title: Gene expression profiles regulated by Tead2 mutants, Yap, and cell density in NIH3T3 cells

status: Public on Nov 21 2008

city: Chuo-ku, Kobe

first: Mitsunori

last: Ota

state: Hyogo

address: Minatojima-minamimachi 2-2-3

department: CENTER FOR DEVELOPMENTAL BIOLOGY

institute: RIKEN

summary:
Regulation of organ size is important for development and tissue homeostasis. In  Drosophila, Hippo signaling controls organ size by regulating the activity of a TEAD  transcription factor, Scalloped, through modulation of its coactivator protein Yki. The  role of mammalian Tead proteins in growth regulation, however, remains unknown.  Here we examined the role of mouse Tead proteins in growth regulation. In NIH3T3  cells, cell density and Hippo signaling regulated the activity of Tead proteins by  modulating nuclear localization of a Yki homologue, Yap, and the resulting change in  Tead activity altered cell proliferation. Tead2-VP16 mimicked Yap overexpression,  including increased cell proliferation, reduced cell death, promotion of EMT, lack of cell  contact inhibition, and promotion of tumor formation. Growth promoting activities of  various Yap mutants correlated with their Tead-coactivator activities. Tead2-VP16 and  Yap regulated largely overlapping sets of genes. However, only a few of the Tead/Yapregulated  genes in NIH3T3 cells were affected in Tead1-/-;Tead2-/- or Yap-/- embryos. Most  of the previously identified Yap-regulated genes were not affected in NIH3T3 cells or  mutant mice. In embryos, levels of nuclear Yap and Tead1 varied depending on cell  types. Strong nuclear accumulation of Yap and Tead1 were seen in myocardium,  correlating with requirements of Tead1 for proliferation. However, their distribution did  not always correlate with proliferation. Taken together, mammalian Tead proteins  regulate cell proliferation and contact inhibition as a transcriptional mediator of Hippo  signaling, but the mechanisms by which Tead/Yap regulate cell proliferation differ  depending on cell types, and Tead, Yap and Hippo signaling may play multiple roles in  mouse embryos.
We used microarrays to know the gene expression profiles regurated by Tead2-VP16, Tead2-EnR, Yap, and cell density in NIH3T3 cells.

Keywords: Cell density, genetic modification

overall_design: Tead2-VP16-, Tead2-EnR-, Yap- and control vector-expressing cells were cultured at low or high density for RNA extraction and hybridization on Affymetrix microarrays.

first: Takeya

last: Kasukawa


title: Differentially expressed genes in brain tissue from HtrA2 knockout mice

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: genotype comparison

overall_design: This experiment was set out to identify genes that are differentially expressed in brain tissue from the cortex of HtrA2 knockout (KO) mice compared to wild type (WT) littermates. We chose a cortical region since there is no evidence of neuronal loss in this region enabling us to compare mRNA transcripts in identical cellular populations. Brains of littermate WT and HtrA2 KO mice were dissected to obtain cortex tissue at post-natal day 29 (P29). RNA was isolated and samples were processed for hybridisation (6 samples in total, 3 replicates for each genotype).

first: Nicoleta

last: Moisoi

first: L

middle: M

last: Martins

first: Julian

last: Downward


title: Retinoic Acid Enhances Foxp3 Induction Indirectly by Relieving Inhibition from CD4(+)CD44(hi) Cells.

status: Public on Nov 16 2008

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

summary: CD4(+)Foxp3(+) regulatory T (Treg) cells originate primarily from thymic differentiation, but conversion of mature T lymphocytes to Foxp3 positivity can be elicited by several means, including in vitro activation in the presence of TGF-beta. Retinoic acid (RA) increases TGF-beta-induced expression of Foxp3, through unknown molecular mechanisms. We showed here that, rather than enhancing TGF-beta signaling directly in naive CD4(+) T cells, RA negatively regulated an accompanying population of CD4(+) T cells with a CD44(hi) memory and effector phenotype. These memory cells actively inhibited the TGF-beta-induced conversion of naive CD4(+) T cells through the synthesis of a set of cytokines (IL-4, IL-21, IFN-gamma) whose expression was coordinately curtailed by RA. This indirect effect was evident in vivo and required the expression of the RA receptor alpha. Thus, cytokine-producing CD44(hi) cells actively restrain TGF-beta-mediated Foxp3 expression in naive T cells, and this balance can be shifted or fine-tuned by RA.

overall_design: All gene expression profiles were obtained from highly purified T cell populations sorted by flow cytometry. To reduce variability, cells from multiple mice were pooled for sorting, and replicates were generated for essentially all groups. RNA from 0.5-3 x 105 cells was amplified, labeled, and hybridized to Affymetrix M430v2 microarrays. Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

first: Jonathan

middle: A

last: Hill

first: Jason

last: Hall

first: Cheng-Ming

last: Sun

first: Qi

last: Cai

first: Norbert

last: Ghyselinck

first: Pierre

last: Chambon

first: Yasmine

last: Belkaid

first: Daine

last: Mathis

first: Christophe

last: Benoist


title: Pilot study: Basal gene expression in bone

status: Public on Nov 15 2008

first: Simon

middle: Charles

last: Rawlinson

address: 4 Newark Street

institute: Bart's and The London School of Medicine and Dentistry

summary:
Pilot study
Analysis of basal gene expression of the protective bones of the skull (parietals), weight-bearing bones of the limb (ulnae) and mandibular bone and teeth

overall_design: RNA extraction from normal bone

middle: C


title: Gene expression analyses of PR action in the mammary gland of ovariectomized mice

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
Beyond demonstrating a critical role for progesterone receptor signaling in normal mammary epithelial proliferation, the progesterone receptor knockout mouse disclosed the progesterone receptor along with its effector pathways as key determinants of mammary neoplastic progression.  Despite these advances, however, further progress in our mechanistic understanding of progesterone’s involvement in mammary morphogenesis and tumorigenesis is contingent upon defining the essential effector pathways responsible for transducing the progesterone signal into a mammary proliferative and/or pro-survival response.  Toward this goal, a judiciously chosen acute progesterone treatment regimen together with microarray methods was applied to the mammary gland of the normal mouse to uncover new effectors that operate immediately downstream of the progesterone mammary signal.  Examination of the resultant progesterone-responsive transcriptome disclosed “inhibitor of differentiation or DNA binding 4” (Id4) as a molecular target acutely induced by progesterone in the murine mammary epithelium.
Keywords: time course

overall_design: Microarray analysis was performed on mammary tissue total RNA obtained from ovariectomized mice previously treated with progesterone for 4, 16, 28, and 76 hours.  For each hormone treatment time-point, mammary gland microarray data from sesame oil (vehicle) treated mice was included as controls.  Total mammary gland RNA from each time-point and treatment group was interrogated using the Affymetrix GeneChip Mouse Genome 430 2.0 Array.  For a given time-point and treatment group, three sets of mice (5 mice in each set) were used for gene expression profiling; mammary RNA pooled from each set was hybridized to one microarray chip.  Therefore, a total of 15 mice (or 3 microarray chips) were used per time-point and treatment group.

first: John

last: Lydon

first: Rodrigo

last: Fernandez


title: Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140

status: Public on Nov 14 2008

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: MicroRNAs (miRNAs) are short noncoding RNA molecules regulating the expression of mRNAs. Target identification of miRNAs is computationally difficult due to the relatively low homology between miRNAs and their targets. We present here an experimental approach to target identification where the cartilage-specific miR-140 was overexpressed and silenced in cells it is normally expressed in separate experiments. Expression of mRNAs was profiled in both experiments and the intersection of mRNAs repressed by miR-140 overexpression and derepressed by silencing of miR-140 was identified. The intersection contained only 49 genes, although both treatments affected the accumulation of hundreds of mRNAs. These 49 genes showed a very strong enrichment for the miR-140 seed sequence implying that the approach is efficient and specific. 21 of these 49 genes were predicted to be direct targets based on the presence of the seed sequence. Interestingly, none of these were predicted by the published target prediction methods we used. One of the potential target mRNAs, Cxcl12, was experimentally validated by Northern blot analysis and a luciferase reporter assay.

overall_design: Each condition was profiled in triplicate. For over-expression experiment cells were transfected with siRNA-140 (miR-140 mimick) or siRNA-96 (as a control). For suppresion experiment cells were transfected with LNA-antimicroRNA-140 (suppressing endogenous miR-140) or LNA-antimicroRNA-449 (as a control).

first: Francisco

last: Nicolas

first: Tamas

last: Dalmay

first: Frank

last: Schwach

first: Vincent

last: Moulton

first: Sakari

last: Kauppinen

first: Morten

last: Lindow


title: TLR-mediated type I IFN induction in pDCs requires the rapamycin-sensitive PI3K-mTOR-p70S6K pathway

city: Atlanta

first: Weiping

last: Cao

state: GA

address: 954 Gatewood Road

department: Emory Vaccine Center

institute: Emory University

summary:
Robust type I interferon (IFN-alpha/beta) production in plasmacytoid dendritic cells (pDCs) is critical for anti-viral immunity. Here we demonstrated a role for the mammalian target of rapamycin (mTOR) pathway in regulating interferon production by pDCs. Inhibition of mTOR or the ‘downstream’ mediators of mTOR p70S6K1,2 kinases during pDC activation via Toll-like receptor 9 (TLR9) blocked the interaction of TLR9 with the adaptor MyD88 and the subsequent activation of interferon response factor 7 (IRF7), resulting in impaired IFN-alpha production. Microarray analysis confirmed that inhibition of mTOR by the immunosuppressive drug  rapamycin suppressed anti-viral and anti-inflammatory gene expression. Consistent with this, targeting rapamycin-encapsulated microparticles to antigen-presenting cells in vivo resulted in a diminution of IFN-alpha production in response to CpG DNA or the yellow fever vaccine virus strain 17D.  Thus, mTOR signaling plays a critical role in TLR-mediated IFN-alpha responses by pDCs.

CpGA is a TLR9 agonist.

overall_design: pDCs were isolated from mouse spleen or human PBMC. The effect of rapamycin on pDCs IFN-alpha production as induced by TLR ligands was studied. The mechanism of rapamycin effect was dissected in RAW cell line.

first: Santhakumar

last: Manicassamy

first: Hua

last: Tang

first: Sudhir

last: Kasturi

first: Ali

last: Pirani

first: Niren

last: Murthy

first: Bali

last: Pulendran


title: Comparative analysis of Drd1+ Medium Spiny Neurons, Drd2+ Medium Spiny Neurons, Motor Neurons, and Purkinje Neurons

city: New York

first: Nathaniel

last: Heintz

state: NY

address: 1230 York Ave, Box 260

institute: HHMI/Rockefeller University

summary:
The cellular heterogeneity of the brain confounds efforts to elucidate the biological properties of distinct neuronal populations.
Using Bacterial Artificial Chromosome (BAC) transgenic mice which express EGFP-tagged ribosomal protein L10a in defined cell populations, we have developed a methodology to affinity purify polysomal mRNAs from genetically defined cell populations in the brain.
The utility of this approach is illustrated by the comparative analysis of four types of neurons, revealing hundreds of genes that distinguish these four cell populations.
We find that even two morphologically indistinguishable, intermixed subclasses of medium spiny neuron display vastly different translational profiles and present examples of the physiological significance of such differences.
This genetically targeted  Translating Ribosome Affinity Purification (TRAP) methodology is a generalizable method useful for the identification of molecular changes in any genetically defined cell type in response to genetic alterations, disease, or pharmacological perturbations.

Keywords: Cell Type Comparison

overall_design:
For each cell population, three independent TRAP replicates were collected, and total RNA from both the immunoprecipitate and unbound fractions were seperately amplified and hybridized.
For each tissue, several representative unnbound fractions are provided to serve as controls.  Biological replicates are GCRMA normalized within groups.
Following averaging of replicates, we recommend further global normalization between groups, using affymetrix biotinylated controls, to correct for any broad biases in scanning and hybridization.
Finally for many analyses, we also recommend filtering to remove those probesets with low IP/UB fold change values from each cell type.
Researchers can contact us for spreadsheets where these additional steps have been completed.

first: Myriam

last: Heiman

first: Anne

last: Schaefer

first: Shiaoching

last: Gong

first: Jayms

last: Peterson

first: Michelle

last: Day

first: Keri

middle: E

last: Ramsey

first: Mayte

last: Suárez-Fariñas

first: Cordelia

last: Schwarz

first: Dietrich

last: Stephan

first: D

middle: J

last: Surmeier

first: Paul

last: Greengard


title: Comparative analysis of Drd1+ Medium Spiny Neurons, Drd2+ Medium Spiny Neurons, cocaine treatment

overall_design:
For each cell type and treatment (cell = D1 or D2, treatment = acute or chronic, saline or cocaine) three independent TRAP replicates were collected, and total RNA from the immunoprecipitates were  amplified and hybridized.
Data were normalized with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile.
Data were then converted to log2 scale.
We recommend that only genes where more than one sample has a normalized intensity larger than 16 (4 in log2 scale) should be kept in the analysis.


title: A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

status: Public on Nov 08 2008

city: St. Louis

first: Thaddeus

middle: S.

last: Stappenbeck

state: MO

address: 660 S. Euclid Avenue, Box 8118

department: Pathology and Immunology

institute: Washington University in St. Louis

summary: Susceptibility to Crohn's disease, a complex inflammatory disease involving the small intestine, is controlled by over 30 loci. One Crohn's disease risk allele is in ATG16L1, a gene homologous to the essential yeast autophagy gene ATG16 (ref. 2). It is not known how ATG16L1 or autophagy contributes to intestinal biology or Crohn's disease pathogenesis. To address these questions, we generated and characterized mice that are hypomorphic for ATG16L1 protein expression, and validated conclusions on the basis of studies in these mice by analysing intestinal tissues that we collected from Crohn's disease patients carrying the Crohn's disease risk allele of ATG16L1. Here we show that ATG16L1 is a bona fide autophagy protein. Within the ileal epithelium, both ATG16L1 and a second essential autophagy protein ATG5 are selectively important for the biology of the Paneth cell, a specialized epithelial cell that functions in part by secretion of granule contents containing antimicrobial peptides and other proteins that alter the intestinal environment. ATG16L1- and ATG5-deficient Paneth cells exhibited notable abnormalities in the granule exocytosis pathway. In addition, transcriptional analysis revealed an unexpected gain of function specific to ATG16L1-deficient Paneth cells including increased expression of genes involved in peroxisome proliferator-activated receptor (PPAR) signalling and lipid metabolism, of acute phase reactants and of two adipocytokines, leptin and adiponectin, known to directly influence intestinal injury responses. Importantly, Crohn's disease patients homozygous for the ATG16L1 Crohn's disease risk allele displayed Paneth cell granule abnormalities similar to those observed in autophagy-protein-deficient mice and expressed increased levels of leptin protein. Thus, ATG16L1, and probably the process of autophagy, have a role within the intestinal epithelium of mice and Crohn's disease patients by selective effects on the cell biology and specialized regulatory properties of Paneth cells.

overall_design: 4 Samples: 2 replicates of Atg16-hypomorph Paneth cells and 2 replicates of Wildtype Paneth cells.


title: Basal gene expression in bone (mice and rat)

first: Simon

last: Rawlinson

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: A translational profiling approach for the molecular characterization of CNS cell types

summary:
The cellular heterogeneity of the brain confounds efforts to elucidate the biological properties of distinct neuronal populations.
Using Bacterial Artificial Chromosome (BAC) transgenic mice which express EGFP-tagged ribosomal protein L10a in defined cell populations, we have developed a methodology to affinity purify polysomal mRNAs from genetically defined cell populations in the brain.
The utility of this approach is illustrated by the comparative analysis of four types of neurons, revealing hundreds of genes that distinguish these four cell populations.
We find that even two morphologically indistinguishable, intermixed subclasses of medium spiny neuron display vastly different translational profiles and present examples of the physiological significance of such differences.
This genetically targeted  Translating Ribosome Affinity Purification (TRAP) methodology is a generalizable method useful for the identification of molecular changes in any genetically defined cell type in response to genetic alterations, disease, or pharmacological perturbations.

This SuperSeries is composed of the SubSeries listed below.


title: Effect of an anti-myostatin antibody on skeletal muscle gene expression in mice

status: Public on Nov 22 2008

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

summary:
More than 2,000 genes appear to be upregulated or downregulated in skeletal muscle of mice with constitutive knockout of myostatin (Steelman et al., FASEB J 20:580-2, 2006). This study was done to determine whether inhibition of myostatin activity in mature mice has similar effects on the pattern of gene expression.

Keywords: Differential expression in treated and control mice

overall_design: Ten samples from JA16 antibody-treated mice were compared with 10 samples from saline-treated mice


title: Application of a translational profiling approach for the comparative analysis of CNS cell types.

summary:
Comparative analysis can provide important insights into complex biological systems. As demonstrated in the accompanying paper, Translating Ribosome Affinity Purification (TRAP), permits comprehensive studies of translated mRNAs in genetically defined cell populations following physiological perturbations.
To establish the generality of this approach, we present translational profiles for twenty four CNS cell populations, and identify known cell-specific and enriched transcripts for each population.
We report thousands of cell-specific mRNAs that were not detected in whole tissue microarray studies, and provide examples that demonstrate the benefits deriving from comparative analysis.
To provide a foundation for further biological and in silico studies, we provide a resource of sixteen transgenic mouse lines, their corresponding anatomic characterization, and translational profiles for cell types from a variety of CNS structures.
This resource will enable a wide spectrum of molecular and mechanistic studies of both well known and previously uncharacterized neural cell populations.

Keywords: Cell Type Comparison

overall_design:
For each cell population, three independent TRAP replicates were collected, and total RNA from both the immunoprecipitate and unbound fractions were seperately amplified and hybridized.
For each tissue, several representative unbound fractions are provided to serve as controls.  Biological replicates are GCRMA normalized within groups.
Following averaging of replicates, we recommend further global normalization between groups, using affymetrix biotinylated controls, to correct for any broad biases in scanning and hybridization.
Finally for many analyses, we also recommend filtering to remove those probesets with low IP/UB fold change values from each cell type.
Researchers can contact us for spreadsheets where these additional steps have been completed.

first: Joseph

middle: P

last: Doyle

middle: D

last: Dougherty

first: Eric

middle: F

last: Schmidt

first: Tanya

middle: R

last: Stevens

first: Guojun

last: Ma

first: Sujata

last: Bupp

first: Preana

last: Shrestha

first: Rajiv

last: Shah

first: Martin

middle: L

last: Doughty

first: Shiaching


title: SIRT1 redistribution on chromatin promotes genome stability but alters gene expression during aging

status: Public on Nov 26 2008

first: Philipp

last: Oberdoerffer

department: Pathology

type: Genome binding/occupancy profiling by array


title: The time-dependent response of placental trophoblast stem cells to hyperosmolar stress

status: Public on Nov 04 2008

city: Detroit

first: wenbo

last: xu

state: MI

address: 3127 Scott Hall ,540 East Canfield

institute: wayne state university

summary:
Stress induces undifferentiated stem cells to differentiate in a way that looks like normal differentiation
We used hyperosmolar stress as a generic, energy-depleting stressor and tested for the global changes in the transcriptional response of placental trophoblast stem cells
Keywords: Time course for stressed stem cells to assay for differentiative and homeostatic responses

overall_design: Placental trophoblast stem cells were subjected to 0, 0.5, 2, 6, and 24 hours of hyperosmolar stress and then assayed by Affymetrix 430MOE V2 whole mouse genome arrays.

first: Jian

last: Liu

first: Daniel

last: Rappolee


title: Heat shock effects on testes from C57BL/6 and AKR/N mouse strains

status: Public on Nov 01 2008

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

summary: Cryptorchidism and scrotal heating result in abnormal spermatogenesis but the mechanism(s) proscribing this temperature sensitivity are unknown.  It was previously reported that the AKR/N or MRL/MpJ-+/+ mouse testis is more heat resistant than the testis from the C57BL/6 strain.  We have attempted to probe into the mechanism(s) involved in heat sensitivity by examining global gene expression profiles of normal and heat-treated testes from C57BL/6, AKR/N and MRL/MpJ-+/+ mice by microarray analysis.  In the normal C57BL/6 testis, 415 and 416 transcripts were differentially expressed (at least two-fold higher or lower) when compared to the normal AKR/N and MRL/MpJ-+/+ testis, respectively.  The AKR/N and MRL/MpJ-+/+ strains revealed 268 differentially expressed transcripts between them.  There were 231 transcripts differentially expressed between C57BL/6 and two purported heat-resistant strains, AKR/N and MRL/MpJ-+/+.  Next, the testes of C57BL/6 and AKR/N mice were exposed to 43ºC for 15 min and harvested at different time points for TUNEL studies and microarrays.  An increase of TUNEL-positive germ cell numbers was significant 8 hr after heat exposure in the C57BL/6 mouse.  However, this increase was not observed in the AKR/N mouse until 10 hr after heat exposure.  All tubules showed germ cell loss and disruption in C57BL/6 testis 24 hr after heat shock.  In contrast, although a number of seminiferous tubules showed an abnormal morphology 24 hr post-heat shock in the AKR/N mouse, many tubules still retained a normal structure.  Numerous transcripts exhibited differential regulation between the two strains within 24 hours after heat exposure.  The differentially expressed transcripts in the testes 8 hr after heat exposure were targeted to identify the genes involved in the initial response rather than those due to germ cell loss.  Twenty transcripts were significantly down-regulated and 19 genes were up-regulated by hyperthermia in C57BL/6 and did not show a parallel change in the AKR/N testis.  Conversely, heat shock resulted in 30 up-regulated transcripts and 31 down-regulated transcripts in AKR/N that were not similarly regulated in C57BL/6.  A number of genes shared similar differential expression patterns and differential regulation by hyperthermia in both strains of mice.  Taken together, the present study indicates the diverse genetic backgrounds in the three strains lead to major differences in normal testis gene expression profiles while the differences in heat shock responses involves a significantly smaller number of genes.  The data generated may provide insights regarding gene networks and pathways involved in heat stress and their relationship to spermatogenesis.

overall_design: Total RNA of testes from two different strains of mice, C57BL/6 and AKR/N were analyzed using microarray 430.20 chip.  Duplicates were used in controls and treated samples at 8hr, 10hr, 12hr, 24hr after heat shock at 43C for 15 min.  All mice were 8 weeks old.

first: Ying

last: Li

first: Qing

last: Zhou

first: Randy

last: Hively

first: Christopher

last: Small

first: Michael

last: Griswold


title: CBA/CaJ mouse cochlea gene expression profile

first: Joe

middle: Claud

last: Adams

address: 243 Charles St.

department: Otolaryngology

institute: Massachusetts Eye & Ear Infirmary

summary:
This data set is intended as a public resource documenting the identity of roughly 10,000 genes that are abundantly expressed in the mouse cochlea. The data have many uses, including for making comparisons with proteomics studies, and for comparisons of expression profiles with other mouse strains and with other species. The CBA/CaJ strain was chosen because of its lack of known vulnerabilities to premature cochlear degeneration or to extreme reactions to cochlear stresses. It may therefore be considered a “normal” mouse. No experimental manipulations were done on the mice of this study. Contamination of the results by genes expressed in the surrounding petrous bone and from those in  blood cells was minimized.

Keywords: normal controls

overall_design: 8 replicates, pooled ears from each of 8 mice


title: Gene expression profile of testes from three mouse strains, AKR/N, C57BL/6 and MRL/MpJ+/+

summary: Cryptorchidism and scrotal heating result in abnormal spermatogenesis but the mechanism(s) proscribing this temperature sensitivity are unknown.  It was previously reported that the AKR/N or MRL/MpJ-+/+ mouse testis is more heat resistant than the testis from the C57BL/6 strain.  We have attempted to probe into the mechanism(s) involved in heat sensitivity by examining global gene expression profiles of normal and heat-treated testes from C57BL/6, AKR/N and MRL/MpJ-+/+ mice by microarray analysis.  In the normal C57BL/6 testis, 415 and 416 transcripts were differentially expressed (at least two-fold higher or lower) when compared to the normal AKR/N and MRL/MpJ-+/+ testis, respectively.  The AKR/N and MRL/MpJ-+/+ strains revealed 268 differentially expressed transcripts between them.  There were 231 transcripts differentially expressed between C57BL/6 and two purported heat-resistant strains, AKR/N and MRL/MpJ-+/+.

overall_design: Total RNA of testes from 3 different strains of mice, C57BL/6, AKR/N and MRL/MpJ-+/+,  were analyzed using microarray  430.20 chip. All mice were 8 weeks old, 2 mice/strain.


title: Aryl Hydrocarbon Receptor Regulates Distinct Dioxin-Dependent and Dioxin-Independent Gene Batteries

city: Toronto

first: Paul

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

summary:
Conventional biochemical and molecular techniques identified previously several genes whose expression is regulated by the aryl hydrocarbon receptor (AHR). We sought to map the complete spectrum of AHR-dependent genes in male adult liver using expression arrays to contrast mRNA profiles in Ahr-null mice (Ahr–/–) with those in mice with wild-type AHR (Ahr+/+). Transcript profiles were determined both in untreated mice and in mice treated 19 h earlier with 1000 µg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Expression of 456 ProbeSets was significantly altered by TCDD in an AHR-dependent manner, including members of the classic AHRE-I gene battery, such as Cyp1a1, Cyp1a2, Cyp1b1, and Nqo1. In the absence of exogenous ligand, AHR status alone affected expression of 392 ProbeSets, suggesting that the AHR has multiple functions in normal physiology. In Ahr–/– mice, only 32 ProbeSets exhibited responses to TCDD, indicating that the AHR is required for virtually all transcriptional responses to dioxin exposure in liver. The flavin-containing monooxygenases, Fmo2 and Fmo3, considered previously to be uninducible, were highly induced by TCDD in an AHR-dependent manner. The estrogen receptor alpha as well as two estrogen-receptor-related genes (alpha and gamma) exhibit AHR-dependent expression, thereby extending cross-talk opportunities between the intensively studied AHR and estrogen receptor pathways. p53 binding sites are over-represented in genes down-regulated by TCDD, suggesting that TCDD inhibits p53 transcriptional activity. Overall, our study identifies a wide range of genes that depend on the AHR, either for constitutive expression or for response to TCDD.
Keywords: treatment-control and mutant-wildtype

overall_design: Mice bearing wild-type or genetically deleted AHRs were treated with corn oil vehicle or TCDD, and their livers analyzed by expression arrays.

first: Nathalie

last: Tijet

first: Ivy

last: Moffat

first: Allan

middle: B

last: Okey

first: Jouko

last: Tuomisto

first: Raimo

last: Pohjanvirta


title: Gene expression analysis of cells sensitive to necrosis (L929) and cells sensitive to apoptosis (NIH3T3).

status: Public on Oct 31 2008

first: Junying

last: Yuan

address: 240 Longwood Avenue

department: Department of Cell Biology

summary: To explore gene expression profiles of cells sensitive to necrosis (such as L929 cells) and those sensitive to apoptosis (such as NIH3T3 cells), we conducted expression microarray analysis of L929 cells and NIH3T3 cells.

overall_design: Total RNA of 2 samples of unstimulated L929 cells or 2 samples of unstimulated NIH3T3 cells were extracted by Trizol followed by RNeasy. The quantity, purity and integrity of RNA were evaluated by UV spectrophotometry and RNA-nano Bioanalyzer. Sample processing and hybridization on Mouse Genome 430 2.0 GeneChip microarrays (Affymetrix) were performed according to manufacturer’s instructions. Genes that are differentially expressed in L929 cells relative to NIH3T3 cells were identified as having an FDR-adjusted p-value <0.05 and a fold-change >1.5.

first: Junichi

last: Hitomi

first: Dana

last: Christofferson

first: Aylwin

last: Ng

first: Jianhua

last: Yao

first: Alexei

last: Degterev

first: Ramnik

last: Xavier


title: Expression data of Naïve Treg and Tumor associated Treg cells

first: Yu

last: Zhao

address: 660 S. Euclid

institute: Washington University

summary:
Naïve Treg cells were purified from the resting spleens of FoxP3-GFP knock-in mice made in the 129/SvJ strain.
Ascites Treg cells were tumor-associated FoxP3-GFP+ cells sorted from the tumor ascites of 129/SvJ mice IP-injected with 1 x 10e6 RMAS cells 5 days earlier; Spleen-T Treg cells were purified from the spleens of the same tumor-bearing mice.

Keywords: in vivo samples

overall_design: Affymetrix MOE430v2 arrays were used to perform gene expression studies.  The purity of the sorted Treg cells is >99%.

first: Xuefang

last: Cao

first: Timothy

last: Ley


title: Induction of systemic disease-specific salivary biomarker profiles in mouse cancer models

status: Public on Nov 11 2008

city: Los Angeles

first: David

last: Wong

state: CA

address: 73-017 CHS, 10833 Le Conte Ave

department: Dental Research Institute School of Dentistry

institute: University of California at Los Angeles

summary: Saliva (oral fluids) is an emerging biofluid poised for clinical diseases detection. Although the rationale for oral diseases applications (e.g. oral cancer) is clear, the rationale and relationship between systemic diseases and saliva biomarkers are unknown. In this study, we used mouse models of melanoma and non-small cell lung cancer and compared the transcriptome biomarker profiles of tumor-bearing mice to those of control mice. Microarray analysis showed that salivary transcriptomes were significantly altered in tumor-bearing mice vs. controls. Analysis of the transcriptomes in the mouse tumors, serum, salivary glands and saliva revealed that salivary biomarkers have multiple origins. Furthermore, we identified that the expression of two groups of significantly altered transcription factors Runx1, Mlxipl, Trim30 and Egr1, Tbx1, Nr1d1 in melanoma-bearing mice that can potentially be responsible for 82.6% of the up-regulated genes expression and 62.5% of the down-regulated gene expression in the mice saliva, respectively. We also confirmed that the ectopic production of nerve growth factor (NGF) in the melanoma tumor tissue as a tumor-released mediator that can induce expression of the transcription factor Egr-1 in the salivary gland. Taken together, our data support the conclusion that upon systemic disease development, a disease-specific change occurs in the salivary biomarker profile. Although the origins of the disease-specific salivary biomarkers are both systemic and local, stimulation of salivary gland by mediators released from remote tumors play an important role in regulating the salivary surrogate biomarker profiles.

overall_design:
Mice (either C57BL/6 mice or DBA/2 mice) were randomly assigned to control group and tumor group (15 animals per group). Melanoma mice model was induced by subcutaneous (s.c.) injection of B16-F1 cells in 0.1 ml PBS into the lower-right flank of C57BL/6 mice. The lung cancer model was established by s.c. injection of KLN-205 cells in DBA/2 mice. Control animal were injected with PBS alone. Established tumors were observed after 2-3 weeks.

When tumors reached 15 mm in diameter saliva was collected and the mice were sacrificed. Mild anesthesia was induced. Mice saliva was stimulated, obtained and immediately placed in pre-schilled 1.5-ml microcentrifuge tubes. Collection was completed in 20 minutes and samples were stored at -80ºC until analyzed.In addition, Blood was collected in BD Vacutainer tubes containing clot activator (BD Biosciences). Salivary gland and tumor tissue were removed from mice, snap-frozen in liquid nitrogen and stored at -80ºC.

Salivary,salivary gland, serum or tumor RNA was isolated using the RNeasy Mini Kit (Qiagen) as described previously. There are 15 mice in the control group or tumor group (totally 30 C57BL/6 mice for melanoma mouse model, another 30 DBA/2 mice for lung cancer mouse model). Samples derived from 5 mice in each group were pooled and RNA extracted. The pooling is necessary to ensure sufficient salivary mRNA can be obtained for microarray analyses. Isolated total RNA was treated with recombinant DNase (Ambion, Austin, TX). For microarray analysis, mRNA from mouse saliva, gland or tumor was linearly amplified using the RiboAmp RNA Amplification kit (Molecular Devices, Sunnyvale, CA). After purification, cDNA were in vitro transcribed and biotinylated using GeneChip Expression 3’-Amplification Reagents for in vitro transcription labeling (Affymetrix, Santa Clara, CA). The labeled RNAs was subsequently fragmented, hybridization and scanning.

first: KAI

last: GAO

first: Zhou

last: Hui

first: Lei

last: Zhang

first: Jin

middle: W

last: Lee

first: Qing

last: Zhou

first: James

last: Farrel

first: Guido

last: Eibl

middle: T


title: Expression study of liver smaples of 2-days old  Mfp2 knockout mice as compared to wild type

status: Public on Nov 06 2008

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

summary:
Study on gene expression in multifunctional protein 2 deficient mice. Liver samples of two days old mice in normal conditions are used. In total 8 arrays were hybridized corresponding to 4 KO mice and 4 WT mice Results: Cholesterol synthesis is induced and ppar alpha targets also differentially expressed between KO and WT.
Keywords: Knockout gene expression study; genetic modification

overall_design: Liver samples, 4 KO mice and 4 WT mice

first: E

middle: V

last: van Themaat

first: K

last: Martens


title: Comparative analysis of Drd1+ Medium Spiny Neurons and Drd2+ Medium Spiny Neurons

first: Nathaniel

last: Heintz

overall_design:
For each cell population,  D1 and D2, three independent TRAP replicates were collected, and total RNA from the immunoprecipitates were  amplified and hybridized.
Data were normalized with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile.
Data were then converted to log2 scale.
We recommend that only genes where more than one sample has a normalized intensity larger than 16 (4 in log2 scale) should be kept in the analysis.

first: Myriam

last: Heiman

first: Anne

last: Schaefer

first: Shiaoching

last: Gong

first: Jayms

last: Peterson

first: Michelle

last: Day

first: Keri

last: Ramsey

first: Mayte

last: Suárez-Fariñas

first: Cordelia

last: Schwarz

first: Dietrich

last: Stephan

first: D

last: Surmeier

first: Paul

last: Greengard


title: Interferon-γ-dependent regulatory circuits in immune inflammation highlighted in diabetes

city: Houston.

first: Jason

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

summary: We demonstrate diverse roles of interferon–gamma (IFN-γ) in the induction and regulation of immune-mediated inflammation using a transfer model of autoimmune diabetes. The diabetogenic CD4+BDC2.5 (BDC) T cell clone upon transfer into NOD.scid mice induced destruction of islets of Langerhans leading to diabetes. Administration of a neutralizing antibody to IFN-γ (H22) resulted in long term protection (LTP) from diabetes, with inflammation but persistence of a significant, albeit decreased numbers of β-cells. BDC T cells were a mixture of cells expressing high, intermediate and low levels of the T cell receptor. Clonotype-low BDC T cells were required for LTP. Furthermore, islet infiltrating leukocytes in the LTP mice contained Foxp3+CD4 T cells. Islet inflammation in both diabetic and LTP mice was characterized by heavy infiltration of macrophages. Gene expression profiles indicated that macrophages in diabetic mice were M1-type, while LTP mice contained M2-differentiated. The LTP was abolished if mice were treated with either an antibody depleting CD4 T cells, or a neutralizing antibody to CTLA-4, in this case, only at a late stage. Neutralization of IL-10, TGF-β, GITR or CD25 had no effect. Transfer of only clonotype-high expressing BDC T cells induced diabetes but in contrast, H22 antibodies did not inhibit diabetes. While clonotype high T cells induced diabetes even when IFN-γ was neutralized, paradoxically, there was reduced inflammation and no diabetes if host myeloid cells lacked IFN-γ receptor. Hence, using monoclonal CD4 T cells, IFN-γ can have a wide diversity of roles, depending on the setting of the immune process.

overall_design: Pancreatic islets were laser-capture microdissected from mice injected with diabetogenic T cells. One cohort of mice also received injections with anti-interfereon gamma monoclonal antibody, which protected those mice from developing diabetes. RNA prepared from islets was amplified and analyzed by Affymetrix GeneChips. Each GeneChip was prepared from RNA pooled from 5 mice at each timepoint. GeneChips were prepared from RNA extracted at different days following injection of T cells. The following days were assayed day 0 (i.e., untreated), day 3 (for diabetic and protected islets), day 4 (diabetic and protected), day 5 (only for protected, as diabetic islets were too edematous to dissect), day 8 (diabetic and protected).

first: Emil

last: Unanue

first: Boris

last: Calderon


title: Gene expression analysis of ctrl_islets versus VhlhKO_islets

city: Zurich

first: Jens

last: Zehetner

state: Zurich

address: Schafmattstrasse 18

department: Cell Biology

country: Switzerland

institute: ETH Zurich

summary: Understanding the nature of the various glucose-derived signals for insulin secretion (both triggering and amplifying) is essential for gaining insight into the functional failure of the beta-cells in diabetes and the development of drugs for correcting this problem. The beta-cells uniquely couple changes in cellular metabolism to electrical activity and thus insulin release. In mice, beta-cell specific deletion of the von Hippel-Lindau (VHL) tumor suppressor protein leads to the activation of a HIF transcription program that includes genes involved in glycolysis, suppression of mitochondrial activity and lactate production. This reprogramming of cellular metabolism results in abnormal insulin secretion properties.

overall_design: Three batches of isolated islets from each genotype where used for RNA isolation and Affymetrix measurements.

first: Carsten

last: Danzer

first: Wilhelm

last: Krek


title: Multi-stage analysis of gene expression in C57/B6 mouse liver development

status: Public on Oct 30 2008

city: Beijing

first: Tingting

last: Li

address: Hai Dian

department: Automatioon

country: China

institute: Tsinghua University

summary:
The liver performs a number of essential functions for life. The development of such a complex organ relies on finely regulated gene expression profiles which change over time in the development and determine the phenotype and function of the liver.
We used high-density oligonucleotide microarrays to study the gene expression and transcription regulation at 14 time points across the C57/B6 mouse liver development, which include E11.5 (embryonic day 11.5), E12.5, E13.5, E14.5, E15.5, E16.5, E17.5, E18.5, Day0 (the day of birth), Day3, Day7, Day14, Day21, and normal adult liver. With these data, we made a comprehensive analysis on gene expression patterns, functional preferences and transcriptional regulations during the liver development.

Keywords: time course

overall_design: Totally 25 microarrays have been used in this experiment, and 11 of the 14 time points have two technique repeat experiments.

first: Jian

last: Huang

first: Xuegong

last: Zhang

first: Zeguang

last: Han


title: Comparision of expression profile between wild-type and Slc39a13 knockout chondrocytes

status: Public on Nov 07 2008

city: Yokohama

first: Toshiyuki

last: Fukada

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN

summary:
In order to explore molecules whose expression is controlled by Slc39a13, we investigated gene expression profiling of primary chondrocyte isolated from wild-type and Slc39a13 knockout mice.
Keywords: knockout vs wild-type

overall_design: wild-type vs Slc39a13 knockout

first: Tatsuya

last: Furuichi

first: Hiroshi

last: Kitamura

first: Osamu

last: Ohara

first: Shiro

last: Ikegawa

first: Toshio

last: Hirano


title: Microarray analysis of Foxa2 mutant mouse embryos

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary:
Background:  The Spemann/Mangold organizer is a transient tissue critical for patterning the gastrula stage vertebrate embryo and formation of the three germ layers. Despite its important role during development, there are still relatively few genes with specific expression in the organizer and its derivatives. Foxa2 is a forkhead transcription factor that is absolutely required for formation of the mammalian equivalent of the organizer, the node, the axial mesoderm and the definitive endoderm (DE). However, the targets of Foxa2 during embryogenesis, and the molecular impact of organizer loss on the gastrula embryo, have not been well defined.
Results:  To identify genes specific to the Spemann/Mangold organizer, we performed a microarray-based screen that compared wild-type and Foxa2 mutant embryos at late gastrulation stage (E7.5). We could detect genes that were consistently down-regulated in replicate pools of mutant embryos versus wild-type, and these included a number of known node and DE markers. We selected 314 genes without previously published data at E7.5 and screened for expression by whole mount in situ hybridization. We identified 10 novel expression patterns in the node and 5 in the definitive endoderm. We also found significant reduction of markers expressed in secondary tissues that require interaction with the organizer and its derivatives, such as cardiac mesoderm, vasculature, primitive streak, and anterior neuroectoderm.
Conclusions: The genes identified in this screen represent novel Spemann/Mangold organizer genes as well as potential Foxa2 targets. Further investigation will be needed to define these genes as novel developmental regulatory factors involved in organizer formation and function.  We have placed these genes in a Foxa2-dependent genetic regulatory network and we hypothesize how Foxa2 may regulate a molecular program of Spemann/Mangold organizer development. We have also shown how early loss of the organizer and its inductive properties in an otherwise normal embryo, impacts on the molecular profile of surrounding tissues.

overall_design:
Microarrays:
Tetraploid embryos were derived as previously described (Nagy et al. 1990; Nagy et al. 1993) using Foxa2 null ES cells (Dufort et al. 1998). Wild type embryos were collected from timed matings of ICR mice. Wild type or tetraploid embryos were collected at E7.5 and staged accordingly (Downs and Davies 1993). Embryos were between mid-streak and head-fold stages and the extra-embryonic regions were removed by dissection. The embryo proper, including extra-embryonic tetraploid-derived VE, was retained and multiple samples were pooled for total RNA isolation using Trizol reagent. Numbers of E7.5 embryos collected and pooled were as follows: wild type 1 (n=53), wild type 2 (n=50), Foxa2 null 1 (n=53), Foxa2 null 2 (n=48). Total RNA from each of the four embryo pools was processed for Affymetrix Murine Genome U74Av2 GeneChip analysis as previously described (Lickert et al. 2005).

Data analysis:
Affymetrix MAS 5.0 software was applied to the U74Av2 GeneChip data to target normalize the global expression level to 1000, and provide present, absent and fold change calls in a cross-comparisons of all replicate mutant samples over the two replicate wild-type samples. Next probe sets with absent calls in all samples were removed from the data set. As well, all samples with illogical calls were also removed, for example a probe set with an increase call that was called absent in the sample with the higher level of expression. Lastly, we filtered the data to include only probe sets that showed a statistical change call in two or more (2/4) of the cross comparisons.

MOE430v2 GeneChips were analyzed as follows in the R statistical programming language (R Core Development Team, 2006; see Additional File 11 for details). Probeset summaries were calculated according to the MAS 5.0 algorithm. Logarithmic summary values were normalized by the loess smoother applied to the M-A scale transform. Statistical testing for differential expression between mutant and wild-type was performed on single probe level taking the duplicate chips into account employing the Wilcoxon paired rank test. The p-value threshold was adjusted by either family-wise error rate (FWER, Bonferroni procedure) or the false discovery rate (FDR, Bejamini-Hochberg technique). Significant probesets were tested for enrichment of GO terms by the hypergeometric distribution testing with the annotation as available from the GO consortium on March 25th, 2005.

first: Doris

last: Kinzel

first: Brian

last: Cox

first: Christine

last: Bell

first: Janet

last: Rossant

first: Heiko

last: Lickert


title: Comparative analysis of Drd1+ Medium Spiny Neurons, Drd2+ Medium Spiny Neurons and whole brain

first: Nathaniel

last: Heintz

summary:
The cellular heterogeneity of the brain confounds efforts to elucidate the biological properties of distinct neuronal populations.
Using Bacterial Artificial Chromosome (BAC) transgenic mice which express EGFP-tagged ribosomal protein L10a in defined cell populations, we have developed a methodology to affinity purify polysomal mRNAs from genetically defined cell populations in the brain.
The utility of this approach is illustrated by the comparative analysis of four types of neurons, revealing hundreds of genes that distinguish these four cell populations.
We find that even two morphologically indistinguishable, intermixed subclasses of medium spiny neuron display vastly different translational profiles and present examples of the physiological significance of such differences.
This genetically targeted  Translating Ribosome Affinity Purification (TRAP) methodology is a generalizable method useful for the identification of molecular changes in any genetically defined cell type in response to genetic alterations, disease, or pharmacological perturbations.

Keywords: Cell Type Comparison

overall_design:
For each RNA source (D1, D2, and WB), three independent TRAP or total RNA replicates were collected, and total RNA from the immunoprecipitates or homogenized tissue was  amplified and hybridized.
Data were normalized withinin two groups (IP and WB) with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile.
Data were further normalized to the expression values of several positive control genes and to a constant value of 0.01.
Data were then converted to log2 scale.
We recommend that only genes where more than one sample has a normalized intensity larger than 16 (4 in log2 scale) should be kept in the analysis.

first: Myriam

last: Heiman

first: Anne

last: Schaefer

first: Shiaoching

last: Gong

first: Jayms

last: Peterson

first: Michelle

last: Day

first: Keri

last: Ramsey

first: Mayte

last: Suárez-Fariñas

first: Cordelia

last: Schwarz

first: Dietrich

middle: A

last: Stephan

first: D

last: Surmeier

first: Paul

last: Greengard


title: T cell-suppression by programmed cell death 1 ligand 1(PD-L1) on IFNg-treated retinal pigment epithelial cells

status: Public on Oct 24 2008

city: Tokyo

first: Yuri

last: Futagami

address: 1-5-45 Yushima Bunkyoku

department: Ophthalmology

institute: Tokyo Medical and Dental University

summary:
Adult (6- to 8-week-old) C57BL/6 purchased from CLEA Japan Inc. (Tokyo, Japan) were used as donors ocular pigment epithelium (PE). To cultivate retinal PE (RPE) eyes were cut into two parts along a circumferential line posterior to the ciliary process, creating a ciliary body-deficient posterior eyecup.  The eyecup was then incubated in 0.2% trypsin (Biowhitaker) for 1 hr.  These tissues were triturated to make a single cell suspension, and then re-suspended in the medium.
Keywords: Comparison

overall_design: Comparison of gene expression pattern in Mouse Primary Cultured Cell Lines (RPE, RPE+IFNg).

first: Sunao

last: Sugita

first: Shintaro

last: Horie

first: Hiroyuki

last: Aburatani

first: Manabu

last: Mochizuki


title: Strains for eQTL CNV Analysis

city: Jupiter

first: Mathew

last: Pletcher

state: FL

address: 5353 Parkside Dr

institute: Scripps Florida

summary:
Background
Haplotype association mapping is a recently developed method that can be used to identify expression Quantitative Trait Loci (eQTLs).  The underlying genomic structure of the haplotype can be defined by single nucleotide polymorphisms (SNPs), variable number tandem repeats (VNTRs) and copy number variations (CNVs).  Microarray genotyping platforms are able to interrogate all three genomic polymorphisms simultaneously.   Combined with gene expression data, these data allow for the elucidation of sites responsible for the regulation of transcription.
Results
Thirty three inbred strains were genotyped on a microarray platform to assess possible contributions of polymorphic regions to gene expression.  Over one hundred million statistical correlations were made between probe performance on genotyping and gene expression microarrays.  This analysis provided 10,655 trans associations and 31 cis associations.  Further investigation of one of the cis associations revealed that a 84kb region of MMU3 acts as a haplotype-specific locus control region for the glutathione-S-transferase mu family in multiple tissues.  In the strains that share the minor haplotype, reductions in mRNA levels in members of the Gst mu family are observed.
Conclusions
We have identified a haplotype containing a putative locus control region for the Gst mu family gene cassette.  In the strains with affected haplotype, Gst mu expression is drastically reduced.  The reduction in Gst mu levels has important relevance for pharmacology and toxicology studies.  The reduction of Gst mu levels in general, and Gstm5 in particular, has implication in models of dopamine metabolism, Parkinson’s disease, and chemical neurotoxicity.
Keywords: Liver gene expression, no treatment

overall_design:
Samples GSM262266-GSM262267, GSM262270-GSM262272 representing liver gene expression Samples from 10 week old male mouse livers were analyzed in a confirmation study of an identified eQTL.  Samples came from pools of three animals, and were compared across strains.

The genotyping summary output file and associated .CEL files are linked below as supplementary files.  Briefly:
After hybridization and staining the arrays are scanned on an Affymetrix Scanner 3000 7G 4C using four distinct filters, one for each DNA base (A, C, G, T). These scanned images are saved at .dat files. A grid is superimposed on the .dat array image such that each element of the grid brackets a feature. Once the grid has been applied, GCOS computes one intensity value for each cell, and saves these values in a .CEL file. A .CEL file is generated for each possible base (A, C, G, T). Only the .CEL files are read by GTGS.
The .CEL files computed by GCOS are then imported into GTGS and analyzed. The experiments are then clustered together and used to generate a normalized profile of each probe. From the clustered profiles a genotype call is made for every specific probe on an individual chip. These genotyped calls are then exported from GTGS into a .txt file containing assay id, sample id and relative intensity values for each DNA base over the entire set of SNPs analyzed.

first: Kevin

last: Hayes

first: Brandon

middle: M

last: Young


title: Oncogenesis of T-ALL and non-malignant consequences of overexpressing NOTCH1

status: Public on Oct 27 2008

city: Houston

first: Alexei

last: Protopopov

address: 1901 East Rd

department: IACS

institute: UT MD Anderson Cancer Center

summary:
We have determined the consequences of ICN1 overexpression from retroviral vectors introduced into bone marrow cells.
Even though the tumors consist of phenotypically heterogeneous cells, no evidence for tumor stem cells was found.

overall_design: Expression analysis, array-based comparative genomic hybridization and spectral karyotyping.

first: Xiaoyu

last: Li

first: Fotini

last: Gounari

first: Khashayarsha

last: Khazaie

first: Harald

last: von Boehmer


title: Gene expression changes in multiple brain regions of a mouse MPTP model of Parkinson's disease

status: Public on Oct 21 2008

city: Fairfax

first: Daniel

last: Sforza

state: VA

address: 4400 University Drive

department: Computational and Data Sciences

institute: George Mason University

summary:
In Parkinson’s disease (PD), the progressive loss of substantia nigra dopamine cells has been associated with their vulnerability to oxidative stress, inflammation, and mitochondrial dysfunction. To identify multiple gene transcription alterations that may potentially underlie early stages of related degenerative processes in brain, we used the subcrhonic MPTP mouse model of PD and microarray analysis at 4 days post-MPTP when neurotoxic activity is maximal. Since PD results in gene changes throughout the brain, we assessed MPTP's effects in multiple regions: frontal cortex, striatum and midbrain.
Keywords: neurotoxic response

overall_design: Mus musculus adults were randomly assigned to either MPTP or saline treatment groups. Brain regions of interest (frontal cortex, striatum and midbrain) were dissected from both groups for RNA extraction and hybridization on Affymetrix microarrays.

first: Parvana

last: Hartenstein

first: Goran

last: Lacan

first: William

last: Melega

first: Arthur

last: Toga


title: Genome-Wide Mapping of in Vivo Protein-DNA Interactions

city: Hayward

first: Shujun

last: Luo

address: 25861 Industrial Blvd

institute: Illumina inc

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element–1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [±50 base pairs (bp)], which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity [ROC (receiver operator characteristic) area ≥ 0.96] and statistical confidence (P < 10−4), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.

overall_design: Exam NRSF binding in Jurkat T cell line

first: David

middle: S

last: Johnson

first: Ali

last: Mortazavi

first: Richard

last: Myers

first: Barbara

last: Wold


title: Comparision of expression profile between wild-type and Slc39a13 knockout osteoblasts

first: Toshiyuki

last: Fukada

summary:
In order to explore molecules whose expression is controlled by Slc39a13, we investigated gene expression profiling of primary osteoblast isolated from wild-type and Slc39a13 knockout mice.
Keywords: knockout vs wild-type

first: Hiroshi

last: Kitamura

first: Osamu

last: Ohara

first: Toshio

last: Hirano


title: Identification of PU.1 target genes by expression profiling of PUER cells

status: Public on Oct 11 2008

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

institute: Institute of Human Genetics

summary:
PU.1 is a key transcription factor for macrophage differentiation. Novel PU.1 target genes were identified by mRNA profiling of PU.1-deficient progenitor cells (PUER) before and after PU.1 activation. We used two different types of Affymetrix DNA-microarrays (430 2.0 arrays and ST 1.0 exon arrays) to characterize the global PU.1-regulated transcriptional program underlying the early processes of macrophage differentiation.

Keywords: time course

overall_design: Uninduced and 24h 4-hydroxy-tamoxifen (OHT) induced PUER cells were cultured before RNA extraction and hybridization on Affymetrix Mouse Genome 430 2.0 and Mouse Exon ST 1.0 microarrays. Triplicates before (0h) and after (24h) induction of PU.1 were analyzed.

first: Karin

last: Weigelt


title: Vancomycin nephrotoxicity assessed by DNA microarray

status: Public on Oct 23 2008

city: Menlo Park

first: Hanna

middle: Hongchin

last: Ng

address: 333 Ravenswood Avenue

institute: SRI International

summary:
The glycopeptide antibiotic vancomycin (VCM) represents one of the last lines of defense against methicillin-resistant Staphylococcus aureus infections. However, vancomycin is nephrotoxic, but the mechanism of toxicity is still unclear.
The goal of this study was twofold: (1) gain insights into the molecular mechanisms of vancomycin nephrotoxicity at the genomic level and (2) evaluate potential biomarkers (gene expression profiles) of vancomycin-induced kidney injury
Keywords: Dose response

overall_design: Groups of 6 female BALB/c mice were treated with 7 daily iv or ip doses of vancomycin (50, 200, and 400 mg/kg) or saline, and sacrificed on Day 8

first: Christine

last: Dieterich


title: Expression data from early mouse embryo eye development, specifically optic fissure.

status: Public on Oct 08 2008

city: Bethesda

first: Jacob

last: Brown

state: MD

address: 10 Center Drive

institute: NEI

summary:
The different stages of the optic fissure can be clearly visualized by making sagittal sections through the mouse eye during early development which represent the optic fissure at open (E10.5), closing (E11.5) and fused (E12.5) states.  Laser capture microdissection (LCM) was employed to dissect tissue from the margins of the optic fissure consisting of the outer (presumptive RPE) and inner (presumptive neurosensory retina) layers of the retina.
An approximately square-shaped block of optic fissure (50 x 50 mm) was dissected from each side of the fissure.  Two rounds of linear amplification were performed on RNA isolated from each of the samples prior to microarray hybridization.  Expression data were gathered in biological triplicate at E10.5, E11.5 and duplicate at E12.5, each array representing pooled optic fissure tissue from three embryos from a single litter.  Expression signals were ascertained from 45,101 probe sets and normalized across arrays.

Keywords: Time course

overall_design: Differential gene expression over the course of three days in laser capture microdissected tissue from wild type mouse embryos.

first: Sunit

last: Dutta

first: Kapil

last: Bharti

first: Robert

last: Bonner

first: Peter

middle: J

last: Munson

first: Igor

last: Dawid

first: Amana

last: Akhtar

first: Ighovie

last: Onojafe

first: Ramakrishna

last: Alur

first: Jeffrey

last: Gross

first: J

last: Hejtmancik

first: Xiaodong

last: Jiao

first: Wai

middle: Y

last: Chan

first: Brian

last: Brooks


title: Analysis of genes regulated by FoxD3 in B16-F10 mouse melanoma cells

status: Public on Oct 15 2008

city: Davis

first: Aaron

last: Thomas

address: One Shields Ave.

department: MCB

institute: University of California, Davis

summary: We wished to examine the genes regulated by FoxD3 in pigment cells to gain understanding in how FoxD3 represses melanoblast specification in the neural crest.  For technical reasons, we could not use neural crest cells, so we used melanoma cells, since they are derived from neural crest cells.  To this end, we transfected B16-F10 mouse melanoma cells with constructs expressing FoxD3, or FoxD3-VP16, in which the C-terminal portion of FoxD3 (which contains the transcriptional repression domain) has been replaced by the VP16 transcriptional activation domain.

overall_design:
The base vector used for these studies was pMES, which expresses the gene of interest under control of the chick beta-actin promoter.  EGFP is also expressed from the bicistronic mRNA through the use of an IRES.

B16-F10 cells were transfected with either empty pMES, pFoxD3 (which contains FoxD3 inserted into pMES), or pFoxD3-VP16 (similar to pFoxD3, except that the C-terminal portion of FoxD3, which contains the transcriptional repression domain, has been replaced by the transcriptional activation domain of VP16).

24 hours after transfection, EGFP-positive cells were collected by FACS and those cells were subjected to microarray analysis.

first: Carol

last: Erickson


title: EOM and TA Sp cell comparison

status: Public on Oct 09 2008

city: Philadelphia

first: Murat

last: Budak

state: PA

institute: University of Pennsylvania

summary:
Using Affymetrix GeneChips, we analyzed expression profiles of SP cells from EOM and TA. 348 differentially expressed transcripts defined the EOM-SP transcriptome: 229 upregulated in EOM-SP and 119 in TA-SP.
Keywords: Expression Profiling

overall_design: Six independently separated EOM and six TA SP cell preparations were used for microarray analysis using the Affymetrix® Mouse 430 ver 2.0 GeneChip arrays.

first: Eugenia

last: Pacheco-Pinedo

first: Sasha

last: Bogdanovich

first: Louise

middle: H

last: Jorgensen

first: Henrik

last: Schroeder

first: Neal

last: Rubinstein

first: Tejvir

last: Khurana


title: p53+/- mouse osteosarcoma RNA array (with mc3T3 and one RS control)

status: Public on Oct 10 2008

first: Ou

last: Ma

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

summary: RNA expression profiles from 12 (twelve) osteosarcomas arisen from p53+/- mouse were compared with a mc3T3 osteoblast control, and a rhabdomyosarcoma expression profile which was from a mouse with the same genetic background.

overall_design: Total RNA was extracted from 12 osteosarcomas and 1 rhabdomyosarcoma, both arisen from p53+/- mice. Total RNA was also extracted from a cultured mc3T3 osteoblast cell line as control. RNA microarray was performed on the 14 samples, and expression profiles were compared.

first: Lawrence

last: Donehower


title: Gene expression changes related to postnatal handling

first: mark

last: alter

address: 125 S. 31st Street

department: Center for Neurobiology and Behvior

summary: Postnatal handling in rodents leads to decreased anxiety-like behavior in adulthood.  We used microarrays to look at gene expression differences in the CA1 region of the hippocampus in female mice subjected to postnatal handling compared to controls.

overall_design: Balb c/J offspring were briefly separated from mothers for 15 minutes each morning on postnatal days 1-14 (handled group) or left undisturbed.  At 8 weeks of age mice were tested in the open-field and light-dark behavioral paradigms to verify a handling-induced behavioral phenotype.  2 weeks after behavioral testing, animals were sacrificed and the CA1 region was microdissected.  CA1 regions were stored at -20C in RNA later.  RNA was extracted from 8 samples (4 handled and 4 non-handled) using Trizol.  RNA was extracted from second group of animals (7 handled and 10 non-handled) using Qiagen RNA/DNA columns.  All total RNA samples were double round amplied and labeled using standard Affymetrix protocols and hybridized to Mouse 430_2.0 arrays in parallel.

first: Mark

last: Alter


title: The RPE transcriptional response to light damage

status: Public on Oct 07 2008

city: Baltimore

first: Amir

last: Rattner

address: 725 North Wolfe St., PCTB Room 805

department: Molecular Biology and Genetics

institute: Johns Hopkins University

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

overall_design: BALBc mice were dark adapted for one week. To produce light damage a subset of the mice were then exposed to 6,000 lux white fluorescent light for 1.5 hours. RPEs were collected for RNA extraction 24 hours after light damage.

first: Leila

last: Toulabi

first: John

last: Williams

first: Huimin

last: Yu

first: Jeremy

last: Nathans


title: Expression data from MatDp(dist2) and PatDp(dist2) mice

city: London

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 MatDp(dist2) and PatDp(dist2) mice (newborn whole head). Identification of highly differentially expressed transcripts.

overall_design: Pairwise array comparative analyses were performed using MAS5/GCOS where the sample genotype varied between the compared arrays: MatDp(dist2) vs PatDp(dist2), distal T(2:9)11H translocation breakpoint.

first: Ruth

last: McCole

first: Kathryn

last: Woodfine

first: Andrew

last: Wood

first: Rebecca

last: Oakey


title: The Effects of Resiquimod Treatment on the Asthma Transcriptome

status: Public on Oct 04 2008

city: Montreal

first: Pierre

last: Camateros

state: Quebec

address: 1650 Cedar Ave

department: Experimental Medicine

institute: McGill University

summary:
Resiquimod is a nucleoside analog belonging to the imidazoquinoline family of compounds which is known to signal through Toll-like receptor 7.  Resiquimod treatment has been demonstrated to inhibit the development of allergen induced asthma in experimental models.  Despite this demonstrated effectiveness, little is known about the molecular events responsible for this effect.  The aim of the present study was to elucidate the molecular processes which were altered following resiquimod treatment and antigen challenge in a mouse model of allergic asthma.  Employing microarray analysis, we have characterized the “asthmatic” transcriptome of the murine lung and determined that it includes genes involved in: the control of cell cycle progression, airway remodelling, the complement and coagulation cascades, and chemokine signalling.  We have demonstrated that systemic resiquimod administration resulted in the recruitment of NK cells to the lungs of the mice, although no causal relationship between NK cell recruitment and treatment efficacy was found.  Furthermore, results of our studies demonstrated that resiquimod treatment resulted in the normalization of the expression of genes involved with airway remodelling and chemokine signalling, and in the modulation of the expression of genes including cytokines and chemokines, adhesion molecules, and B-cell related genes, involved in several aspects of immune function and antigen presentation.  Overall, our findings identified several genes, important in the development of asthma pathology, that were normalized following resiquimod treatment thus improving our understanding of the molecular consequences of resiquimod treatment in the lung milieu.

Keywords: Disease and treatment state analysis

overall_design: A total of 18 samples, from 6 sets of biological replicates, were analyzed. 9 A/J and 9 C57BL/6 mice were divided into three equal groups.  All animals were sensitized to ovalbumin, one group received PBS aerosol challenges, the other two received 1% ovalbumin aerosol challenges.  Of the two ovalbumin challenged groups, one recieved resiquimod 24hours before each challenge.

first: Rob

last: Sladek

first: Thomas

last: Hudson

first: Danuta

last: Radzioch


title: Expression data from BWF1 mice

status: Public on Oct 28 2008

city: Los Angeles

first: Ram

middle: Pyare

last: Singh

address: 1000 Veteran Ave

department: Rheumatology/Medicine

institute: David Geffen School of Medicine at UCLA

summary:
Microarray analysis was performed on BWF1 mice spleenocyte cells in control and pCONS treated mice.
Microarray analysis identified many genes differentially expressed in control vs pCONS treated mice spleenocytes. Some of the genes were uperegulated and some of the genes were down regulated. Microarray analysis was performed in CD4, CD8, and whole spleenocyte WBC cells.

Keywords: One week after pCONS injection

overall_design: RNA was isolated from the mice spleenocytes from control and pCONs treated mice one week after treatment.

middle: P

first: Bevra

last: Hahn


title: Gene activation by Rag-mediated DNA double strand breaks

status: Public on Oct 12 2008

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: The objective is to identify genes that are differentially expressed following the introduction of DNA double strand breaks (DSBs) by the Rag proteins in murine pre-B cells. Cells lacking Artemis are used since the Rag-induced DSBs will not be repaired and, thus, will provide a continuous stimulus to the cell. Cells lacking Artemis and Atm are used to determine which gene expression changes depend on Atm and cells lacking Artemis that express an I kappa B alpha dominant negative are used to determine which gene expression changes depend on NFkB.

overall_design: Murine v-abl-transformed pre-B cells were treated with 3 uM STI571 for 48 hours. Cell types included Wild type (3 biological replicates), RAG-2-deficient (3 biological replicates), Artemis-deficient (3 biological replicates), Artemis and ATM-deficient (2 biological replicates, each with a technical replicate), and Artemis-deficient expressing dominant negative IkB (3 biological replicates). Each sample was hybridized once using Affymetrix Mouse Genome 2.0 GeneChip arrays (Mouse 430 v2, Affymetrix, Santa Clara, CA). Data were analyzed using the RAG-2-deficient samples as the controls.  Additionally, purified bone marrow pre-B cells were harvested from RAG-1-deficient (2 biological replicates) and Artemis-deficient (2 biological replicates) mice with an IgH transgene.  Each sample was hybridized once using Affymetrix Mouse Genome 2.0 GeneChip arrays (Mouse 430 v2, Affymetrix, Santa Clara, CA). Data were analyzed using the RAG-1-deficient:IgH samples as the controls.

first: Andrea

last: Bredemeyer

first: Beth

last: Helmink

first: Cindy

last: Innes

first: Lisa

last: McGinnis

first: Grace

middle: K

last: Mahowald

first: Eric

last: Gapud

first: Laura

last: Walker

first: Jennifer

last: Collins

first: Brian

last: Weaver

last: MandikNayak

first: Robert

last: Schreiber

first: Paul

last: Allen

first: Michael

last: May

first: Richard

last: Paules

first: Craig

last: Bassing

first: Barry

last: Sleckman


title: Plasmacytoid dendritic cells (pDCs) from E2-2 heterozygous mice

status: Public on Oct 02 2008

city: New York

first: Babacar

last: Cisse

address: West 168th St HHSC 609

department: Microbiology

institute: Columbia Uinversity

summary:
Analysis of expression profiles of pDCs from wild type and heterozygous E2-2 mice. Results show the control by E2-2 of the expression of pDC-enriched genes.

Keywords: Genome-wide expression analysis

overall_design: Duplicates of both wild type and heterozygous pDCs were used


title: Gene expression profile of mouse embryonic stem cells (D3-pOCT-mESC) grown in low concentrations of nitric oxide

status: Public on Oct 17 2008

city: Seville

first: Rafael

middle: A.

last: Tapia Limonchi

state: Seville

address: Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93

department: Department of Cell Therapy and Regenerative Medicine

country: Spain

institute: Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)

summary: In order to identify the genes regulated in mouse embryonic stem cells (mESC) by the effect of low concentrations of nitric oxide (NO), we analysed the transcriptome of cells treated with NO and compared it to those of cells cultured in the absence of leukemia inhibitory factor (LIF), and in the presence of LIF. We used the cell line D3-pOct4, which carries the enhanced Green Fluorescence Protein gene (eGFP) under the control of the Oct-4 promotor. This line is continuously maintained in the undifferentiated state in the presence of LIF, in comparison with the wild type line .

overall_design: D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF, in the absence of LIF, and in the absence of LIF supplemented with 2uM of diethylenetriamine nitric oxide adduct (DETA)/NO (Sigma) used as donor of nitric oxide.  Treatments were maintained for seven days. RNA was extracted and analyzed by Bioanalyzer of Agilent. The cDNA microarray chip used was Mouse Genome 430_2.0 (Affymetrix) and the data were analyzed with GeneChip Operating System v1.4.0.036 using global scaling as the normalization method.

first: Juan

middle: R

last: Tejedo

first: Gladys

last: Cahuana

first: Sergio

last: Mora Castilla

first: Mario

last: Bautista

first: Franz

last: Martin

first: Bernat

last: Soria

first: Francisco

last: Bedoya


title: High temporal resolution profiling of NIH3T3 cells

status: Public on Oct 03 2008

last: Hughes

address: 421 Curie Bvd, Brb 835

institute: UPenn

summary:
High-temporal resolution profiling was performed on NIH3T3 fibroblasts to detect rhythmic transcripts

Keywords: time course

overall_design: Samples were collected every hour for 48 hours from forskolin-synchronized NIH3T3 cells.  Samples were analyzed using Affymetrix arrays.

first: John

last: Hogenesch


title: High-temporal resolution profiling of mouse liver

summary:
High-temporal resolution profiling was performed on mouse liver to detect rhythmic transcripts

Keywords: time course

overall_design: Samples were collected every hour for 48 hours from 3-5 mice per time point from liver.  Samples were pooled and analyzed using Affymetrix arrays.

first: Satchin

last: Panda

first: Luciano

last: DeHaro


title: Gene expression differences between high and low exploratory genetically identical mice

first: mark

last: alter

summary: Genetically identical inbred mice exhibit substantial stable individual variability in exploratory behavior.  We used microarrays to look at gene expression differences in the hippocampus in female mice separated by stable differences in exploratory behavior

first: Mark

last: Alter


title: Genomic profile of IL10-/- knocked out colitis model

status: Public on Nov 01 2008

city: Granada

first: Antonio

last: Suarez

state: Granada

address: Pharmacy Faculty, Campus Cartuja s/n

department: Biochemistry and Molecular Biology

institute: University of Granada

summary:
Objetives: study and characterization of the IL10-/- knocked out colitis model in mice at genomic level and the study of the influence of bacteria in the development of the disease.
Keywords: Differentially expressed genes analysis

overall_design:
We used three groups of animasl: 1)IL10-/- mice grown under conventional condition, 2)IL10-/- mice grown under specific pathogen free (SPF) conditions, 3) Wild type mice grown under conventional conditions (CONTROL group). For each group, we recovered samples at 7, 9 and 12 weeks after birth According to colon length and colonic damage, three replicates were selected for each time point and each group (27 samples), for genomic analysis.
RNA was extracted from homogenized full-thickness colonic tissues in Trizol® reagent (Invitrogen) and purified with RNeasy affinity columns (Qiagen), according to manufacturer´s protocol. The microarray analysis was performed by Progenika Biopharma (Bilbao, Spain) on GeneChip® Rat Genome 230 2.0 Array (Affymetrix). All sample labeling (biotin), hybridization, staining and scanning procedures were carried out using Affimetrix, standard protocols (www.affymetrix.com). Normalization was carried out using Bioconductor sofware (affyPLM package).

first: Trinidad

last: Montero

last: Suárez

first: Xavier

last: Llor

first: Miguel

last: Gassull

first: Angel

last: Gil


title: Gene expression profiling in the lung and liver of low and high dose Perfluorooctanoic Acid exposed mouse fetuses

city: Research Triangle Park

first: Mitchell

middle: B

last: Rosen

department: Reproductive Toxicology

institute: U.S. EPA

summary:
Exposure to PFOA during gestation altered the expression of genes related to fatty acid catabolism in both the fetal liver and lung.  In the fetal liver, the effects of PFOA were robust and also included genes associated with lipid transport, ketogenesis, glucose metabolism, lipoprotein metabolism, cholesterol biosynthesis, steroid metabolism, bile acid biosynthesis, phospholipid metabolism, retinol metabolism, proteosome activation, and inflammation.  These changes are consistent with activation of PPAR alpha.  Non-PPAR alpha related changes were suggested as well.

Keywords: gene expression, microarray,PFOA, mouse, fetus, liver

overall_design:
Experiment 1: High Dose: Thirty timed-pregnant CD-1 mice were orally dosed from gestation day 1-17 with either 0, 5, or 10 mg/kg/day PFOA in water.  At term, fetal lung and liver were collected, total RNA prepared, and samples pooled from three fetuses per litter.  Five biological replicates consisting of individual litter samples were then evaluated for treatment group using Affymetrix mouse 430_2 microarrays.

Experiment 2: Low Dose: Thirty timed-pregnant CD-1 mice were orally dosed from gestation day 1-17 with either 0, 1, or 3 mg/kg/day PFOA in water.  At term, fetal lung and liver were collected, total RNA prepared, and samples pooled from three fetuses per litter.  Five biological replicates consisting of individual litter samples were then evaluated for treatment group using Affymetrix mouse 430_2 microarrays (note one microarray from the lung + 1mg/kg/day dose group was excluded from the study due to high background).

Please note that each dose experiment had separate concurrent controls.

first: Julie

last: Thibodeaux

first: Carmen

last: Wood

first: Robert

middle: D

last: Zehr

first: Judith

middle: E

last: Schmid

first: Christopher

last: Lau


title: Cooperative actions of p53 and Pten in normal and neoplastic progenitor cell renewal and differentiation

status: Public on Oct 01 2008

city: Boston

first: Hongwu

last: Zheng

state: MA

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
Glioblastoma (GBM) is a highly lethal brain tumor presenting as one of two subtypes with distinct clinical histories and molecular profiles. The primary GBM subtype presents acutely as high-grade disease that typically harbors EGFR, PTEN and Ink4a/Arf mutations, and the secondary GBM subtype evolves from the slow progression of low-grade disease that classically possesses PDGF and p53 events1.  Here, we show that concomitant CNS-specific deletion of p53 and Pten in the mouse CNS generates a penetrant acute-onset high-grade malignant glioma phenotype with striking clinical, pathological and molecular resemblance to primary GBM in humans.  This genetic observation prompted p53 and PTEN mutational analysis in human primary GBM, demonstrating unexpectedly frequent inactivating mutations of p53 as well the expected PTEN mutations.  Integrated transcriptomic profling, in silico promoter analysis and functional studies of murine neural stem cells (NSCs) established that dual, but not singular, inactivation of p53 and Pten promotes an undifferentiated state with high renewal potential and drives elevated c-Myc levels and its associated signature.  Functional studies validated increased c-Myc activity as a potent contributor to the impaired differentiation and enhanced renewal of p53-Pten null NSCs as well as tumor neurospheres (TNSs) derived from this model.  c-Myc also serves to maintain robust tumorigenic potential of p53-Pten null TNSs. These murine modeling studies, together with confirmatory transcriptomic/promoter studies in human primary GBM, validate a pathogenetic role of a common tumor suppressor mutation profile in human primary GBM and establish c-Myc as a key target for cooperative actions of p53 and Pten in the regulation of normal and malignant stem/progenitor cell differentiation, self-renewal and tumorigenic potential.
We used microarrays to detail the gene expression difference of the p53-null and p53/Pten-doubly null neural stem cell after differentiation .

Keywords: cell type comparison

overall_design: transcriptome comparisons of 2 independent p53-null with 3 p53/Pten double-null murine NSCs at 1 day post exposure to the differentiation inducer.

first: Ronald

last: DePinho


title: Expression data from mouse microvascular transcriptomes

status: Public on Sep 27 2008

city: Stockholm

first: Liqun

last: He

address: Scheelesvag 2

country: Sweden

institute: Karolinska Institute

summary:
Little is known about the pan-microvascular transcriptome, particularly considering gene transcripts and their encoded proteins that can be considered as vascular-selective in their expression.
Using a combination of publicly available and our own transcript profiles, we identified a core set of gene transcripts, which are specifically and broadly expressed in the microvasculature.
Keywords: cell type comparison, developmental regulation

overall_design: There are three different samples, each have three biological repeats. Comparisons were carried out between the samples.

first: Elisabet

last: Wallgard


title: Study of activity-regulated genes in mouse primary cultured neurons

status: Public on Sep 24 2008

first: Yingxi

last: Lin

address: Enders 250, 300 Longwood Avenue

department: Neurology/Neurobiology

institute: Children' Hospital/Harvard Medical School

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

overall_design: Refer to individual Series


title: Aquaporin-11 knockout effect on kidney

city: Bunkyo-ku, Tokyo

first: Shinji

last: Okada

address: 1-1-1 Yayoi

institute: The University of Tokyo

summary:
Aquaporin-11 (AQP11), a new member of the aquaporin family, is localized in the endoplasmic reticulum (ER).  Aqp11–/– mice neonatally suffer from polycystic kidneys derived from the proximal tubule.  Its onset is proceeded by the vacuolization of ER.  However, the mechanism for the formation of vacuoles and the development of cysts remain to be clarified.  Here, we show that Aqp11–/– mice and polycystic kidney disease animals share a common pathogenic mechanism of cyst formation.
Keywords: Geneexpression profile of Aqp11 knokout mouse kidney

overall_design: Aqp11+/– mice, originally generated in a 129/SvEvBrd background (4), were back-crossed 10–11 times to a C57/BL6 background.  Heterozygous mice were interbred to obtain knockout (Aqp11–/–) and wild-type littermates (Aqp11+/+).  The genotypes of offsprings were analyzed by PCR using tail DNA as a template.  All animal experiments were approved by the Animal Care Committee of the University of Tokyo.  One-week-old mice were sacrificed by cervical dislocation.  Kidneys were rapidly excised on ice, washed in ice-cold phosphate-buffered saline, immersed in RNAlater (Ambion) and stored at –20°C.  Total RNA was isolated using TRIzol Reagent (Invitrogen) and cleaned up using an RNeasy minikit with DNase treatment (Qiagen).  The RNA quality and quantity were examined by agarose-gel electrophoresis and a spectrophotometer (GE Healthcare).  Five pairs of Aqp11+/– mice were interbred, and we obtained 7 Aqp11+/+ and 9 Aqp11–/– offsprings.  Three micrograms of total RNA obtained from each kidney was individually reverse-transcribed, amplified, and labeled using GeneChip One-Cycle Target Labeling and Control Reagent package (Affymetrix) according to the manufacturer’s protocol.  Labeled cRNA was hybridized to GeneChip Mouse Genome 430 2.0 Array (Affymetrix) (a total of 16 samples on 16 different arrays).  The arrays were washed, stained using Fluidics Station (Affymetrix), and then scanned with the GeneChip Scanner (Affymetrix).  Data collection was performed using GeneChip Operating Software (Affymetrix).  The quality of collected data was checked by scatter plot analysis.

first: Takumi

last: Miasaka

first: Yasuko

last: Tanaka

first: Ichiro

last: Matsumoto

first: Kenichi

last: Ishibashi

first: Sei

last: Sasaki

first: Keiko

last: Abe


title: Conserved Transcriptional Response of Rodent Liver to TCDD: Mouse

status: Public on Sep 19 2008

city: Toronto

first: Paul

middle: C

last: Boutros

address: 101 College Street, Suite 800

institute: Ontario Institute for Cancer Research

summary:
Background
Mouse and rat models are mainstays in pharmacology, toxicology and drug development – but differences between strains and between species complicate data interpretation and application to human health. Dioxin-like polyhalogenated aromatic hydrocarbons represent a major class of environmentally and economically relevant toxicants. In mammals dioxin exposure leads to a broad spectrum of adverse affects, including hepatotoxicity of varying severity. Several studies have shown that dioxins extensively alter hepatic mRNA levels. Surprisingly, though, analysis of a limited portion of the transcriptome revealed that rat and mouse responses diverge greatly (Boverhof et al. Toxicol Sci 94:398–416, 2006).

Results
We employed oligonucleotide arrays to compare the response of 8,125 rat and mouse orthologs. We confirmed that there is limited inter-species overlap in dioxin-responsive genes. Rat-specific and mouse-specific genes are enriched for specific functional groups which differ between species, conceivably accounting for species-specificities in liver histopathology. While no evidence for the involvement of copy-number variation was found, extensive inter-species variation in the transcriptional-regulatory network was identified; Nr2f1 and Fos emerged as candidates to explain species-specific and species-independent responses, respectively.

Conclusion
Our results suggest that a small core of genes is responsible for mediating the similar features of dioxin hepatotoxicity in rats and mice but non-overlapping pathways are simultaneously at play to result in distinctive histopathological outcomes. The extreme divergence between mouse and rat transcriptomic responses appears to reflect divergent transcriptional-regulatory networks. Taken together, these data suggest that both rat and mouse models should be used to screen the acute hepatotoxic effects of drugs and toxic compounds.

overall_design: Wild-type C57BL/6 mice were treated with 1000 ug/kg TCDD (n=6) or with cornoil vehicle as control (n=5) for 19 hours. Their livers were then excised, RNA extracted, and the resulting samples hybridized to Affymetrix MOE430-2 arrays to survey changes in the transcriptome profile.

first: Raimo

last: Pohjanvirta

first: Allan

last: Okey


title: Prediction of left ventricle systolic dysfunction in mice using gene expression profiling

city: stanford

first: Rani

last: Agrawal

address: 300 Pasteur Drive, Dept of Anesthesia

department: Anesthesia

institute: Stanford University

summary:
We tested the hypothesis that a set of differentially expressed genes could be used to predict cardiovascular phenotype in mice after prolonged catecholamine stress.

Keywords: Treatment

overall_design: We observed that WT FVB and B2KO mice developed systolic dysfunction in response to continuous catecholamine infusion while WT C57 mice developed diastolic dysfunction.  Using these mice as the derivation cohort, we identified a set of 83 genes whose differential expression correlated with left ventricle systolic dysfunction.  The gene set was then used to accurately predict development of left ventricle systolic dysfunction in a separate group of mice (WT B6129SF2/J) after catecholamine stress.

first: Andrew

last: Patterson


title: Transcriptional profile of rapidly stimulated atrial myocytes: Conservation with human atrial fibrillation

city: Nashville

first: yajun

last: yi

state: TN

address: 2215 Garland Ave

institute: vanderbilt univ

summary:
Atrial fibrillation (AF) is a progressive arrhythmia for which current therapy is inadequate. During AF, rapid stimulation causes atrial remodeling that promotes further AF. The cellular signals that trigger this process remain poorly understood, however, and elucidation of these factors would likely identify new therapeutic targets. We have previously shown that immortalized mouse atrial (HL-1) myocytes subjected to 24 hr of rapid stimulation in culture undergo remodeling similar to that seen in animal models of atrial tachycardia (AT) and human AF. This preparation is devoid of confounding in vivo variables that can modulate gene expression (e.g., hemodynamics). Therefore, we investigated the transcriptional profile associated with early atrial cell remodeling. RNA was harvested from HL-1 cells cultured for 24 hr in the absence and presence of rapid stimulation and subjected to microarray analysis. Data were normalized using Robust Multichip Analysis (RMA), and genes exhibiting significant differential expression were identified using the Significance Analysis of Microarrays (SAM) method. Using this approach, 919 genes were identified that were significantly altered with rapid stimulation (763 up-regulated and 156 down-regulated). For many individual transcripts, changes typical of AF/AT were observed, with marked up-regulation of genes encoding BNP and ANP precursors, heat shock proteins, and MAP kinases, while novel signaling pathways and molecules were also identified. Both stress and survival response were evident, as well as up-regulation of multiple transcription factors. Genes were also functionally classified based on cellular component, biologic process, and molecular function using the Gene Ontology database to permit direct comparison of our data with other gene sets regulated in human AF and experimental AT. For broad categories of genes grouped by functional classification, there was striking conservation between rapidly stimulated HL-1 cells and AF/AT. Results were confirmed using real-time quantitative RT-PCR on 13 genes selected by physiological relevance in AF/AT and regulation in the microarray analysis (up, down, and nonregulated). Rapidly-stimulated atrial myocytes provide a complementary experimental paradigm to explore the initial cellular signals in AT remodeling to identify novel targets in the treatment of AF.
Keywords: stimulated atrial myocytes human atrial fibrillation

overall_design: HL-1 cell expression profile in vitro with and without rapid electric stimulation


title: Npas4-regulated genes in mouse hippocampal neurons

summary:
we performed a  DNA microarray experiment to identify activity-regulated genes that are misregulated in the absence of Npas4.
Keywords: Primary neuron culture, depolarization, activity-dependent, Npas4

overall_design: We infected mouse hippocampal neurons with lentivirus expressing Npas4-RNAi or control-RNAi @ 3 DIV and depolarized the neurons @ 8 DIV with 50 mM of KCl for 0, 1, 3 or 6 hours. Neurons were lysed, mRNA isolated and hybridized to Affymetrix arrays. Data were collected from 3 independent experiments.

first: Michael

last: Greenberg


title: Murine postpartum testis developmental time course (0 to 35 day)

status: Public on Sep 18 2008

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

summary:
Murine testis developmental time course created from tissue samples collected from birth through adulthood and hybridized to M430_2 chips in duplicate.

Keywords: time-course

overall_design: Time course of gene expression in the murine postpartum testis development (duplicates in day 0, 3, 6, 8, 10, 14, 18, 20, 30, 35). Total 20 samples.

last: Griswold

first: Christopher

middle: L

last: Small

first: James

last: Shima


title: Characteristic Transcriptional Profiling of Rhythmic mRNA Expression in the Murine Distal Colon

status: Public on Sep 15 2008

city: Ann Arbor

first: Willemijntje

middle: A

last: Hoogerwerf

state: MI

address: 2215 Fuller Road

department: Internal Medicine

institute: VA Ann Arbor Healthcare System (111D)

summary:
To identify a cohort of rhythmically expressed genes in the murine Distal Colon,microarrays were used to measure gene expression over a 24-hour light/dark cycle.The rhythmic transcripts were classified according to expression patterns, functions and association with physiological and pathophysiological processes of the colon including motility, colorectal cancer formation and inflammatory bowel disease.
Keywords: time series

overall_design: Mice were maintained for 2 weeks on a 12 hour light/dark (LD) cycle (lights on 7 AM, lights off 7 PM) prior to all experiments. For the reference experiment, mice had ad libitum access to food. Samples were collected every four hours, at 0400, 0800, 1200, 1600, 2000 and 2400, starting 1 hour after the lights went on.  Total RNA was isolated by modified guanidinium thicyanate-phenol-chloroform extraction method and was treated with DNase I (Promega, Madison, WI) at 37 oC for 30 minutes.Hybridizations and Scaning were done as per Affymetrix techniques. Three MOE 430 plus 2.0 chips were used per time point.

first: Mala

last: Sinha