A/B are activated by many cytokines, including erythropoietin.  Stat5a/b-/- mice are severely anemic and die perinatally, but no link has been made to iron homeostasis.  To study the function of STAT5A/B in vivo, we deleted the floxed Stat5a/b locus in hematopoietic cells with a Tie2-Cre transgene.  These mice exhibited microcytic, hypochromic anemia, as did lethally irradiated mice transplanted with Stat5a/b-/- fetal liver cells.  Flow cytometry and RNA analyses of erythroid cells from mutant mice revealed a 50% reduction in Tfr1 mRNA and protein.  We detected STAT5A/B binding sites in the first intron of the Tfr1 gene and found that expression of constitutively active STAT5A in an erythroid cell line increased Tfr1 levels.  Chromatin immunoprecipitation experiments confirmed the binding of STAT5A/B to these sites.  We conclude that STAT5A/B is an important regulator of erythroid progenitor iron uptake via its control of Tfr1 transcription.

Keywords: genetic modification

overall_design: Isolated Ter119-positive fetal liver cells from three to five E14.5 embryos of the same genotype were combined, and total RNA was extracted using TRIzol reagent (Life Technologies) with two additional ethanol precipitations.  RNA quality was verified using an Agilent Bioanalyzer (Agilent Technologies).  Microarray analyses were performed using Affymetrix Mouse Genome 430 2.0 array GeneChips (Affymetrix).   Up- and down-regulated genes were selected based on P values of <0.05 and fold changes of >1.5 or -1.5 as assessed by ANOVA using Partek Pro software (Partek).  To determine specific pathways, gene pathway analysis was obtained using the statistically significant gene list (P<0.05) represented on the chip.

first: Yongzhi

last: Cui

first: Bingmei

first: Weiping

last: Chen

first: Lothar

last: Hennighausen


title: Mouse model of Osteosarcoma

city: Boston

first: Carl

last: Walkley

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary:
expression analysis from a genetically engineered mouse model of osteosarcoma
determine the expression profile of mouse osteosarcoma
Keywords: disease state analysis

overall_design: 3 control in vitro differentiated WT primary osteoblasts; 15 primary osteosarcoma; 4 OS cell lines; 4 secondary tumours

first: Stuart

last: Orkin


title: Runx transcriptional program for control of cell adhesion and survival

status: Public on Jun 12 2008

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

summary:
The Runx genes are important in development and cancer, where they can act either as oncogenes or tumour supressors. We compared the effects of ectopic Runx expression in established fibroblasts, where all three genes produce an indistinguishable phenotype entailing epithelioid morphology and increased cell survival under stress conditions. Gene array analysis revealed a strongly overlapping transcriptional signature, with no examples of opposing regulation of the same target gene. A common set of 50 highly regulated genes was identified after further filtering on regulation by inducible RUNX1-ER. This set revealed a strong bias toward genes with annotated roles in cancer and development, and a preponderance of targets encoding extracellular or surface proteins reflecting the marked effects of Runx on cell adhesion.

Keywords: Comparative study of gene targets regulated by overexpression of the different Runx family members

overall_design: 6 samples (expression of different Runx family members); 5 in duplicate, 1 single.  2 control samples (empty vector) in duplicate. Cultures of Runx expressing cells were grown to confluence, treated with ethanol +/- 4OHT tamoxifen for 24 hours and harvested  for RNA extraction and hybridization on Affymetrix microarrays

first: Sandy

last: Wotton

first: Anne

last: Terry

first: Anna

last: Kilbey

first: Alma

last: Jenkins

first: Ewan

last: Cameron

first: James

middle: C

last: Neil


title: Age-associated increase in aneuploidy and changes in gene expression in mouse eggs.

status: Public on Jun 07 2008

city: Philadelphia

first: Hua

last: Pan

state: PA

address: 415 S University Avenue

department: Department of Biology

institute: University of Pennsylvania

summary: An increase in the incidence of aneuploidy is well documented with increasing maternal age, in particular in human females. Remarkably, little is known regarding the underlying molecular basis for the age-associated increase in aneuploidy, which is a major source of decreased fertility in humans. Using mouse as a model system we find that eggs obtained from old mice (60-70 weeks of age) display a 6-fold increase in the incidence of hyperploidy as assessed by chromosome spreads. Expression profiling of transcripts in oocytes and eggs obtained from young and old mice reveals that approximately 5% of the transcripts are differentially expressed in oocytes obtained from old females when compared to oocytes obtained from young females (6-12 weeks of age) and that this fraction increases to approximately 33% in eggs. The latter finding indicates that the normal pattern of degradation of maternal mRNAs that occurs during oocyte maturation is dramatically altered in eggs obtained from old mice and could therefore be a contributing source to the decline in fertility. Analysis of the differentially expressed transcripts also indicated that the strength of the spindle assembly checkpoint is weakened and that higher errors of microtubule-kinetochore interactions constitute part of molecular basis for the age-associated increase in aneuploidy in females. Last, BRCA1 expression is reduced in oocytes obtained from old females and RNAi-mediated reduction of BRCA1 in oocytes obtained from young females results in perturbing spindle formation and chromosome congression following maturation

overall_design: We profiled the global gene expression in GV & MII oocyte by maternal aging, and identified the genes differentially expressed.

first: Pengpeng

last: Ma

first: Wenting

last: Zhu

first: Richard

last: Schultz


title: Ca2+ oscillatory pattern in fertilized mouse eggs affects gene expression and development to term.

summary: The Ca2+ oscillations initiated by the fertilizing sperm (but terminating concomitant with pronucleus formation) apparently ensure that the events constituting egg activation occur in the correct temporal order; early events (e.g., cortical granule exocytosis) require fewer oscillations than later events (e.g., recruitment of maternal mRNA). Whether the Ca2+ signaling events impact long-term development, in particular development to term, is unknown. Using fertilized eggs that have undergone the first few Ca2+ oscillations, we developed procedures that result either in inhibiting or stimulating the natural pattern of Ca2+ signaling of inseminated eggs. Although the incidence of development to the blastocyst stage is unaltered by these procedures, fewer offspring are born following embryo transfer, indicating that developmental competence of the blastocysts is reduced. Interestingly, embryo transfer experiments reveal that when the natural regime of Ca2+ oscillations is precociously interrupted, the incidence of implantation is compromised whereas hyper-stimulation of Ca2+ signaling events compromises post-implantation development. Moreover, although there was no major difference in the overall growth rates of the offspring, those obtained following hyper-stimulation exhibited a far greater variability in their weight. Analysis of global patterns of gene expression by microarray analysis revealed that approximately 20% of the transcripts are mis-regulated when too few oscillations are experienced by the embryo and EASE analysis indicates that genes preferentially involved in RNA processing and polymerase II transcription are differentially affected. In addition, a set of genes involved in cell adhesion is also mis-expressed and could thus be mechanistically linked to the observed reduced implantation. Only about 3% of the transcripts were mis-regulated following hyper-stimulation, and EASE analysis indicates that genes preferentially involved in metabolism are differentially affected. In toto, these results indicate that a range Ca2+ signaling events following fertilization (an excess or reduction) has long-term effects on both gene expression and development to term.

overall_design: We profiled the global gene expression in the blastocysts by treatment of Ca2+ oscillations, and identified the genes differentially expressed.

first: Jean-Pierre

last: Ozil

first: Bernadette

last: Banrezes

first: Szabolcs

last: Tóth


title: Differential expression between FHL2-/-  and WT MEFs.

status: Public on Jun 06 2008

city: Paris

first: Yu

last: Wei

address: 28, rue Dr Roux

department: Virologie

country: France

institute: Institut Pasteur

summary:
The LIM-only protein FHL2 acts as a transcriptional modulator that positively or negatively regulates multiple signaling pathways. We recently reported that FHL2 cooperates with CBP/p300 in the activation of ß-catenin/TCF target gene cyclin D1. In this paper, we demonstrate that FHL2 is associated with the cyclin D1 promoter at the TCF/CRE site, providing evidence that cyclin D1 is a direct target of FHL2. We show that deficiency of FHL2 greatly reduces the proliferative capacity of spontaneously immortalized mouse fibroblasts which is associated with decreased expression of cyclin D1 and p16INK4a, and hypophosphorylation of Rb. Reexpression of FHL2 in FHL2-null fibroblasts efficiently restores cyclin D1 levels and cell proliferative capacity, indicating that FHL2 is critical for cyclin D1 activation and cell growth. Moreover, ectopic cyclin D1 expression is sufficient to override growth inhibition of immortalized FHL2-null fibroblasts. Gene expression profiling revealed that FHL2 deficiency triggers a broad change of the cell cycle program that is associated with downregulation of several G1/S and G2/M cyclins, E2F transcription factors and DNA replication machinery, thus correlating with reduced cell proliferation. This change also involves downregulation of the negative cell cycle regulators, particularly INK4 inhibitors, which could counteract the decreased expression of cyclins, allowing cells to grow. Our study illustrates that FHL2 can act on different aspects of the cell cycle program to finely regulate cell proliferation.
Keywords: mouse embryonic fibroblasts derived from FHL2-/- and WT mouse embryos (14.5 days)

overall_design: Two biological genotypes, FHL2-/- and WT MEF cells. Three spontaneously immortalized clones of each genotype were analyzed using Affymetrix arrays.


title: Effect of age, calorie restriction and resveratrol on gene expression in mouse heart, brain, and skeletal muscle

status: Public on Jun 10 2008

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

summary:
Resveratrol in high doses has been shown to extend lifespan in some studies in invertebrates and to prevent early mortality in mice fed a high-fat diet. We fed mice from middle age (14-months) to old age (30-months) either a control diet, a low dose of resveratrol (4.9 mg kg-1 day-1), or a calorie restricted (CR) diet and examined genome-wide transcriptional profiles.
We report a striking transcriptional overlap of CR and resveratrol in heart, skeletal muscle and brain. Both dietary interventions inhibit gene expression profiles associated with cardiac and skeletal muscle aging. Gene expression profiling suggests that both CR and resveratrol may retard some aspects of aging through alterations in chromatin structure and transcription. Resveratrol, at doses that can be readily achieved in humans, fulfills the definition of a dietary compound that mimics some aspects of CR.
Keywords: aging intervention study

overall_design: Heart, neocortex tissue, and gastrocnemius muscle was collected from young and old mice at 5 and 30 months of age, respectively; mice were subjected to either a calorie restricted diet or a control diet supplemented with resveratrol

middle: L


title: gene expression of CTCF-depleted mouse oocyte

status: Public on Jun 05 2008

summary: CTCF is a multifunctional nuclear factor involved in epigenetic regulation.  We have used transgenic RNA interference to deplete maternal stores of CTCF from growing mouse oocytes, and identified the potential target genes

overall_design: We profiled the global gene expression in the wild type and CTCF-depleted GV oocytes, and identified a set of target genes.

first: Le-Ben

last: Wan

first: Yong

last: Chen

first: Jun

first: Andrew

last: Fedoriw

first: Keith

middle: E

last: Latham

first: Marisa

last: Bartolomei


title: Gene expression in murine memory versus naive B cells (1st generation and 2nd generation screens)

city: New Haven

first: Mary

middle: M.

last: Tomayko

state: CT

department: Dermatology

institute: Yale University

summary:
Memory B cells play essential roles in the maintenance of long-term immunity and may be important in the pathogenesis of autoimmune disease, but how these cells are distinguished from their naïve precursors is poorly understood. To address this, it would be important to understand how gene expression differs between memory and naive B cells in order to elucidate memory-specific functions. Using model systems that help overcome the lack of murine memory-specific markers and the low frequency of antigen-specific memory and naïve cells, we undertook a global comparison of gene expression between memory B cells and their naive precursors.
1st generation screen:
These data represent our first generation comparison of gene expression between murine naïve and memory splenic B cells. Naïve NP-binding splenic B cells were FACS purified from unimmunized mVh186.2 transgenic Balb/c mice. Memory B cells were generated by immunizing mVh186.2 transgenic Balb/c mice with 2 doses of NP-CGG in alum delivered i.p. 6 weeks apart. After a minimum of 12-weeks rest, NP-binding splenic B cells were isolated by FACS. Total RNA was extracted, cRNA synthesized and labeled and hybridized to Affymetrix mouse 430 2.0 chips.
2nd generation screen:
These data represent our second generation comparison of gene expression between murine naïve and memory splenic B cells. Naïve NP-binding AA4.1neg splenic B cells were FACS purified from unimmunized mVh186.2 transgenic Jk KO Balb/c mice. Memory B cells were generated from these naive precursors after adoptive transfer into recipients that mount poor endogenous NP-responses. 12-weeks post i.p. immunization with NP-CGG in alum, NP-specific splenic memory  B cells  were isolated by FACS. Total RNA was extracted, cRNA synthesized and labeled and hybridized to Affymetrix mouse 430 2.0 chips.

Memory/Naïve comparison data linked below as Supplementary files.

Keywords: Cell type comparison

overall_design:
1st generation screen: 7 samples, 3-4 biological replicates each of murine splenic naïve and memory B cells
2nd generation screen: 8 samples, 4 biological replicates each of murine splenic naïve and memory B cells

first: Mark

middle: J

last: Shlomchik


title: Gene Expression Data in R26Pax3 palates

status: Public on Jun 01 2008

first: Jonathan

middle: A.

last: Epstein

address: 421 Curie Blvd

department: Cell and Developmental Biology

summary:
We used microarrays to detail the global programme of gene expression underlying palate development by persistent expression in R26Pax3 mice and identified distinct classes of up-regulated and down-regulated genes during this process.
Keywords: palate development

overall_design: Palatal shelves were dissected at E14.5 for RNA extraction and hybridization on Affymetrix microarrays. Wild type and R26Pax3/Pax3 littermates were used.

first: Meilin

last: Wu

last: Li

first: Kurt

last: Engleka

first: Bo

last: Zhou

first: MinMin

last: Lu

first: Joshua

middle: B

last: Plotkin


title: RLSC and MMH-D3 cell lines

status: Public on Jun 03 2008

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

summary:
Increasing evidence provide support that the mammalian liver contains stem/progenitor cells, but their molecular phenotype, embryological derivation,  cell biology as well as of their role in the liver cell turnover and regeneration remain to be further clarified.
We report the isolation, characterization and reproducible establishment in line of a resident liver stem cell (RLSC) with immunophenotype and differentiative potential distinct from other previously reported liver precursor/stem cells. RLSCs, derived from foetal and neonatal murine livers as well as from immortalized hepatocytic MMH lines and established in lines, are Sca+, CD34-, CD45-, alfa-fetoprotein+, albumin-. This immunophenotype suggests a non-haematopoietic origin. RLSCs transcriptional profile, defined by microArray technology, highlighted the expression of a broad spectrum of “plasticity-related genes” and “developmental genes” suggesting a multi-differentiative potential.
RLSCs, indeed, spontaneously differentiate into hepatocytes and cholangiocytes and, when cultured in appropriate conditions, into mesenchymal and neuro-ectodermal cell lineages, such as osteoblasts/osteocytes, chondrocytes, astrocytes and neuronal cells.
 RLSCs capability to spontaneously differentiate into hepatocytes, the lack of albumin expression and the broad differentiative potentiality locate them in a pre-hepatoblast/liver precursor cells hierarchical position.
In conclusion, RLSCs may provide an useful tool to improve liver stem cell knowledge and to assess new therapeutic approaches for liver diseases.
Keywords: cell type comparison

overall_design: We compared the gene expression profile of a RLSC line to that of the previously characterised hepatocytic differentiated cell line MMH-D3 (ref Amicone), using Affymetrix Mouse430_2 GeneChip array.

first: Alice

last: Conigliaro

first: Marta

last: Colletti

first: Carla

last: Cicchini

first: Mateus

last: Guerra

first: Roberta

last: Zini

first: Veronica

last: Bordoni

first: Francesca

last: Siepi

first: Martina

last: Leopizzi

first: Marco

last: Tripodi

first: Laura

last: Amicone


title: Effect of BMPR2-R899X mutation in lung with and without elevated RVSP

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

summary:
Familial pulmonary arterial hypertension (fPAH) is associated with mutations in BMPR2. Many of these mutations occur in the BMPR2 tail domain, leaving the SMAD functions intact. In order to determine the in vivo consequences of BMPR2 tail domain mutation, we created a smooth-muscle specific doxycycline inducible BMPR2 mutation with an arginine to termination mutation at amino acid 899. When these SM22-rtTA x TetO7-BMPR2R899X mice had transgene induced for 9 weeks, starting at 4 weeks of age, they universally developed pulmonary vascular pruning as assessed by fluorescent microangiography. Approximately half the time the induced animals developed elevated right ventricular systolic pressures (RVSP), associated with extensive pruning, muscularization of small pulmonary vessels, and development of large structural pulmonary vascular changes. These lesions included large numbers of macrophages and T-cells in their adventitial compartment, as well as CD133 positive cells in the lumen. Small vessels filled with CD45 positive and sometimes CD3 positive cells were a common feature in all SM22-rtTA x TetO7-BMPR2R899X mice. Gene array experiments show changes in stress response, muscle organization and function, proliferation and apoptosis, and developmental pathways before RVSP increases. Our results show that the primary phenotypic result of BMPR2 tail domain mutation in smooth muscle is pulmonary vascular pruning leading to elevated RVSP, associated with early dysregulation in multiple pathways with clear relevance to PAH. This model should be useful to the research community in examining early molecular and physical events in the development of PAH, and as a platform to validate potential treatments.
Keywords: Disease state analysis

overall_design: Each array is an individual female mouse, age-matched, with two mice & arrays used for each of controls (transactivator only), BMPR2-R899X with normal RVSP, and BMPR2-R899X with high RVSP.

first: Julie

last: Harral

first: Kirk

last: Lane

first: Yupu

last: Deng

first: Brian

last: Ickes

first: Sebastian

last: Albu

first: Daniel

last: Crona

first: Duncan

last: Stewart

first: Karen

last: Fagan


title: Transcription Profiling of Lung Adenocarcinomas of c-Myc-Transgenic Mice

status: Public on May 31 2008

city: Hannover

first: Jürgen

last: Borlak

address: Nikolai-Fuchs-Strasse 1

country: Germany

institute: Fraunhofer Institut

summary:
The transcriptional regulator c-Myc is the most frequently deregulated oncogene in human tumors. Targeted overexpression of this gene in mice results in distinct types of lung adenocarcinomas. By using microarray technology, alterations in the expression of genes were captured based on a female transgenic mouse model in which, indeed, c-Myc overexpression in alveolar epithelium results in the development of bronchiolo-alveolar carcinoma (BAC) and papillary adenocarcinoma (PLAC).
In this study, we analyzed exclusively the promoters of induced genes by different in silico methods in order to elucidate the c-Myc transcriptional regulatory network.
Keywords: c-myc transgenic versus non-transgenic

overall_design: For gene expression analysis, RNA was isolated from lung tissue of either 16 c-Myc-transgenic or 16 non-transgenic control female mice. Identical amounts of RNA from 4 individuals of one group were pooled, such that 4 pools of 4 mice per group could be analyzed. Each pool was analysed in one microarray experiment.

first: Susanne

last: Reymann


title: Transcriptional profiling of Tmprss6-deficient mouse liver

status: Public on Jun 04 2008

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

summary: Matriptase-2 (Tmprss6), a recently described member of the TTSP family, is an essential regulator of iron homeostasis. Tmprss6-/- mice display an overt phenotype of alopecia and a severe iron deficiency anemia. These hematological alterations found in Tmprss6-/- mice are accompanied by a marked up-regulation of hepcidin, a negative regulator of iron export into plasma.

overall_design: Tmprss6-deficient mice were generated by gene targeting. Total RNA was extracted from liver samples from control and Tmprss6-deficient male mice after o/n fasting. Transcriptional profiling was analyzed using GeneChip Mouse 430 2.0 arrays.

first: Alicia

middle: R

last: Folgueras

first: Fernando

last: Martin de Lara

first: Alberto

last: Pendas

first: Cecilia

last: Garabaya

first: Francisco

last: Rodriguez

first: Aurora

last: Astudillo

first: Teresa

last: Bernal

first: Ruben

last: Cabanillas

first: Carlos

last: Lopez-Otin

first: Gloria

last: Velasco


title: The in vivo effect of actin cytoskeletal abnormalities on gene expression

status: Public on May 30 2008

first: Sakae

last: Ikeda

address: 425-G Henry Mall Room 5350 Genetics/Biotech

department: Department of Medical Genetics

institute: University of Wisconsin-Madison

summary:
Remodeling of the actin cytoskeleton through actin dynamics (assembly and disassembly of filamentous actin) is known to be essential for numerous basic biological processes.  In addition, recent in vitro studies provided evidence that actin dynamics participate in the control of gene expression.  A spontaneous mouse mutant, corneal disease 1 (corn1), is deficient for a regulator of actin dynamics, destrin (DSTN; also known as actin depolymerizing factor or ADF), and develops epithelial hyperproliferation and neovascularization in the cornea.  Dstncorn1 mice exhibit the actin dynamics defect in the corneal epithelial cells as evidenced by increased filamentous actin, offering an in vivo model to investigate the physiological significance of the transcriptional regulation by actin dynamics.  To examine the effect of the Dstncorn1 mutation on gene expression, we performed a microarray analysis using the cornea from Dstncorn1 and wild-type control mice.  A dramatic alteration of gene expression was observed in the Dstncorn1 cornea, with 1,226 annotated genes differentially expressed.  Functional annotation of these genes revealed that most significantly enriched functional categories are associated with actin and/or cytoskeleton.  Among genes that belong to these categories, a considerable number of serum response factor (SRF) target genes were found, indicating the existence of the actin-SRF pathway of transcriptional regulation in vivo.  A comparative study using an allelic mutant strain, Dstncorn1-2J, with milder corneal phenotypes also suggested that the severity of the actin dynamics defect correlates with the level of gene expression changes.  Our study provides evidence that actin dynamics have a strong impact on gene expression in vivo.
Keywords: Comparative gene expression

overall_design: Microarray analysis was performed in triplicate with RNA from each genotype, A. BY H2bc H2-T18f/SnJ (A. BY wild-type), A. BY H2bc H2-T18f/SnJ-Dstncorn1/J (Dstncorn1), C57BL/6J (B6 wild-type), C57BL/6JSmn-Dstncorn1-2J/J (Dstncorn1-2J), and C.129S2(B6)-Il8rbtm1Mwm/J (Il8rb-/-), hybridized to three Affymetrix MG 430 2.0 arrays.

first: Angela

last: Verdoni

first: Natsuyo

last: Aoyama

first: Akihiro


title: Effect of Evi-1 deletion in hematopoietic stem cells

status: Public on May 29 2008

city: Tokyo

first: Susumu

last: Goyama

address: 7-3-1 Hongo, Bunkyo-ku

department: Hematology

country: Japan

institute: Tokyo University

summary: To identify the target genes of Evi-1 in hematopoietic stem cells (HSCs), we carried out genome-wide transcriptional analysis using wild-type and Evi-1-deleted HSCs.

overall_design: Lineage(-), Sca-1(+), c-Kit(+) cells derived from Evi-1(flox/flox) mice were transduced with GFP or Cre-GFP expressing retroviruses. GFP(+) cells were sorted and  and analyzed by Affymetrix® Mouse Genome 430 2.0 Array® for gene expression. Two independent experiments were performed.

first: Go

last: Yamamoto

first: Munetake

last: Shimabe

first: Tomohiko

last: Sato

first: Motoshi

last: Ichikawa

first: Seishi

last: Ogawa

first: Shigeru

last: Chiba

first: Mineo

last: Kurokawa


title: Hookworm-Induced Persistent Changes to the Immunological Environment of the Lung

city: Baltimore

first: Joshua

last: Reece

address: 615 N. Wolfe Street

department: MMI

institute: Johns Hopkins University BSPH

summary:
Infection with Nippostrongylus brasiliensis results in persistent changes to the lung environment. Cytokine profiling reveals a sustained increase in both Th1 and Th2 transcripts. Cellular populations of macrophages display an alternative phenotype, with upregulation of YM1, Arg1, Mrc1 as well as Class II MHC. These alternatively activated alveolar macrophages (AAAMs) also increase drastically in number. Subsequent challenge with house dust mite (HDM) Dermatophagoides pteronyssinus shows a reduced allergic phenotype, with decreased fold changes in effector cell cytokines of both the Th1 and Th2 variety indicative of the new regulatory environment established in the lung by helminth infection. Histological examination of the lung environment reveals a significant decrease in eosinophila and reduced mucous production by bronchial epithelial cells.
Keywords: Timecourse, Infection, Allergy Model

overall_design: BALB/c mice were challenged with 500 infectious L3 stage Nippostrongylus brasiliensis larvae subcutaneously. Mice were allowed to resolve their infection, then were sensitized twice with 75 allergy units (AU) of HDM bound to 1mg of alum intraperitoneally. Two challenge doses of 50AU HDM in PBS were given intranasally one day apart, then lungs were harvested at 6, 24 and 72 hours post challenge. Mice were analyzed by histology, immunohistochemistry, real time RT-PCR and affymetrix gene array analysis using full genome chips.

first: Mark

last: Siracusa

first: Cory

middle: F

last: Brayton

last: Southard

first: Joseph

last: Urban

first: Alan

last: Scott


title: Differentiated, partially- and fully-reprogrammed MEFs/B-cells

status: Public on May 28 2008

first: Tarjei

last: Mikkelsen

address: 7 Cambridge Center

institute: Broad Institute

summary:
Expression profiles generated during dissection of the molecular mechanisms underlying direct reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells, iPS).
Keywords: Cell type comparison/Timecourse

overall_design: 2 technical replicates of B lymphocytes, partially reprogrammed (MCV8, MCV6, BIV1), MEF-iPS(Oct4) and B-iPS(Nanog) cell lines.

first: Jacob

last: Hanna

first: Eric

last: Lander

first: Alexander

last: Meissner


title: Identification of novel monosodium urate crystal-induced mRNAs

status: Public on May 23 2008

city: Rahway

middle: P

last: Menetski

state: NJ

address: PO Box; RY80M-162

department: Molecular Profiling

institute: Merck & Co

summary:
Objective. To identify novel monosodium urate (MSU) crystal-induced mRNAs by transcript profiling of isolated murine air pouch membranes.
Methods. Nine hours after injecting crystals into air pouches, membranes were meticulously dissected away from the adjacent soft tissues. mRNA expression differences between inflamed and control membranes were determined by oligonucleotide microarray analysis. Induction of selected mRNAs was validated by real-time relative quantitative reverse transcriptase PCR (qPCR) in pouch membranes and murine peritoneal macrophages.
Results. Eleven of the 12 most highly upregulated mRNAs related to innate immunity and inflammation. They included mRNAs encoding histidine decarboxylase (the enzyme that synthesizes histamine), interleukin (IL)-6, the cell surface receptors PUMA-g and TREM-1, and the polypeptides Irg1 and PROK-2. MSU crystals induced dramatic rises in these mRNAs in the pouch membrane within 3-8 hours after the surge in pro-inflammatory cytokine (IL-6, IL-1beta and TNFalpha) and immediate early gene (Egr-1) transcription, which occurred 1h after crystal injection. MSU crystals induced these mRNAs in cultured macrophages with similar kinetics but lower fold changes. In keeping with their downregulation by MSU crystals according to the microarrays, qPCR confirmed that TREM-2 and granzyme D mRNAs decreased 79% and 94%, respectively, in MSU crystal inflamed membranes.
Conclusions. This analysis disclosed several genes previously not implicated in MSU crystal inflammation. Their rise after the early surge in cytokine mRNAs suggests that they may, for instance, amplify or perpetuate inflammation. Transcript profiling of the isolated air pouch membrane promises to be a powerful tool to identify genes acting at different stages of inflammation.

overall_design:
Mouse strain: female Balb/C,  6-8 weeks old
Number of mice= 6.
Air pouches raised on back for 7 days by injecting 2ml of sterile air.
On day 7, injection of 1ml PBS or 2mg MSU crystals in 1ml PBS (n=3 each)
9 h after injection, dissection of the air pouch membranes from the adjacent soft tissues, RNA extraction with RNeasy columns. Pooling of RNA from the 3 control pouches or the 3 MSU crystal pouches.  Processing and labeling of 5ug aliquots in the U Penn microarray core according to standard Affy protocols. Hybridization to Affy Mo430_2 oligonucleotide microarrays.

first: Frank

last: Pessler

first: C

last: Mayer

first: S

last: Jung

first: E

last: Behrens

first: L

last: Dai

first: H

last: Schumacher


title: Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype

status: Public on May 25 2008

city: Rochester

first: Hartmut

last: Land

state: NY

address: 601 Elmwood Avenue, Box 633

department: Biomedical Genetics

institute: University of Rochester Medical Center

summary:
Understanding the molecular underpinnings of cancer is of critical importance to developing targeted intervention strategies. Identification of such targets, however, is notoriously difficult and unpredictable. Malignant cell transformation requires the cooperation of a few oncogenic mutations that cause substantial reorganization of many cell features and induce complex changes in gene expression patterns.  Genes critical to this multi-faceted cellular phenotype thus only have been identified following signaling pathway analysis or on an ad hoc basis. Our observations that cell transformation by cooperating oncogenic lesions depends on synergistic modulation of downstream signaling circuitry suggest that malignant transformation is a highly cooperative process, involving synergy at multiple levels of regulation, including gene expression.  Here we show that a large proportion of genes controlled synergistically by loss-of-function p53 and Ras activation are critical to the malignant state.  Remarkably, 14 among 24 such 'cooperation response genes' (CRGs) were found to contribute to tumor formation in gene perturbation experiments.  In contrast, only one in 14 perturbations of genes responding in a non-synergistic manner had a similar effect. Synergistic control of gene expression by oncogenic mutations thus emerges as an underlying key to malignancy and provides an attractive rationale for identifying intervention targets in gene networks downstream of oncogenic gain and loss-of-function mutations.
Keywords: Oncogenic mutation-specific comparison

overall_design: Contains 50 samples total, 10 replicates each of parental cell line YAMC, plus bleo/Neo vector control, mp53-expressing, Ras-expressing and mp53/Ras cells.  Polysomal RNA from each sample was run on Affymetrix GeneChip® Mouse Genome 430 2.0 Arrays.

first: Helene

last: McMurray

first: Erik

last: Sampson

first: Shaw-Ree

last: Chen

first: Peter

last: Salzman

first: Lev

last: Klebanov

first: Andrei

last: Yakovlev


title: Interlocking transcriptomics, proteomics and toponomics technologies for brain tissue analysis in murine hippocampus

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
We have correlated transciptomics, proteomics and toponomics analyses of hippocampus tissue of inbred C57/BL6 mice to analyse the interrelationship of expressed genes and proteins at different levels of organization. We find that transcriptome and proteome levels of function are highly conserved between different mice, while the topological organization (the toponome) of protein clusters in synapses of the hippocampus is highly individual, with only few interindividual overlaps (0.15 %). In striking contrast, the overall spatial patterns of individual synaptic states, defined by protein clusters, have boundaries within a strict and non-individual spatial frame of the total synaptic network. The findings are the first to provide insight in the systems biology of gene expression on transcriptome, proteome and toponome levels of function in the same brain subregion. The approach may lay the ground for designing studies of neurodegeneration in mouse models and human brains.
Keywords: brain proteome, transcriptome, toponome, synapses

overall_design: 4 biological replicates, all wild type

first: Marcus

last: Bode

first: Martin

last: Irmler

first: Manuela

last: Friedenberger

first: Caroline

last: May

first: Klaus

first: Christian

last: Stephan

first: Helmut

last: Meyer

first: Christiane

last: Lach

first: Reyk

last: Hillert

first: Andreas

last: Krusche

first: Katrin

last: Marcus

first: Walter

last: Schubert


title: Effect of 5HTT knockout and heterozygosity in whole mouse lung

first: James

last: West

summary:
Rationale: While modulation of the serotonin transporter (5HTT) has shown to be a risk factor for pulmonary arterial hypertension for almost 40 years, there is a lack of in vivo data about the broad molecular effects of pulmonary inhibition of 5HTT. Previous studies have suggested effects on inflammation, proliferation, and vasoconstriction. The goal of this study was to determine which of these were supported by alterations in gene expression in serotonin transporter knockout mice. Methods: Eight week old normoxic mice with a 5-HTT knock-out (5HTT-/-) and their heterozygote(5HTT+/-) or wild-type(5HTT+/+) littermates had right ventricular systolic pressure(RVSP) assessed, lungs collected for RNA, pooled, and used in duplicate in Affymetrix array analysis. Representative genes were confirmed by quantitative RT-PCR and western blot. Results: RVSP was normal in all groups. Only 124 genes were reliably changed between 5HTT-/- and 5HTT+/+ mice. More than half of these were either involved in inflammatory response or muscle function and organization; in addition, some matrix, heme oxygenase, developmental, and energy metabolism genes showed altered expression. Quantitative RT-PCR for examples from each major group confirmed changes seen by array, with an intermediate level in 5HTT+/- mice. Conclusions: These results for the first time show the in vivo effects of 5HTT knockout in lungs, and show that many of the downstream mechanisms suggested by cell culture and ex vivo experiments are also operational in vivo.  This suggests that the effect of 5HTT on pulmonary vascular function arises from its impact on several systems, including vasoreactivity, proliferation, and immune function.
Keywords: Genetic modification

overall_design: Comparison of whole lung total RNA from pools of wild-type, heterozygote, and knockout 5HTT mice to determine the pulmonary effects of loss of 5HTT expression.

first: Daniel

last: Crona

first: Julie

last: Harral

first: Serge

last: Adnot

first: Saadia

last: Eddahibi


title: Expression data from epidermis of epithelial activated beta-catenin mutant mouse embryo

status: Public on May 20 2008

city: New York

first: Sarah

last: Millar

address: Icahn Building, Floor 13 Room 020C, 1425 Madison Ave

department: Developmental, Cell and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

summary:
β-catenin signaling is required for hair follicle development, but it is unknown whether it is sufficient to activate expression of hair follicle genes in embryonic skin. To address this we profiled gene expression in epidermis from E15.5 KRT14-Cre Ctnnb1(Ex3)fl/+ embryos carrying an activating mutation in epithelial beta-catenin, and control littermate embryos.
Keywords: Genetic modification

overall_design:
Total epidermal RNA from two KRT14-Cre Ctnnb1(Ex3)fl/+ and two control littermate E15.5 embryos was hybridized to Affymetrix GeneChip Mouse Genome MOE430 2.0 oligonucleotide microarrays.

Appended below is Table S1: Full list of differentially expressed genes in KRT14-Cre Ctnnb1(Ex3)fl/+ mutant compared with control littermate epidermis at E15.5, including normalization and filter parameters. Fold change, listed in the second column, gives the ratio of normalized control : mutant transcript levels.

first: Yuhang

last: Zhang


title: PPARalpha-mediated effects of dietary lipids on intestinal barrier gene expression

status: Public on May 22 2008

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary:
Background: The selective absorption of nutrients and other food constituents in the small intestine is mediated by a group of transport proteins and metabolic enzymes, often collectively called ‘intestinal barrier proteins’. An important receptor that mediates the effects of dietary lipids on gene expression is the peroxisome proliferator-activated receptor alpha (PPARα), which is abundantly expressed in enterocytes. In this study we examined the effects of acute nutritional activation of PPARα on expression of genes encoding intestinal barrier proteins. To this end we used triacylglycerols composed of identical fatty acids in combination with gene expression profiling in wild-type and PPARα-null mice. Treatment with the synthetic PPARα agonist WY14643 served as reference.
Results: We identified 74 barrier genes that were PPARα-dependently regulated 6 hours after activation with WY14643. For eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and oleic acid (OA) these numbers were 46, 41, and 19, respectively. The overlap between EPA-, DHA-, and WY14643-regulated genes was considerable, whereas OA treatment showed limited overlap. Functional implications inferred form our data suggested that nutrient-activated PPARα regulated transporters and phase I/II metabolic enzymes were involved in a) fatty acid oxidation, b) cholesterol, glucose, and amino acid transport and metabolism, c) intestinal motility, and d) oxidative stress defense.
Conclusion: We identified intestinal barrier genes that were PPARα-dependently regulated after acute activation by fatty acids.This knowledge provides a better understanding of the impact dietary fat has on the barrier function of the gut, identifies PPARα as an important factor controlling this key function, and underscores the importance of PPARα for nutrient-mediated gene regulation in intestine.
Keywords: metabolic state analysis

overall_design: Pure bred wild-type (129S1/SvImJ) and PPARα-null (129S4/SvJae) mice were treated for 6 hours with the synthetic triacylglycerols triolein [oleic acid (OA, C18:1)], trieicosapentaenoin [eicosapentaenoic acid (EPA, C20:5)] or tridocosahexaenoin [ocosahexaenoic acid (DHA, C22:6)], or the potent PPARα agonist WY14,643. Two weeks before the start of the experiment, mice were put on a modified AIN76A diet, in which corn oil was replaced by olive oil. At the day of the experiment mice were fasted for four hours. At 9 AM mice were dosed by oral gavage with 400 µl of a 0.1% WY14643 suspension in 0.5% carboxymethyl cellulose, or 400 µl of the synthetic triacylglycerols. Six hours after the gavage the mice were anaesthetized, small intestines were removed, flushed with ice-cold PBS and remaining fat and pancreatic tissue was carefully removed. Total RNA was then isolated. RNA of 4-5 biological replicates was hybridized to Affymetrix 430-2.0 plus arrays. Five microgram total RNA was labelled according to the ENZO-protocol, fragmented and hybridized according to Affymetrix's protocols.

first: Heleen

last: De Vogel - van den Bosch

first: Meike

last: Bünger

first: Philip

last: de Groot

first: Hanneke

last: Bosch - Vermeulen

first: Michael

last: Müller


title: Expression data from skin, dermis, and epidermis of epithelial activated beta-catenin mutant mouse embryo

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

overall_design: Refer to individual Series


title: Expression data from dermis of epithelial activated beta-catenin mutant mouse embryo

summary:
β-catenin signaling is required for hair follicle development, but it is unknown whether it is sufficient to activate expression of hair follicle genes in embryonic skin. To address this we profiled gene expression in dermis from E15.5 KRT14-Cre Ctnnb1(Ex3)fl/+ embryos carrying an activating mutation in epithelial beta-catenin, and control littermate embryos.
Keywords: Genetic modification

overall_design:
Total dermal RNA from two KRT14-Cre Ctnnb1(Ex3)fl/+ and two control littermate E15.5 embryos was hybridized to Affymetrix GeneChip Mouse Genome MOE430 2.0 oligonucleotide microarrays.

Appended below is Table S2: Full list of differentially expressed genes in KRT14-Cre Ctnnb1(Ex3)fl/+ mutant compared with control littermate dermis at E15.5, including normalization and filter parameters. Fold change, listed in the second column, gives the ratio of normalized mutant : control transcript levels.


title: Expression data from skin of epithelial activated beta-catenin mutant mouse embryo

summary:
β-catenin signaling is required for hair follicle development, but it is unknown whether it is sufficient to activate expression of hair follicle genes in embryonic skin. To address this we profiled gene expression in skin dissected from E14.5 KRT14-Cre Ctnnb1(Ex3)fl/+ embryos carrying an activating mutation in epithelial beta-catenin, and control littermate embryos.
Keywords: Genetic modification

overall_design:
Total skin RNA from two KRT14-Cre Ctnnb1(Ex3)fl/+ and two control littermate E14.5 embryos was hybridized to Affymetrix GeneChip Mouse Genome MOE430 2.0 oligonucleotide microarrays.

Appended below is Table S3: Full list of differentially expressed genes in KRT14-Cre Ctnnb1(Ex3)fl/+ mutant compared with control littermate intact skin at E14.5, including normalization and filter parameters. Fold change, listed in the second column, gives the ratio of normalized mutant : control transcript levels.


title: Choroid plexus function in B10.pl WT mice versus B10.PL RAG-/- mice (carri-affy-mouse-302760)

status: Public on May 17 2008

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Previous work has led us to examine the differences in the choroid plexus function in B10.pl WT mice versus B10.PL RAG-/- mice. We believe that there is a difference between those that are normal functioning and those that are lymphocyte deficient.
To determine the gene expression profile of the choroid plexus in wild type mice as compared to those that are lymphocyte deficient.
We hypothesize that there is altered expression in the genes that mediate cellular adhesion in choroid plexus from wild type mice as compared to those that are lymphocyte deficient.
8-10 week old animals (age and sex matched) were injected with Evan's blue post anesthetization. After waiting an hour the animals were euthanized and their brains were extracted and placed in RNALater for 24 hours. The brains were then sliced sagitally

Keywords: RAG mutant, choroid plexus

middle: D

last: Carrithers


title: Histones associated with downregulated genes are hypo-acetylated in Huntington’s disease models

city: Charlestown

first: Ghazaleh

last: Sadri-Vakili

department: Neurology

institute: Massachusetts General Hospital

summary:
Transcriptional dysregulation plays a major role in the pathology of Huntington's disease (HD). However, the mechanisms causing selective downregulation of genes remain unknown. Histones regulate chromatin structure and thereby control gene expression; recent studies have demonstrated a therapeutic role for histone deacetylase (HDAC) inhibitors in polyglutamine diseases. This study demonstrates that despite no change in overall acetylated histone levels, histone H3 is hypo-acetylated at promoters of downregulated genes in R6/2 mice, ST14a and STHdh cells, as demonstrated by in vivo chromatin immunoprecipitation. In addition, HDAC inhibitor treatment increases association of acetylated histones with downregulated genes and corrects mRNA abnormalities. In contrast, there is a decrease in mRNA levels in wild-type cells following treatment with a histone acetyltransferase inhibitor. Although changes in histone acetylation correlate with decreased gene expression, histone hypo-acetylation may be a late event, as no hypo-acetylation is observed in 4-week-old R6/2 mice. Nevertheless, treatment with HDAC inhibitors corrects mRNA abnormalities through modification of histone proteins and may prove to be of therapeutic value in HD.
Keywords: cell type comparison and disease state analysis

overall_design:
Total RNA was isolated from STHdh7/7 and STHdh111/111 cell lines by extraction with TRI-Reagent (Sigma-Aldrich, St Louis, MO) and purified further over RNeasy columns (Qiagen, Valencia, CA). Fifteen µg of total RNA was pooled for each sample and used to generate labeled cRNA probes according to the Affymetrix GeneChip protocol. Biotinylated cRNA probes were hybridized to MOE40.3K oligonucleotide microarrays using the Affymetrix Fluidics Station 400 according to the manufacturer's standard protocol. Microarray analysis Chips were developed, scanned, and normalized using global scaling. All quality control parameters calculated by Affymetrix GCOS Software were monitored (38).  The images of the chips were analyzed to find spotted or damaged array regions and to ensure data quality (39).  The Presence/Absence calls from Affymetrix MAS5 were monitored and compared throughout the different samples.
All data were normalized using the GeneChip Robust MultiChips Analysis (GCRMA) algorithm (40, 41), performed with R in BioConductor.
The processed images of the arrays were analyzed for quality control, we found all the samples to be of equal very good quality, with an average of 40.5% ± 1.44% Present calls with a range of 38% to 42.4%, (the background, noise, spike in controls, housekeeping genes presented a variability over the 8 samples less than 7% pre-normalization). In addition, 31.55% of the probe sets were called Present or Marginal in all the 8 samples and 44.6% were called Absent in all the 8 samples, showing a good consistency of the quality between the samples and between the groups compared.

first: Bérengère

last: Bouzou

first: Caroline

last: Benn

first: Mee-Ohk

last: Kim

first: Prianka

last: Chawla

first: Ryan

last: Overland

first: Kelly

last: Glajch

first: Eva

last: Xia

first: Zhihua

last: Qiu

first: Steven

last: Hersch

first: Timothy

middle: W

last: Clark

first: George

last: Yohrling

first: Jang-Ho

last: Cha


title: Transcriptome and proteome analysis of early embryonic mouse brain development

first: Johannes

last: Beckers

summary:
Embryonic mouse brain development involves a sequential differentiation of multipotent progenitor cells into neurons and glia. Using microarrays and large 2-D electrophoresis, we investigated the transcriptome and proteome of mouse brains at embryonic days 9.5, 11.5 and 13.5. During this developmental period, neural progenitor cells shift from proliferation to neuronal differentiation. As expected, we detected numerous expression changes between the time points investigated but interestingly, the rate of alteration was about 10% to 13% of all proteins and mRNAs during every two days of development. Furthermore, up- and downregulation was balanced. This was confirmed for two additional stages of development, embryonic day 16 and 18. We hypothesize that during embryonic development, the rate of protein expression alteration is rather constant due to a limitation of cellular resources such as energy, space and free water. The similar complexity found at the transcriptome and proteome level at all stages suggests, that changes in relative concentration of gene products rather than an increased number of gene products dominate throughout cellular differentiation. We found that metabolism and cell cycle related gene products were downregulated in expression when precursor cells switched from proliferation to neuronal differentiation (day 9.5 to 11.5), whereas neuron specific gene products were upregulated. A detailed analysis revealed their implication in differentiation related processes such as rearrangement of the actin cytoskeleton as well as Notch and Wnt signaling pathways.
Keywords: time course, development, transcriptome, proteome

overall_design:
3 embryonic stages:
E9.5: 6 biological replicates
E11.5: 4 biological replicates
E13.5: 6 biological replicates

first: Daniela

last: Hartl

first: Martin

last: Irmler

first: Irmgard

last: Römer

middle: T

last: Mader

first: Lei

last: Mao

first: Claus

last: Zabel

last: Hrabé de Angelis

first: Joachim

last: Klose


title: Translation state array analysis of Mouse embryonic stem cells and embryoid bodies

status: Public on May 14 2008

city: Seattle

first: Charles

last: Murry

state: WA

address: 815 Mercer st., Rm # 454

department: Pathology

institute: University of Washington

summary:
Stem cell differentiation is known to involve changes in RNA expression, but little is known about translational control during differentiation.  We comprehensively profiled gene expression during differentiation of embryonic stem cells (ESCs) into embyroid bodies (EBs) by integrating conventional transcriptome analysis with global assessment of ribosome loading.  Differentiation was accompanied by an anabolic switch, characterized by global increases in transcript abundance, polysome content, protein synthesis rates and protein content.  Furthermore, 78% of expressed transcripts showed increased ribosome loading, thereby enhancing translational efficiency.  Elevated protein synthesis was accompanied by enhanced phosphorylation of eIF-4E binding protein, suggesting regulation by the mTOR pathway.
Some transcripts were under exclusive translational control, including Activated Transcription Factor 5 (ATF5) a b-zip transcription factor, Deleted in Colon Cancer (DCC) the tumor suppressor and Wnt1, the beta-catenin agonist.  Parsimonious translation in ESCs may provide a layer of quality control to prevent inappropriate gene expression in the pluripotent state.
Keywords: Translation state array analysis during embryonic stem cell differentiation

overall_design: Embryonic stem cells (ESC) maintained in an undifferentiated state and day-5 Embryoid bodies (EB) were selected for RNA was extraction and hybridization on Affymetrix 430_2 mouse expression arrays. For polysome fractionation,  twelve fractions collected from the gradients were combined to form four pools. One ml of each pool (Pools: 1-4) was used for RNA isolation, labeling and hybridization for undifferentiated ESCs (UD1, UD2, UD3 and UD4) and EBs (EB1, EB2, EB3 and EB4). In parallel, total RNA was also isolated from unfractionated lysates for transcript abundance analysis.  Three biological replicates of ESCs and EB cultures were used for polysome fractionation and total RNA analysis.

first: Prabha

last: Sampath

first: David

middle: K

last: Pritchard

first: Lil

last: Pabon

first: Hans

last: Reinecke

first: Stephen

last: Schwartz

last: Morris


title: CD8 T cells stimulated with IL-2 complex in vivo

first: Michael

last: Bevan

address: I604H HSC, 1959 NE Pacific Street

department: Immunology

institute: Univerisity of Washington, HHMI

summary:
IL-2 signals into CD8 T cells have a programming and regulatory role in driving cells to full effector and memory differentiation. This study was designed to look for IL-2 target genes that affect CD8 T cell responses.

Keywords: Time-course, cytokine treatment

Keywords: Expression profiling by array

overall_design: Treatment of mice with IL-2/anti-IL-2 immune complexes (IL-2 complex) stimulates all fraction of CD8 T cells in vivo. Because STAT5 phosphorylation peaked 1 h after injection of the IL-2 complex, gene expression in CD8 T cells was compared at 0 h (no treatment), 1 h and 3 h post treatment. Two mice were used for each time point.

first: Daisuke

last: Kamimura


title: C2C12 differentiation time course to observe changes between myoblasts and myotubes

status: Public on May 13 2008

city: Cambridge

first: Qicheng

last: Ma

address: 250 Mass Ave

institute: Novartis

summary:
This analysis compares various timepoints from Day -1, 50% confluency myoblasts to Day 5 post differentiation myotubes.
Consecutive timepoints and myoblasts vs. myotubes are compared.
Keywords: time course

http://www.biodatamining.org/content/1/1/4

overall_design: 8 time points from Day -1 to Day 5, three replicates for each time point.

first: Adel

last: Bakhtiarova

first: Penelope

middle: A

last: Kosinski

first: Daniel

last: Kemp


title: Ventilator-induced lung injury in C57BL\6 mice

status: Public on May 15 2008

city: San Francisco

first: James

last: Frank

address: 4150 Clement St

institute: UCSF

summary:
This study was undertaken to examine differential gene expression across the whole genome during short-term ventilator-induced lung injury in mice, a commonly used model of acute lung injury, as compared with spontaneous ventilation.
Keywords: Disease state analysis

overall_design: Mice were anesthetized with isoflurane followed by ketamine/xylaxine. Saline (0.25 ml) was given every hour ip. A tracheotomy tube was placed and the mice were ventilated with an initial peak airway pressure of 20 cmH2O approximating a tidal volume of 20 ml/kg and without end-expiratory pressure. Ventilation was continued for 3h. Tidal volume was not adjusted. Body temperature was monitored with a digital rectal thermometer and maintained at 37C with a heating table and external heating lamp. Control mice were treated identically, but were not mechanically ventilated (i.e. breathed spontaneously). There were 5 biological relicates in each group.

last: Erle

first: Yuanyuan

last: Xiao

first: Charlie

last: Wray


title: Role of small intestine in the development of dietary fat-induced obesity and insulin resistance in C57BL/6J mice.

first: Guido

last: Hooiveld

summary:
Obesity and insulin resistance are two major risk factors underlying the metabolic syndrome. To gain more insight in the role of the small intestine in the etiology of these metabolic disorders, a microarray study was performed on small intestines (SI) of C57BL/6J mice that were fed a high fat diet mimicking the fatty acid composition of a Western-style human diet. The mice became obese and developed dietary fat-induced glucose intolerance. For gene expression profiling, the small intestines were subdivided in three equal parts along the longitudinal axis. The most pronounced effects of dietary fat were detected in part 2 of the small intestine. The biological processes that were most extensively modulated on a high fat diet were related to lipid metabolism, especially β- and ω-fatty acid oxidation seemed to play an important role, cell cycle and inflammation/immune response. An additional secretome analysis revealed differentially expressed secreted proteins, such as Il18, Ffgf15, Mif, Igfbp3 and Angptl4, which might provoke systemic effects in peripheral organs by influencing their metabolic homeostasis. Furthermore, many of the dietary fat-modulated genes and biological processes in small intestine were previously already associated with obesity and/or insulin resistance. Together, the data of this exploratory study provided various leads for an essential role of the small intestine in development of obesity and/or insulin resistance.
Keywords: time course

overall_design: After a run-in period of 3 weeks on a low-fat diet, 9 weeks old mice were fed a high- (HF) or a low-fat (LF) purified diet for 2, 4, and 8 weeks (n=6 per diet, per time point). Body weight was recorded weekly and after 7 weeks of diet intervention an oral glucose tolerance test was performed. At the end of the experiment, mice were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%). The small intestines were excised and the adhering fat and pancreatic tissue were carefully removed. The small intestines were divided in three equal parts along the proximal to distal axis (SI 1, SI 2 and SI 3).

first: Nicole

last: de Wit

first: Hanneke

last: Bosch-Vermeulen

first: Philip

last: de Groot

first: Mechteld

last: Grootte Bromhaar

first: Jenny

last: Jansen

last: Müller

first: Roelof

last: van der Meer


title: Liver and cecum from mice exposed to aflatoxin B1 (AFB1) and/or Helicobacter hepaticus

status: Public on May 09 2008

city: Chapel Hill

first: Arlin

last: Rogers

state: NC

address: Campus Box 7431

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina

summary:
We evaluated aflatoxin B1-induced liver tumor promotion by H. hepaticus. Microarrays of liver and cecum from female mice were used to evaluate the individual and combined transcriptional effects of AFB1 and H. hepaticus
Keywords: Tumor co-promotion study

overall_design: C3H/HeN mice were inoculated with 7 ug/g BW AFB1 or vehicle IP at 10 days of age, and gavaged with H. hepaticus or broth at 3 weeks; necropsied at 40 weeks


title: Virus-Induced Airway Disease in Mice (C57BL/6J, d21/d49)

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

address: Campus Box 8116, 660 S. Euclid Ave.

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

summary:
Analysis of gene expression in lungs of C57BL/6J mice that develop chronic airway disease phenotypes after a single Sendai virus infection, compared with mice treated with UV-inactivated virus.
Keywords: disease state analysis

overall_design: Whole lung RNA was analyzed from 3 mice per condition per time point for days 21 and 49 post infection, Sendai virus versus UV-inactivated virus, C57BL/6J mouse strain.

first: Edy

middle: Y

last: Kim

first: John

last: Battaile

first: Yingjian

last: You

first: Eugene

last: Agapov

first: Mitchell

middle: H

last: Grayson

first: Loralyn

last: Benoit

first: Derek

last: Byers

first: Yael

last: Alevy

first: Jennifer

last: Tucker

first: Suzanne

last: Swanson

first: Rose

last: Tidwell

first: Jeffrey

last: Tyner

last: Morton

first: Mario

last: Castro

first: Deepika

last: Polineni

first: G

last: Patterson

first: Reto

last: Schwendener

last: Allard

first: Gary

last: Peltz

first: Michael

last: Holtzman


title: Long-term hematopoietic stem cells and the proto-oncogene Pbx1

status: Public on May 07 2008

city: Rozzano

first: Francesca

last: Ficara

state: MI

address: via Manzoni 56

institute: CNR/Istituto Clinico Humanitas

first: Mark

last: Murphy

first: Min

last: Lin

middle: L

last: Cleary


title: ELAV-like protein HuD overexpression and pulldown (perro-affy-mouse-482241)

status: Public on May 06 2008

first: Winnie

last: Liang

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.
Besides binding and stabilizing the GAP-43 mRNA, HuD was shown to bind in vitro or in vivo the mRNAs of acetylcholinesterase, tau, p21, neuroserpin, and MARCKS among others.  To identify additional targets of HuD, we propose to pull down the RNAs bound to myc-tagged HuD in vivo in the brains of HuD transgenic mice, to isolate these bound RNAs and use these to probe DNA microarrays. We will use pull downs using non-immune IgGs as controls.

To test our hypothesis we propose 2 specific aims:
1) To identify the targets of HuD in HuD overexpressor mice and
2) To compare these target mRNAs to those we identified  previously  as having increased levels of expression in the hippocampus of HuD transgenic mice (see protocol # Perrone-Bizzozero-5R01NS030255-12) and/or those that show increased expression in dentate granule cells of HuD transgenic mice ( protocol # perro-affy-mouse-309741)

Based upon the role of the RNA-binding HuD in neuronal development and synaptic plasticity, we expect that HuD targets will include mRNAs for proteins involved in these processes.
All mice are in C57BL/6 background and are male approximately 60 days old. To identify target of HuD in our transgenic mice, we will homogenize the homogenize the hippocampi  (2 per animal) of 3 transgenic mice and use these protein extracts for immunoprecipitation assays. Briefly, transgenic myc-tagged HuD protein will be immunoprecipitated using myc-tag antibodies and protein-G agarose beads and samples will be sent to T-Gen for RNA isolation, single round amplification and probing of DNA microarrays. We will use non-immune IgG as a negative control.
Conditions:
Pooled Extracts from 3 transgenic mice IP with myc-tag antibodies: Triplicates
Pooled extract from 3 transgenic mice IP with non-immune IgGs (negative control): duplicates

Keywords: dose response

first: Nora

middle: I

last: Perrone-Bizzozero


title: Cranial neural crest cells of E11.5 wild type and FAK mutants (valle-affy-mouse-480721)

summary:
Cranial neural crest cells (NCC) give rise to the majority of the cartilage, bone, connective tissue, and sensory ganglia in the head, and also participate in the remodeling of the cardiac outflow tract and pharyngeal arch arteries during cardiovascular development. Our preliminary results show that targeted deletion of focal adhesion kinase (FAK) in murine NCC results in cardiovascular and craniofacial alterations, resembling human congenital heart diseases The objective of this project is to elucidate the underlying mechanisms by which FAK mediates NCC function during development.
Compare gene expression in cranial neural crest cells of E11.5 wild type and FAK mutants.
FAK is a tyrosine kinase that transduces integrin and growth factor signaling pathways. Abnormal growth factor signaling leads to cardiovascular malformations caused by deficient cardiac NCC function. However, a direct role for FAK in NCC morphogenesis has not been demonstrated. We will test the hypothesis that FAK is a downstream target of essential growth factor signaling in cranial neural crest cells during development.
1) Generate E11.5 mouse embryos that are either control (FAK+/flox) or NCC specific FAK knockout (Wnt1Cre;FAKflox/flox). 2) Determine genotype by PCR. 3) Dissect head and torax from the different genotypes. 4) Obtain NCC from dissected tissue by magnetic cell sorting using p75 antibody. 5) Prepare total RNA from speciments. We will pool the NCC from 3 different embryos of the same genotype, and send total RNA to TGEN for probe preparation, hybridization and array result analysis.
Keywords: other

first: Louis

last: Reichardt


title: Rosiglitazone Treatment Reduces Diabetic Neuropathy in STZ treated DBA/2J mice

status: Public on May 10 2008

city: Ann Arbor

first: Timothy

middle: David

last: Wiggin

address: 109 Zina Pitcher Pl., Rm 5368

institute: University of Michigan

summary:
Diabetic Neuropathy (DN) is a common complication of diabetes.  Currently, there is no drug treatment to prevent or slow the development of DN.  Rosiglitazone (Rosi) is a potent insulin sensitizer and may also slow the development of DN by a mechanism independent of its effect on hyperglycemia.  A two by two design was used to test the effect of Rosi treatment on the development of DN.  Streptozotocin-induced diabetic DBA/2J mice were treated with Rosi.  DN and oxidative stress were quantified, and gene expression was profiled using the Affymetrix Mouse Genome 430 2.0 microarray platform.  An informatics approach identified key regulatory elements activated by Rosi.  Diabetic DBA/2J mice developed severe hyperglycemia, DN and elevated oxidative stress.  Rosi treatment did not affect hyperglycemia but did reduce oxidative stress and prevented development of thermal hypoalgesia.  Two novel transcription factor binding modules were identified that may control genes correlated to changes in DN following Rosi treatment: SP1F_ZBPF and EGRF_EGRF.  Rosi treatment reduced oxidative stress and DN independent of its insulin sensitizing effects. Gene expression profiling identified two novel targets activated by Rosi treatment.  These targets may be useful in designing drugs with the same efficacy as Rosi in treating DN but with fewer undesirable effects.
Keywords: disease and treatment analysis

overall_design:
There were 4 groups:
Control
Control + Rosi
Diabetic (Type 1)
Diabetic + Rosi

Affymetrix chips were run on five mice from each group.  One chip (in the Control group) failed quality control measures and was excluded.

first: Matthias

last: Kretzler

first: Subramaniam

last: Pennathur

first: Kelli

last: Sullivan

first: Frank

middle: C

last: Brosius

first: Eva

last: Feldman


title: Microarray analysis of CD4+T cells in murine arthritis

status: Public on May 01 2008

city: Memphis

first: Jian

last: Yan

address: 956 Court Ave

department: Orthopedics Surgery

institute: University of Tennessee Health Science Center

summary:
Although activated CD4+ T cell-driven overproduction of cytokines, especially TNF and IL1, is generally regarded as the major factor in the development of rheumatoid arthritis (RA), little is known about the precise role of CD4+ T cells in the initiation and progression of this disease. In this study, this issue was addressed using a time-course microarray analysis in a mouse model of RA, Il1rn deficient mice.No obvious cytokine gene expression changes reflecting T cell activation was observed in CD4+ T cells in the Il1rn deficient mice during the course of spontaneous arthritis. On the contrast, majority of dysregulated genes were those predominantly expressed in myeloid lineage cells, suggesting T cell reprogramming involvement in arthritis development. Distinct gene expression patterns were identified for different stages of disease, including downregulated expression of immunoglobulin heavy chain constant region genes and increased expression of inflammatory genes in the early phase, and downregulation of MHC class II genes in the late phase. The common changes occurred in both early and late phases included upregulation of Arl2bp and Mfap1, which are involved in the regulation of cytoskeletal dynamics.
Keywords: Time course

overall_design: Two KO mice and three WT mice for each time point (1 month and 4 month) were used for this study.

first: Yan

last: Jiao

first: Weikuan

last: Gu

first: John

middle: M

last: Stuart


title: Keap1-dependent gene expression determined in the liver using conditional Keap1 knockout mice vs. genetic control mice

first: William

middle: O

last: Osburn

state: MD

address: 615 N. Wolfe St

department: Environmental Health

institute: Johns Hopkins Bloomberg School of Public Health

summary:
To compare hepatic gene expression in conditional Keap1 knockout (Alb-Cre:Keap1(flox/-)) and genetic control mice. Disruption of Keap1-mediated repression of Nrf2 signaling was expected to result in increased expression of Nrf2-regulated genes.
Keywords: comparative expression profiling

overall_design: Hepatic gene expression was compared in conditional Keap1 knockout and genetic control mice (Alb-Cre:Keap1(flox/+)) mice.  Male 9 week old mice were used, n=3/group.

first: Melinda

middle: S

last: Yates

first: Patrick

last: Dolan

first: Karen

last: Liby

first: Michael

middle: B

last: Sporn

first: Keiko

last: Taguchi

first: Masayuki

last: Yamamoto

first: Thomas

last: Kensler


title: Expression data from early and adult stages of mouse development

city: genoa

first: Domenico

last: Albino

address: L.go R. Benzi, 10

institute: National Institute for Cancer Research (IST)

summary:
DNA repair genes have been shown to be expressed in the early stages of mammalian development probably to reduce possible replication errors and genotoixc damages.  Several birth defects and some cancers are due to inappropriate or defective DNA repair machinery indicating that a right activity of DNA repair genes in the early stages of fetal development are essential for an appropriate DNA function.  Neuroblastoma (NB), an embryonal tumor deriving from neural crest cells (NCCs) is diagnosed in about 30% of patients within the first year of life. Moreover, several reports show that NB can be detected in foetus and in neonatal period.
To assess gene expression profiling of DNA repair genes during early stage of development, we performed a genome-wide analysis of Neural Crest cells (NCCs) generating a gene expression database that can help to better understand the gene(s) involved in both genetic and cancer diseases. We found 11 genes involved in DNA repair activity during mouse embryo development overexpressed in early stages. Six out 11 were never been described in mouse embryology.
Keywords: time course

overall_design: Mouse embryos were collected at successive stages of early and adult development stages for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of NCCs by Laser Capture Microdissection (LCM) from embryos and adult in order to analyze DNA repair genes during mouse development. To that end, we collected cells at three time-points: at embryonal stage of 8.5 dpc: E8.5 (neural tube closure); at embryonal stage of 13.5dpc: E13.5 (dorsal root ganglion); at adult stage of 3 months postnatal: P90 (adrenal medulla).

first: Stefano

last: Moretti


title: Identification of phase-specific arthritis-related genes in mice

summary:
Rheumatoid arthritis (RA), one of the most common polygenic diseases, is characterized by a chronic, progressive inflammation mainly in joints and has an unknown etiology. Numerous studies have revealed the significance of cytokines TNF and IL-1 in the onset and progression of RA. Due to the complexity of interactions among different cytokines and immune cells, little is known about the precise molecular mechanisms underlying RA. In this study, oligonucleotide microarray analysis and a mouse model of RA, IL-1 receptor antagonist deficient mice were used to address this issue. Two hundred and ninety transcripts were found to be dysregulated greater than or equal to 2-fold in the diseased mice. Phase-specific gene expression changes were identified, including early increase and late decrease of heat shock protein coding genes and Cyr61. Moreover, common gene expression changes were also observed, especially the upregulation of paired-Ig-like receptor A (Pira) in both early and late phases of arthritis. We conclude that common and distinct gene expression change patterns that were identified globally may represent novel opportunities for better control of RA through early diagnosis and development of alternative therapeutic strategies.
Keywords: Time course

overall_design: Six wild-type and 6 Il1rn deficient BALB/c mice at 1 month and 4 month (3 for each time point) were used for microarray analysis of splenic gene expression profiling.

first: Feng


title: Differentially regulated genes in LT-HSC from control or Pbx1-null mice

first: Francesca

last: Ficara

summary:
Self-renewal is a defining characteristic of stem cells, however the molecular pathways underlying its regulation are poorly understood.  Here we demonstrate that conditional inactivation of the Pbx1 proto-oncogene in the hematopoietic compartment results in a progressive loss of long-term hematopoietic stem cells (LT-HSCs) that is associated with concomitant reduction in their quiescence, leading to a defect in the maintenance of self-renewal as assessed by serial transplantation.  Transcriptional profiling revealed that multiple stem cell maintenance factors are perturbed in Pbx1-deficient LT-HSCs, which prematurely express a large subset of genes, including cell cycle regulators, normally expressed in non-self-renewing multipotent progenitors.  A significant proportion of Pbx1-dependent genes are associated with the Tgf-b pathway, which serves a major role in maintaining HSC quiescence.  Pbx1-deficient LT-HSCs are unable to up-regulate the cyclin dependent kinase inhibitor p57 in response to Tgf-b, providing a mechanism through which Pbx1 maintenance of stem cell self-renewal is achieved.
Keywords: genetic modification

overall_design: Highly efficient Pbx1 deletion was induced with poly(I:C) in 3 young MxCre+.Pbx1f/f mutant or 2 MxCre-.Pbx1f/f control mice. LT-HSC (Lin-cKit+Sca1+CD34-CD135-) cells were prospectively sorted from bone marrow of individual mice harvested 4 weeks after the last injection of poly(I:C).

first: Mark

middle: J

last: Murphy

first: Min

last: Lin

last: Cleary


title: GNF Mouse GeneAtlas V3

status: Public on Apr 29 2008

city: San Diego

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary: High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we profiled gene expression from  a diverse array of normal tissues, organs, and cell lines in mice.  Keywords: multiple tissues

overall_design: Multiple tissues were taken from naïve male C57BL6 mice for hybridization to MOE430_2 arrays

first: Jane

last: Lattin

first: Kate

last: Schroder

first: Andrew

last: Su

first: Jie

last: Zhang

first: Tim

last: Wiltshire

first: Kaoru

last: Saijo

first: Christopher

last: Glass

first: David

last: Hume

first: Stuart

last: Kellie

first: Matthew

last: Sweet


title: Trans-10, cis-12 conjugated linoleic acid activates the integrated stress response pathway in adipocytes

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

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

overall_design: Refer to individual Series


title: Expression data from Rb family (Rb, p130 and p107) deficient Hematopoietic stem Cells

status: Public on Apr 25 2008

city: palo alto

first: Patrick

last: Viatour

address: 350 pasteur drive

institute: Stanford University

summary:
Loss of Rb family in HSCs results in a severe phenotype, such as enhanced proliferation and increase in stem cell number. In addition, HSCs were higly mobilized but failed to transplant. Rb family deficient mice rapidly exhibit a myeloproliferative disease with eosinophilic characteristics. Meanwhile, the lymphoid compartment was severely decreased, due to high apoptotic activity in this lineage.
Keywords: unpaired WT versus Rb family deficient KLS

overall_design:
We used mice that harbor floxed alleles for the Rb family and we induced the recombination by 6 weeks of age. KLS (c-Kit+ Lin - Sca-1+) cells were sorted 2 months after the recombination.
Total of 6 hybridizations done.  One Sample was excluded from our analysis based on high background and anomalous control probeset values.

first: Julien

last: Sage


title: Differentially regulated genes in normal LT-HSC vs ST-HSC

last: Ficara

summary:
Self-renewal is a defining characteristic of stem cells, however the molecular pathways underlying its regulation are poorly understood.  Here we demonstrate that conditional inactivation of the Pbx1 proto-oncogene in the hematopoietic compartment results in a progressive loss of long-term hematopoietic stem cells (LT-HSCs) that is associated with concomitant reduction in their quiescence, leading to a defect in the maintenance of self-renewal as assessed by serial transplantation.  Transcriptional profiling revealed that multiple stem cell maintenance factors are perturbed in Pbx1-deficient LT-HSCs, which prematurely express a large subset of genes, including cell cycle regulators, normally expressed in non-self-renewing multipotent progenitors.
Keywords: cell type comparison

overall_design: LT-HSC (Lin-cKit+Sca1+CD34-CD135-) and ST-HSC (Lin-cKit+Sca1+CD34+CD135-) cells were prospectively sorted from the BM of MxCre-.Pbx1f/f control mice harvested 4 weeks after the last injection of poly(I:C).

last: Murphy

first: Michael


title: Prospective isolation of functionally distinct radial glial subtypes - lineage and transcriptome analysis

status: Public on May 29 2008

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

institute: Helmholtz Zentrum Muenchen

summary:
Since the discovery of radial glia as the source of neurons, their heterogeneity in regard to neurogenesis has been described by clonal and time-lapse analysis in vitro. However, the molecular determinants specifying neurogenic radial glia differently from radial glia that mostly self-renew remain ill-defined. Here, we isolated two radial glial subsets that co-exist at mid-neurogenesis in the developing cerebral cortex and their immediate progeny. While one subset generates neurons directly, the other is largely non-neurogenic but also gives rise to Tbr2-positive basal precursors, thereby contributing indirectly to neurogenesis. Isolation of
these distinct radial glia subtypes allowed determining interesting differences in their transcriptome. These transcriptomes were also strikingly different from the transcriptome of radial glia isolated at the end of neurogenesis. This analysis therefore identifies, for the first time, the lineage origin of basal progenitors and the molecular differences of this lineage in comparison to directly neurogenic and gliogenic radial glia.

overall_design: Comparison of radial glial subtypes

first: Luisa

last: Pinto

middle: T

last: Mader

first: Martin

last: Irmler

first: Marco

last: Gentilini

first: Frederico

last: Santoni

first: Alessandro

last: Bulfone

first: Paolo

last: Malatesta

first: Magdalena

last: Götz

first: Daniela

last: Drechsel

first: Robert

last: Blum

first: Ronny

last: Stahl


title: Placental and decidual timecourse samples normalized and modeled with an undissected e17 sample

status: Public on Apr 23 2008

city: Stanford

first: Kirstin

last: Knox

address: 300 Pasteur Dr.

department: Genetics

institute: Stanford Univeristy

summary:
We used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0).  For these samples, at each stage the fetal placenta and maternal decidual tissues were dissected and profiled separately (See series 1).
For this experiment (Series 2), placental and decidual timecourse samples were normalized and modeled with two undissected (including placental and decidual tissue) e17 placentas to allow for scaling of values for comparison to the undissected placenta samples used in the publicly available mouse GeneAtlas dataset
Keywords: time course

overall_design: Mouse placentas were obtained from timed pregnant female mice at each timepoint, and fetal tissues were used to confirm embryo staging.  For all dissected samples, fetal placenta and maternal decidual tissues were dissected and pooled separately for each litter prior to RNA extraction and hybridization on Affymetrix microarrays.

first: Julie

last: Baker


title: Timecourse of developing mouse placenta, with placental and decidual tissues profiled separately

summary:
We used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0).
At each stage, the fetal placenta and maternal decidual tissues were dissected and profiled separately
Keywords: time course

overall_design: Mouse placentas were obtained from timed pregnant female mice at each timepoint, and fetal tissues were used to confirm embryo staging.  Fetal placenta and maternal decidual tissues were dissected and pooled separately for each litter prior to RNA extraction and hybridization on Affymetrix microarrays.


title: Expression data from developing mouse placenta


title: Coordinated Regulation of Signaling Pathways and Biological Processes during Liver Development

status: Public on Apr 18 2008

city: Boston

first: Hasan

middle: Huseyin

last: Otu

address: 4 Blackfan Circle Rm. 238

department: Medicine

institute: Harvard Medical School

summary:
Understanding congenital liver disease requires elucidation of the signaling pathways and transcriptional events in the developing liver.  Comprehensive assessment of gene expression between 10.5 and 16.5 dpc in the developing mouse liver and comparison with adult liver and non-hepatic embryonic tissue was validated with real-time PCR and in situ hybridization.  The broad nature of the analysis provides insights into patterns of genetic control of hepatogenesis.  Pathways implicated in human disease are highly regulated at the transcriptional level.  Rather than activating or inhibiting a pathway or biological process by altering the expression of a single signaling molecule, transcriptional changes in large numbers of genes in a pathway or process are regulated in a coordinated manner.  For example, both TGF-beta and Notch signaling is inhibited during hepatogenesis not just by decreasing transcription of multiple pathway members, but also with a complementary increase in the transcription of a pathway inhibitor.  Similarly, genes related to specific biological processes exhibit strong temporal synchronization in which multiple members of the pathway have similar transcriptional regulation over time.  Global coordination of signaling or functional families at the transcriptional level may be a mechanism to produce robustness of the desired outcomes. In addition, this comprehensive analysis provides a database for the further study of transcriptional events during liver development by identifying liver-specific, highly regulated genes.
Keywords: time course

overall_design: In order to provide transcriptional profile of the developing liver compared both to normal adult liver and non-hepatic embryonic tissueswe performed high-density microarray analysis using Affymetrix MG 430 2.0 chips for embryonic liver samples at 10.5, 11.5, 12.5, 13.5, 14.5, and 16.5 days post conception (dpc), embryo-minus liver tissues at 10.5, 11.5, 12.5, and 14.5 dpc, and normal 10-week-old adult mouse liver. Each sample consisted of at least five embryos.

first: Karen

last: Ho

first: Handan

last: Can

first: Seth

last: Karp


title: Dorsal root ganglion (katz-affy-mouse-210210)

status: Public on Apr 19 2008

city: Phoenix

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
The molecular identity of touch sensation is still largely unknown. We choose an extrem and very specific example, touch sensation of pennis glan, to study this problem. It's known from previous retro-grade labeling result that only one DRG in rat innervate the pennis glan, which makes it idea for microarry analysis.
To clone the mechanosensory receptor specifically or highly expressed in the primary sensory neurons innervating pennis glan.
There is a specific mechanosensory receptor in the primary sensory neurons innervating pennis glan.
1. Retrograde labeling the innervating nerve by DiI
2. Dissect DRGs, dissociate neurons and pick up the fluorescent cells.
3. Pool around 20 positive cells and 50 control cells (big diameter neuron and small to medium diameter neuron respectively), purify total RNA.
4. Two rounds of amplification
5. Affymetrix analysis
Keywords: dorsal root ganglion, touch sensatiion

first: Lawrence

last: Katz


title: Gene expression profiles of detrusor, stroma and urothelium isolated from SMGA (Actg2) transgenic neonatal bladders using LCM. (GUDMAP Series ID: 20)

status: Public on Apr 22 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 and laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing urogenital system. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. The data submitted here represents the gene expression profiles of compartmental bladder tissues collected through laser capture microscopy.
Keywords: Gene expression comparison from developing regions of the mouse postnatal day 1 and postnatal day 2 urogenital system.

overall_design: Bladders were isolated from newborn SMGA/EGFP transgenic mice, embedded in OCT, frozen and sectioned (8 microns).  Detrusor, stroma and urothelium were isloated using laser capture microscopy.   The caps were frozen on dry ice and stored at -80 degrees C until RNA was extracted for gene expression analysis. Laser captured and total RNA isolated for gene expression analysis using the Affymetrix MOE430 microarray chip.

first: James

last: Lessard

first: Nick

middle: E

last: Maull