title: Microarray Analysis of Retinal Gene Expression in the DBA/2J Model of Glaucoma

status: Public on Nov 04 2005

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

address: 20 South, 2030 East Rm. 320 BPRB

department: Neurobiology & Anatomy

institute: University of Utah

summary:
Purpose: The DBA/2J mouse is a model for secondary angle-closure glaucoma due to iris atrophy and pigment dispersion, which ultimately leads to increased intraocular pressure (IOP). We sought to correlate changes in retinal gene expression with glaucoma-like pathology by performing microarray analysis of retinal RNA from DBA/2J mice at 3 months before disease onset, and at 8 months, after IOP elevation. Methods: IOP was monitored monthly in DBA/2J animals by Tono-Pen and animals with normal (3 months) or elevated IOP (8 months) were identified. RNA was prepared from 3 individual retinas at each age, and the RNA was amplified and used to generate biotin-labeled probe for high density mouse Affymetrix arrays (U430.2). A subset of genes was selected for confirmation by quantitative RT-PCR using independent retina samples from DBA/2J animals at 3, 5 and 8 months of age, and compared to retinas from C57BL/6J control animals at 3 and 8 months. Results: There were changes in expression of 68 genes, with 32 genes increasing and 36 genes decreasing at 8 months versus 3 months. Upregulated genes were associated with immune response, glial activation, signaling and gene expression, while down-regulated genes included multiple crystallin genes. Significant changes in 9 upregulated genes and 2 downregulated genes were confirmed by quantitative RT-PCR, with some showing changes in expression by 5 months. Conclusions: DBA/2J retina shows evidence for glial activation and an immune-related response following IOP elevation, similar to what has been reported following acute elevation of IOP in other models.
Keywords: retina, glaucoma, DBA/2J, elevated intraocular pressure

first: Michael

last: Steele

first: Denise

last: Inman

first: David

middle: J

last: Calkins

first: Philip

last: Horner


title: The Oct4 and Nanog transcription network that regulates pluripotency in mouse embryonic stem cells

status: Public on Feb 08 2006

city: Singapore

first: Huck Hui

last: Ng

state: Singapore

address: 60 Biopolis street, #02-01 Genome

department: Cell and Medical Biology

country: Singapore

institute: Genome Institute of Singapore

summary:
A) We profiled gene expression changes during ES cell differentiation

B) We profiled gene expression changes when Pou5f1 or Nanog is knockdown upon RNAi
Keywords: Array Based

overall_design:
A) Mouse ES cells were induced to differentiate by 3 different chemical treatments. The RNAs were hybridized onto custom-made microarrays.

B) We used siRNA to knockdown Pou5f1 or Nanog in mouse ES cells. The RNAs from control and knockdown cells were hybridized onto Affymetrix Mouse Genome 430 2.0 microarrays

first: Yuin-Han

last: Loh

first: Qiang

last: Wu

first: Joon-Lin

last: Chew

first: Vinsensius

middle: B

last: Vega

first: Weiwei

last: Chang

first: Xi

last: Chen

first: Guillaume

last: Bourque

first: Joshy

last: George

first: Bernard

last: Leong

first: Jun

last: Liu

first: Kee-Yew

last: Wong

first: Ken

middle: W

last: Sung

first: Charlie

middle: H

last: Lee

first: Xiao-Dong

last: Zhao

first: Kuo-Ping

last: Chiu

first: Leonard

last: Lipovich

first: Vladimir

middle: A

last: Kuznetsov

first: Paul

last: Robson

first: Lawrence

last: Stanton

first: Chia-Lin

last: Wei

first: Yijun

last: Ruan

first: Bing

last: Lim

first: Huck-Hui


title: Skeletal muscle allotypes

status: Public on Sep 27 2005

city: Cleveland

first: Henry

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

country: USA

institute: Case Western Reserve University

summary:
Expression profiling of 8 skeletal muscles from adult C57BL mice.  Extraocular, temporalis, anterior digastric, sternocleidomastoid, triceps, diaphragm, quadraceps femoris (vastus lateralis), and tibialis anterior were evaluated using Affymetrix 430 v.2 arrays.
Keywords: parallel sample


title: Gene expression in MEFs in response to treatment with dipyridyl and trichostatin A

status: Public on Oct 24 2005

city: Memphis

middle: K.

last: Brindle

state: TN

address: 332 N Lauderdale

department: Biochemistry

institute: St Jude Children's Research Hospital

summary:
The CH1 protein interaction domain of the transcriptional coactivators p300 and CBP is thought to interact with HIF-1alpha and this interaction is thought to be critical to the expression of HIF-1alpha target genes in response to hypoxia. Trichostatin A (TSA), an inhibitor of histone deacetylases, has been reported to repress the expression of HIF-1alpha target genes.  To test the requirement of the CH1 domain and TSA for gene expression in response to dipyridyl (a hypoxia mimetic), primary mouse embryonic fibroblasts (MEFs) were generated from C57Bl/6x129/Sv F2 e14.5 embryos that contain a deletion in the CH1 domain of three of four alleles of CBP and p300. The remaining allele of p300 or CBP was a conditional knock out allele. Control MEFs with only a single conditional knockout allele of p300 or CBP were also generated. At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated with ethanol vehicle  or 100ng/ml TSA with 5% carbon dioxide at 37 C in a humid chamber for 30 min., followed by ethanol vehicle or 100 umdipyridyl (DP) for an additional 3hrs.  Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Keywords: genetic modification, dose response

overall_design: 16 samples; 4 genotypes [CBP+/flox (flox1), p300 +/flox (flox2), CBP CH1/flox;p300 CH1/CH1 (triCH1flox1),CBP CH1/CH1;p300 CH1/flox (triCH1flox2)] , 4 treatments (EtOH, TSA, dipyridyl (DP) and TSA+DP).

first: Lawryn

last: Kasper

first: Fayçal

last: Boussouar

first: Kelli

last: Boyd

first: Wu

last: Xu

first: Michelle

last: Biesen

first: Jerold

last: Rehg

first: Troy

last: Baudino

first: John

middle: L

last: Cleveland

middle: K


title: Ezh2 deficient T-cell

status: Public on Sep 01 2005

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
Lymph node T cells isolated from Ezh2fl/fl or Ezh2 deficient mice
Keywords: repeat sample

first: I-hsin

last: Su

first: Alexander

last: Tarakhovsky


title: Aging Liver Profiles of the Long Lived Prop-1 Mutant Mouse (Ames) and Wild Type Controls

status: Public on Aug 18 2005

city: Galveston

first: James

last: DeFord

state: TX

address: 301 University Blvd.

department: Human Biological Chemistry and Genetics

institute: University of Texas at Galveston

summary:
To compare and contrast genetic signatures from livers of young and aged Ames dwarf mice with their wild type controls.
Keywords: Time Course

overall_design: 25 micrograms of liver RNA was isolated from  young (5 dwarfs, 5 wildtype), middle aged (5 dwarfs, 5 wild type) and aged (5 dwarf, 6 wild type) mice for use in hybridization of Affymetrix gene chips according to Affymetrix protocols.

middle: M

last: Guigneaux

first: William

last: Boylston

last: Papaconstantinou


title: Burden-2R01NS036193-06A1

status: Public on Jul 06 2005

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
These experiments are designed to discover genes that are expressed selectively by synaptic nuclei in skeletal muscle with the particular goal of identifying genes that regulate motor axon growth and differentiation.
We plan to isolate RNA from the dissected synaptic region of skeletal muscle and from the non-synaptic region of skeletal muscle and to identify the genes that are expressed at higher levels in the synaptic than non-synaptic region.
Previously, we showed that motor axons fail to stop and differentiate in mice lacking MuSK, a receptor tyrosine kinase that is activated by motor neuron-derived Agrin.  We hypothesize that MuSK activation normally leads to the production of a retrograde stop/differentiation signal that is encoded by a gene that is expressed preferentially in synaptic nuclei.  In the absence of MuSK signaling, the retrograde signaling is not produced by synaptic nuclei, and consequently motor axons wander aimlessly over the muscle.
We obtain 6 to 8 micrograms of total RNA from the dissected synaptic or non-synaptic region from a single P21 mouse diaphragm muscle.  This is a standard procedure in the lab, and we have used these methods to analzye gene expression and to generate high-quality cDNA libraries.  Because the synaptic zone is narrower in the left hemi-diaphragm, we will isolate RNA from this half of the diaphragm.  In order to isolate sufficient RNA (5 micrograms from each sample), we will pool the synaptic and non-synaptic regions from two hemi-diaphragms.  In order to reduce experimental variability, we wish to analzye expression in six samples: three samples of synaptic RNA and three samples of non-synaptic RNA. We will ship the isolated RNA samples to the Consortium in order to generate labeled cDNA, to screen Affymetrix mouse oligo arrays and to assist in the analysis. Several genes, including the subunits of the acetylcholine receptor, MuSK, acetylcholinesterase, and utrophin are known to be expressed preferentially in synaptic nuclei; thus, these genes serve as internal controls for the reliability and effectiveness of the screen.  Most other genes, several of which we have analyzed in previous studies, including actin, GAPDH, runx1, nogoC, creatine kinase, etc. are expressed uniformly in skeletal muscle; thus, expression of these genes should be equally represented in synaptic and non-synaptic regions.
Keywords: other

overall_design: as above

first: S

last: Burden


title: Gene inductions in response to BCR-crosslinking in TAK1-deficient B cell

status: Public on Aug 11 2005

city: Suita

first: Shizuo

last: Akira

state: Osaka

address: 3-1, Yamada-oka

department: Host Defense

country: Japan

institute: Research Institute for Microbial Diseases Osaka University

summary:
BCR-induced gene expression profile in wild-type and B cell-specific TAK1-deficient B cells; to elucidate how TAK1 regulates BCR-mediated proliferative response
Keywords: ordered

overall_design: Purified splenic B cells (CD43 negative) were treated with or without anti-IgM (20 micloG/mL) for 4 h. Total RNA was extracted with an RNeasy kit (Qiagen), double-stranded DNA was synthesized from 10 micloG of total RNA with the SuperScript Choice System (Invitrogen) primed with T7-(dT) 24 primer. These cDNAs were used to prepare biotin-labeled cRNA by an in vitro transcription reaction performed using T7 RNA polymerase in the presence of biotinylated-ribonucleotides, according to the manufacturer’s protocol (Enzo Diagnostics). The cRNA product was purified using an RNeasy kit, fragmented, and hybridized to Affymetrix mouse expression array A430.2 microarray chips, according to the manufacturer’s protocol (Affymetrix). The hybridized chips were stained, washed, and scanned with a GeneArray Scanner (Affymetrix).

first: Shintaro

last: Sato


title: Targets of FGFR2-IIIb signalling in the hair follicle

status: Public on Jul 20 2005

city: Freiburg

first: Thomas

last: Schlake

country: Germany

institute: Max-Planck-Institute of Immunobiology

summary:
rationale: comparison of gene expression profiles in wildtype and Foxn1::dnFGFR2-IIIb transgenic hair follicles; identification of targets that mediate the effects seen in transgenic hair follicles
results: as already suggested by the phenotype, the molecular abnormalities appear to be restricted to the hair shaft medulla; Igfbp5 is an important mediator of transgene-dependent effects
Keywords: ordered


title: Exaggerated neuroinflammation and sickness behavior in aged mice after activation of the peripheral innate immune system

status: Public on Sep 12 2005

city: Urbana

first: Rodney

middle: W.

last: Johnson

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: Univ of Illinois in Urbana

summary:
Acute cognitive impairment (i.e., delirium) is common in elderly emergency department patients and frequently results from infections that are unrelated to the central nervous system. Since
activation of the peripheral innate immune system induces brain microglia to produce inflammatory cytokines that are responsible for behavioral deficits, we investigated if aging exacerbated neuroinflammation and sickness behavior after peripheral injection of
lipopolysaccharide (LPS). Microarray analysis revealed a transcriptional profile indicating the presence of primed or activated microglia and increased inflammation in the aged brain.
Furthermore, aged mice had a unique gene expression profile in the brain after an intraperitoneal injection of LPS, and the LPS-induced elevation in the brain inflammatory cytokines and oxidative stress was both exaggerated and prolonged compared with adults. Aged mice were anorectic longer and lost more weight than adults after peripheral LPS administration. Moreover, reductions in both locomotor and social behavior remained 24 h later in aged mice, when adults had fully recovered, and the exaggerated neuroinflammatory response in aged mice was not reliably paralleled by increased circulating cytokines in the periphery. Taken together, these data
establish that activation of the peripheral innate immune system leads to exacerbated neuroinflammation in the aged as compared with adult mice. This dysregulated link between the
peripheral and central innate immune system is likely to be involved in the severe behavioral deficits that frequently occur in older adults with systemic infections.
Keywords: Aging, cytokines, brain, inflammation, behavior

overall_design: In this study, adult and aged mice were injected intraperitoneal with sterile saline or Escherichia coli LPS (0.33 mg/kg, ~10 µg/mouse; serotype 0127:B8, Sigma). This dosage of LPS was used because it induces a mild transient sickness behavior in young adults. Mice were killed 4 h after saline or LPS injection by CO2 asphyxiation. Blood samples were collected and brains were removed, separated in half at the longitudinal fissure, frozen in liquid nitrogen, and stored (-80°C) until assaying. Total RNA was later isolated from some brain samples for microarray analysis (n=3).

first: Johnathan

middle: P

last: Godbout

first: Jing

last: Chen

first: Jayne

last: Abraham

first: Amy

middle: F

last: Richwine

first: Brian

last: Berg

first: Keith

last: Kelley


title: Expression profiling of GATA-1 wild type and mutant fetal megakaryocytes

status: Public on May 14 2005

city: Boston

first: Zhe

last: Li

state: MA

department: Division of Hematology/Oncology

institute: Children's Hospital Boston

summary:
Background:
Children with Down syndrome (DS) are predisposed to acute megakaryoblastic leukemia (AMKL, or AML M7) and a related myeloid disorder, referred to as transient myeloproliferative disorder (TMD), or transient leukemia (TL). Recently, acquired mutations in the erythroid/megakaryocytic lineage-specific transcription factor GATA-1 have been identified in megakaryoblasts from virtually all DS patients with AMKL (DS-AMKL), as well as in nearly all DS neonates with TMD. These mutations prevent synthesis of full-length GATA-1, but lead to synthesis of a truncated GATA-1 protein (GATA-1s) that lacks the N-terminal transactivation domain.
To determine the in vivo requirement of GATA-1 N-terminal domain in hematopoiesis and to model DS megakaryocytic leukemia initiated by GATA-1 mutation, we generated a GATA-1 knockin allele with a truncation at this domain (GATA-1deltaN). ES cells bearing this mutant allele generated a unique type of large Thrombopoietin (Tpo)-dependent megakaryocytes-containing colonies, when differentiated in vitro. Fetal livers from mice carrying this mutant allele contained elevated numbers of CD41+ cells throughout embryonic development, especially during mid-gestation. In in vitro hematopoietic colony assays, mutant cells from yolk sacs and mid-gestation fetal livers gave rise to a large number of macroscopic hyperproliferative megakaryocytic colonies (CFU-MKs). Consistent with that, when mutant fetal liver progenitors were cultured in liquid medium in the presence of Tpo, the derived megakaryocytes displayed marked hyperproliferation and grew for longer period of time than WTs.

Specific aims:
To understand the molecular basis for the megakaryocytic hyperproliferation phenotype of the GATA-1deltaN mutants, we plan to profile gene expression patterns of fetal liver-derived primary megakaryocytes and megakaryocytic progenitors from the GATA-1deltaN mutants and compare them with WTs, as well as GATA-1deltaNeodeltaHS mutants (GATA-1– megakaryocytes).

Experimental design:
E12.5 fetal livers were harvested from either GATA-1 WT and mutant embryos. Single cell suspensions were made from these livers and the cells were cultured in liquid medium in the presence of Tpo for 3 days. On day 3, primary megakaryocytes were enriched by a BSA gradient, and further enriched by anti-CD41 antibody and magnetic microbeads. Megakaryocytic progenitors were collected by FACS sorting for small cells in the same culture that express low level of CD41. Total RNAs were then prepared from these two populations and submitted for microarray profiling.

Conclusions:
When examining genes that are normally upregulated upon megakaryocyte differentiation (many of this class are megakaryocyte-specific genes), we found in GATA-1deltaN megakaryocytes, the majority of these genes are upregulated, although not to the full extent as seen in WTs. In contrast, this class of genes is largely not upregulated in GATA-1deltaNeodeltaHS megakaryocytes, which are blocked at an immature stage of differentiation. Genes that are downregulated during megakaryocyte differentiation include those that are normally repressed by GATA-1. Among genes that are not properly downregulated in GATA-1deltaN megakaryocytes, five transcription factors (Myc, Myb, GATA-2, PU.1, Ikaros) are of particular interest. Inadequate GATA-1s-mediated repression of transcription factors required for proliferation of hematopoietic progenitors (Myc, Myb and GATA-2) and for specifying lineage choices other than megakaryocyte/erythrocyte (PU.1 and Ikaros) may contribute to hyperproliferation of GATA-1deltaN megakaryocytes.

Keywords = GATA-1
Keywords = megakaryocyte
Keywords = mouse model
Keywords: other

first: Stuart

last: Orkin


title: Transcriptional Profiling of the Metanephric Kidney

status: Public on Jul 01 2005

city: Berlin

first: Kai

middle: Martin

last: Schmidt-Ott

address: Robert-Roessle-Str. 10

department: Differentiation and Regeneration of Kidney Epithelia

institute: Max-Delbrueck Center for Molecular Medicine

summary:
In this study we identify molecules with highly restricted expression patterns during the initial stages of metanephric development, when the ureteric bud has entered the metanephric mesenchyme and initiated branching morphogenesis. Using the Affymetrix Mouse Genome 430 2.0 Array, we compare gene expression patterns in ureteric bud tips, stalks and metanephric mesenchymes from mouse E12.5 embryos. To identify conserved molecular pathways, we also analyze transcriptional profiles in rat E13.5 ureteric buds and metanephric mesenchymes using the Affymetrix Rat Genome U34 Set. Taken together, these data sets help to identify conserved and highly localized transcripts in the metanephric kidney.
Keywords = Mus musculus
Keywords = Rattus norvegicus
Keywords = metanephric mesenchyme
Keywords = ureteric bud
Keywords = ureteric bud tips
Keywords = ureteric bud stalks
Keywords = molecular screen for spatially restricted transcripts
Keywords: other

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

first: Jun

last: Yang

first: Xia

first: Howard

last: Wang

first: Neal

last: Paragas

first: Kiyoshi

last: Mori

first: Jau-Yi

first: Mario

last: Schiffer

first: Erwin

last: Bottinger

first: Jonathan

last: Barasch


title: Aortae of 32 weeks old apoE mice

status: Public on May 04 2005

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

summary:
Aortae of 32 weeks old apoE mice versus wild type mice on a C57BL/6J Background.
Keywords = mouse aorta microarray
Keywords: other


title: Regulatory T cell lineage specification by Foxp3

status: Public on Mar 23 2005

city: Seattle

first: Jeffrey

last: Rasmussen

state: WA

department: Immunology

institute: University of Washington

summary:
Examination of CD4+ T cells from Foxp3-GFP knock-in mice. Aim is to understand the genetic program governed by Foxp3 in T cells by comparison of CD4 T cells subdivided into four groups based on expression of Foxp3 and CD25.
Keywords = regulatory T cells
Keywords = Foxp3
Keywords: repeat sample

first: Jason

middle: D

last: Fontenot

first: Luke

last: Williams

first: James

last: Dooley

first: Andy

middle: G

last: Farr

first: Alexander

middle: Y

last: Rudensky


title: Mouse preimplantation development

status: Public on Apr 01 2005

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary:
We examined expression profiles of genes that could be regulated by the MAPK pathways during mouse preimplantation development.  We used Affymetrix GeneChips for microarray analysis, and three independent experiments were carried out.  8-cell stage embryos were treated or untreated with MAPK inhibitors, and blastocyst stage embryos were recruited for the study.  Hybridization was carried out with the GeneChip Mouse Expression Set 430 or GeneChip Mouse Genome 430 2.0 Array following Affymetrix instructions.  The array was then washed and stained using the GeneChip fluidics station according to the manufacture's instructions.  Hybridized arrays were scanned using an Affymetrix GeneChip Scanner.  Expression analysis was performed using GeneChip Operating Software 1.0 (Affymetrix) and scaled to an average probe set intensity of 500.
Keywords: other

first: Momoko

last: Maekawa

first: Takuya

last: Yamamoto


title: Analysis of Germ Stem Cell loss in a murine model of ERM deficiency

city: St. Louis

first: Kenneth

last: Murphy

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary:
ERM knockout mice were produced.  Testis develop a Sertoli cell only
syndrome, which appears complete by 10 weeks of age in male ERM knockout mice.

Three sets of Affymetrix comparisons were made.
#1 and #2,  Wt or ERM knockout testis from 4 week old males, totaly RNA.
This time preceeds any significant histologic difference between the wt or
knockout.  The results was the finding that only a very specific set or
markers for spermatogonial STEM CELLs were found to be greatly reduced in the ERM knockout.

#3 and #4.  The sertoli cell line TM4 was transduced with a retroviral
ERM.  The wild type TM4 cell line was compared to this TM$-ERM cell line,
with the finding that only a few genes were increased in the TM4-ERM line.

#5, #6 and #7.  Primary Sertoli cells were purified from 4 week old wild
type or ERM knockout or from 10 week old ERM knockout mice and compared.
Keywords: other

first: C

last: Chen

first: K


title: DC response to ISD vs CpG

status: Public on Mar 01 2005

city: New Haven

first: Daniel

middle: B

last: Stetson

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

summary:
Bone marrow-derived dendritic cells were left untreated or stimulated with lipid-transfected double-stranded DNA or CpG oligonucleotides for four hours before harvesting.
Keywords: other

first: Ruslan

last: Medzhitov


title: Characterize CREB target genes in different tissue types

status: Public on Mar 02 2005

city: La Jolla

first: Xinmin

last: Zhang

state: CA

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

summary:
The CREB family of transcription factors stimulates cellular gene expression following phosphorylation at a conserved serine (Ser133 in CREB1) in response to cAMP and other extracellular signals. In order to characterize CREB target genes in various tissues, we give a cAMP agonist, forskolin (FSK), to cell lines or primary cultures and monitor the gene expression. To eliminate CREB-independent effects of FSK on cellular gene expression, we employed a dominant negative form of CREB called A-CREB, which dimerizes selectively with and blocks the DNA binding activity of CREB but not other bZIP family members. Therefore, genes that are induced by cAMP and the induction was blocked by A-CREB treatment likely represents CREB target genes.

Notes:
1) In HEK293T cells, besides the Control+FSK+(FSK-ACREB) experiments, a different set of experiments showing FSK effect on 1hr and 4hr is included. The two sets of data in HEK293T were generated at different times with different batch of cells, and comparison should be limited within each set. The cAMP induced genes at 1hr, however, was similar between the two sets.
2) These is no ACREB data for pancreatic islets or hepatocytes. For hepatocytes, however, we have included fasting liver and refed liver in additional to FSK treated primary hepatocytes. During fasting, glucagon induces cAMP increase in the liver and CREB is activated.  Therefore, a more reliable list of CREB target genes in hepatocytes can be obtained by selecting those genes are that induced both during fasting and in FSK treated primary culture.
Keywords: parallel sample

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: Gianluca

last: Canettieri

first: Michael

last: Conkright

first: John

last: Hogenesch

first: Marc

last: Montminy


title: heart/muscle-specific MnSOD-deficient mouse

status: Public on Feb 05 2005

city: Itabashi-ku

first: Takuji

last: Shirasawa

state: Tokyo

department: Molecular Gerontology

institute: Tokyo Metropolitan Institute of Gerontology

summary:
To investigate the pathological significance of excess oxidative stress in the heart, we generated heart/muscle-specific manganese superoxide dismutase (MnSOD) -deficient mice on a C57BL/6 background using the Cre-loxP system uder the control of the muscle reatin kinase (MCK) promoter. The mutant mice developed progressive congestive heart failure with dilated cardiomyopathy and physical disability and died with a median survival rate of 15.4 ± 4.0 weeks. The pathological changes in our model were compatible with human cardiac aging. To investigate the transcriptional alterations in the mutant heart, we carried out an Affymetrix microarray analysis for comparison between the mutant and normal heart at 16 weeks of age.
Keywords = Mn-SOD
Keywords = manganese superoxide dismutase
Keywords = knockout
Keywords = heart failure
Keywords = heart
Keywords = muscle
Keywords: parallel sample

first: Hidetoshi

last: Nojiri

first: Takahiko

last: Shimizu

first: Toshiaki

last: Tachibana

first: Hiroshi

last: Ishikawa

first: Yutaka

last: Ohta

first: Manabu

last: Sami

first: Hisashi

last: Kurosawa

first: Ronald

last: Kahn


title: Effect of knocking out SOCS3 in mouse ES cells

status: Public on Feb 02 2005

city: Parkville

first: Ken

last: Simpson

state: Victoria

address: 1G Royal Parade

department: Genetics and Bioinformatics

country: Australia

institute: The Walter and Eliza Hall Institute

summary:
Series contains four arrays - two wildtype, two null.  The experiment studied the effect of knocking out SOCS3 in mouse ES cells.
Keywords: other

first: Ariel

last: Forrai

first: Kristy

last: Boyle

first: Adam

last: Hart

first: Lynne

last: Hartley

first: Steven

last: Rakar

first: Tracy

last: Willson

first: Andrew

middle: W

last: Roberts

first: Warren

middle: S

last: Alexander

first: Anne

last: Voss

first: Lorraine

last: Robb


title: Gata-1 Knock Down - Wild Type Megakaryocyte Gene Expression

status: Public on May 06 2005

city: Chicago

first: John

last: Crispino

institute: The University of Chicago

summary:
Hematopoietic progenitor cells were isolated from 13.5 day mouse fetal livers by lineage depletion and expanded for three days. Fetal livers were isolated from both wild type and Gata-1 knock embryos. Gata-1 knock embryos contain a deletion of the Gata-1 promoter sequence that results in undetectable levels of Gata-1 protein specifically in the megakaryocyte lineage. Following progenitor outgrowth  megakaryocytes were enriched in a differentiation media for three days and isolated on a discontinuous BSA gradient. The resulting megakaryocytes were >90% pure as determined by acetylcholinesterase staining. These cells were lysed in Trizol and the resulting RNA was used for hybridization.
Keywords = Gata-1
Keywords = Megakaryocytes
Keywords: other

last: Muntean


title: Effect of aldosterone on gene expression in the heart

status: Public on Nov 01 2005

first: Alexander

last: Turchin

address: 221 Longwood Avenue

department: Division of Endocrinology

institute: Brigham and Women's Hospital

summary:
Aldosterone is known to have a number of direct adverse effects on the heart, including fibrosis and myocardial inflammation. However, genetic mechanisms of aldosterone action on the heart remain unclear.
This experiment investigated of temporal changes in gene expression profile of the whole heart induced by acute administration of a physiologic dose of aldosterone in the mouse. mRNA levels of 34,000 known mouse genes were measured at eight time points after aldosterone administration using oligonucleotide microarrays and compared to those of the control animals who underwent a sham injection. A novel software tool (CAGED) designed for analysis of temporal microarray experiments using a Bayesian approach was used to identify genes differentially expressed between the aldosterone-injected and control group.
CAGED analysis identified twelve genes as having significant differences in their temporal profiles between aldosterone-injected and control groups. All of these genes exhibited a decrease in expression level 1-3 hours after aldosterone injection followed by a brief rebound and a return to baseline. These findings were validated by quantitative RT-PCR. The differentially expressed genes included phosphatases, regulators of steroid biosynthesis, inactivators of reactive oxygen species, and structural proteins. Several of these genes are known to functionally mediate biochemical phenomena previously observed to be triggered by aldosterone administration, such as phosphorylation of ERK1/2. These results provide the first description of cardiac genetic response to aldosterone and identify several potential mediators of known biochemical sequelae of aldosterone administration in the heart.

Methods:
Male C57BL6 mice were injected with aldosterone 10 mcg/kg (experimental group) or vehicle (control group) at time 0. Five animals were sacrificed at each of the following time points in each group: 0, 0.5, 1, 2, 3, 4, 5, and 12 hours from injection. Hearts were removed and total RNA extracted from the hearts of all five animals at each time point / experimental condition was pooled for gene expression analysis.
Keywords: time series

overall_design: Time series of effect of aldosterone on gene expression in the mouse heart

first: Christine

middle: Z

last: Guo

first: Gail

last: Adler

first: Vincent

last: Ricchiuti

first: Isaac

last: Kohane

first: Gordon

middle: H

last: Williams


title: Neuroprotective effects of erythropoietin. Wilson-5R01NS028208-15

status: Public on Nov 24 2004

first: Winnie

last: Liang

summary:
Hypoxic-ischemic (HI) injury in the developing brain is a common cause of disability in children, and there are no effective treatments at this time. Erythropoietin (EPO) has recently gained interest as a neuroprotective drug, and EPO and its receptor are expressed within the central nervous system. We have recently shown that pretreatment with EPO markedly reduced brain injury caused by unilateral hypoxic-ischemic insult in 7 day old mice. EPO did not reduce early signs of neuronal injury at 6 hours, but significantly protected the neonatal brain when assessed 24 hours and 7 days after HI. The mechanism of this delayed protection is unclear, but is thought to involve transcription of neuroprotective genes, possibly subsequent to activation of NFkB.  By comparing gene expression in EPO- and vehicle- (VEH) treated mice after HI, we should gain insight into the mechanisms underlying the neuroprotective effects of EPO and may identify additional targets for therapeutic interventions.
We will compare gene expression patterns in 7-day old mouse forebrain after 1) VEH pretreatment plus sham surgery, 2) VEH pretreatment plus HI, and 3) EPO pretreatment plus HI.  We will thus identify genes induced by HI in the developing brain and characterize changes in gene expression caused by EPO pretreatment. We will use the model of neonatal hypoxic-ischemic injury and EPO treatment parameters that were used in our prior studies demonstrating neuroprotection. Based on the time-course of neuroprotection defined in our prior study and the pharmacokinetic profile of EPO, we will examine gene expression 18 hours after HI.
We hypothesize that changes in gene expression after EPO pretreatment underlie the neuroprotective effects of this cytokine after neonatal hypoxic ischemic injury.
We will examine gene expression in 3 groups:  1) 1) VEH pretreatment + sham surgery, 2) VEH pretreatment + HI, and 3) EPO pretreatment + HI.  EPO (5U/g, i.p.) or VEH was injected in 7 day old mice, drawn from 4 litters, with 3 to 4 pups per treatment group in each litter.  One hour later, the right common carotid artery was ligated under isoflurane anesthesia, animals were allowed to recover for 90 min and were then placed in hypoxic chambers (10% oxygen, balance nitrogen) for 50 min.  The animals subjected to sham surgery received isoflurane anesthesia for a comparable period, incision and dissection to visualize  the common carotid artery, but no ligation and no hypoxia.  Eighteen hrs later, animals were anesthetized with isoflurane and the right hemisphere was rapidly dissected and placed in RNA Later (Qiagen) at 4C.  Total RNA was isolated using an RNeasy lipid tissue mini kit (QIAzol lysis and RNeasy purification, Qiagen).  RNA concentrations were determined spectrophotometrically and an aliquot of each sample was examined by gel electrophoresis to screen for degradation.  Samples were stored at -80C.  After quality control screening, we selected 5 male and 5 female samples per treatment group (extra samples were reserved).  We plan to pool 1 male and 1 female for each microarray sample and we plan to run 5 microarrays from each treatment group, for a total of 15 microarrays.  We would like to have Agilent Bioanalyzer quality control assays on the individual samples carried out by the consortium before pooling. We will send 10 micrograms of each sample for Agilent QC and subsequent pooling of equimolar amounts.   We would like to use Affymetrix mouse gene chips (please advise which specific chips are available; are you using the GeneChip Mouse Expression array 430A or the GeneChip Mouse Genome 430 2.0 Array?).
Keywords: dose response

first: Mary Ann

last: Wilson


title: Identification of genes that are dysregulated in the telencephalon of Dlx1/2 mutants. Rubenstein-2R01MH049428-11

summary:
The Dlx homeodomain transcription factors are implicated in regulating the function of inhibitory neurons; therefore understanding their functions will provide insights into disorders such as epilepsy, mental retardation, autism and cerebral palsy.
Identify genes that are dysregulated in the telencephalon of Dlx1/2 mutants. I am sending separate samples of the Basal Ganglia (BG) and cortex (Ctx).
Comparing gene expression in the embryonic basal ganglia and cortex in wild type and dlx1/2 mutant mice will provide information regarding the types of genes that are downstream of Dlx1/2 function.
Perform gene array analyses in duplicate or triplicate; compare expression profile of total RNA from wild type and dlx1/2 telencephalons. I am sending separate samples of the Basal Ganglia (BG) and cortex. I want to perform gene expression comparison between: 1) wild type and dlx1/2 basal ganglia (BG) 2) wild typee and dlx1/2 cortex (ctx) Age of all mice has been indicated as 14 days to satisfy system requirements, however all mice are embryonic day 14.5.
Keywords: other

last: Rubenstein


title: Resistance to thyroid hormone (RTH) and PPARa activation

status: Public on Sep 26 2005

first: Norman

last: Buroker

address: 4800 Sand Point Way N.E.

institute: Seattle Children's Hospital

summary:
In this study we used the d337T TRb transgenic mouse that has been created to reproduce the human genetic disease known as resistance to thyroid hormone (RTH) as a model to determine if the d337T TRb mutation would have an effect on PPARa activation.  A single amino acid deletion (d337T)  abrogates thyroid hormone (T3) binding and transforms the thyroid hormone receptor (TRb) into a constitutive repressor.  The principle goal was to determine if T3 regulates myocardial energy metabolism through its nuclear receptors.  We introduced a known PPARa activator (WY14, 643) into control and d337T TRb transgenic mice then examined cardiac gene expression using Affymetrix 430_2  expression arrays and RT-PCR.  We compared the gene expression of  PPARa, RXRb and TRa,b and three PPARa target genes among four studies groups [control, control with WY14, 643, d337T TRb, and d337T TRb with WY14, 643] consisting of seven mice per group.  Microarray analysis revealed that these genes responded to the WY14, 643 treatments of control and d337T TRb mice.  Analysis of the array and RT-PCR data indicates that mRNA expression levels of PPARa and mRXRb decrease after a six hour drug treatment in both control and d337T TRb mice (P<0.01) as did the array mRNA expression levels for TRa & b (P<0.025).  Three target genes (AMPD3, PDK4 and UCP3) of PPARa were up regulated in control and down regulated in the d337T TRb transgenic mouse, indicating a direct action on these metabolic genes when the TRb becomes a repressor.   In conclusion, PPARa activation by WY14, 643 has a positive effect on control mice and a negative effect on the TRb transgenic mice which supports our hypothesis that T3 regulates myocardial energy metabolism through its nuclear receptors.
Keywords: treatment and deletion effects

overall_design: 7 control, 7 deletion strain individuals, 7 controls with a PPARalpha activator, 7 deletion strain individuals with a PPARalpha activator

middle: E

first: Martin

last: Young

first: Kyle

last: Serikawa

first: Ming

last: Ge

first: Xue-Han

last: Ning

first: Caimiao

last: Wei

first: Michael

last: Portman


title: Microarray Based Comparison of two Amplification Methods For Nanogram Amounts of Total RNA

status: Public on May 28 2004

city: Manhattan

first: Philine

last: Wangemann

state: KS

address: 1600 Dension Avenue

department: Anatomy and Physiology

institute: Kansas State University

summary:
Two T7 based methods One round of Amplification (Affymetrix) and Two round of Amplification were compared to two Ribo-SPIA based systems, RiboSPIA and pico Ribo SPIA systems. Data for One Round of amplification , Two round of amplification and RiboSPIA are listed here.
All Hybridisation were performed using Affymetrix Mouse 430-2 gene chips.  Data were all scaled to 500 and scaling factor average was 3.6 +/- 0.9, background intensities 46 +/- 5 , noise 2.9 +/- 0.6, rawQ 1.5 +/- 0.2
Keywords: other

first: Ruchira

last: Singh

first: Rajanikanth

middle: J

last: Maganti

first: Sairam

middle: V

last: Jabba


title: C57BL/6 Benchmark Set for Early Cardiac Development

status: Public on Jun 24 2004

city: Cambridge

first: Martina

last: Schinke

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

institute: Harvard University

summary:
Timed matings were performed using C57BL/6 mice and pregnant females sacrificed starting at embryonic day (E) 10.5, and then in daily intervals until E14.5.  Gene expression was be further analyzed at E16.5 and E18.5, to monitor changes in gene expression related to maturation of the heart.  At stage 10.5, the rostral and caudal parts of the embryo were removed and the middle part, which includes the heart, was subjected to expression analysis.  From embryonic day 11.5 on, we isolated embryonic hearts and separated the ventricular from the atrial chambers.

Keywords = heart
Keywords = development
Keywords = cardiac
Keywords: time-course

first: Patrick

last: Jay

first: Jeff

last: Brown

first: Seigo

last: Izumo


title: Strain-dependent effects of alcohol on early mouse embryos

status: Public on Mar 11 2004

city: Louisville

first: Thomas

last: Knudsen

state: KY

address: 501 S Preston St

department: Birth Defects Center

institute: University of Louisville

summary:
EXPERIMENT: Microarray expression profiles derived from the cranial neural folds (headfold) of neurulation-stage mouse embryos 3.0h after maternal alcohol exposure on 8 d.p.c.
ANIMAL MODEL: Pregnancies from 2 substrains of C57BL/6 mice that differ in relative risk of Fetal Alcohol Syndrome (FAS): C57BL/6J (B6J) high-risk condition, and C57BL/6NCrl (B6N) low-risk condition.
EXPOSURE: Dams dosed with ethanol (EtOH) by intraperitoneal injection at 2.9 g EtOH per kg body weight. Controls received vehicle (saline) alone. A third group of dams received EtOH + 4.0 mg/kg PK11195, a specific high-affinity ligand to the 18 KDa mitochondrial peripheral benzodiazepine receptor site.
INTERVAL: High blood alcohol content must be sustained in dams for several hours to invoke FAS and is traditionally accomplished by a double injection of EtOH 4.0h apart. Since these embryos were harvested for genetic analysis 1h before dams would have gotten the second alcohol injection, the interval represents a snapshot of the critical response, prior to the second maternal injection that invokes greater risk. Counter-exposure to PK11195 significantly lowers the adverse response of B6J embryos to EtOH.
PLATFORM: Two independent assays run. The first dataset (PE), run April 2002 – January 2003, used samples pooled from 2 litters (PE) and the platform was a two-channel MPS621 array (http://www.lifesciences.perkinelmer.com/). This platform has 4800 sequence-verified gene elements derived from over 50 different human cDNA libraries reflecting a variety of well-annotated cellular processes and disease pathways. The second dataset (AF), run between May 2005 – November 2005, used samples pooled from 1 litter and the platform was Affymetrix GeneChip® Mouse Genome 430A 2.0 Array (http://www.affymetrix.com/). The MG430A 2.0 platform has 45,102 oligonucleotide probe cells representing approximately 14,000 well-characterized genes in the draft mouse genome assembly. The corresponding GEO samples are GSM12218 - GSM12227 for the two-channel PE arrays, and GSM136067 - GSM136078 for the one-channel AF arrays.
Keywords = fetal alcohol syndrome
Keywords = alcohol-related birth defects
Keywords = EtOH
Keywords = PK11195
Keywords = embryo
Keywords = strain differences
Keywords: Ordered

overall_design: Assay of early mouse embryos during pathogenesis of Fetal Alcohol Syndrome (FAS). Replicate RNA samples were arrayed by one-channel oligonucleotide (Affymetrix) or two-channel cDNA (Perkin-Elmer) platforms.

first: Kimberly

middle: R

last: Nemeth

first: Amar

first: Maia

middle: L

last: Green


title: SCCOR_MouseLung_Simva_LPS

status: Public on Oct 26 2004

city: Baltimore

first: Shwu-Fan

last: Ma

state: MD

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins University

summary:
This series contain mouse lung samples treated with Simvastatin and LPS and corresponded controls.
Keywords: other

first: Jeffrey

last: Jacobson

first: Joseph

last: Barnard

first: Dmitry

last: Grigoryev

first: Joe

middle: G. N.

last: Garcia


title: Rosenfeld-5R01NS034934-14

status: Public on Jul 06 2005

city: Phoenix

first: Winnie

last: Liang

institute: Translational Genomics

summary:
Using targeted gene deletion, we have firmly established that the Class IV POU domain transcription factor Brn-3.2 controls a developmental program regulating axon pathfinding in the mouse visual system. We have isolated and identified downstream gene targets of Brn-3.2, using Representational Difference Analysis (RDA), on cDNA populations derived from wildtype and Brn-3.2-/- retina at the appropriate embryonic stage. One of these candidate genes, the Homeodomain Interacting Protein Kinase 2 (HIPK2), is postulated to be a transcriptional coregulator, based on its in vitro interactions with repressor homeodomain proteins of the NK class, as well as other components of repressor complexes. HIPK2 has also been shown to be involved in post-translational modification of two major transcriptional regulators, p53 and CtBP. Expression of a dominant-negative form of HIPK2 in sensory neurons affects the innervation patterns of their target tissues, suggesting an axon pathfinding defect.
The aim of this project is to identify targets for the Homeodomain Interacting Protein Kinase 2 (HIPK2), that we isolated as a downstream gene target of the class IV POU domain transcription factor Brn-3.2, and to investigate their function in the Brn-3.2 dependent pathway regulating axon pathfinding.
We hypothesize that the genes regulated by HIPK2 will play a critical role in axon pathfinding and that the results of this study will provide novel insights into the molecular mechanisms of axon pathfinding, and possibly neural plasticity and regeneration, and therefore, be of great interest to the field of neurobiology in general.
In order to uncover potential biological role(s) of HIPK2 in neural development, and particularly axon pathfinding, we generated transgenic mouse models for in vivo studies. Our preliminary observations in transgenic mice, indicate that a form of the molecule expected to act as a dominant-negative and designed to be expressed in sensory neurons, affects the innervation patterns of their target tissues, suggesting an axon pathfinding defect. We plan to take advantage of this model to identify genes regulated by HIPK2, and which are likely to be involved in axon pathfinding. To this end, we will compare gene expression profiles in sensory neurons isolated wild-type and transgenic mice. In our experimental paradigm, the trigeminal ganglion represents the ideal sensory structure in which to perform such an analysis: 1) High levels of transgene can be expressed in the trigeminal ganglion, as assessed by the expression of LacZ from the bicistronic construct which contains IRES-LacZ downstream of a dominant negative form of HIPK2.  2) The trigeminal ganglion can be dissected at embryonic day 13.5, when the phenotype is apparent, with ease and free of contamination from surrounding tissues.  3) The amounts of RNA that can be isolated from a single ganglion are in the range of 200-300 ng, which should be sufficient for microarray analysis following linear amplification of RNA. One series will be carried out with transgenic embryos and a control series will be carried out with wildtype littermates. Animals will be prepared and sacrificed by a standard protocol. Tissue will be rapidly dissected from E13.5 trigeminal ganglion, frozen in liquid nitrogen, and stored at -80C until RNA is extracted. RNA will be prepared using RNeasy Micro Kit. We will be providing 4 tissue samples for each of the wildtype and transgenic animals to mitigate any expression differences resulting from mouse to mouse variation.
Keywords: other

first: M

last: Rosenfeld


title: NHGRI_Melanoma_class

status: Public on Jan 22 2001

city: Bethesda

first: Michael

last: Bittner

department: Cancer Genetics Branch

institute: NHGRI, NIH

summary:
This series represents a group of cutaneous malignant melanomas and unrelated controls which were clustered based on correlation coefficients calculated through a comparison of gene expression
profiles.
Keywords: other


title: Microarray Based Comparison of three Amplification Methods For Nanogram Amounts of Total RNA

status: Public on Dec 21 2004

first: Philine

last: Wangemann

summary:
Two T7 based methods One round of Amplification (Affymetrix) and Two round of Amplification were compared to two Ribo-SPIA based systems, RiboSPIA and pico Ribo SPIA systems. Data for Pico-RiboSPIA are listed here.
All Hybridisation were performed using Affymetrix Mouse 430-2 gene chips.  Data were all scaled to 500.
For 12 chips performed with pico Ribo SPIA the scaling factor average was 2.0 +/- 0.3, background intensities 74.4 +/- 12.7 , noise 3.9 +/- 0.6, rawQ 2.5 +/- 0.3
Keywords: ordered

first: Ruchira

last: Singh

first: Rajanikanth

last: Maganti

first: Sairam

first: Martin

last: Wang

first: Glenn

last: Deng

first: Joe Don

last: Heath

first: Nurith

last: Kurn


title: Myocilin effect on retina. Russell-7U24NS043571-02

status: Public on Oct 14 2004

summary:
Glaucoma is a neurodegenerative disease in which vision is lost as a result of the apoptosis of retinal ganglion cells. When the trabecular meshwork cells,  that regulate aqueous humor outflow, are stressed as they are in some forms of glaucoma, they considerably up-regulated secretion of a protein called myocilin into the aqueous. The function of this protein is unclear; but since some aqueous humor flows to the posterior of the eye, the effects of myocilin will also be felt by the retinal cells. We have a transgenic mouse that secretes large amounts of myocilin into aqueous humor. In these mice, there is a deposition of myocilin on membranes of certain cells suggesting myocilin might have some signaling functions. This signaling function could explain why stresses that increase intraocular pressures can increase the likelihood for glaucoma, cause the myocilin to be secreted at very high levels by the trabecular meshwork. Myocilin may be important in treating glaucoma.
This experiment will determine if myocilin is altering gene expression in the retina. The results should show variations in expression levels and will give us some indication of the pathways that are important to preserve retinal ganglion cells after a diagnosis of glaucoma.
Our hypothesis is that myocilin is acting like a signaling protein in the eye. It acts not only in the anterior segment but also in retina as a result of the flow of some aqueous to the back of the eye. This signaling function is protective to certain ocular cells. This function of myocilin may influence cells in the retina and may counter the apoptotic signals in the retinal ganglion cells that occur during glaucoma.
Retinas from transgenic mice and from mice of the same strain that do not have the transgene will be dissected. The mice will be three weeks of age. Because of the small size of the retina, samples will be pooled to obtain the RNA necessary to run the microarray. Three control and three transgenic samples will be run and compared with each other. We have data indicating that myocilin is at high levels in the aqueous humor of the transgenic animals.
Keywords: dose response

first: Paul

last: Russell