title: MOE430A Analysis of Dll3 mutant vs. wild-type 9.5 dpc presomitic mesoderm

summary: Delta-like 3 (Dll3) is a divergent ligand and modulator of the Notch signaling pathway only identified so far in mammals. Null mutations of Dll3 disrupt cycling expression of Notch targets Hes1, Hes5, and Lfng, but not of Hes7.  Compared with Dll1 or Notch1, the effects of Dll3 mutations are less severe for gene expression in the presomitic mesoderm, yet severe segmentation phenotypes and vertebral defects result in both human and mouse.  Reasoning that Dll3 specifically disrupts key regulators of somite cycling, we carried out functional analysis to identify targets accounting for the segmental phenotype. Using microdissected embryonic tissue from somitic and presomitic mesodermal tissue, we identified new genes enriched in these tissues, including Limch1, Rphn2, and A130022J15Rik.  Surprisingly, we only identified a small number of genes disrupted by the Dll3 mutation. These include Uncx, a somite gene required for rib and vertebral patterning, and Nrarp, a regulator of Notch/Wnt signaling in zebrafish and a cycling gene in mouse. To determine the effects of Dll3 mutation on Nrarp, we characterized the cycling expression of this gene from early (8.5 dpc) to late (10.5 dpc) somitogenesis. Nrarp displays a distinct pattern of cycling phases when compared to Lfng and Axin2 (a Wnt pathway gene) at 9.5 dpc but appears to be in phase with Lfng by 10.5 dpc.  Nrarp cycling appears to require Dll3 but not Lfng modulation.  In Dll3 null embryos, Nrarp displayed static patterns.  However, in Lfng null embryos, Nrarp appeared static at 8.5 dpc but resumed cycling expression by 9.5 and dynamic expression at 10.5 dpc stages.  By contrast, in Wnt3a null embryos, Nrarp expression was completely absent in the presomitic mesoderm.  Towards identifying the role of Dll3 in regulating somitogenesis, Nrarp emerges as a potentially important regulator that requires Dll3 but not Lfng for normal function.

overall_design: To enrich for genes in the presomitic mesoderm that are specifically disrupted by Dll3 mutation, we compared microdissected tissues from wild-type and Dll3 mutant embryos. We generated biological replicate pools from Dll3+/+ (wild-type) or Dll3neo/neo embryos for a total of six pools. Microarray analysis using Affymetrix MOE430A arrays was carried out on the biological pool triplicates for both wild-type and mutant genotypes.

first: Duncan


title: (AKR/J x PyMT)F1 versus (DBA/2J x PyMT)F1 tumor expression data

status: Public on Nov 30 2008

city: Bethesda

first: Kent

last: Hunter

state: MD

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

country: USA

institute: National Cancer Institute

summary:
F1 hybrids from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses display a 20-fold difference in mammary tumor metastatic capacity, due to differences in inherited polymorphisms.  Expression studies were performed to determine whether polymorphism-driven gene expression signatures predictive of outcome could be generated from mouse tumor tissues

Keywords: Basal transcription profiles

overall_design: Mammary tumors from adult F1 animals from (AKR/J x PyMT) and (DBA/2J x PyMT) outcrosses was collected and arrayed on Affymetrics chip to identify basal differences in gene expression between the different genotypes

middle: W


title: AHR mediated gene expression changes in immature DN thymocytes and thymic emigrants

status: Public on Nov 25 2008

city: Duesseldorf

first: Markus

last: Frericks

address: Auf'm Hennekamp 50

department: Immunology

country: Germany

institute: Institute for Environmental Research

summary: Effect of an immunosupressive dose of TCDD, a ligand for the aryl hydrocarbon receptor, on the gene expression profile of fetal DN thymocytes and thymic emigrants

overall_design: C57BL6 mice were mated and the pregnant dams sacrifice at day 15 of gestation. Fetal thymic lobes were prepared and cultured for 6 days on culture inserts (5-6 lobes/culture insert). Medium, containing either 10 nM TCDD or solvent control was exchanged every 48 hours. At day six (gestation day 21, corresponding to birth), single cell suspensions of the thymocytes were prepared and CD4-CD8- cells isolated by MACS sorting. Purity of the population was checked FACS analysis, to be greater 95%. RNA was purified (TRIZOL), amplified (Ambion Kit) and processed (Affymetrix standard protocol) according to manufacturers instructions. Raw cell files were processed with the bioconductor affy package

first: Marc

last: Majora

first: Charlotte

last: Esser


title: IGFBP-3 is regulated by Gli signaling in cartilage tumors.

status: Public on Mar 06 2009

city: toronto

first: benjamin

last: alman

state: ontario

address: 555 university avenue

department: Developmental and stem cell biology

country: Canada

institute: Hospital for Sick Children

summary: Mice that develop benign cartilage lesions due to overexpression of Gli2 in chondrocytes developed lesions similar to chondrosarcomas when also deficient in p53.  Gli2 overexpression and p53 deficiency had opposing effects on chondrocyte differentiation, but had additive effects negatively regulating apoptosis.  Regulation of Igfbp3 expression and IGF signaling by Gli and p53 integrated their effect on apoptosis.  Treatment of human chondrosarcomas or fetal mouse limbs explants with IGFBP3 or by blocking IGF increased the apoptosis rate, and mice expressing Gli2 developed substantially fewer tumors when also deficient for Igf2.  IGF signaling meditated apoptosis regulates the progression to malignant chondrosarcoma.

overall_design: The CH10T1/2 cell line was stably transfected with either the R150C variant PTHR1 present in enchondromas (Hopyan, S., Gokgoz, N., Poon, R., Gensure, R. C., Yu, C., Cole, W. G., Bell, R. S., Juppner, H., Andrulis, I. L., Wunder, J. S., and Alman, B. A. (2002). A mutant PTH/PTHrP type I receptor in enchondromatosis. Nat Genet 30, 306-310)  or a wild type PTHR1, as previously reported (Mau, E., Whetstone, H., Yu, C., Hopyan, S., Wunder, J. S., and Alman, B. A. (2007). PTHrP regulates growth plate chondrocyte differentiation and proliferation in a Gli3 dependent manner utilizing hedgehog ligand dependent and independent mechanisms. Dev Biol 305, 28-39).  Cells were grown overnight in serum free media and treated with either 10− 7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA), or carrier alone for one hour.  RNA was isolated from the cells CH10T1/2 cells expressing either the R150C variant PTHR1 or wild type PTHR1.  RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer, which was then transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using Enzo BioArray High Yield RNA labeling kit (Enzo Diagnostics, New York, NY). The cRNA labeling and hybridizations were then performed according to Affymetrix GeneChip Protocol (Affymetrix Inc., Santa Clara, CA). The chips were scanned for fluorescence signal detection. Affymetrix - GeneChip® Mouse Genome 430A 2.0 Array was utilized.

first: Elaine

last: Mau

first: Benjamin

last: Alman


title: Effect of TCDD Exposure on purified splenic CD8 T cells

summary:
8-12 week, female C57BL/6 mice were injected with 10 µg/kg TCDD or solvent control. CD8+ T cells from spleen were FACS purified and submitted to transcription profiling
Keywords: TCDD, AHR, Immunosupression peripheral T cells, CD8 T cells, Toxicogenomics

overall_design: For each group 4 female C57BL/6 mice were treated, spleen surgically removed and single cell suspensions generated. Cell suspensions were pooled, and CD8 positive T cells purified (purity > 99%). RNA was isolated using TRIzol and amplified using the Ambion message AMP kit. Target lableing and hybridization was performed using Affymetrix standard protocols

first: Cahrlotte


title: Effect of an AhR-/- on transcription in CD4 T cells from the spleen.

summary:
CD4+ T cells from 8-12 week female mice were isolated from wt and AhR-/- mice 24h after  injection of 10µg/kg TCDD or solvent control.
Keywords: TCDD, AHR, immunosuppression

overall_design: Each experiment was performed in biological duplicates from 4 pooled animals. Since TCDD treatment showed only marginal impact on the gene expression (~10 transcripts effected in wt mice) wt - ko comparisons were performed on pooled profiles from TCDD and solvent mice.


title: Endometrial hyperplasia and carcinoma

status: Public on Nov 20 2008

city: New York

first: Ayesha

last: Joshi

state: NY

address: 1300 York Avenue, Pathology

department: Pathology and Laboratory Medicine

institute: Weill Medical College of Cornell University

summary:
Using mouse models of endometrial tumorigenesis based on two of the most common molecular alterations found in primary human UEC we sought to characterize the transition from CAH to carcinoma to identify clinically useful biomarkers.
In order to identify novel candidate genes associated with invasion, global gene expression profiles were compared from uteri with extensive CAH and carcinoma.
Keywords: Gene expression profiling

overall_design: RNA was extracted from uterine segments with either CAH or invasive carcinoma from  Pten+/-;Mlh1-/- , Pten+/-;Mlh1+/+ and Wild type female mice. The RNA was hybridized to Affymetrix mouse 430A chip in order to determine changes in global gene expression patterns

first: Hong

last: Wang

first: Lora

last: Ellenson


title: The effects of dietary curcumin on colonic gene expression in TNBS-induced colitis

status: Public on Nov 22 2008

city: Tucson

first: Pawel

middle: R.

last: Kiela

state: AZ

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

summary:
Curcumin is a potent anti-inflammatory compound capable of preventing chemically induced colitis in mice.
We used microarray analysis to detail the global programme of colonic gene expression in BALB/c mice fed standard or 2% curcumin-supplemented diet and treated with control or TNBS (trnitrobenzene-sulfonic acid, 2 mg/mouse) enema.

Keywords: Diet and disease effect.

overall_design: 6-8 week old BALB/c mice were treated with respecive diet two days prior to enema administration (day 0) and sacrificed on day 7. Whole colon was dissected from  mice and their wild-type littermates and total RNA isolated for microarray analysis using Affymetrix murine MOE430 mouse array set. RNA was pooled from 3 mice in each dietary/treatment group.

middle: R


title: Thymic deletion in B10 430B

status: Public on Nov 01 2008

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

summary:
Microarray analysis of thymic deletion in the B10 mouse strain
The gene expression patterns of thymocytes at the pre-selection stage and undergoing positive selection or negative selection were compared in the  C57BL/10-H2k (B10k) strain. In order to sort thymocytes homogenously undergoing positive selection the 3A9 TCRHEL transgenic was used, which directs thymocyte development towards a MHC class II-restricted HEL-reactive lineage. To sort thymocytes homogenously undergoing negative selection, the 3A9 TCRHEL transgenic was crossed to the insHEL transgenic, which expresses HEL under the control of the insulin promoter in the thymic stroma, leading to efficient negative selection at the early single positive (CD4+CD8low) stage. To prepare the samples, thymic cell suspensions from female 6-8 week old B10k mice, either 3A9 TCRHEL or 3A9 TCRHEL x insHEL transgenics, were stained with CD4-FITC, CD69-PE, CD8-PerCP, and 1G12 supernatant (which recognises the 3A9 TCRHEL complex) followed by anti-IgG1-APC, and sorted. Pre-selection cells (from both transgenics) were defined as CD4+CD8+CD69-1G12low. Cells undergoing positive selection (from 3A9 TCRHEL transgenics) or negative selection (from 3A9 TCRHEL x insHEL transgenics) were defined as CD4+CD8lowCD69+1G12high.
Keywords: repeat

overall_design: Single positive or double positive thymocytes from B10 mice were compared to those from B10 TCRHEL transgenic mice. 3 biological replicaes were used for each of the 4 different groups of thymocytes.

first: Adrian

last: Liston


title: Analysis of Aiolos and OBF-1 deletions in bone marrow from 7 week old mice

status: Public on Nov 03 2008

city: Basel

first: Edward

middle: James

last: Oakeley

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary:
The chromatin regulator Aiolos and the transcriptional coactivator OBF-1 have been implicated in regulating aspects of B cell maturation and activation. Mice lacking either of these factors have a largely normal early B cell development. However, when both factors are eliminated simultaneously a block is uncovered at the transition between pre-B and immature B cells, indicating that these proteins exert a critical function in developing B lymphocytes. In mice deficient for Aiolos and OBF-1, the numbers of immature B cells are reduced, small pre-BII cells are increased and a significant impairment in immunoglobulin light chain DNA rearrangement is observed. We identified genes whose expression is deregulated in the pre-B cell compartment of these mice. In particular, we found that components of the pre-BCR, such as the surrogate light chain genes l5l5 and VpreB, fail to be efficiently silenced in double-mutant mice. Strikingly, developmentally regulated nuclear repositioning of the l5l5 gene is impaired in pre-B cells lacking OBF-1 and Aiolos. These studies uncover a novel role for OBF-1 and Aiolos in controlling the transcription and nuclear organization of genes involved in pre-BCR function.

OBF-1 or Aiolos or both were deleted and the gene expression profiles for these animals investigated using Affymetrix arrays

Keywords: Genetic modifications

overall_design: Two control wildtype animals, then duplicates for each of the single Aiolos or OBF-1 mutants and further duplicates for the Aiolos/OBF-1 double mutants

middle: J

first: Alexander

last: Karnowski

first: Patrick

last: Matthias


title: Differentially regulated genes in HtrA2 knockout MEFs upon rotenone treatment

status: Public on Dec 01 2008

city: London

first: Kristina

last: Klupsch

address: 44 Lincoln's Inn Fields

department: London Research Institute

country: United Kingdom

institute: Cancer Research UK

summary:
Cellular stress responses can be activated following functional defects in organelles such as mitochondria and the endoplasmic reticulum. Mitochondrial dysfunction caused by loss of the serine protease HtrA2 leads to a progressive movement disorder in mice and has been linked to parkinsonian neurodegeneration in humans. Here we demonstrate that loss of HtrA2 results in transcriptional up-regulation of nuclear genes characteristic of the integrated stress response, including the transcription factor CHOP, selectively in the brain. We also show that loss of HtrA2 results in the accumulation of unfolded proteins in the mitochondria, defective mitochondrial respiration and enhanced production of reactive oxygen species that contribute to the induction of CHOP expression and to neuronal cell death. CHOP expression is also significantly increased in Parkinson’s disease patients’ brain tissue. We therefore propose that this brain-specific transcriptional response to stress may be important in the advance of neurodegenerative diseases.

Keywords: stress response to rotenone treatment

overall_design: This experiment was set out to identify genes that are differentially regulated upon rotenone treatment in HtrA2 knockout (KO) mouse embryonic fibroblasts (MEFs) compared to wild type (WT) MEFs. Primary MEFs were isolated and at passage 4 subjected to treatment with vehicle (control) or 1 μM rotenone (rot) for 4 hrs. 3 replicates were performed. RNA was isolated and samples were processed for hybridisation (12 samples in total).

first: Nicoleta

last: Moisoi

first: L

middle: M

last: Martins

first: Julian

last: Downward


title: Integrative Genome-wide Analysis of Glioblastoma.

status: Public on Oct 30 2008

city: Rennes

first: Marie

last: de Tayrac

address: 2 avenue du Professeur Léon Bernard

country: France

type: Genome variation profiling by genome tiling array

type: Expression profiling by genome tiling array

summary:
Glioblastoma multiforme shows multiple chromosomal aberrations, the impact of which on gene expression remains unclear. To investigate this relationship and to identify putative initiating genomic events, we integrated a paired copy number and gene expression survey in glioblastoma using whole human genome arrays. Loci of recurrent copy number alterations were combined with gene expression profiles obtained on the same tumor samples. We identified a set of 406 ‘cis-acting DNA targeted genes’ corresponding to genomic aberrations with direct copy-number-driving changes in gene expression, defined as genes with either significantly concordant or correlated changes in DNA copy number and expression. Functional annotation revealed that these genes participate in key processes of cancer cell biology, providing insights into the genetic mechanisms driving glioblastoma. The robustness of the gene selection was validated on an external microarray data set including 81 glioblastomas and 23 non-neoplastic brain samples. The integration of array CGH and gene expression data highlights a robust ‘cis-acting DNA targeted genes’ signature that may be critical for glioblastoma progression, with two tumor suppressor genes PCDH9 and STARD13 that could be involved in tumor invasiveness and resistance to etoposide.
Keywords: Glioblastoma Multiforme, array CGH, microarray, data integration

overall_design:
Glioblastoma multiforme (n=19) and non-neoplastic brain samples (n=4) were analysed.
CGH-array were performed in a dye-swap experiment. Tumor DNA was hybridized with the corresponding patient blood DNA as reference to identify somatic changes only. Whole genome expression microarray were performed for the same GBMs with particular care to provide paired data sets.
For each brain tumor sample: a snap-frozen tumor block was cryodissected in 10µm sections. The first section as well as sections obtained every 100µm were stained to analyze tissue with at least 70 percents of tumoral cells and to exclude necrotic areas and widespread blood vessels. The adjacent sections were alternatively pooled in different tubes for RNA and DNA extractions, thus allowing a comparison between closely related biological materials.
The non-neoplastic brain samples (N) were also analysed by expression microarray to provide gene expression measurements expressed as log2 ratio (GBM vs mean N) and to allow testing procedure.

first: Amandine

last: Etcheverry

first: Stephan

last: Saïkali

first: Marc

last: Aubry

first: Abderrahmane

last: Hamlat

first: Véronique

last: Quillien

first: Marie-Dominique

last: Galibert

first: Jean

last: Mosser


title: Gene analysis of the developing brain of embryos from STZ induced diabetic mice

status: Public on Oct 01 2008

city: Singapore

first: S Thameem

last: Dheen

address: Medical Drive 10

country: Singapore

institute: National University of Singapore

summary:
Maternal diabetes causes congenital malformations in various organs in fetuses. This study was aimed to investigate the differential gene expression profiling in developing brains of embryos from diabetic mice.
Keywords: disease state analysis

overall_design: Totally six samples were used. Three brains of the embryos from control normal mice was hybridized on three chips separately. And three malformed brains of the embryos from experimental diabetic mice was hybridized on three chips separately.

first: Boran

last: Jiang

first: Thameem

first: Dinesh

middle: K

last: Srinivasan

first: Manikandan

last: Jayapal


title: Expression profiling of a high-fertility mouse line by microarray analysis and qPCR.

status: Public on Sep 22 2008

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

institute: Leibniz Institute for Farm Animal Biology

summary:
The objective of the present study was to identify genes that are involved in increasing the ovulation number in mouse line FL1 that had been selected for high fertility performance.
Keywords: Comparative gene expression profiling

overall_design: Ovaries from 30 animals of line FL1 and of the control line DUKsi were collected at the metestrous stage, combined to 6 pools each, and processed for microarray analysis.

first: Gerd

last: Nürnberg


title: Global gene expression analysis of undifferentiated H1 hESC, and hEB cells differentiated with SF BVF2H conditions

status: Public on Aug 23 2008

city: Baltimore

first: Wayne

last: Yu

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

summary:
Global gene expression analysis of human embryoid body (hEB) differentiations during differentiation in serum free conditions in the presence of BMP4, VEGF, and FGF2 growth factors
A total of 5 samples are analyzed. Each sample is taken at each time point. There is no replicate. H1_hESC_day0 sample is used as control to compare to other samples

Keywords: Cell differentiation

overall_design: Cell differentiation compares to undifferentiated status in a time-course of 3-, 5-, 7- and 10-day without replicates.

first: Elias

middle: T

last: Zambidis


title: mRNA regulation in normal or TNF-a/IL-4-activated bronchial epithelial cells (BEAS-2B)

status: Public on Oct 14 2008

city: Houston

first: David

middle: S

last: Loose

state: TX

address: 6431 Fannin St, MSB 4.130

department: Integrative Biology & Pharm

institute: University of Texas

summary: Illumina microarray experiment on BEAS-2B cells. Cells  were seeded 24 h before TNF-a/IL-4 (50 ng/ml) treatment that lasted for 18 h. Cytoplasmic RNA of both normal and activated BEAS-2B cells were collected for microarray. Cells  were seeded 24 h before TNF-a/IL-4 (50 ng/ml) treatment that lasted for 18 h.

overall_design: Biological triplicate control and IL4/TNf samples.

first: Ann-Bin

last: Shyu

first: Yuxin

last: Zhai

first: Zhenping

last: Zhong

first: Chyi-Ying

middle: A

last: Chen

first: Zhenfang

last: Xia


title: Prox-1 promotes invasion of kaposiform hemangioendotheliomas

status: Public on Aug 04 2008

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

institute: ETH Zurich

summary:
Kaposi’s sarcoma (KS) is the most frequently occurring malignant tumor in patients infected with the human immunodeficiency virus. Recent studies have revealed that infection of vascular endothelial cells with Kaposi's sarcoma-associated herpes virus in vitro results in a lymphatic re-programming of these cells, with potent induction of the lymphatic marker genes podoplanin and VEGFR-3 which is mediated by upregulation of the transcription factor Prox1. However, the potential effects of Prox1 expression on the biology of KS and, in particular, on the aggressive and invasive behavior of KS tumors in vivo have remained unknown. We stably expressed Prox1 cDNA in the two mouse hemangioendothelioma cell lines EOMA and Py-4-1, well-established murine models for kaposiform hemangioendothelioma. Surprisingly, we found that expression of Prox1 was sufficient to induce a more aggressive behavior of tumors growing in syngenic mice, leading to enhanced local invasion into the muscular layer and to cellular anaplasia.  This enhanced malignant phenotype was associated with upregulation of several genes involved in proteolysis, cytoskeletal reorganisation and migration. Together, these results indicate that Prox1 plays an important, previously unanticipated role in mediating the aggressive behavior of vascular neoplasms such as Kaposi's sarcoma.
Keywords: Overexpression of Prox1 in Py-4-1 cell line.

overall_design: Total cellular RNA was extracted from two stably Prox1-expressing Py-4-1 cell clones and from two control-transfected Py-4-1 cell clones.

first: Soheil

last: Dadras

first: Adrienne

last: Skrzypek

first: Lynh

last: Nguyen

first: Jack

last: Arbiser

first: Martin

middle: C

last: Mihm

first: Michael

last: Detmar


title: Transcriptome analysis of Foxp3- CD25- regulatory T cells

status: Public on Aug 21 2008

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
The concept of immune regulation/suppression has been well-established. With thymus-derived CD4 CD25  regulatory T (TR) cells, it became clear that a variety of additional peripherally induced TR cells play vital roles in protection from many harmful immune responses including intestinal inflammation. In the present study, we have analyzed in vivo-induced Ag-specific CD4 TR cells with respect to their molecular and functional phenotype. By comparative genomics we could show that these Ag-specific TR cells induced by chronic Ag stimulation in vivo clearly differ in their genetic program from naturally occurring thymus-derived CD4 CD25  TR cells. This distinct population of induced TR cells express neither CD25 nor the TR-associated transcription factor Foxp3. Strikingly, CD25 is not even up-regulated upon stimulation. Despite the lack in Foxp3 expression, these in vivo-induced CD25  TR cells are able to interfere with an Ag-specific CD8  T cell-mediated intestinal inflammation without significant increase in CD25 and Foxp3 expression. Thus, our results demonstrate that in vivo-induced Ag-specific TR cells represent a distinct population of Foxp3 CD25  TR cells with regulatory capacity both in vitro and in vivo.

Keywords: cell type comparison

overall_design: To define the molecular signature of Ag-specific in vivo-induced dtg CD25 TR cells in comparison to naturally occurring CD25 TR cells, we performed comparative gene expression profiling by Affymetrix microarray analysis. Sorted splenic wild-type (WT) TR cells, stg TR cells, dtg CD25-  TR cells, dtg CD25+  TR cells, in vitro-stimulated stg 16h TA cells, stg 3d TA cells as well as stg TN cells, were included in the experiment and analyses were performed in triplicates.

first: Wiebke

last: Hansen

first: Jan

last: Buer


title: Gene Expression Analysis of laser-microdissected motorneurons in Spinal Muscular Atrophy (SMA)

status: Public on Aug 06 2008

city: Milan

first: Stefania

last: Corti

address: via F. Sforza 35

department: Neurological Sciences

country: Italy

institute: University of Milan

summary:
Spinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. Stem cell transplantation could represent a therapeutic approach for motor neuron diseases such as SMA.  We examined the theraputics effects of a spinal cord neural stem cell population and their ability to modify SMA phenotype.
Microarray technology was used to assess the global gene expression profile of laser-microdissected motoneurons obtained by transplanted and veichle treated SMA, and wildtype mice.
Keywords: Comparative Gene Expression Analysis

overall_design: The microarray data derived from three different groups: wildtype controls (vehicle treated), transgenic SMA (vehicle treated) and transplanted SMA mice. Each population consists of three RNA profiling samples.

first: Dario

last: Ronchi


title: Neonatal and embyronic CNS of mice with maternal or paternal duplication of proximal chromosomes 7 and 15 (430A)

status: Public on Jul 25 2008

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary:
Gene expression profiling was performed on CNS tissue from neonatal mice carrying the T9H translocation and maternal or paternal duplication of proximal Chromosomes 7 and 15.  Our analysis revealed the presence of two novel paternally expressed intergenic transcripts at the PWS/AS locus.  The transcripts were termed Pec2 and Pec3 for paternally expressed in the CNS.Our analysis also revealed imprinting of Magel2, Mkrn3, Ndn,Ube3a and Usp29, as well as Pec2 and Pec3 in embryonic brain, 15.5 dpc, and provided a survery of biallelically expressed genes on proximal Chromosomes 7 and 15 in embryonic and neonatal CNS.

Keywords: genetic modification, developmental comparison

overall_design: Fourteen samples were analyzed by microarray analysis using GeneChip 430A:  Six different biological samples were analyzed in duplicate:  RNAs were from neonatal cortex and cerebellum, and from whole brain of 15.5 dpc embryos, purified from mice carrying either maternal or paternal duplication of proximal chromosomes 7 and 15.    In addition, one hybridization each was performed on 13.5 dpc embryonic brain RNA from mice carrying the same duplications.

first: Judith

last: Singer-Sam

first: Victoria

middle: L

last: Buettner


title: Mechanism of alopecia in the new hairless mutant Hos: HR-1 mouse

status: Public on Jul 11 2008

city: Tokyo

first: Tomomi

last: Soshin

address: Yayoi 1-1-1

department: Graduate School of Agricultural and Life Sciences

country: Japan

institute: the University of Tokyo

summary:
The Hos: HR-1 mouse strain (HR-1) is an autosomal resessive mutant strain which is widely used in pharmacological and dermatological studies in Japan.  Although HR-1 mice have been believed to be Hr gene mutants based on their distinctive alopecia phenotype, there are no reports on either the genetic nature of the Hr gene or mechanism of alopecia.  The present study clarified that the HR-1 mice carry a C to T transition in the Hr gene, which causes a proline to serin amino acid change in the functional domain of translated HR protein.  It is well known that HR plays an important role in hair follicle regression, and loss of HR function triggers distinctive alopecia with the presence of premature apoptosis in the regressing hair follicle.  However, the detailed function of HR protein is still uncertain.  To clarify the mechanism by which HR dysfunction causes hair loss, here we performed microarray analysis on the mRNA samples obtained from the regressing hair follicles of the homozygous (HrHos / HrHos) and heterozygous (+/HrHos, control) Hr mutant mice using laser capture microdissection.  Our results showed increased expression of apoptosis-related and cell-cycle-repressive genes and decreased expression of cell-cycle-promoting genes, suggesting inhibition of the cell cycle at G0/G1.  These findings strongly suggest that the loss of HR function leads to high expression of cell cycle inhibitors, resulting in the hair loss with premature apoptosis in the hair matrix.
Keywords: genetic analysis

overall_design: Homozygous (HrHos / HrHos) and heterozygous (+/HrHos) Hr mutant mice of the same N1 littermates obtained from a male Hos: HR-1 mouse and a female heterozygous F1 offspring (+/HrHos) between an HR-1 mouse and an ICR mouse were used at day 14 postpartum.  +/HrHos mice were used as controls because the Hr gene mutantion is autosomal recessive and the morphological appearance of +/HrHos is as same as that of wild-type mice. Four samples (two from +/HrHos and two from HrHos / HrHos) were analyzed. All RNA samples were extracted from hair follicles of dorsal skin using Laser capture microdissection.

first: Taro

last: Okada

first: Yoshiyuki

last: Ishii

first: Makio

last: Takeda

first: Ryoichi

last: Otsuka

first: Hiroyuki

last: Nakayaam

first: Kunio

last: Doi


title: Neonatal and embyronic CNS of mice with maternal or paternal duplication of proximal chromosomes 7 and 15 (430B)

overall_design: Eight samples were analyzed by microarray analysis using GeneChip 430B (no biological replicates).  RNAs were from neonatal cortex and cerebellum, and from whole brain of 13.5 and 15.5 dpc embryos, purified from mice carrying either maternal or paternal duplication of proximal chromosomes 7 and 15.


title: Comparative analysis of gene expression in ob/ob leptin-treated and ob/ob saline-treated lungs.

status: Public on Jun 01 2008

first: vikas

last: misra

address: 615 N. Wolfe street, E6609

department: Environmental health sciences

institute: Johns Hopkins University School of public health

summary:
We hypothesize that gene expression in the lungs of these differentially-treated mice are divergent thus contributing to the disparity in their phenotypes. More specifically, (1) Effects of Leptin-treatment of ob/ob postnatal mice lungs are known to be volume-dependent from 2 to 10 wks of age, and are independent of the hypometabolism associated with leptin deficiency. ; (2) Leptin is critical to postnatal lung remodeling, particularly related to enlarged alveolar surface area. In order to test these hypotheses at the gene expression level, we utilized microarray analysis to examine transcriptional differences between lungs of leptin or saline-treated ob/ob postnatal mice.
Keywords: leptin, ob, lung

overall_design: This study utilizes microarray analysis to test these hypotheses. Three sets of lungs were harvested from both treatments (Leptin or Saline) at around 1 mo. postnatal. RNA was isolated and used for global gene expression profiling (Affymetrix Mouse 430A array). Statistically significant gene expression was determined as a minimum 6 counts of 9 pairwise comparisons, minimum 1.5-fold change, and p < 0.05.

first: Kewu

last: Huang

first: Richard

last: Rabold

first: Eric

last: Abston

first: Brian

last: Schofield

first: Vikas

last: Misra

first: Hannah

last: Lee

first: Shyam

last: Biswal

first: Wayne

last: Mitzner

first: Clarke

middle: G

last: Tankersley

first: Ewa

last: Galdzicka


title: murine CD4+ and CD8+ T-cells from wildtype and Gfi knockout cells

status: Public on Jul 22 2008

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
to compare the transcriptomes of naïve CD4+ and CD8+ T-cells from Gfi1-knockout cells with wildtype cells, spleenocytes  from wildtype and Gfi-knockout C57Bl/6 mice were isolated, stained with CD44, CD4 and CD8 antibodies and separated by using a FACS Diva (Becton Dickinson). Total RNAs isolated from 2 mice each (approximately 2xE06 cells) were pooled and subjected to microarray analysis on Affymetrix MOE430A_2.0 arrays
Keywords: knockout mice

overall_design: 4 samples, 1 replicate per group

first: Denise

last: Pargmann

first: Raif

last: Yücel

first: Christian

last: Kosan

first: Simone

last: Schimmer

first: Ulf

last: Dittmer

first: Tarik

last: Möröy


title: Role of AhR in thymocyte emigration in vivo

status: Public on Nov 25 2008

city: Duesseldorf

first: Markus

last: Frericks

address: Auf'm Hennekamp 50

institute: Institute for Environmental Research

summary:
Over-activation of the aryl hydrocarbon receptor by TCDD in mice leads among other phenotypes to a severe thymic atrophy accompanied by immunosuppression. TCDD causes a block in thymocyte maturation and a preferential emigration of immature CD4-CD8- DN thymocytes (recent thymic emigrants) into the periphery. As part of this study gene expression profiles from DN thymocytes and thymic emigrants were generated from TCDD and solvent control mice
Keywords: Affymetrix, TCDD, CD4-CD8- thymocytes, Thymus involution, thymic emigration, Ahr

overall_design: Female, 6-8 week old C57BL6 mice were i.p. injected with 10 µg/kg TCDD. After 5 days mice were anesthezised and FITC injected into their thymi. after 24h mice were sacrificed and CD4-CD8-FITC+ cells isolated from thymus (thymocytes) and spleen (recent thymus emigrants).

first: Vladimir

last: Temchura

first: Charlotte

last: Esser


title: A novel tumor-promoting function resided in the 5’ untranslated region of vegf mRNA

status: Public on Apr 04 2008

city: Tokushima

first: Tomoko

last: Kawai

address: 3-18-15 Kuramoto-cho

department: Stress Science

institute: Institue for Health Biosciences, The University of Tokushima Graduate School

summary:
VEGF165 is one of the key regulators of tumor development. Using HCT116 cells transfected with full-length vegf mRNA, full-length vegf mRNA with mutations of H9D and L14E, mutated vegf mRNAs lacking untranslated regions (UTRs), and 5’UTR mutated between nt 591 and nt 746, we found that vegf 5’UTR resided an anti-apoptotic activity against chemotherapy independently of VEGF165. We next established HCT116 clones stably expressing vegf 5’UTR or the mutated vegf 5’UTR. The cells expressing 5’UTR, but not the mutated UTR, showed the drug-resistant phenotype, anchorage-independent growth, and rapid tumor growth when implanted in athymic nude mice. Microarray and real-time PCR showed that the vegf 5’UTR-expressing tumors up-regulated anti-apoptotic genes including mia and down-regulated pro-apoptotic genes including fas, pdcd1, nrg1, and bax. Microarray analysis also revealed specific down-regulation of IFN-inducible genes (43 genes) in the growing tumors. HCT116 cells stably transcribing vegf 5’UTR decreased STAT1 expression and IFN alpha-STAT1 pathway. In addition to 5-fluorouracil treatment, the vegf 5’UTR-expressing tumors did not respond to IFN alpha therapy at all. This novel tumor-promoting function in the vegf 5’UTR may partly explain the insufficiency of the VEGF-VEGFR strategies and suggest a vegf-targeted silencing strategy as a more effective anti-tumor therapy.
Keywords: genetic modification

overall_design: We established HCT116 clones stably expressing vegf 5’UTR (vegf 5’-G5) and vegf 5’UTR mutated between nt 591 and nt 746 (vegf 5’ mut-D5) and implanted into the left and the right flanks of the identical mouse, respectively. The generated tumors on day 14 after injection were removed and total RNA was extracted from each tumor using RNeasy mini (Qiagen). After removing contaminated DNA by DNaseI treatment, 10 micro grams each of RNA of vegf 5’-G5-derived tumor from 3 individual mice was mixed and prepared for microarray analysis as sample RNA. The reference RNA of vegf 5’ mut-D5-derived tumor was arranged in the same manner. The quality of both RNA samples was confirmed using an Agilent 2100 Bioanalyzer. Microarray analysis was then performed: briefly, 1 µg of sample RNA (vegf 5’-G5) and reference RNA (vegf 5’ mut-D5) were converted to cDNA with oligo dT conjugated T7 promoter primer and reverse transcriptase. These cDNAs were amplified using T7 RNA polymerase while labeling with either Cy5-CTP or Cy3-CTP (Low RNA Fluorescent Linear Amplification Kit, Agilent Technologies). 750 ng of Cy3 and Cy5-labeled cRNA were mixed and hybridized on an Agilent 22k human 1A array in a hybridization oven at 65oC for 17 h as rotating. Following hybridization and washing of a slide according to manufacture’s protocol, the arrays were scanned using the Agilent DNA Microarray Scanner (G2565BA) and microarray images were analyzed using Agilent Feature Extraction Software (v7.5). The final signal intensity was resulted from subtracting background signal from row spot signal. The gene expression level was presented as ratio of sample intensity against reference intensity.

first: Kiyoshi

last: Masuda

first: Shigetada

last: Teshima-Kondo

first: Mina

last: Mukaijo

first: Naoko

last: Yamagishi

first: Yoshiko

last: Nishikawa

first: Kensei

last: Nishida

first: Kazuhito

last: Rokutan


title: murine T-cells from wildtype and Gfi1 knockout mice activated by anti-CD3 plus anti-CD28 for 0 to 24h

first: Ludger

last: Klein-Hitpass

summary:
To compare the transcriptomes of T-cells from Gfi1-knockout cells with wildtype cells, spleenocytes  from wildtype and Gfi-knockout C57Bl/6 mice were isolated using panT-cell kit  in an AutoMACS device (Miltenyi). Cells were cultured with anti-CD3 plus anti-CD28 antibodies (2 µg antibody/ml) for the indicated time period. Total RNAs was isolated and subjected to microarray analysis on Affymetrix MOE430A_2.0 arrays.
Keywords: time course, wt and Gfi1 knockout

overall_design: 8 samples, 1 replicate per group

first: Denise

last: Pargmann


title: Cellular pathways involved in the adaptation and progression of motor neuron injury in the mouse model of familial ALS

status: Public on Mar 27 2008

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
Microarray analysis has been applied to the study of ALS in order to investigate gene expression in whole spinal cord homogenates of SOD1 G93A mice and human ALS cases, although the massive presence of glial cells and inflammatory factors has made it difficult to define which gene expression changes were motor neuron specific. Recently, laser capture microdissection (LCM), combined with microarray analysis, has allowed the identification of motor neuron specific changes in gene expression in human ALS cases.
The aim of the present study is to combine LCM and microarray analysis to study how motor neurons in the spinal cord of transgenic SOD1 G93A mice and transgenic SOD1 WT respond to stimuli determined by the presence of the human mutant protein throughout the evolution of the stages in motor neuron injury
Keywords: Murine motor neurons

overall_design: Motor neurons have been isolated from the spinal cord of G93A mice and non transgenic littermates at different time points and the transcription expression profile of the isolated motor neurons has been analysed

first: Laura

last: Ferraiuolo

first: Hazel

last: Holden

last: Kasher

first: Janine

last: Kirby

first: Pamela

last: Shaw


title: Comparison of murine masticatory and limb skeletal muscle

status: Public on May 09 2008

city: Philadelphia

first: Elisabeth

last: Barton

state: PA

address: 240 S. 40th Street

department: Anatomy and Cell Biology

institute: University of Pennsylvania Dental School

summary:
Distinctions between craniofacial and axial muscles exist from the onset of development and throughout adulthood. The masticatory muscles are a specialized group of craniofacial muscles that retain embryonic fiber properties throughout adulthood, suggesting that the developmental origin of these muscles may govern a pattern of expression that differs from limb muscles. To determine the extent of these differences, expression profiling of total RNA isolated from the masseter and tibialis anterior (TA) muscles of adult female mice was performed, which identified transcriptional changes in unanticipated functional classes of genes in addition to those associated with fiber type. In particular, the masseters displayed a reduction of transcripts associated with load-sensing and anabolic processes, and heightened expression of genes associated with stress. Consistent with these observations were a significantly smaller fiber cross-sectional area in masseters, significantly elevated load-sensing signaling (phosphorylated Focal Adhesion Kinase (FAK)), and increased apoptotic index in masseters compared to TA muscles. Based on these results, we hypothesize that masticatory muscles may sense and respond to load differently than limb muscles, where the drive for anabolic processes is reduced, and cell stress mediated processes are enhanced. These results establish a novel classification for the masseter muscle in the spectrum of skeletal muscle allotypes, and may provide insight into the molecular basis for specific muscle-related pathologies associated with masticatory muscles.
Keywords: skeletal  muscle, developmental origin, craniofacial muscles

overall_design: Tissues were isolated from normal adult female mice (C57Bl/6), age 6 months. Paired comparisons between masseter and tibialis anterior muscles were performed on all present genes using "Significance Analysis of Microarrays" (SAM) to identify differentially expressed genes between masticatory and axial muscles.

first: Marianna

last: Evans

first: Kevin

last: Morine

first: Cyelee

last: Kulkarni


title: Neonatal and embyronic CNS of mice with maternal or paternal duplication of proximal chromosomes 7 and 15

first: Xiwei

last: Wu

summary:
Gene expression profiling was performed on CNS tissue from neonatal mice carrying the T9H translocation and maternal or paternal duplication of proximal Chromosomes 7 and 15.  Our analysis revealed the presence of two novel paternally expressed intergenic transcripts at the PWS/AS locus.  The transcripts were termed Pec2 and Pec3 for paternally expressed in the CNS.Our analysis also revealed imprinting of Magel2, Mkrn3, Ndn,Ube3a and Usp29, as well as Pec2 and Pec3 in embryonic brain, 15.5 dpc, and provided a survery of biallelically expressed genes on proximal Chromosomes 7 and 15 in embryonic and neonatal CNS.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Expression data from UPD12 mice

status: Public on Apr 14 2008

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

summary:
Comparison of gene expression levels between matUPD12 and patUPD12 15.5 dpc whole embryo or placenta samples (maternal versus paternal uniparental disomy of Chr 12). Identification of highly differentially expressed transcripts.
Keywords: genetic modification

overall_design: Pairwise array comparative analyses were performed using MAS5/GCOS where sample age and tissue were matched, while the sample genotype varied between the compared arrays: matUPD12 vs patUPD12.

first: Kathryn

last: Woodfine

first: Rebecca

last: Oakey

first: Dionne

last: Gray

first: Anne

last: Ferguson-Smith


title: Apc1638N intestinal tumors vs WT intestinal mucosa

status: Public on Apr 01 2008

city: Rotterdam

first: Claudia

last: Gaspar

address: Dr. Molenwaterplein 40, PO Box 2040

department: Experimental Pathology

country: Netherlands

institute: ErasmusMC

summary:
The majority of sporadic colorectal cancer cases are initiated by mutations in the APC tumor suppressor gene leading to constitutive activation of the Wnt/b-catenin signaling pathway and adenoma formation. Several pre-clinical models carrying germline mutations in the endogenous mouse Apc tumor supressor gene have been generated and their phenotype characterized. The predisposition of these mouse models to multiple intestinal adenomas closely resembles the FAP phenotype at the molecular, cellular and phenotypic level and may prove valuable to elucidate the molecular and cellular mechanisms underlying colorectal tumorigenesis. The goal of this study is to establish an expression signature characteristic of intestinal tumors characterized by the inactivation of Apc.
Keywords: Tumor vs Normal intestinal cells

overall_design: We have compared 3 intestinal tumor samples collected from the mouse model Apc1638N against 2 normal intestinal samples collected from wild type C57Bl6/J animals. In both cases only epithelial cells were used for the signature since we have collected our samples were laser capture microdissected.

first: Joana

last: Cardoso

first: Patrick

last: Franken

first: Lia

last: Molenaar

first: Hans

last: Morreau

first: Gabriela

last: Moslein

first: Julian

last: Sampson

first: Judith

last: Boer

first: Renee

middle: X

last: de Menezes

first: Riccardo

last: Fodde


title: Comparison of SCG expression profiles from Bax null versus NGF-Bax double null mice

status: Public on Apr 09 2008

first: David

middle: D

last: Ginty

address: 725 N. Wolfe St.

department: Neuroscience

institute: Johns Hopkins University School of Medicine

summary:
We report that developmental competition between sympathetic neurons for survival is critically dependent on a sensitization process initiated by target innervation and mediated by a series of feedback loops.  Target-derived nerve growth factor (NGF) promoted expression of its  receptor TrkA in neurons and prolonged TrkA-mediated signals.  NGF also controlled expression of brain derived neurotrophic factor (BDNF) and neurotrophin-4 (NT4), which, through the receptor p75, can kill neighboring neurons with low retrograde NGF–TrkA signaling whereas neurons with high NGF–TrkA signaling are protected.  Perturbation of any of these feedback loops disrupts the dynamics of competition.  We suggest that three target-initiated events are essential for rapid and robust competition between neurons: sensitization, paracrine apoptotic signaling, and protection from such effects.
Keywords: comparative gene expression analysis

overall_design: This experiment examine gene expression differences in superior cervical ganglia fro P0 bax null versus NGF-Bax double null animals. The Bax genotype was used in order to prevent the neuronal cell death normally observed in the NGF null animal.

first: Christopher

last: Deppmann

first: Stefan

last: Mihalas

first: Nikhil

last: Sharma

first: Bonnie

middle: E

last: Lonze

first: Ernst

last: Niebur


title: Altered Genomic Expression of Immune and Metabolic Pathways in a Murine Model of Diesel Enhanced Allergic Sensitization

status: Public on Mar 26 2008

city: carrboro

first: Tina

last: Stevens

state: NC

address: 138 marlowe ct

institute: UNC

summary:
Diesel exhaust (DE) has been shown to enhance allergic sensitization in animals following high dose instillation or chronic inhalation exposure scenarios.  The purpose of this study was to determine if short term exposures to diluted DE enhance allergic immune responses to antigen, and identify possible mechanisms using microarray technology. BALB/c mice were exposed to filtered air or diluted DE to yield particle concentrations of 500 or 2000 µg/m3 4 hr/day on days 0-4.  Mice were sensitized intranasally with ovalbumin (OVA) antigen or saline on days 0-2, and 18 and all were challenged with OVA on day 28. Mice were necropsied either 4 hrs after the last DE exposure on day 4, or 18, 48, and 96 hrs after challenge.  Immunological endpoints included OVA-specific serum IgE, biochemical and cellular profiles of bronchoalveolar lavage (BAL), and cytokine production in the BAL. OVA-sensitized mice exposed to both concentrations of DE had increased eosinophils, neutrophils, lymphocytes, and IL-6 post-challenge compared to OVA control, while DE/saline exposure yielded increases in neutrophils at the high dose only.  Microarray analysis demonstrated distinct gene expression profiles for the high dose DE/OVA and DE/saline groups. DE/OVA induced pathways involved in oxidative stress and metabolism while DE in the absence of allergen sensitization modulated cell cycle control, growth and differentiation, G-proteins, and cell adhesion pathways.  This study shows for the first time early changes in gene expression induced by the combination of diesel exhaust inhalation and antigen sensitization, which resulted in stronger development of an allergic asthma phenotype.
Keywords: dose response

overall_design: Lung RNA was isolated from mice exposed to filtered air,  500 ug/m3 DE, or 2000 ug/m3 DE with or without OVA for a total of 6 exposure groups.  Each group had 4 replicates for a total of 24 microarrays.

first: T

first: M

middle: I

last: Gilmour

first: W

last: Linak

first: S

last: Hester

first: Q

last: Krantz


title: KCl depolarization-regulated genes in mouse cortical neurons

status: Public on Sep 24 2008

city: Boston

first: Yingxi

last: Lin

state: MA

address: Enders 250, 300 Longwood Avenue

department: Neurology/Neurobiology

institute: Children' Hospital/Harvard Medical School

summary:
we used DNA microarray analysis to identify genes that are induced by neuronal activity in excitatory neurons at the time when inhibitory synapses are forming and maturing on them.
Keywords: Primary neuron culture, depolarization, activity-dependent

overall_design: We cultured cortical neurons for 7 DIV until the process of inhibitory synapse development was underway, and then depolarized the neurons with 50 mM of KCl to activate L-type voltage-sensitive calcium channels (L-VSCCs) for 0, 1 or 6 hours, the cells were lysed, mRNA isolated and hybridized to Affymetrix arrays. Data were collected from 3 independent experiments.

first: Michael

last: Greenberg


title: Expression data from Newborn mice infected with Shigella flexneri

status: Public on Mar 20 2008

city: Paris

first: Thierry

last: Pedron

address: 28 rue du Docteur Roux

department: Biologie cellulaire et Infection

institute: Pasteur Institute

summary:
In order to identify the developmental changes controlling the switch from disease susceptibility to resistance, we performed global gene expression analysis on non-infected and infected intestinal tissues taken from 4-day- and 7-day-old animals.
Keywords: time course of infection

overall_design: RNA from intestinal tissues of 4-day- or 7-day-old mice infected or not with invasive (INV+) or non-invasive (INV-) Shigella strains during 2 or 4 hours were hybridized on Murine MOE430A Affymetrix Genechip.

first: Maria-Isabel

last: Fernandez

first: Béatrice

last: Regnault

first: Céline

last: Mulet

first: Myriam

last: Tanguy

first: Philippe

last: Jay

last: Sansonetti

last: Pédron


title: Microarray analysis of mdx mice expressing high levels of utrophin: therapeutic implications for DMD

status: Public on Apr 23 2008

city: Oxford

first: Dilair

last: Baban

address: Roosevelt Drive

department: Wellcome Trust Centre Human Genetics

institute: University of Oxford

summary:
Duchenne Muscular Dystrophy (DMD) is a fatal muscle wasting disorder caused by dystrophin deficiency. Previous work suggested that increased expression of the dystrophin-related protein utrophin in the mdx mouse model of DMD can prevent dystrophic pathophysiology.   Physiological tests showed that the transgenic mouse muscle functioned in a way similar to normal muscle.  More recently, it has become possible to analyse disease pathways using microarrays, a sensitive method to evaluate the efficacy of a therapeutic approach.  We thus examined the gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line expressing utrophin.  The data confirm that the expression of utrophin in the mdx mouse muscle results in a gene expression profile virtually identical to that seen for the normal mouse.  This study confirms that a strategy to up-regulate utrophin is likely to be effective in preventing the disease.
Keywords: Global gene expression profile

overall_design: Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.

first: Kay

last: Davies


title: CD49 Sorted Stem Cells, time 0

status: Public on Mar 01 2008

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
CD49 Sorted Stem Cells, time 0, Dulac labeling protocol (NOTE: the dulac protocol amplifies from a small number of cells and the results may be difficult to compare with other more standard microarray analyses.)
Keywords: other

overall_design: this experiment include 2 samples and 12 replicates


title: Embryonic stem cells differentiated into embryoid bodies. vs cells grown in regular growth conditions

summary:
Embryonic stem cells differentiated into embryoid bodies. Their expression pattern will be compared to that of the same cells grown in regular growth conditions. A study of the differential gene expression of these two populations should reveal genes whose expression is necessary for the maintenance of the stem cell phenotype.
Keywords: other


title: Transcriptome analysis of murine macrophages in response to infection with Streptococcus pyogenes

status: Public on Mar 14 2008

first: Robert

last: Geffers

address: Inhoffenstr. 7

institute: HCI - Helmholtz Centre for Infection Research

summary:
The complex response of murine macrophages to infection with Streptococcus pyogenes was investigated at the level of gene expression using a high-density oligomer microarray. More than 400 genes were identified as being differentially regulated. Many of the up-regulated genes encoded molecules were involved in immune response and inflammation, transcription, signalling, apoptosis, cell cycle, electron transport and cell adhesion. Of particular interest was the up-regulation of proinflammatory cytokines, typical of the classically activated macrophages (M1 phenotype) such as TNF-?, IL-1 and IL-6, and also the up-regulation of anti-inflammatory mediators such as IL-1ra and IL-10 associated with macrophage alternative activation (M2 phenotype). Furthermore, the gene encoding inducible nitric oxide synthase (iNOS), an enzyme typically implicated in classical activation was not induced in infected macrophages. Instead, the gene encoding arginase, a competitor for the iNOS substrate arginine and involved in the alternative activation pathway was up-regulated in S. pyogenes-infected cells. Thus, the microarray-based gene expression analysis demonstrated that S. pyogenes induced an atypical activation program in macrophages with some but not all features of classically or alternatively activation phenotypes. The microarray data also suggested that the bactericidal activity of macrophages against S. pyogenes is mediated by phagocyte oxydase since p47phox was up-regulated in infected cells. Indeed, the in vivo and in vitro killing of S. pyogenes was markedly diminished in the absence of functional phagocyte (p47phox-/-) but not in the absence of iNOS (iNOS-/-). Understanding how macrophages respond to S. pyogenes at the molecular level may facilitate the development of new therapeutic paradigms.
Keywords: infection response

overall_design: Total RNA was isolated from highly purified F4/80+ cells obtained from the peritoneal cavity of C3H/HeN infected and uninfected control mice and hybridized to an Affymetrix GeneChip MOE430A.

first: R

first: E

last: Medina


title: Gene Expression Changes Between 3-Month-Old Epiphycan/Biglycan Double-null and Wildtype Mice

city: Houston

first: Jason

last: Schultz

address: 2121 W. Holcombe Bvld

institute: Texas A&M HSC-IBT

summary:
Epiphycan/Biglycan double-null mice develop age-dependant osteoarthritis. This study aims to elucidate the gene expression changes which happen early in the disease (3 Months) in order to identify possible contributors to disease devleopment and progression.

Note: CEL files for GSM230344 and GSM230347 are not available
Keywords: osteoathritis, SLRP, biglycan, epiphycan

overall_design: Two wildtype and three epiphycan/biglycan-null arrays were performed using Affymetrix Genechip technology. For each chip, the tibio-femoral joints of three male mice (6 joints per sample) were pooled and RNA extracted, labeled, and hybridized.

middle: B

first: Magnus

last: Hook

first: Wei

last: Zhou


title: Rnf41 is associated with anxiety like behavior, major depression and beta carboline induced seizure

status: Public on Jun 30 2008

city: Dallas

first: Sanghyeon

last: Kim

address: 5323 Harry Hines Blvd.

institute: UT Southwestern medical center

summary:
The molecular etiology of invididual differences in complex behavior traits and susceptibility to psychiatric illness remains incomplete. Using an unbiased genetic approach in a mouse model, Quantitative Trait Loci (QTL) influencing anxiety-like behaviors and beta-carboline-induced seizure vulnerability have been mapped to the distal portion of mouse chromosome 10 and an interval specific congenic strain (ISCS; A.B6chr10; 66 cM to telomere) was developed. This A.B6chr10 strain facilitated defining the behavioral influences of this region as well as gene expression profiling to identify candidate gene(s) underlying this QTL. By microarray studies, an unsuspected E3 Ubiquitin Ligase, Ring Finger 41 (Rnf41 / Neuregulin Receptor Degrading Protein1; Nrdp1) was differentially expressed in the region of interest, comparing the hippocampi of A/J vs A.B6chr10 mice as well as A/J vs B6 mice. By RT-PCR, Rnf41 expression levels were significantly increased 1.5 and 1.3-fold in the hippocampi of C57BL6/J and A.B6chr10 mice compared to A/J mice, respectively. In addition, protein levels of Rnf41 were increased in hippocampi of B6 mice compared to A/J mice across postnatal development with a 5.5-fold difference at P56. Among LxS recombinant inbred mice (N=33), Rnf41 hippocampal mRNA expression levels were significantly correlated with open field behavior (r= .454, p=.0073). Re-analyzing a microarray database of human post-mortem prefrontal cortex (Brodmann’s Area 46/10), RNF41 mRNA expression levels were reduced significantly in patients with major depression and bipolar disorder compared to unaffected controls. Overall, Rnf41 is a pleiotropic candidate gene for anxiety-like behaviors, depression, and vulnerability to seizures. RNF41 and its binding partners provide novel etiological pathways for influencing behavior, highlighting a potential role for the ubiquitin proteasome system in psychiatric illness.
Keywords: strain difference, genetic variation

overall_design:
Microarray
Affymetrix GeneChip: From three independent pools (3 hippocampi /pool) of total RNA for each line, probe was labeled, hybridized as one pool per GeneChip, using a total of six mouse MOE 430 arrays (Affymetrix, Santa Clara, CA). The sequential steps of reverse transcriptions, purification of ds cDNA, in vitro transcription and labeling of cRNA with biotin (Enzo BioArray High Yield RNA Transcript Labeling Kit), fragmentation of cRNA, hybridization to gene chips in a Affymetrix fluidics station 400 system, staining with streptavidin-phycoerythrin, washings, and scannings with a GeneArray Scanner were performed as described in the detailed protocols of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA) by the UTSW Microarray Core. The Affymetrix two GeneChip MOE 430 A and B set contains more than 45,000 probe sets, interrogating the expression level of 34,000 mouse gene transcripts.
Illumina Microarray	For the P0.5 microarray study, total RNA from a whole brain was individually used per Sentrix Mouse-6 BeadChip (Illumina, San Diego, CA), allowing individual samples to be evaluated and an increased sample size, namely six P0.5 mouse brains for each of three lines (A/J, B6, A.B6chr10). The Sentrix Mouse-6 BeadChip contains total 47,769 gene-specific, 70-mer oligonucleotide probes. Total RNA from each brain tissue of P0.5 mice was extracted in Trizol as above, reverse transcribed, labeled, and hybridized with a microarray according to the manufacturer’s detailed protocol (Illumina, San Diego, Ca.). Briefly, total RNA was reverse transcribed, then in vitro transcribed to cRNA and labeled with biotin-16-UTP. The labeled probe was hybridized to Illumina's Sentrix mouse-6 Expression BeadChips (Illumina, San Diego, CA), washed, and scanned with Illumina's BeadStation 500GX Genetic Analysis System in the UTSW Microarray core.

first: S

last: Zhang

first: K

last: Choi

last: Reister

first: A

middle: F

last: Baykiz

first: H

last: Gershenfeld


title: Mouse neurospheres

summary:
Seven day old platelet-derived growth factor-generated neurospheres cultured from the embryonic ganglia
Keywords: other

overall_design: this experiment include 3 samples and 30 replicates


title: Role for AP-1 transcription factors (c-Jun, c-Fos) in prostate cancer progression and clinical outcome of prostate tumor

status: Public on Jun 27 2008

city: New York

first: Cory

last: Abate-Shen

address: 1130 St. Nicholas Ave

department: Urology

institute: Columbia University

summary:
In our investigations of the molecular pathways of prostate tumorigenesis in Nkx3.1; Pten mutant mice using gene expression profiling, we now find that the AP-1 transcription factors, c-Jun and c-Fos, are significantly up-regulated during cancer progression. Forced expression of c-Fos and c-Jun in prostate cancer cells results in increased tumorigenicity, activation of Erk MAP kinase, and enhanced survival in the absence of androgens, which are hallmarks of disease progression. In humans, Jun and Fos proteins are significantly up-regulated during prostate cancer progression and significantly correlated with activation of Erk MAP kinase. Most notably, expression of Jun is associated with disease recurrence independent of other currently used prognostic indicators.
These analyses reveal a hitherto unappreciated role for AP-1 transcription factors in prostate cancer progression vis-à-vis Erk MAP kinase signaling, as well as the identification of a novel marker of disease recurrence, namely c-Jun.

Keywords: Stages of Prostate Cancer

overall_design: Mouse prostate was collected from wild-type or the Nkx3.1; Pten compound mutant mice at the age of 8-16 months. One lobe of dosolateral prostate was snap-frozen in OCT and stored at -80ºC for laser capture microdissection (LCM). To obtain androgen-independent lesions, mice were castrated at 7 to 14 months of age. Mice were sacrificed for analysis at 8 to 16 months of age and one dosolateral prostatic lobe was snap-frozen in OCT and stored at -80ºC for LCM. Approximate 1000 Prostate epithelial cells were isolated from normal prostate, dysplasia, prostatic intraepithelial neoplasia (PIN) or cancer lesions using PixCell IIE LCM system (Arcturus), followed by RNA linear amplification and labeling using Small Sample Labeling Protocol VII (Affymetrix). Samples were labeled using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific) and were hybridized to MOE430A GeneChips containing 22,690 well characterized mouse genes/ESTs (Affymetrix).

first: Xuesong

last: Ouyang


title: Mouse liver gene expression after 4.5 days of repeated combined acoustic and restraint stress vs. control

status: Public on Jun 01 2008

city: Greifswald

first: Maren

last: Depke

address: F.-L.-Jahn-Str. 15a

department: Department of Functional Genomics

institute: Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics

summary:
Stress is a powerful modulator of neuroendocrine, behavioral and immunological functions. After 4.5 days of repeated combined acoustic and restraint stress as a murine model of chronic psychological stress severe metabolic dysregulations became detectable in female BALB/c mice. Stress-induced alterations of metabolic processes that were found in a hepatic mRNA expression profiling were verified by in vivo analyses. Repeatedly stressed mice developed a hypermetabolic syndrome with severe loss of lean body mass, hyperglycemia, dyslipidemia, increased amino acid turn-over, and acidosis. This was associated with hypercortisolism, hyperleptinemia, insulin resistance, and hypothyroidism. In contrast, after a single acute stress exposure changes in expression of metabolic genes were much less pronounced and predominantly confined to gluconeogenesis, probably indicating that metabolic disturbances might be initiated already early but will only manifest in repeatedly stressed mice .Thus, in our murine model, repeated stress caused severe metabolic dysregulations leading to a drastic reduction of the individual's energy reserves. Under such circumstances stress may further reduce the ability to cope with new stressors such as infection or cancer.
Keywords: stress response

overall_design: Two biological experiments of repeated combined acoustic and restraint stress were performed, which consist each of a repeatedly stressed group and an untreated control group. Liver RNA expression profiles were analyzed in technical duplicates using pools of 8 or 9 individual RNAs of each group.

first: Uwe

last: Völker

first: Christine

last: Schütt

first: Cornelia

last: Kiank


title: Expression data from mouse liver after combined acoustic and restraint stress compared to non-stressed control mice

summary:
Stress is a powerful modulator of neuroendocrine, behavioral and immunological functions. After 4.5 days of repeated combined acoustic and restraint stress as a murine model of chronic psychological stress severe metabolic dysregulations became detectable in female BALB/c mice. Stress-induced alterations of metabolic processes that were found in a hepatic mRNA expression profiling were verified by in vivo analyses. Repeatedly stressed mice developed a hypermetabolic syndrome with severe loss of lean body mass, hyperglycemia, dyslipidemia, increased amino acid turn-over, and acidosis. This was associated with hypercortisolism, hyperleptinemia, insulin resistance, and hypothyroidism. In contrast, after a single acute stress exposure changes in expression of metabolic genes were much less pronounced and predominantly confined to gluconeogenesis, probably indicating that metabolic disturbances might be initiated already early but will only manifest in repeatedly stressed mice .Thus, in our murine model, repeated stress caused severe metabolic dysregulations leading to a drastic reduction of the individual's energy reserves. Under such circumstances stress may further reduce the ability to cope with new stressors such as infection or cancer.

This SuperSeries is composed of the SubSeries listed below.


title: E2F4 wt and knockout neurospheres

status: Public on Feb 13 2008

first: Theodore

last: Perkins

summary:
E2F4 wild and knockout type neurospheres from E12.5 forebrain. E2F4 transcription factor regulates the expression of the genes which are required for neural stem cell expansion in the developing mouse brain. The results of microarray analysis will help to identify the signaling pathways affected by E2F4 deletion and refine the neural stem cell regulatory mechanism.
Keywords: other

overall_design: This experiment include 2 samples on 2 platforms for a total of 4 Samples.


title: Myoblasts and Myotubes

summary:
Satellite cells play an important role in post-natal growth and regeneration of skeletal muscle. They can be defined as a population adult muscle stem cells based on their self renewal capability and ability to differentiate into skeletal muscle fibers. Functional Retinoblastoma protein (pRb) is essential for the process of skeletal muscle differentiation in satellite cell derived primary myoblasts. Furthermore, the biochemical function of pRb is largely associated with its ability to interact with chromatin modifying factors such as histone deacetylases (HDACs) and histone methyltransferases thus inhibiting transcription of target gene promoters. Hence, expression profiling of pRb null primary myoblasts and myotubes will provide a global picture of the downstream targets of pRb transcriptional regulation in relation to cell cycle control, apoptosis inhibition, and muscle differentiation.
Keywords: other

overall_design: This experiment includes 4 samples with 3 replicates each on 2 platforms for a total of 24 Samples.


title: RML Prion and mock-infected murine neuroblastoma cells

status: Public on Feb 25 2008

city: Zurich

first: Gino

last: Miele

address: Schmelzbergstrasse 12

department: Institute for Neuropathology

institute: University Hospital Zurich

summary:
Affymetrix genechip profiling analsysis (MOE430A and MOE430B) of murine neuroblastoma cells infected with either RML prion strain or mock brain homogenate
Keywords: Affymetrix gene expression profiling

overall_design: Parental N2a cells were split into 6 aliquots, 3 of which were infected with RML prions and 3 of which were mock-infected with normal brain homogenate.  There are three biological replicates in total for each experimental group.

first: Adriano

last: Aguzzi


title: Diagnosis of Acute Lung Rejection by Gene Expression Profiling of Bronchoalveolar Lavage Cells

status: Public on Jan 01 2008

city: Minneapolis

first: Jeff

last: Lande

state: MN

address: 420 Washington Avenue SE

department: Medicine

institute: University of Minnesota

summary:
Acute lung rejection is a risk factor for chronic rejection, jeopardizing the long-term survival of lung transplant recipients. At present, acute rejection is diagnosed by transbronchial lung biopsies, which are invasive, expensive, and subject to significant sampling error. In this study, we sought to identify groups of genes whose collective expression in BAL cells best classifies acute rejection versus no-rejection. BAL samples were analyzed from 32 unique subjects whose concurrent histology showed acute rejection (n=14) or no rejection (n=18).  Global BAL cell gene expression was measured using Affymetrix U133A microarrays.  The nearest shrunken centroid method with 10-fold cross validation was used to define the classification model.  250 runs of the algorithm were performed to determine the range of misclassification error and the most influential genes in determining classifiers. The estimated overall misclassification rate was below 20%. Seven transcripts were present in every classifier and 52 transcripts were present in at least 70% of classifiers; these transcripts were notable for involvement with T-cell function, cytotoxic CD8 activity, and granulocyte degranulation. The proportions of both lymphocytes and neutrophils in BAL samples increased with increasing probability of acute rejection; this trend was more pronounced with neutrophils. We conclude that there is a prominent acute rejection-associated signature in BAL cells characterized by increased T-cell, CD8+ cytotoxic cell, and neutrophil gene expression; this is consistent with established mechanistic concepts of the acute rejection response.
Keywords: Disease State Analysis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Lung transplant recipients surviving at least 30 days after transplantation at the University of Minnesota were eligible for enrollment in the study.  The study was approved by the University’s Institutional Review Board, and all patients provided written informed consent.  Subjects underwent scheduled surveillance (n = 22) and clinically indicated (decreased pulmonary function tests or new radiographic abnormalities) bronchoscopies (n = 10), in which 100-200 cc of sterile saline was instilled into a single anatomic location (right middle lobe or lingula), and recovered using gentle suction.  4-6 transbronchial biopsies (TBB) were obtained from the same subsegmental location as the BAL, and 4-6 additional TBB were obtained from the lower lobe of the same lung.  After sending samples for clinical tests, approximately 50 ml of the recovered BAL effluent was immediately placed on ice.  BAL cell counts and differentials were determined with a hemocytometer.  Specimens from subjects with active bronchopulmonary infections (as determined by history, exam, chest radiograph, and the results of routine laboratory tests and cultures) were excluded from analysis.
All biopsy specimens were graded according to standard International Society for Heart and Lung Transplantation criteria8.  Vascular and airway cellular infiltrate were scored separately on A (vascular) and B (airway) scales, each score ranging from 0 to 48;23;24.  For the purposes of this analysis, acute rejection was defined as a combined A+B score greater than or equal to 2; and no-rejection was defined as a combined A+B score less than 2.
The BAL samples used in this study were selected according to strict criteria that were designed to maximize potential differences in gene expression between acute rejection and non-acute rejection BAL samples; and to minimize bias from confounding factors.  Each subject (n=32) was represented by one BAL sample in this study.  Control subjects and samples (n=14) were selected according to the following criteria: 1) A+B score was 0 or 1 for all biopsies collected from each subject during his/her post-transplant course; 2) at least three biopsies had been graded from each subject; 3) the subject had survived at least one year post-transplant; 4) the selected BAL sample was culture negative for pathogenic bacteria, fungi, and viruses; and 5) the selected sample was from a patient that had not developed BOS or was collected at least 6 months prior to the development of BOS.  Rejection subjects and samples (n=18) were selected according to the following criteria: 1) the BAL sample was culture negative for pathogenic bacteria, fungi, and viruses; 2) for subjects with more than one acute rejection sample, we used the first acute rejection sample (A+B score > 1); 3) BOS grade was 0 at the time of BAL sampling (although some subjects subsequently developed BOS).

first: Jeffrey

first: Jagadish

last: Patil

last: Li

first: Todd

middle: R

last: Berryman

first: Richard

last: King

first: Marshall

last: Hertz


title: ETV6-NTRK3 fusion oncoprotein transduces NIH 3T3 cells

status: Public on Dec 14 2007

first: Zhe

department: Division of Hematology/Oncology

institute: Children's Hospital Boston

summary:
We report a mouse model that recapitulates expression of the ETV6-NTRK3 (EN) fusion oncoprotein, the product of the t(12;15)(p13;q25) translocation characteristic of human secretory breast carcinoma. Activation of EN expression in mammary tissues by Whey acidic protein (Wap) promoter-driven Cre leads to fully penetrant, multifocal malignant breast cancer with short latency. We provide genetic evidence that committed bipotent or CD61+ luminal alveolar progenitors, are targets of tumorigenesis. Furthermore, EN transforms these otherwise transient progenitors through activation of the AP1 complex.
To study the initial effects of ETV6-NTRK3 (EN) mediated transformation, we retrovirally transduced NIH 3T3 cells and generated microarray expression profiling data of EN transduced 3T3 cells as well as control 3T3 cells. Using gene set enrichment analysis (GSEA), we identified a signature involving the AP1 transcriptional complex in EN transduced 3T3 cells.
Keywords: genetic modification, cell type comparison

overall_design: We retrovirally transduced NIH 3T3 cells with either EN, or controls (either the empty vector or a kinase-dead version of EN with a mutation at the kinase domain of NTRK3). We then prepared total RNAs from these cells and collected microarray expression profiling data from them using Affymetrix mouse MOE430A chips.

first: Cristina

last: Tognon

first: Poul

middle: H

last: Sorensen

first: Stuart

last: Orkin


title: High cholesterol diet and phenobarbital affect cholesterol homeostasis and drug metabolism

status: Public on Nov 27 2007

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
High cholesterol diet and xenobiotic treatment induce changes in cholesterol homeostasis and drug metabolism. Mice were either 7 days on high cholesterol diet or were treated with phenobarbital. Liver samples were anayzed using Affymetrix GeneChip MOE430A.
Keywords: treatment and diet effects

overall_design: One group of mice was treated 50 mg/kg of phenobarbital in vehicle (5% DMSO in corn oil). Untreated group was injected vehicle only. Third group was 7 days on 1% (w/w) cholesterol diet prior vehicle treatment. After 10 hours animals were sacrificed and total RNA was isolated from liver. Total RNA from two animals was pooled resulting in 4 pools per group. These pools were analyzed using Affymetrix GeneChip MOE430A.

first: Adrian

last: Roth

first: Renate

last: Loser

first: Urs

last: Meyer


title: Androgenetic, Gynogenetic and Fertilized Mouse Blastocysts

status: Public on Dec 01 2007

first: Theodore

summary:
The study of genomic imprinting in mammals started with analysis of parthenogenetic embryos. At the phenotypic level, embryos with two maternal genomes and no paternal genome proceed through early development unimpaired, and only begin to fail after implantation. The most recognizable early defect is reduced or non-existent trophoblast, the tissue that gives rise to the placenta. We applied the procedure for establishing Trophoblast Stem cells (TS cells) developed in the Rossant lab to parthenogenetic embryos, and were successful in making four different TS cell lines, three from MI oocyte derived blastocysts and one from MII derived blastocysts. Initial molecular characterization, including microarray analysis, indicates that these cells are indistinguishable from fertilized TS cells, with the single exception of null expression of the paternally expressed gene Snrpn.
The only significant difference between parthenogenetic and fertilized TS cells was the frequency with which they could be derived. In our hands, fertilized blastocyst outgrowths produced TS cells at robust rates (10-12 colonies per blastocyst), while parthenogenetic blastocyst outgrowths produced only 4 colonies in 50 outgrowths, 100 times less frequently than fertilized embryos. This led us to hypothesize that those few TS cells that arose in parthenogenetic outgrowths were probably a result of very low frequency stochastic variation in the imprint status of a gene or genes required for either establishment or maintenance of stem cells, or both. The corollary to this hypothesis posits that the early failure of parthenogenetic embryos, and in particular parthenogenetic trophoblast, is a function of impaired stem cell function. This raises the intriguing possibility that microarray comparisons of parthenogenetic, fertilized and androgenetic blastocysts may reveal the identities of genes important for stem cell biology. To this end, my colleague Keith Latham, at the Fels Institute, Temple University, Philadelphia, made amplified cDNAs from pools of ten each of androgenetic, gynogenetic, or fertilized blastocysts. Three separate pools for each type of embryo were prepared for microarray analysis. The embryos were all produced by nuclear transfers between zygotes, a difficult technique that is Keith's special expertise. He used the Brady/Iscove protocol to generate quantitative 3' end biased cDNAs. We would like to compare the transcriptomes of these embryos using the MOE430 2.0 arrays. We expect that important insights into the biology of uniparental embryos in general, and stem cells in particular may be revealed.
Keywords: other

overall_design: this experiment include 3 samples and 18 replicates


title: Sex-specific early response to pressure overload in mice

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

institute: Max Planck Institute for Molecular Genetics

summary:
Pressure overload (PO) leads first to cardiac hypertrophy and later to heart failure. In mice, PO leads to sex differences in cardiac morphology and function.  However, early sex differences in gene regulation that precede sex differences in function have not yet been identified.
To identify such changes, we developed a model of PO that is characterized by compensated hypertrophy without sex differences after 2 weeks and by heart failure with sex differences after 9 weeks. We used transverse aortic constriction (TAC) or sham-operation in male and female mice and analyzed gene expression by microarray experiments.
Keywords: the influence of gender on hypertrophic gene expression

overall_design: The gene expression induced by pressure overload in female and male mice in comparison to sham operated control mice was investigated. For each of these four conditions four biological replicates were performed and the individual samples were hybridized seperately on Affymetrix RAE 430A GeneChip Arrays.

first: Sebastian

last: Brokat

first: Patricia

last: Ruiz Noppinger

first: Christian

last: Grohe

first: Vera

last: Regitz-Zagrosek


title: Analysis of gene expression during neurite outgrowth and regeneration

status: Public on Dec 04 2007

city: Princeton

first: Moriah

last: Szpara

state: NJ

address: 301 Schultz

department: Molecular Biology

institute: Princeton University

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

overall_design: Refer to individual Series


title: Organ-Derived Dendritic Cells Have Differential Effects on Alloreactive T Cells

status: Public on Oct 31 2007

first: Jeremy

last: Grubin

address: 411 East 67th Street Rm K425

institute: Memorial Sloan Kettering Cancer Center

summary:
Transcriptional response of murine allogeneic T cells (B10.BR) after
stimulation with different organ-derived (spleen, liver, peripheral and
mesenteric lymph nodes) dendritic cells (C57BL/6) in vitro
Keywords: gene expression array-based, count

overall_design: We stimulated B10.BR T cells with dendritic cells derived from different C57BL/6 organs for four days and then performed array experiments on the T cells.

first: Theo

last: Kim

first: Marcel

last: van den Brink


title: Spontaneous SCC induced by the somatic inactivation of Rb1 and Trp53 tumor suppressors in mouse stratified epithelia

status: Public on Nov 14 2007

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary:
The squamous cell carcinomas represent the aggressive type of non melanoma skin cancer, the most frequent malignancy among human population. We have studied here the possible relationship between these two pathways in skin using epidermal-specific mutant mice. Loss of p53, but not pRb, produces spontaneous tumor development, indicating that, contrary to pRb, p53 is the predominant tumor suppressor acting in mouse epidermis. The simultaneous inactivation of pRb and p53 does not aggravate the epidermal phenotype observed in Rb-deficient mice in terms of proliferation and/or differentiation. However, in doubly deficient mice spontaneous skin tumor development is severely accelerated. The tumors are aggressive, undifferentiated and display a hair follicle origin. Detailed analysis indicates that the acceleration is mediated by premature activation of the EGFR/Akt pathway, resulting in increased angiogenesis. The molecular characteristics of this model provide valuable tools to understand epidermal tumor formation, and may ultimately contribute to the development of therapies for the treatment of aggressive squamous cancer.
Keywords: Squamous cell carcinoma, Epidermis, Tumorigenesis, pRb, p53, Akt, Angiogenesis

overall_design: Pools from RNA whole skin extracts from 3 animals of same genotype were done and analyzed, per duplicate, in mouse microarrays. Comparison was performed between the 4 different genotypes.

first: Ana

last: Martínez-Cruz

first: Mirentxu

last: Santos

first: María

last: Lara

first: Carmen

last: Segrelles

first: Sergio

last: Ruiz

first: Marta

last: Moral

first: Corina

last: Lorz

first: Ramón

last: García-Escudero

first: Jesús

middle: M

last: Paramio


title: Expression profiles of mouse medulloblastoma

status: Public on Oct 12 2007

city: Cambridge

first: Junhao

last: Mao

address: 16 Divinity Ave., BL 1048

department: MCB

institute: Harvard University

summary:
Dysregulatio of Hh signaling has been shown to be involved in the formation of human medulloblastoma. We generated a mouse model (CAGGS-CreER;R26-SmoM2) of Hh related tumors.
We used microarray to profile gene expression in Hh induced mouse medulloblastoma and identified distinct classes of up-regulated or down-regulated genes during Hh dependent tumorigenesis .
Keywords: Tumor vs wild type tissue

overall_design: Medulloblastoma samples and adjacent wild type cerebellar tissue from CAGGS-CreER;R26-SmoM2 mice were isolated for RNA extraction and hybridization on Affymetrix microarrays.

first: Keith

last: Ligon

first: David

last: Rowitch

first: Andy

last: McMahon


title: Gene Expression in S49 Deathless (D-) cell variant

status: Public on Dec 12 2007

city: Claremont

first: Alexander

last: Zambon

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

summary:
The second messenger cAMP acts via protein kinase A (PKA) to induce apoptosis by mechanisms that are poorly understood. Here, we assessed a role for mitochondria and analyzed gene expression in cAMP/PKA-promoted apoptosis by comparing wild-type (WT) S49 lymphoma cells and the S49 variant, D- (cAMP-deathless), which lacks cAMP-promoted apoptosis but has wild-type levels of PKA activity and cAMP-promoted G1 growth arrest. Treatment of WT, but not D-, S49 cells with 8-CPT-cAMP for 24 h induced loss of mitochondrial membrane potential, mitochondrial release of cytochrome c and Smac and increase in caspase-3 activity. Gene expression analysis (using Affymetrix 430 2.0  Arrays) revealed that WT and D- cells incubated with 8-CPT-cAMP have similar, but non-identical, extents of cAMP-regulated gene expression at 2h (~800 transcripts) and 6h (~1000 transcripts) (|Fold|>2, P<0.06); by contrast, at 24h ~2500 and ~1100 transcripts were changed in WT and D- cells, respectively. Using an approach that combined regression analysis, clustering and functional annotation to identify transcripts that showed differential expression between WT and D- cells, we found differences in cAMP-mediated regulation of mRNAs involved in transcriptional repression, apoptosis, the cell cycle, RNA splicing, Golgi and lysosomes. The 2 cell lines differed in CREB phosphorylation and expression of the transcriptional inhibitor Icer and in cAMP-regulated expression of genes in the Inhibitor of apoptosis (IAP) and Bcl families. The findings indicate that cAMP/PKA-promoted apoptosis of lymphoid cells occurs via mitochondrial-mediated events and imply that such apoptosis involves gene networks in multiple biochemical pathways.
Keywords: time course

overall_design: S49 D- cells were treated with 8-CPT-cAMP over the course of 24 hours. Cells were prepared for hybridization to microarrays at times 0-untreated, 2h, 6h, and 24h after treatment with 8-CPT-cAMP. Experimental replicates were as follows n=4 for time 0 and n=3 for 2, 6, and 24h post treatment.

first: Lingzhi

last: Zhang

first: Paul

last: Insel


title: Gene profiling approaches help to define the specific functions of retinoblastoma family in epidermis

status: Public on Nov 13 2007

first: Ramon

last: Garcia-Escudero

summary:
The epidermal-specific ablation of Rb gene leads to increased proliferation, aberrant differentiation, and the disengagement of these processes in vivo and in vitro. These differences in phenotype are more severe with the loss of p107, demonstrating the functional compensation between pRb and p107. As p107 and p130 also exert overlapping functions in epidermis, we have generated Rb(F19/F19)K14cre;Rbl2-/- (pRb-;p130-) mice to analyze possible functional redundancies between pRb and p130. The epidermal phenotype was very similar between pRb- and pRb-;p130- mice, suggesting that pRb and p130 activities are not redundant in epidermis. Importantly, we can correlate the proliferation differences with specific changes in gene expression between pRb-, pRb-;p107- and pRb-;p130- primary keratinocytes using microarray analysis, and explain the phenotypes in the context of altered E2F expression and functionality. Our findings support a model in which the distinct retinoblastoma family members, in conjunction with E2F members, play a central role in regulating epidermal homeostasis through specific or overlapping activities.
Keywords: skin, pRb, transgenic mice, p130

overall_design: Total RNA from pooled cells from each genotype were analyzed, per duplicate (pRb-/-;p107-/-, or pRb-/-;p130-/-) or triplicate (wild type, or pRb-/-), in mouse microarrays. Comparison was performed between the 4 different genotypes.

first: Jesus


title: p107 acts as a tumor suppressor in pRb-deficient epidermis.

summary:
The specific deletion of Rb gene in epidermis leads to altered proliferation and differentiation, but not to the development of spontaneous tumors. Our previous data have demonstrated the existence of a functional compensation of Rb loss by Rbl1 (p107) in as the phenotypic differences with respect to controls are intensified. However, the possible evolution of this aggravated phenotype, in particular in relationship with tumorigenesis, has not been evaluated due to the premature death of the double deficient mice. We have now investigated whether p107 can also act as a tumor suppressor in pRb-deficient epidermis using different experimental approaches. We found spontaneous tumor development in doubly-deficient skin grafts. Moreover, Rb-deficient keratinocytes are susceptible to Ha-ras-induced transformation, and this susceptibility is enhanced by p107 loss. Further functional analyses, including microarray gene expression profiling, indicated that the loss of p107, in the absence of pRb, produces the reduction of p53-dependent pro-apoptotic signals. Overall, our data demonstrate that p107 behaves as a tumor suppressor in epidermis in the absence of pRb and suggest novel tumor-suppressive roles for p107 in the context of functional p53 and activated Ras
Keywords: epidermis, tumorigenesis, pRb, p107, Ras, p53, apoptosis

first: Mirentxu

first: Ana

last: Martínez-Cruz

first: Pilar

last: Hernandez

last: Martinez-Palacio


title: Mouse Liver Regeneration

status: Public on Dec 13 2007

city: Taipei

first: Ann-Ping

last: Tsou

address: 155, Li-Nong St., Sec.2

department: Inst. Biotechnology in Medicine

country: Taiwan

institute: National Yang-Ming University

summary:
The goal of this study is to obtain an expression profile of regenerating mouse livers. We used microarray analysis to study the gene groups coordinately expressed temporally during mouse a liver regeneration. One of the syn-expression groups that showed a sharp rise in gene expression immediately after hepatectomy contains a set pancreatic exocrine genes. The syn-expression profile of pancreatic genes and the pancreatic-specific transcription factors Ptf1a and Ipf1 was confirmed using real-time PCR. Electron microscopic examination showed the presence of morphological features reminiscent of pancreatic acinar cells with the presence of characteristic zymogen granules and ER organization. These results indicate that there is a transient liver-to-pancreas transdifferentiation event at the beginning of liver regeneration. A strong coordinated up-regulation of pancreatic genes was found to accompany the injury response in the pancreas, suggesting a compensatory mechanism for pancreatic functions. There seems to be a relationship between the induction of pancreatic genes and acute phase response at the beginning of liver regeneration.
Keywords: gene expression array-based (RNA / in situ oligonucleotide)

overall_design:
Total RNA was extracted from livers of mice recovered at
various hours after partial hepatectomy (PHx 4h, 8h, 12h, 36h,
48h, 72h). We grouped livers of four to six mice together for
RNA extraction. Genes showed differentially up- or downregulated
by two-fold with respect to the normal mouse livers
were identified using GeneSpring software version 7.2 (Silicon
Genetics, Agilent Technologies).

first: Yat-Pang

last: Chau

first: Hsin-Hui

last: Chang

first: Chia-Lin

last: Liu

first: Yi-Ying

last: Lu

first: Chien-Der

last: Lin

first: Jia-Liang

last: Jiang

first: Ying-Ru

last: Ke

first: Jen-Hwey

last: Chiu

first: Chin-Wen

last: Chi

first: Chen-Kung

last: Chou

first: Ming-Ta

last: Hsu


title: Constitutively active Akt induces ectodermal defects and impaired BMP signaling

status: Public on Oct 25 2007

first: Ramon

summary:
Aberrant activation of the Akt pathway has been implicated in several human pathologies including cancer. However, current knowledge on the involvement of Akt signaling in development is limited. Previous data have suggested that Akt-mediated signaling may be an essential mediator of epidermal homeostasis through cell autonomous and non-cell autonomous mechanisms. Here we report the developmental consequences of deregulated Akt activity in the basal layer of stratified epithelia, mediated by the expression of a constitutively active Akt1
(myrAkt) in transgenic mice. Contrary to mice overexpressing wilt type Akt1 (Aktwt), these myrAkt mice display, in a dose-dependent manner, altered development of ectodermally derived organs such as hair, teeth, nails and epidermal glands. To identify the possible molecular mechanisms underlying these alterations, gene profiling approaches were employed. We demonstrate that constitutive Akt activity disturbs the bone morphogenetic protein (BMP)-dependent signaling pathway, which leads to alterations in adult epidermal stem cells. Collectively, we show that epithelial tissue development and homeostasis is dependent on proper regulation of Akt expression and activity.
Keywords: ectodermal development, Akt1, skin, transgenic mice

overall_design: Two (transgenic mice L60, L84 and LA) or three pools (control mice LC) from RNA whole skin extracts of same genotype were done and analyzed, individually, in mouse microarrays. Comparison was performed between the 4 different genotypes.

first: Carmen

last: Segrelles

first: Marta

last: Moral

first: Corina

last: Lorz

last: Santos

first: Jerry

first: José

last: Cascallana

first: Maria

last: Lara

first: Steve

last: Carbajal

first: Ramón

last: García-Escudero

first: Linda

last: Beltran

last: Segovia

last: Bravo

first: John

last: DiGiovanni

first: Jesús

last: Paramio