title: Microarray analysis of mouse ear tissue exposed to bis-(2-chloroethyl) sulfide

status: Public on Dec 22 2005

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

summary:
Sulfur mustard (SM) is a potent alkylating agent. We are developing medical countermeasures to reduce the injury caused by SM exposure. Screening in the mouse ear vesicant model has identified three effective compounds: dimercaprol (British anti-lewisite), indomethacin, and octyl homovanillamide (OHV). To identify gene expression changes that correlate with compound efficacy we used oligonucleotide microarrays to compare gene expression profiles in vehicle-exposed skin, SM-exposed skin, and skin pretreated with each compound before SM exposure. Mice were topically exposed on the inner surface of the right ear to SM alone or pretreated for 15 min with one of the compounds and then exposed to SM. Left ears were vehicle-exposed. Ear tissue was harvested 24 hr later for ear weight determination (an endpoint indicating compound efficacy). The exposure groups were: methylene chloride (sulfur mustard vehicle); ethanol (drug vehicle); 0.08 mg sulfur mustard; 6.25 mg dimercaprol 15 min before 0.08 mg sulfur mustard; 1.34 mg indomethacin 15 min before 0.08 mg sulfur mustard; 0.6 mg octylhomovanillamide 15 min before 0.08 mg sulfur mustard; 6.25 mg dimercaprol alone; 1.34 mg indomethacin alone; 0.6 mg octylhomovanillamide alone.  RNA was extracted from the tissues and used to generate oligonucleotide microarray probes. Principal component analysis of the gene expression data revealed partitioning of the samples based on drug treatment and SM exposure. Vehicle-exposed mouse ears clustered away from the other treatment groups. SM-exposed mouse ears pretreated with dimercaprol or OHV clustered more closely with vehicle-exposed ears, while SM-exposed mouse ears pretreated with indomethacin clustered more closely with SM-exposed ears. This clustering of the samples is supported by the ear weight data, in which the indomethacin group has ear weights closer to the SM-exposed group, whereas the dimercaprol and OHV groups have ear weights closer to the vehicle-exposed group.  Correlation coefficients were calculated for each gene based on the correlation between gene expression level and ear weight. These data provide the basis for understanding what gene expression changes are important in the development of effective SM medical countermeasures.
Keywords: ordered

overall_design: Exposure of mouse ears to sulfur mustard alone, sulfur mustard preceded by drug treatment, or vehicle compounds.  Naïve controls were also included.  Biological replicates of at least n=3 were examined for each exposure condition.

first: J

first: A

middle: I

last: Hege

first: C

last: Phillips

first: L

middle: D

last: Orzolek

last: Sylvester

last: Bossone

last: Henemyre-Harris

first: R

middle: C

last: Kiser

first: Y

last: Choi

last: Schlager

last: Sabourin


title: Global and gene-specific analyses show distinct roles for Myod and Myog at a common set of promoters

status: Public on Mar 01 2006

city: Seatttle

first: Yi

last: Cao

state: WA

address: 1100 Fairview Ave. N

department: Human Biology

country: USA

institute: Fred Hutchinson CRC

summary:
We used a combination of genome-wide and promoter-specific DNA binding and expression analyses to assess the functional roles of Myod and Myog in regulating the program of skeletal muscle gene expression. Our findings indicate that Myod and Myog have distinct regulatory roles at a similar set of target genes. At genes expressed throughout the program of myogenic differentiation, Myod can bind and recruit histone acetyltransferases. At early targets, Myod is sufficient for near full expression; whereas, at late expressed genes Myod initiates regional histone modification but is not sufficient for gene expression. At these late genes, Myog does not bind efficiently without Myod, however, transcriptional activation requires the combined activity of Myod and Myog. Therefore, the role of Myog in mediating terminal differentiation is, in part, to enhance expression of a subset of genes previously initiated by Myod.
Keywords: Myod, Myogenin, muscle differentiation, regulatory network, gene expression

overall_design: Mouse embryonic fibroblasts isolated from Myod-/-Myf-/- mice were tranduced with either MDER or MDER+Myog. MDER was activated by the addition of beta-estradiol. Cells were induced to differentiate for various times, and triplate samples were collected from the indicated time points.

first: Stephen

middle: J

last: Tapscott


title: Mechanically stimulated fibroblast from different fetal mouse tissues using Affy MOE430 chip set

status: Public on Jan 01 2006

city: Sheffield

first: Steve

last: Winder

address: Western Bank

department: Department of Biomedical Science

country: United Kingdom

institute: University of Sheffield

summary:
In order to test the hypothesis that fibroblasts from different tissues are phenotypically distinct from one another, we have subjected tendon, skin and corneal fibroblasts of fetal mouse to mechanical stimulation by fluid flow and analyzed the transcriptional responses of the cells using Affymetrix MOE430 chip set containing two arrays MOE430A and MOE430B.
Keywords: cell type comparison, stress response

overall_design: The experiment is done using Affymetrix MOE430 chip set containing two arrays MOE430A - platform GPL339 and MOE430B - platform MOE340. Three biological replicates for tendon, skin and corneal fibroblasts subjected to mechanical stimulation as well as not stimulated (control) were analyzed yielding 18 samples per chip (36 in total).

first: Jennifer

middle: R

last: Mackley

last: Ando

first: Pawel

last: Herzyk


title: p107 knockout vs. wild type neurospheres

status: Public on Dec 09 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary:
The ganglionic eminence was dissected and neurospheres were cultured from the brain of E13.5 embroys. RNA was isolated from neurospheres cultured from p107-/- embryos and their wildtype littermates. P107 knockout mice have previously been shown to have an increased number of stem cells and enhanced stem cell self renewal. With the microarray experiment we are hoping to discover the genes involved in stem cell number and self renewal along with p107.
Keywords: other

overall_design: this experiment include 2 samples and 14 replicates


title: Gene Expression in Embryonic Stem Cells Grown in a Maintenance Serum vs. a Non-maintenance Serum

summary:
Two sets of RNA samples were generated from 3 days growth in different serum lots, lot 6999 and lot 6473. Lot 6999 has been pre-screened for embryonic stem cell maintenance and is routinely used for that purpose. Lot 6473 failed all tests for embryonic stem cell maintenance.
Keywords: other

overall_design: this experiment include 2 samples and 12 replicates


title: Putative muscle derived stem cells from mouse.

summary:
Comparison of NRA derived from SCA1+, CD45- MACS purified putative muscle derived stem cells vs. RNA derived from preplating of hind limb muscle cells.
Keywords: other

overall_design: this experiment include 2 samples and 8 replicates


title: Gene Expression Profiles of Undifferentiated and Differentiated Mammospheres

summary:
Mammary gland cells were isolated from 5-8 week old FVB mice and allowed to proliferate as undifferentiated mammospheres in the presence of growth factors (bFGF and EGF). Comparison of the gene expression profiles of undifferentiated mammospheres vs. mammospheres that were allowed to differentiate for 6 days by the removal of growth factors will help to identify genes that are implicated in the maintenance of the mammary gland stem cell compartment.
Keywords: other


title: Osteoblast differentiation time course

summary:
Differentiation Time Course; examination of osteoblast differentation by comparing cells exposed to growth factors with ctrl cells.
Keywords: other

overall_design: this experiment include 7 samples and 42 replicates


title: Effect of radiation on Oct-1 mutant and Wild Type Mouse strains

status: Public on Dec 08 2005

city: Berkely

first: Sanchita

last: Bhattacharya

state: CA

address: 1 Cyclotron Rd

institute: MIT

summary:
WT,WTR,MU and MUR replicates from Affymetrix GeneChip Mouse Expression Set 430 Arrays A and B
Keywords: strain comparison

first: Dean

last: Tantin

first: Caroline

last: Schild-Poulter

first: Caleb

last: Lee

first: Victoria

last: Wang

first: Naomi

last: Rosenberg

first: Robert

last: Hache

first: Phillip

middle: A

last: Sharp


title: Comparison of Hematopoietic Stem Cell, Mast Cell Precursor and Mature Mast Cell Gene Expression

summary:
We are interested in comparing expression patterns of hematopoletic stem cells, mast cell precursors and mature mast cells. Our group recently reported that murine mast cells express CD34, Sca-1 and c-kit. Microarray analysis may uncover other novel surface antigens useful in separating mast cells from stem cells.
Keywords: other


title: Gene Expression Comparison of First Passage vs. Primary Human and Mouse Retinal Sphere Cells

summary:
The pigmented portion of ciliary epithelium in the adult mammalian eye harbors mitotically quiescent retinal sphere cells, which are capable of self-renewal and differentiating into retinal neurons when assayed in vitro; however, very little is known about the molecular mechanism controlling the proliferation and differentiation of these adult retinal stem cells or their molecular resemblance to mutipotent stem/progenitor cells during early eye development. This experiment studies the gene expression of first passage and primary human and mouse retinal sphere cells.
Keywords: other

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: this experiment include 4 samples and 12 replicates


title: 11-Point Time Course Study of Differentiating J1 Embryoid Bodies

status: Public on Dec 06 2005

summary:
An 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Keywords: Time course

overall_design: this experiment include 11 samples and 66 replicates


title: Gene regulatory networks along the small intestinal crypt-villus axis

status: Public on Nov 29 2005

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary:
Genes encoding transcription factors function as hubs in gene regulatory networks because they encode DNA-binding proteins, which bind to promoters that carry their binding sites. In the present work we have studied gene regulatory networks defined by genes with transcripts belonging to different mRNA abundance classes in the small intestinal epithelial cell. The focus is the rewiring that occurs in transcription factor hubs in these networks during the differentiation of the small intestinal epithelial cell while it migrates along the crypt-villus axis and during its development from a fetal endodermal cell to a mature adult villus epithelial cell.
We have generated transcriptome data for mouse small intestinal villus, crypt and fetal intestinal epithelial cells. In addition we have generated metabolome data from crypt and villus cells.
Our results show that the intestinal crypt transcription factor hubs that are rewired during differentiation are involved in the cell cycle process (E2F, NF-Y) and stem cell maintenance (c-Myc). In contrast the villi are dominated by a HNF-4 villus hub, which is rewired during differentiation by the addition of network genes with relevance for lipoprotein synthesis and lipid absorption. Moreover, we have identified a villus NF-kB hub, which was revealed by comparison of the villus and endoderm transcriptomes. The rewiring of the NF-kB villus hub during intestinal development reflects transcriptional activity established by host and microflora interactions. To aid in the mining of our results we have developed a web portal (http://gastro.imbg.ku.dk/mousecv/) allowing easy linkage between the transcriptomic data, biological processes and functions.
Keywords: Cell type comparison

overall_design:
Four different sample categories were analyzed.

1) Small intestinal crypts isolated form 12-weeks old C57BL/6 mice. These samples are in triplicates.

2) Small intestinal villi isolated form 12-weeks old C57BL/6 mice. These samples are in triplicates.

3) Embryonic day 12 mesenchyme. These samples are in quadruplicate. each sample is derived from a pool of mesenchymes (10-40)

4) Embryonic day 12 endoderm. These samples are in quadruplicate. each sample is derived from a pool of endoderms (10-40)

first: Anders

last: Stegmann

first: Jesper

middle: T

last: Troelsen


title: Effects of caerulein on Mist1KO pancreas

status: Public on Nov 23 2005

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 800 Commissioners Rd. E

department: Physiology and Pharmacology/Peadiatrics

institute: The University of Western Ontario/CHRI

summary:
Mouse pancreas from wild type and MistKO animals were induced either with caerulein or saline as control and processed for RNA.  Targets from three biological replicates of each were generated and the expression profiles were determined using Affymetrix Mouse Expression chips 430.  Comparisons between the sample groups allow the identification of genes with differential expression patterns of genes which might contribute to pancreatitis.
Keywords: repeat

overall_design: 3 wild type saline, 3 wild type caerulein, 3 Mist1KO saline and 3 Mist1KO caerulein pancreata were used and biological replicates were analyzed

first: Agnes

last: Kowalik


title: MOE430A study of C57BL/6 brain

status: Public on Nov 28 2005

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
1 week and 8 week male and female brains from littermates of age matched C57BL/6 mice week used to study expression profiles. Affymetrix MOE430A Genechip was used
Keywords: other

first: Marcy

last: Kuentzel

first: Cheryl

last: Eifert

first: Tiffany

last: Devine

first: Paulette

last: McCormick


title: Mouse mammary cell types

status: Public on Dec 02 2005

first: Theodore

last: Perkins

summary:
Gene Expression Profiling of Murine Mammary Stem Cells and Differentiated Derivatives.
Keywords: other

overall_design: this experiment includes 3 samples and 18 replicates


title: ILS/ISS Cerebellum Comparison Affy430

city: Aurora

first: Erik

middle: James

last: MacLaren

state: CO

address: Mail Stop 8303, P.O. Box 6511

department: Pharmacology

institute: University of Colorado at Denver and Health Sciences Center

summary:
Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit a large difference in a number of alcohol and drug related behaviors.  This study examined the expression levels of transcripts in these strains in the cerebellum, which is a major target of ethanol’s actions in the CNS, in order to find differentially expressed candidate genes for these phenotypes. Cerebellum was specifically chosen due to the fact that Purkinje cell sensitivity to ethanol in these strains is highly correlated to "sleep time", the measure of ethanol sensitivity used with these strains. Naive mice were used because differences in sensitivity are observed upon initial exposure to ethanol.
Keywords: cerebellum, naive, untreated

overall_design: Expression was assayed using the Affymetrix Expression Set 430 A and B arrays. Four mice were included in the experiment, two ILS and two ISS.

first: Beth

last: Bennett

first: Thomas

middle: E

last: Johnson

first: James

middle: M

last: Sikela


title: Gene expression under normoxia/hypoxia in mouse embryonic fibroblasts with mutations in the CH1 domains of p300 and CBP

status: Public on Oct 24 2005

city: Memphis

first: Paul

middle: K.

last: Brindle

state: TN

address: 332 N Lauderdale

department: Biochemistry

institute: St Jude Children's Research Hospital

summary:
The CH1 (TAZ) domain of the transcriptional coactivators p300 and CBP has been reported to interact with the transcription factor HIF-1alpha and this interaction is thought to be critical for HIF-1alpha target gene expression in response to hypoxia.  To determine the requirement for the CH1 domain in hypoxia-responsive gene expression, primary mouse embryonic fibroblasts (MEFs) were generated from e14.5 C57B/6x129/Sv F2 embryos that were either wildtype or bore deletion mutations in the CH1 protein binding domains of both alleles of p300 and one allele of CBP (tri_CH1). Subconfluent MEFs were treated with 21% oxygen (normoxia) or 0.1% oxygen (hypoxia) with 5% carbon dioxide at 37 C in a humid chamber for 6hrs. At the start of treatment, medium was removed and replaced with medium (DMEM+10% FBS+pen-strep+ l-glu) that had been preequilibrated overnight in normoxia or hypoxia as appropriate. Immediately after treatment, cells were lysed in Trizol for RNA extraction.
Keywords: genetic modification, dose response

overall_design: 4 samples: two genotypes (1 control, 1 mutant); two treatments (normoxia, hypoxia).

first: Lawryn

middle: H

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

last: Cleveland

middle: K


title: Postnatal Development of Mouse Cochlear Nucleus

status: Public on Oct 15 2005

city: Seattle

first: Julie

last: Harris

department: Otolaryngology-HNS

institute: University of Washington

summary:
Developmental differences in gene expression in the postnatal mouse cochlear nucleus was analyzed at two or three ages using two different array platforms, the Affymetrix Mouse 430A GeneChip or the NIA 15K mouse cDNA microarray.  These ages, P7, P14, and P21 parallel a critical period of neuron survival dependent on input from the auditory nerve.
Keywords: parallel sample

overall_design: Comparison of baseline gene expression in the CN at P7, P14, and P21 using Affymetrix 430A chips or NIA 15K cDNA mouse array.  For Affy chips, 3 replicates were done at P7 and P21, 2 replicates at P14.  For NIA arrays, 5 replicates were done comparing P7 and P21.  There was one dye flip included.

first: Natalie

last: Hardie

first: Olivia

last: Bermingham-Mcdonogh

first: Edwin

middle: W

last: Rubel


title: 10 T1/2 Embryonic Fibroblasts

status: Public on Oct 07 2005

first: Theodore

last: Perkins

summary:
RNA isolates from 10 T1/2 fibroblasts used as baseline control representing gene expression in a terminally differentiated cell type.
Keywords: other

overall_design: this experiment include 1 samples and 6 replicates


title: Transcriptional activation of AhR pathway in keratinocytes

status: Public on Oct 01 2005

city: Tokyo

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

country: Japan

institute: The University of Tokyo

summary:
Occupational and environmental exposure to polycyclic aromatic hydrocarbons (PAHs) has been suggested to provoke inflammatory and/or allergic disorders including asthma, rhinitis and dermatitis.  The molecular mechanisms of this PAH-mediated inflammation remain to be clarified.  Previous studies implied the involvement of PAHs as irritants and allergens, with the reactive oxygen species generated from the oxygenated PAHs believed to be an exacerbating factor.  As well, the possibility exists that PAHs contribute to the pathogenesis through activation of aryl-hydrocarbon receptor (AhR)-mediated transcription, since PAHs are potent inducers of the AhR.  To address this point, we generated transgenic mouse lines expressing the constitutive active form of the AhR in keratinocytes.  In these lines of mice, the AhR activity was constitutively enhanced in the absence of ligands, so that any other direct effects of PAHs and their metabolites could be ignored.  At birth, these transgenic mice were normal, but severe skin lesions with itching developed postnatally.  The skin lesions were accompanied by inflammation and immunological imbalance and resembled typical atopic dermatitis.  Our present study demonstrates that constitutive activation of the AhR pathway causes inflammatory skin lesions and suggests a new mechanism for the exacerbation of inflammatory diseases following exposure to occupational and environmental xenobiotics.
Keywords: transcriptional activation

overall_design: transgenic mice expressing constitutive active form of AhR in keratinocytes vs. non-transgenic mice (wild type littermates)


title: Allograft versus isograft mouse heterotopic tracheal transplant grafts

status: Public on Oct 08 2005

city: Minneapolis

first: Jeff

last: Lande

state: MN

address: 420 Washington Avenue SE

department: Medicine

institute: University of Minnesota

summary:
Exploration of genes associated with acute and chronic rejection associated with obliterative airway disease
Keywords: other

overall_design: Untransplanted trachea (controls; n=5) and trachea transplanted into MHC compatible/incompatible recipients at day 4 (n = 5 compatible/5 incompatible), day 14 (n = 5/5) or day 25 (n = 5/5)

first: Jeffrey

first: Stacy

last: Dalheimer

first: Daniel

last: Mueller

first: Marshall

last: Hertz

first: Richard

last: King


title: Gene expression during oocyte development

status: Public on Sep 26 2005

city: Philadelphia

first: Hua

last: Pan

state: PA

address: 415 S University Avenue

department: Department of Biology

institute: University of Pennsylvania

summary:
oocytes were collected from ovary by follicle stage.  Targets from four biological replicates of each were generated and the expression profiles were determined using Affymetrix MOE430A and B.
Keywords: repeat

overall_design: 4  biological replicates were analyzed

first: Marilyn

last: O'Brien

first: Karen

last: Wigglesworth

last: Eppig

last: Schultz


title: Gene expression in the oocyte at primary follicle stage

status: Public on Sep 19 2005

summary:
oocytes were collected from ovarys of 6 day old female mice.  Targets from four biological replicates of each were generated and the expression profiles were determined using Affymetrix MOE430 A & B.
Keywords: repeat

overall_design: 4 oocyte at primary follicle stage biological replicates were analyzed

last: O’Brien


title: Molecular signatures in skin

status: Public on Sep 20 2005

city: New York

first: Michael

last: Rendl

address: 1428 Madison Avenue

institute: Mount Sinai School of Medicine

summary:
Hair follicle matrix, outer root sheath, dermal papilla cells and melanocytes and a dermal fraction enriched in fibroblasts were FACS isolated from 4d backskins.  Targets from two biological replicates of each were generated and the expression profiles were determined using Affymetrix Mouse Genechip 430A arrays.  Comparisons between the sample groups allow the identification of cell-type specific genes.
Keywords: cell type comparison

overall_design: Mx, ORS, DF, DP and Mc were FACSorted from Lef1-RFP/K14-H2BGFP mice from 4 day old backskins

first: Elaine

last: Fuchs


title: Micromass Time Course

status: Public on Sep 08 2005

first: Claudine

last: James

email: claudinegj@hotmail.com, fbeier@uwo.ca

address: 1151 Richmond Street, Suite 2

department: Physiology and Pharmacology

institute: University of Western Ontario

summary:
Primary micromass cultures derived from 11.5 day old mouse embryo limb buds were cultured for 15 days in differentiating conditions (beta-glycerophosphate and ascorbic acid). Total RNA from differentiating chondrocytes was isolated every three days i.e. days 3,6,9,12 and 15 and hybridized to MOE430A chips. Objective: Gain a view of the temporal gene expression changes occuring during chondrocyte differentiation.
Keywords = micromass culture
Keywords = temporal gene expression
Keywords = mouse
Keywords = chondrocyte differentiation
Keywords: time-course

first: Frank

last: Beier

middle: G


status: Public on Sep 21 2005

city: Madison

first: Alan

last: Attie

state: WI

address: 433 Babcock Drive

institute: University of Wisconsin-Madison

summary:
Coordinated regulation of gene expression levels across a series of experimental conditions provides valuable information about the functions of correlated transcripts. To map gene regulatory pathways, we used microarray-derived gene expression measurements in 60 individuals of an F2 sample segregating for diabetes. We performed correlation analysis among ~40,000 expression traits. By combining correlation among expression traits and linkage mapping information, we were able to identify regulatory networks, make functional predictions to uncharacterized genes, and characterize novel members of known pathways. Using 36 seed traits, we found evidence of coordinate regulation of 160 G-protein coupled receptor (GPCR) pathway expression traits. Of the 160 traits, 50 had their major LOD peak within 8 cM of a locus on chromosome 2, and 81 others had a secondary peak in this region. A previously uncharacterized Riken cDNA clone, which showed strong correlation with stearoyl CoA desaturase 1 expression, was experimentally validated to be responsive to conditions that regulate lipid metabolism. Using linkage mapping, we identified multiple genes whose expression is under the control of transcription regulatory loci. Trait-correlation combined with linkage mapping can reveal regulatory networks that would otherwise be missed if we only studied mRNA traits with statistically significant linkages in this small cross. The combined analysis is more sensitive compared with linkage mapping only.
References:
Kendziorski C., M. Chen, M. Yuan, H. Lan, and A.D. Attie. Statistical Methods for Expression Quantitative Trait Loci (eQTL) Mapping. Biometrics, to appear, 2005.
Lan H, Chen M, Flowers JB, Yandell BS, Stapleton DS, et al. (2006) Combined Expression Trait Correlations and Expression Quantitative Trait Locus Mapping. PLoS Genet 2(1): e6.
Keywords: Genetics of gene expression

overall_design: The F2-ob/ob mice were chosen from a mapping panel that we created to map diabetes related physiological phenotypes (Stoehr et al. 2000). About 110 of these F2-ob/ob mice were also used to map mRNA abundance traits derived by quantitative real-time RT-PCR (Lan et al. 2003). The sixty F2-ob/ob mice that were used to generate microarray-derived mRNA abundance traits were selected from the 110 mice based on a selective phenotyping algorithm (Jin et al. 2004). The F2-ob/ob mice were housed at weaning at the University of Wisconsin-Madison animal care facility on a 12-h light/dark cycle. Mice were provided Purina Formulab Chow 5008 (6.5% fat) and acidified water ad libitum. Mice were killed at 14 weeks of age by CO2 asphyxiation after a 4-hour fast. The livers, along with other tissues, were immediately foil wrapped and frozen in liquid nitrogen, and subsequently transferred to -80 °C freezers for storage. Liver samples were taken from 29 male and 31 females. Total RNA was isolated with RNAzol Reagent (Tel-Test, Inc.) using a modification of the single-step acid guanidinium isothiocyanate phenol-chloroform extraction method according to the manufacturer's protocol. The extracted RNA was purified using RNeasy (Qiagen, Inc.). RNA samples were evaluated by UV spectroscopy for concentration. RNA quality was monitored by visualization on an ethidium bromide-stained denaturing formaldehyde agarose gel. RNA samples were converted to cDNA, and then biotin-labeled cRNA according to Affymetrix Expression Analysis Technical Manual. The labeled samples were hybridized to the M430A, and subsequently the M430B array. The hybridization, washing and scanning steps were carried out by Hong Lan using the Affymetrix core facility at the Gene Expression Center of University of Wisconsin-Madison.

first: Hong

last: Lan

first: Meng

last: Chen

first: Jessica

last: Byers

first: Brian

middle: S

last: Yandell

first: Donnie

last: Stapleton

first: Christine

last: Mata

first: Eric

last: Mui

first: Matthew

last: Flowers

first: Kathryn

last: Schueler

first: Kenneth

middle: F

last: Manly

first: Robert

last: Williams

first: Christina

last: Kendziorski


title: DR4 Control for J1, R1 and V6.5 ES

status: Public on Sep 01 2005

first: Theodore

last: Perkins

summary:
This sample is a control for the J1, R1 and V6.5 ES samples. The DR4 cell type acts as a feeder cell for stem cells and as such is a small contaminant of the embryonic stem cell growth environment.
Keywords: other


title: Altered transcriptome in a motor system spared by ALS: protective vs. adaptive strategies

status: Public on Sep 23 2005

city: Lexington

first: Colleen

last: McMullen

state: KY

address: 800 Rose St MS508

department: Physiology

institute: University of Kentucky

summary:
Amyotrophic lateral sclerosis (ALS) spares the ocular motor system. In this study, we tested the hypothesis that the oculomotor neurons are intrinsically protected in ALS. Using high-density cDNA microarrays, we examined the transcriptome of oculomotor nuclei and spinal cords in mice expressing a human mutant SOD1, the SOD1(G93A) ALS model, at 6 and 10 weeks of age. Comparison of gene expression profiles of these pre-symptomatic SOD1(G93A) mice showed a shift to a proapoptotic state in spinal cords, while the opposite was true in oculomotor nuclei. Seventeen members of the A, B, C and D Hox clusters increased in oculomotor nuclei from 6 to 10 weeks of age; 15 were downregulated in spinal cord. Although only the first 4 classes of a given Hox cluster (e.g., Hoxa1-4) are normally expressed in the developing hindbrain, we found differential expression of mostly the latter classes in both oculomotor nuclei and spinal cords. Also, semaphorin 3B was expressed at 28-fold greater levels in oculomotor nuclei and 61-fold less in spinal cords in 10-week old SOD1(G93A) mice compared to 6-week old mice. Semaphorins 3A and 3E were also differentially regulated. Comparison of gene expression profiles of control SOD1 mice of 6 and 10 weeks of age did not show these changes. Based on these results, we rejected our hypothesis and conclude that the oculomotor nuclei actively adapt to the ALS-inducing mutation.
Supported by NEI and ALSA.
Keywords: disease state analysis

overall_design: Oligonucleotide microarray studies using the Affymetrix system were conducted as described earlier (McMullen et al., 2004).  Biotinylated cRNA was hybridized to Affymetrix Mouse Expression Set 430A GeneChips.  Then, the microarrays were washed and stained with a streptavidin-bound marker, and scanned with a laser scanner.  Resulting microarray data were analyzed with Affymetrix Microarray Suite 5.0 software.  Only those genes with consistent absent/present calls in the three independent replicates per group were considered for further analyses.  Comparisons were crossed such that each oculomotor nuclei sample was compared with each spinal cord sample at the corresponding age.  The Affymetrix software uses the one-sided Wilcoxon’s signed rank test to estimate “increase/no change/decrease” difference calls and fold-changes for each pair-wise comparison.  Only difference calls consistent in all pair-wise comparisons and with average changes greater than 2-fold were considered significant, resulting in a conservative list of genes with changed expression levels.

first: Francisco

last: Andrade


title: DMEM treated WT and PKBa -/- MEFs

city: Basel

first: Edward

last: Oakeley

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

summary:
Mouse embryonic fibroblasts (MEFs) were generated from 13.5-day-old embryos obtained from heterozygous PKBa mice intercrosses (Yang et al., 2003). Briefly, after dissection of head and visceral organs for genotyping, embryos were minced and trypsinized for 30 min at 37°C. Embryonic fibroblasts were then plated and maintained in Dulbecco’s Modified Eagle Medium (DMEM) with 10% foetal calf serum (FCS) (Life Technologies), 100 units/ml of penicillin and 100 mg/ml of streptomycin at 37°C in an atmosphere of 5% CO2. All experiments were performed with wild-type and PKBa-/- MEFs between 15-20 passages. To induce adipocyte differentiation, 2-day-postconfluent cells (day 0) were treated with DMEM supplemented with 10% FCS, 8 mg/ml biotin, 4 mg/ml pantothenate, 0.5 mM 3-isobutyl-1-methylxanthine, 1 mM dexamethasone and 10 mg/ml insulin (all from Sigma). Total RNA was extracted from cells using TRIzol (Invitrogen) according to the manufacturer’s instructions.
Keywords: repeat

overall_design: Time course of DMEM treated WT and PKBa -/- MEFs in quadruplicate

first: Anne

last: Baudry

last: Hemmings


title: C2C12 transcriptome changes in response to hydrogen peroxide

status: Public on Aug 11 2005

summary:
In muscle, reactive oxygen species (ROS) generation increases with strenuous activity, chronic unloading, and inflammatory stimuli; skeletal muscle function is very sensitive to ROS; and there are redox-sensitive signaling pathways. Using myogenic cell cultures, we asked whether hydrogen peroxide (H2O2) induces adaptive changes in skeletal muscle gene expression. H2O2 downregulated or failed to induce antioxidant or apoptotic genes in the myotubes. Instead, H2O2 changed the expression of genes for cytosolic and mitochondrial enzymes, and upregulated inflammatory mediators. Finally, H2O2 had a mostly inhibitory effect on the expression of many transcription factors. The results indicate that mild oxidative stress may induce an adaptive response in skeletal muscle without antioxidant upregulation or apoptosis.
Keywords: Gene Expression, C2C12 Myotubes, Oxidative Stress, Adaptation

overall_design:
Cell Culture:
C2C12 myoblasts (ATCC, Rockville, MD) were cultured in DMEM supplemented with 10% fetal calf serum at 37°C in 5% CO2.  Myoblast differentiation was initiated by switching to differentiation medium (DMEM supplemented with 2% heat-inactivated horse serum) and allowed to continue for 96 hrs. Differentiated myotubes were treated for 2 hours with H2O2 (Sigma-Aldrich, St. Louis, MO) 0, 1, 10, 100, or 1000 μM  in DMEM supplemented with 0.5% heat-inactivated horse serum.
cDNA microarrays:
Total RNA was obtained from treated C2C12 myotubes with TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s recommended protocol.Oligonucleotide microarray studies with Affymetrix Mouse Genome 430A gene chips (n=20 chips) were conducted as described earlier. Microarrays were washed and stained with a streptavidin-bound marker and scanned. Data were analyzed with Affymetrix Microarray Suite 5.0 software. Only genes with consistent absent/present calls in all four independent replicates per group were considered for further analysis. Treatment comparisons were crossed so that each H2O2 sample was compared to each control. The software uses the one-sided Wilcoxon’s signed rank test to estimate “increase/no change/ decrease” difference calls for each pair-wise comparison. Only difference calls consistent in all pair-wise comparisons and with average changes > 1.75 were considered significant, resulting in a conservative list of genes with changed expression levels. Functional classification of genes was based on an extensive literature review.

first: Jennifer

last: Moylan

first: Michael

middle: B

last: Reid


title: Comparison of Gene Expression Profiles of J1 ES and J1 EB Cells.

summary:
Comparison of gene expression profiles of J1 embryonic stem cells and J1 embryoid bodies. This study should reveal genes that, when expressed, are responsible for the maintenance of the stem cell phenotype.
Keywords: other

overall_design: this experiment include 2 samples and 12 replicates


title: Comparison of C212 Myoblasts Infected with a Retrovirus Expressing Pax7d or an Empty Virus (puro)

summary:
C2C12 myoblasts were infected with a retrovirus expressing Pax7d or with an empty virus (puro) as a control. All of the samples originated from the same common pool of parental C2C12. This pool was split into six streams. A single prep of Pax7d-puro virus was split into three volumes and used to infect three of the streams. A single prep of puro-alone virus was similarly split in three and used to infect the remaining three streams. From the point of the infection forward each stream was maintained distinct from the others. Cells were infected and grown simultaneously under identical conditions.
The puro samples may be reused as controls for future experiments, and therefore were immediately hybridized to the MOE430A and MOE430B chips in order to generate a complete dataset. The Pax7d samples, as a specific component of this experiment, were only hybridized to the MOE430A chip as a first-look into the system.
Keywords: other

overall_design: this experiment include 2 samples and 9 replicates


title: Sca1+ primary myospheres

status: Public on Oct 06 2005

summary:
Cells were isolated from muscle (hind leg) of Balb/c mouse (male). Then cells were enriched at FACS by using Sca1 antigen. Cells were grown 4 days in NSC medium, passaged and RNA isolated. Cells were at passage 1.
Keywords: other


title: Intestinal crypt stem and transit cell proliferation and villus cell migration in mice lacking Klf9

status: Public on Dec 08 2006

city: Little Rock

first: Rijin

last: Xiao

state: AR

address: 2020 Marshall Street

institute: Nutrition Center, Arkansas Chidren's Hospital

summary:
Krüppel-like factor 9 (Klf9), a zinc-finger transcription factor, is implicated in the control of cell proliferation, cell differentiation and cell fate in brain and uterus.  Using Klf9 null mutant mice, we have investigated the involvement of Klf9 in small intestine crypt-villus cell renewal and lineage determination.  We report the predominant expression of Klf9 gene in small intestine smooth muscle (muscularis externa).  Jejunums null for Klf9 have shorter villi, reduced crypt stem/transit cell proliferation, and altered lineage determination as indicated by decreased and increased numbers of Goblet and Paneth cells, respectively.  A stimulatory role for Klf9 in villus cell migration was demonstrated by BrdU labeling.  Results suggest that Klf9 controls the elaboration, from small intestine smooth muscle, of molecular mediator(s) of crypt cell proliferation and lineage determination, and of villus cell migration.
Keywords: Genetic modification

overall_design: Total RNA was extracted in parallel from the jejunums of five WT and five Klf9-/- male mice (PND 30) using TRIzol reagent (Invitrogen, Carlsbad, CA).  Conversion of each RNA preparation to corresponding fragmented cRNA.  Fifteen ug of each cRNA was hybridized for 16 hours to an Affymetrix mouse 430A GeneChip.  Ten GeneChips (each corresponding to a single animal) were hybridized, washed and scanned in parallel.  Following the wash, signal amplification, and signal detection steps, GeneChips were scanned (Agilent GeneArray laser scanner) and the resultant images quantified using Affymetrix MAS 5.0 software.

first: Frank

last: Simmen

middle: C

last: Velarde

first: Rachel

middle: D

last: Nicholson

first: Rosalia


title: RETRACTED BY AUTHORS

first: Michaela

middle: Long

last: Tsai

address: 6-160 Jackson Hall, 321 Church St. SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

summary:
Title: Gene Expression in Ara-C Resistance in AML

A microarray study of altered gene expression in acute myeloid leukemia cell lines
Keywords: cell type comparison

Keywords: Expression profiling by array

overall_design: Two highly Ara-C resistant cell lines, B117H and B140H were derived from Ara-C sensitive parental cell lines, B117P and B140P. Variations in gene expression between these resistant/sensitive sets were studied

first: Bin

last: Yin

first: Diane

last: Hasz

first: David

middle: A

last: Largaespada


title: Sca1-CD45 sorted bone marrow

address: 501 Smyth Rd.

institute: Ottawa Hospital Research Institute

summary:
Sca1-CD45 sorted bone marrow
Keywords: other

overall_design: this experiment include 4 samples and 22 replicates


title: Exercise and transcriptional analysis in male eNOS Knockout Mice

status: Public on Jul 20 2005

city: Valhalla

first: Caroline

last: Ojaimi

institute: New York Medical College

summary:
There is cardiac dysfunction in male eNOS (-/-) with age and 50% mortality at 21M. It was of interest to investigate the gene expression profile of aged eNOS (-/-) male in comparison to (+/+) in order to explore the genetic markers and molecular mechanisms leading to heart failure. RNA was extracted from the left ventricle from male (-/-) (n=3) and (+/+) (n=4) at the age of 21M.
Keywords = eNOS knockout
Keywords = microarray
Keywords = exercise
Keywords: other

first: Wei

last: Li

first: Shintaro

last: Kinugawa

first: Heiner

last: Post

first: Anna

last: Csiszar

first: Gabor

last: Kaley

first: Thomas

last: Hintze


title: Altered hepatic gene expression in liver-Cpr-null and Cpr-low mice

status: Public on Jul 16 2005

city: Albany

first: Xinxin

last: Ding

institute: Wadsworth Center, NYSDOH

summary:
NADPH-cytochrome P450 reductase (CPR) is important for the functions of many enzymes, such as microsomal cytochrome P450 (P450) monooxygenases and heme oxygenases. Two mouse models with deficient CPR expression in adults were recently generated in this laboratory: liver-Cpr-null (with liver-specific Cpr deletion) (Gu et al., J. Biol. Chem., 278, 25895–25901, 2003) and Cpr-low (with reduced CPR expression in all organs examined) (Wu et al. J. Pharmacol. Expt. Ther. 312, 35-43, 2005). The phenotypes included a reduced serum cholesterol level and an induction of hepatic P450 in both models, and hepatomegaly and fatty liver in the liver-Cpr-null mouse alone. Our aim was to identify hepatic gene-expression changes related to these phenotypes. Cpr-lox mice, which have normal CPR expression (Wu et al., Genesis, 36, 177-181, 2003.), were used as the control in microarray analysis. A detailed analysis of the gene-expression changes in lipid metabolism and transport pathways revealed potential mechanisms, such as an increased activation of constitutive androstane receptor (CAR) and a decreased activation of peroxisomal proliferators activated receptor alpha (PPAR-gamma) by precursors of cholesterol biosynthesis, that underlie common changes (e.g., induction of multiple P450s and inhibition of genes for fatty acids metabolism) in response to CPR-loss in the two mouse models. Moreover, we also uncovered model-specific gene-expression changes, such as the induction of a lipid translocase (CD36 antigen) and the suppression of carnitine O-palmitoyltransferase 1 (CPT1a) and acyl-CoA synthetase long-chain family member 1 (Acsl1), that are potentially responsible for the severe hepatic lipidosis observed in liver-Cpr-null, but not Cpr-low mice.
Keywords = Cytochrome P450
Keywords = NADPH-cytochrome P450 reductase
Keywords = transgenic mice
Keywords = liver
Keywords = nuclear receptor
Keywords: other

first: Yan

last: Weng

first: Concetta

last: DiRusso

first: Andrew

last: Reilly

first: Paul

middle: N

last: Black


title: R1 Embryonic Stem Cell and Embryoid Body Time Course

status: Public on Jul 22 2005

city: Ottawa

first: Theodore

last: Perkins

summary:
An 11-point time course study comparing R1 embryonic stem cells versus embryoid bodies. Time course 0 hours, 6 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 4 days, 7 days, 9 days, and 14 days.
Keywords: other

overall_design: this experiment include 11 samples and 66 replicates


title: BMPR2 vs hypoxic pulmonary hypertension

status: Public on Jun 10 2005

city: Nashville

first: James

last: West

address: 4200 E 9TH Ave, Box B133

institute: Vanderbilt University

summary:
Comparison of lung from hypoxic PAH to SM22-tet-BMPR2delx4+ PAH, with three different types of control
Keywords: genetic modification, disease state response, stress response

overall_design: One chip each of five conditions, with pooled RNA on each chip to reduce individual variability

first: Yuji

last: Tada

first: Marloes

last: Hoedt-Miller

first: Mark

last: Geraci

first: Takayuki

last: Kuriyama


title: Phosgene exposure in the mouse lung

status: Public on Aug 31 2005

city: Aberdeen Proving Ground

last: Dillman

address: 3100 Ricketts Point Rd

institute: U.S. Army Medical Research Institute of Chemical Defense

summary:
Carbonyl chloride (phosgene) is a toxic industrial compound (TIC) widely used in industry for the production of synthetic products, such as polyfoam rubber, plastics, and dyes.  Exposure to phosgene results in a latent (1-24 hr), potentially life-threatening pulmonary edema and irreversible acute lung injury.  A genomic approach was utilized to investigate the molecular mechanism of phosgene-induced lung injury.  CD-1 male mice were exposed whole-body to either air or a concentration x time (c x t) amount of 32 mg/m3 (8 ppm) phosgene for 20 min (640 mg x min/m3).  Lung tissue was collected from air- or phosgene-exposed mice at 0.5, 1, 4, 8, 12, 24, 48, and 72 hr post-exposure.  RNA was extracted from the lung and used as starting material for the probing of oligonucleotide microarrays to determine changes in gene expression following phosgene exposure.  The data were analyzed using principal component analysis (PCA) to determine the greatest sources of data variability.  A three-way analysis of variance (ANOVA) based on exposure, time, and sample was performed to identify the genes most significantly changed as a result of phosgene exposure.  These genes were rank ordered by p-values and categorized based on molecular function and biological process.  Some of the most significant changes in gene expression reflect changes in glutathione synthesis and redox regulation of the cell, including upregulation of glutathione S-transferase alpha-2, glutathione peroxidase 2, and glutamate-cysteine ligase, catalytic subunit (also known as γ-glutamyl cysteine synthetase).  This is in agreement with previous observations describing changes in redox enzyme activity after phosgene exposure.  We are also investigating other pathways that are responsive to phosgene exposure to identify mechanisms of toxicity and potential therapeutic targets.

Male CD-1 mice were exposed to air or 32 mg per cubic meter phosgene for 20 min and tissue collected at 30 min, 1 hr, 4 hr, 8 hr, 12 hr, 24 hr, 48 hr, or 72 hr before collection and analysis of lung tissue using oligonucleotide microarrays.
Keyword=phosgene
Keyword=mouse
Keyword=lung
Keyword=carbonyl chloride
Keywords: ordered

first: Alfred

last: Sciuito

first: Christopher

last: Phillips

first: L

last: Orzolek

first: Alison

middle: I

last: Hege

last: Moran


title: Gene upregulation by the ATCE1 transcription factor

status: Public on Jun 07 2005

city: Ramat-Gan

first: Stelzer

last: Gil

address: Ramat-Gan

country: Israel

institute: Bar-Ilan University

summary:
ATCE1 is a transcription factor that belongs to the CREB3 subtype of the ATF/CREB transcription factor family.  In order to get an indication of the potential promoters ATCE1 targets, a nuclear form was expressed in NIH 3T3 fibroblasts via transfection and upregulated genes were sought after.
Keywords: Potential promoter targeting

overall_design:
NIH 3T3 cells were transfected with either a pCMV-HA-ATCE1-C-del plasmid, driving the expression the nuclear form of ATCE1, or an empty pCMV-HA vector.
The expression level of transcripts isolated from ATCE1 expressing cells was compared to transcripts obtained from cells transfected with an empty vector that was used as a control.

first: Gil

last: Stelzer

first: Jeremy

last: Don


title: MOE430 whole mouse - mouse colon dilution series - RMA preprocessed

status: Public on Jun 30 2005

city: Cincinnati

first: Johannes

middle: Michael

last: Freudenberg

state: OH

address: 3333 Burnet Ave

department: Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary:
This data is part of a large-scale platform comparison experiment.  Whole mouse and adult mouse colon RNA was mixed at different concentrations (100:0, 75:25, 50:50, 25:75, and 0:100) and distributed across multiple centers for analysis.  Eight microarray platforms and RT-PCR were tested for different labeling protocols, amplification protocols, and data preprocessing approaches in order to maximize data intercomparability.  The role of universal reference RNA was also examined.  Probes of different platforms were matched using gene symbols and/or RefSeq/GenBank accession numbers.  Several different normalization procedures were applied.  Evaluation criteria included linearity, sensitivity/specificity, and reproducibility within and between platforms, labeling methods, and laboratories.
Keywords: dilution series

overall_design: Whole mouse (sacrificed on day 1, strain: C57BL/6) and adult mouse (8 weeks, strain: C57BL/6 ) colon RNA from multiple animals was pooled respectively.  RNA was purified following the manufacturer’s recommendations and integrity was analyzed using an Agilent BioAnalyzer 2100 according to manufacturer instructions. Five RNA samples were created by mixing the two original samples at different concentrations (100:0, 75:25, 50:50, 25:75, and 0:100).  The five master mix samples were then divided into duplicate sets of the five sample RNAs, distributed to individual laboratories, and hybridized to eight different microarray platforms at several different genome centers.  The five samples included here were prepared from 10ng of total RNA using a T7 double amplification protocol as described in Schwab et al., 2003 and hybridized to Affymetrix MOE430 arrays as recommended by the manufacturer using the standard protocol.  No replicates were produced.

first: Sue

last: Kong

first: Anil

last: Jegga

first: Cathy

last: Ebert

first: Shawn

last: Smith

first: Craig

last: Tomlinson

first: Maureen

last: Sartor

first: Mario

last: Medvedovic

first: Michael

last: Wagner

first: Tinghu

last: Qiu

first: Jeff

last: Green

first: Shirley

last: Shurtleff

last: Downing

first: Anika

last: Bissahoyo

first: Jennifer

last: Dackor

first: Haider

last: Syed

first: David

last: Threadgill

first: Stephen

last: Settle

first: Braden

last: Boone

last: Levy

first: Robert

middle: J

last: Coffey

first: Bruce

last: Aronow


title: V6.5 Embryonic Stem Cell and Embryoid Body Time Course

first: Theodore

last: Perkins

summary:
An 11-point time course study comparing V6.5 embryonic stem cells versus embryoid bodies. Time course 0 hours, 6 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 4 days, 7 days, 9 days, and 14 days.
Keywords: other


title: Conditional activation of B-catenin in adult mouse epidermis for 0, 1, or 7 days

status: Public on Jul 15 2005

city: London

first: Fiona

middle: M

last: Watt

address: 44 Lincolns Inn Fields

department: Keratinocyte

institute: Cancer Research UK

summary:
Expression of deltaNB-cateninER allows the time and duration of B-catenin activation to be controlled precisely through the application of 4OHT.  We have shown that B-catenin activation in adult mouse epidermis stimulates de novo hair follicles and the formation of a new bulge and melanocyte niche.  We utilize Affymetrix Mouse Genome 430A 2.0 oligonucleotide arrays to investigate the differential regulation of RNA in skin from 7 week old female deltaNB-cateninER transgenic mice following 0, 1, or 7 days B-catenin activation in the epidermis.  RNA from age and sex matched wild-type littermates was used as a control.
Keywords = Mouse
Keywords = Affymetrix
Keywords = Skin
Keywords = Hair
Keywords = Epidermis
Keywords = Keratinocyte
Keywords = B-catenin
Keywords = Stem Cell
Keywords: time-course

first: Violeta

last: Silva-Vargas

first: Cristina

last: Lo Celso

first: Tyler

last: Ofstad


title: Zoghbi-5R01NS027699-14

status: Public on Jul 06 2005

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
A number of human neurodegenerative diseases result from the expansion of a glutamine repeat within the disease-causing protein. Spinocerebellar ataxia type1 is one such disease, caused by expansion of a polyglutamine tract in the novel protein ataxin-1. To faithfully model SCA1 in the mouse, we generated  knock-in mice carrying 154 CAG repeats in the mouse Sca1 locus. These mice reproduced many aspects of the human disease. Despite ubiquitous expression of the mutant protein, they developed slowly progressive selective neurodegeneration , which is most distinct in Purkinje cells and spinal cord. Alterations in gene expression have been proposed to be involved in the pathogenesis of polyglutamine disease including SCA1, but the changes of gene expression in an authentic disease model have not been characterized. We believe that knowledge of these genes will give insight into the pathophysiology of SCA1 and may ultimately be relevant to the treatment of SCA1.
We will determine gene expression patterns in the cerebellum and forebrain at three different time points.
We propose that the genes whose expression is affected  by mutant ataxin-1 expression are effectors for neuronal dysfunction and neuronal degeneration in the knock-in mice. We also hypothesize the difference in the expression levels of these genes accounts for selective vulnerability of neurons.
We will examine three time points: 4 weeks, 11 weeks, and 20 weeks of age. We have shown that the mice developed motor incoordination as revealed  by rotating rod test as early as 5 weeks of age but it was not until 10 weeks that they start showing clear  neurological  phenotype such as clasping.  At each point, we will compare the pattern between the mutant and wild-type littermate. Animals will be prepared and sacrificed by a standard procedure. Cerebellum and spinal cord are the most affected areas whereas forebrain shows less neurodegeneration. Tissue will be rapidly dissected from cerebellum and forebrain, frozen in liquid nitrogen, and stored at ?80 C until analysis. Tissues will be sent to the centers (as opposed to RNA). We will be providing 9 tissue samples from three litters for each time point to mitigate any expression differences resulting from subtle differences of procedure or environment where the mice grow.
Keywords: time-course

overall_design: as above

first: H

last: Zoghbi


title: Bone marrow and hematopoietic stem cells

status: Public on Sep 15 2005

summary:
Gene expression profiles of sorted bone marrow samples to determine genes implicated in hematopoetic stem cell identity.
Keywords: other

overall_design: this experiment include 6 samples and 32 replicates


title: Transcriptomes analysis of mouse developing forelimb and hindlimb autopods

status: Public on Jun 01 2005

city: Portland

first: Siming

last: Shou

state: OR

address: 3181 Sam Jackson Park Road

department: Medical Genetics

institute: Oregon Health & Science University

summary:
Transcriptomes of mouse embryonic autopods were generated detecting expression of approximately 26179 transcripts in the developing forelimb or hindlimb autopods, representing about 58 % of the probe sets on MOE-430 A/B GeneChip. Three biological replicate array experiments were finished for each condition and MAS5.0 signal were used to do data analysis. Forty-four transcripts with expression differences higher than 2-fold were detected(T test, P<0.05), including Tbx4, Tbx5, Hoxc10 and Pitx1 which were previously shown to be differentially expressed in developing forelimb and hindlimb bud by in situ hybridization and SAGE study (Margulies 2001). RTPCR and in situ experiments confirmed several top differentially expressed genes which were newly discovered by our experiments. Vast amount of transcripts and its family members  such as Bmp, Fgf, Epha, Wnt, T-box and Hox families detected to be highly expressed or differentially expressed in developing autopods, suggesting that the complexity of  transcriptomes of developing autopods and dynamic differential expression and differential combinations of gene expression signals in the developing limb tissue contributes to differences in forelimb versus hindlimb patterning. The differentially expressed genes are the essential factors for morphological diversification of  developing limb structures.

Keywords = microarray
Keywords = mouse
Keywords = autopod
Keywords = limb
Keywords = development
Keywords = gene expression
Keywords = transcriptome
Keywords: repeat sample

first: Scott

last: Stadler

first: Virginia

last: Scott


title: Gene Expression Profiling of 17 beta-Estradiol and Genistein Effects on Mouse Thymus

status: Public on Jul 08 2005

city: Urbana

first: Lei

last: Liu

state: IL

address: 1201 W. Gregory

department: W. M. Keck Center

institute: University of Illinois at Urbana-Champaign

summary:
Compared the effects of Estrogen and its analog Genistein on mouse thymus. Endogenous estrogen were minimized by removal of ovaries. Samples were collected at 4 time points: 0 days, 2 days, 3 days and 6 days from the start of the treatment. Two biological replicates at each time point.
Keywords: comparison of hormone and its analog; Time course

overall_design: Control samples were from the mice that were untreated and at 0 day since treatment. Two treatments (Estrogen injection and Genistein diet) and three time points. Two replicated samples at each time point and each treatment. Total 14 samples.

first: Vimal

last: Selvaraj

last: Bunick

first: Carrol

last: Finnigan-Bunick

first: Rodney

last: Johnson

first: Huixia

last: Wang

first: Paul

last: Cooke


title: Synovial fibroblast activated by IL-1beta; effect of prostacyclin signaling

status: Public on May 20 2005

city: kyoto

first: tetsuya

last: honda

institute: kyoto university

summary:
Synovial fibroblasts were extracted from knee joints of naïve mice(DBA/1J, male 8-12 week old), and passaged 3-4 times. Cells were plated at a concentration of 1 X 106 cells/dish in 60 mm dish in 5 ml of RPMI1640 medium with 1% heat-inactivated FCS at 37°C, 5% CO2. Cells were treated vehicle or stimulated by IL-1beta. In IL-1beta(5ng/ml) stimulated groups, indomethacin (1 μM) and iloprost (1μM) were further added either alone or in combination. After 6 hour stimulation as described above, cells were isolated and frozen by liquid nitrogen, and stored at –80°C before use. Total RNA was extracted by RNAeasy Mini Kit. The RNA sample was labeled for hybridization onto the genechip array according to the standard affymetrix protcols.

Keywords = arthritis prostacyclin
Keywords: other

first: Tetsuya

last: Honda

first: Eri

last: Segi-Nishida

first: Shuh

last: Narumiya


title: mTert overexpression in MEFs

status: Public on May 31 2005

city: Madrid

first: Peter

last: Klatt

department: Molecular Oncology Program

country: Spain

institute: Spanish National Cancer Center (CNIO)

summary:
Recent studies suggest that telomerase promotes cell growth by mechanisms that extend beyond the rescue of critically short telomeres. The in vitro model of mTert overexpressing MEFs recapitulates fundamental aspects of the growth-promoting effects of mTert in vivo. First, in Terc-proficient cells, mTert overexpression favors escape from replicative senescence and enhances anchorage-independent growth in response to oncogenic stress, which fits well with previous data showing that mTert overexpression promotes tumor formation. Second, in Terc-deficient cells, retroviral transduction with mTert results in a delayed onset of immortalization and impairs colony formation in response to oncogenic stress, which is in agreement with the inhibitory effect of mTert overexpression on tumorigenesis in a Terc null mouse background. To unravel the molecular targets of telomerase that impact on cell growth, we compared the transcriptome of MEFs, before and after mTert introduction. We found that ectopic expression of mTert was associated with detectable gene expression changes (greater than 1.5-fold; validated by qRT-PCR) of 26 transcripts. Analysis of the observed transcriptional changes indicates that ectopic expression of mTert suppresses in a coordinated manner functionally related genes with overlapping roles in growth arrest, resistance to transformation, and apoptosis. We show that the majority of the telomerase target genes are growth-inhibitory, transforming growth factor-beta (TGF-beta) -inducible genes and provide functional evidence for the potential of telomerase to abrogate TGF-beta -mediated growth inhibition. Thus, in line with the current view that the diversity of TGF-beta responses is not so much a consequence of the use of different signaling pathways but caused by different ways of reading the output from the same basic pathway, we propose that the telomerase status of a cell creates a gene expression pattern that determines how cells read growth inhibitory signals, among them signals propagated through the TGF-beta pathway.
Keywords: repeat sample

first: Christoph

last: Geserick

first: Eva

last: González-Suárez

first: María

last: Blasco


title: Diet-dependent cardiovascular lipid metabolism controlled by hepatic LXRα

status: Public on May 12 2005

city: Philadelphia

first: Mitchell

middle: A.

last: Lazar

address: 415 Curie Boulevard

institute: University of Pennsylvania

summary:
Microarray analysis of liver RNA from male Low Density Lipoprotein Receptor null mice on C57B6 background expressing human LXR alpha or GFP (control) via adeno-associated virus (AAV2.8) gene transfer, under control of the liver specific human thyroxine binding globulin promoter. Samples are from 8 month old mice, with AAV treatment at age of 10 weeks, on Western diet for 12 weeks prior experiment. The synthetic LXR ligand T0901317 (5mg/kg) or vehicle was administered for 3 days by i.p. injection to designated mice.
Keywords = LXR alpha
Keywords = SREBP1
Keywords = diet
Keywords = lipid metabolism
Keywords = atherosclerosis
Keywords: repeat sample

first: Michael

last: Lehrke

first: Corinna

last: Lebherz

first: Segan

last: Millington

first: Hong-Ping

last: Guan

first: John

last: Millar

first: Daniel

last: Rader

first: James

last: Wilson


title: IFNgamma and 1a,25(OH)2D3 dependent gene expression in bone marrow derived macrophages

status: Public on Apr 21 2005

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
Gene expression profiling of macrophages derived from WT and Vdr deficient mice after stimulation with IFNgamma and/or 1alpha,25(OH)2D3
Keywords = macrophages
Keywords = VDR
Keywords = activated vitamin D3
Keywords = IFNgamma
Keywords = KO mice
Keywords: dose response

first: Laura

last: Helming

first: Jens

last: Böse

first: Jan

last: Ehrchen

first: Thomas

last: Frahm

last: Probst-Kepper

first: Rudi

last: Balling

first: Andreas

last: Lengeling


title: KPAW and wild type eyes

status: Public on Apr 06 2005

city: Lund

first: Tord

last: Hjalt

country: Sweden

institute: Lund University

summary:
Mice over-expressing human PITX2A in cornea by the keratocan upstream
regulatory sequences.

Normalization procedure:
Data normalized to spikes.
Values below 0.01 were set to 0.01.  All of the genes in each sample were divided by the median of a user specified list of positive control genes (chip-to-chip normalization).

Keywords: repeat sample

first: Johan

last: Holmberg

first: Mikael

last: Åkerlund

first: Chia-Yang

last: Liu


title: Beta cells (MIN6) treated with amylin at different times and doses and growth at different concentrations of glucose

status: Public on Apr 12 2005

city: Barcelona

first: Silvia

last: Casas Fontdevila

address: Villarroel, 170

institute: IDIBAPS

summary:
Murine pancreatic beta cell line MIN6 was growth at two different concentrations of glucose (22,2 and 5,5 mM of glucose), 37ºC, 5% CO2 and was treated at four different concentrations of human amylin (0, 1, 10 and 20 uM) during three different times (2, 12 and 24 hours)
Keywords = pancreatic beta cell
Keywords = amylin
Keywords = glucose
Keywords: time-course

last: Casas

first: Jordi

last: Altirriba

first: Anna

last: Novials

first: Sakari

last: Knuutila

first: Ramon

last: Gomis


title: sLTbetaR-Ig treated mLN

status: Public on Mar 04 2005

city: Zürich

first: Christoph

last: Huber

institute: Neuropathology

summary:
treatment of mesenteric lymph nodes with soluble lymphotoxin-beta receptor for 0,1,2,3,27 and 35 days
Keywords: time-course


title: Adipose, dermis and neural embryonic stem cells

status: Public on Mar 03 2005

first: Theodore

last: Perkins

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
The objective is to study gene expression between potential adult stem cells isolated from dermis and adipose tissue compared to embryonic neural stem cells.
Tissue was enzymatically digested and cells were seeded into a tissue culture flask. After 4 days, cells that had grown in suspension were passaged, harvested (by sedimentation, mechanically triturated and replated. Seven days later, cells were passaged again and RNA isolated after another 7 days.
Keywords: other


title: Timecourse of Gene Expression responses to cAMP in S49 Cells

status: Public on Apr 15 2005

city: Claremont

first: Alexander

last: Zambon

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

summary:
Abstract

Although a substantial number of hormones and drugs increase cellular cAMP levels, the global impact of cAMP and its major effector mechanism, protein kinase A (PKA), on gene expression is not known. Here we show that treatment of wild-type S49 lymphoma cells for 24 h with 8-(4-chlorophenylthio)-cAMP (CPT-cAMP), a PKA-selective cAMP analog, alters the expression of ~4500 of ~13,600 unique genes. By contrast, gene expression was unaltered in Kin– S49 cells (that lack PKA) incubated with CPT-cAMP. Changes in mRNA and protein expression of several cell-cycle regulators accompanied cAMP-induced G1-phase cell-cycle arrest of wild-type S49 cells. Within 2 h, CPT-cAMP altered expression of 152 genes that contain evolutionarily conserved cAMP-response elements (CRE) within 5 kb of transcriptional start sites, including the circadian clock gene Per1. Thus, cAMP through its activation of PKA produces extensive transcriptional regulation in eukaryotic cells. These transcriptional networks include a primary group of CRE-containing genes and secondary networks that include the circadian clock.

Keywords: time-course

first: Lingzhi

last: Zhang

first: Simon

last: Minovitsky

first: Joan

last: Kanter

first: Shyam

last: Prabhakar

first: Nathan

last: Salomonis

first: Karen

last: Vranizan

first: Inna

last: Dubchak

first: Bruce

middle: R

last: Conklin

first: Paul

last: Insel


title: Isolation and angiogenesis by endothelial progenitors in the fetal liver

status: Public on Mar 01 2005

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary:
While others have reported that fetal liver contains a population of endothelial progenitors based on expression of cell surface markers or culture assays, this is the first proof of a CD31+Sca1+ progenitor by demonstrating highly efficient in vivo angiogenesis and a direct connection to the host vasculature. We have developed a novel isolation method based on collagenase digestion and culture on a fetal liver-derived feeder layer and demonstrate that the feeder cells or their supernatants are required for endothelial progenitor survival and proliferation. Proteogenomic profiling of the endothelial progenitors and the feeder cells was done with tandem mass spectrometry proteomics using MudPIT and gene transcript expression profiling using high density DNA microarrays. This approach identified a number of gene transcripts, proteins and candidate growth factor pathways that are likely to be involved in endothelial progenitor growth, differentiation and angiogenesis.
Keywords = LEP - Liver Endothelial progenitor
Keywords = Feeder Cells
Keywords = Angiogenesis
Keywords = Proteogenomics
Keywords = Growth Factors
Keywords = Fetal liver
Keywords: parallel sample

first: Stephanie

last: Cherqui

first: Olivier

last: Schussler

first: Johannes

last: Hewel

first: John

last: Yates

first: Daniel

last: Salomon


title: Cell Culture A and B chips leg

status: Public on Feb 19 2005

city: Cleveland

first: Henry

middle: J.

last: Kaminski

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

summary:
Standard Affymetrix Protocol
Keywords = microarray
Keywords = muscle
Keywords: time-course

last: Porter


title: Cardiac grafts pteridine cyclosporinA and NIL treated

status: Public on Feb 28 2005

city: Innsbruck

first: Oliver

middle: Alexander

last: Wrulich

address: Fritz Pregl Strasse 3

country: Austria

institute: Institute of Medical Chemistry and Biochemistry

summary:
Tetrahydrobiopterin compounds prolong allograft survival independent of their effect on nitric oxide synthase activity
Keywords: other

first: Gerald

last: Brandacher

first: Manuel

last: Maglione

first: Stefan

last: Schneeberger

first: Peter

last: Obrist

first: Guntram

last: Thoeni

first: Gabriele

last: Werner-Felmayer

first: Raimund

last: Margreiter

first: Ernst

last: Werner


title: MVC19_expression_profiles

status: Public on Feb 17 2005

city: Boston

first: Wenzhong Xiao

state: MA

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

summary:
gene expression profiles of leukocytes from blood  (WBCs) and spleen harvested at an early (two hours) time point after injury or sham injury in mice subjected to trauma-hemorrhage, burn injury or lipopolysaccharide (LPS)-infusion at three experimental sites
Keywords: other

first: Tanya

last: Logvinenko

first: Bernard

middle: H

last: Brownstein

first: James

last: Lederer

first: William

last: Hubbard

first: Irshad

last: Chaudry

middle: G

last: Remick

last: Baker

first: Wenzhong

last: Xiao

last: Mannick


title: autograft and allograft samples from femur

status: Public on Feb 08 2005

city: Rochester

first: Andrew

last: Brooks

institute: University of Rochester Medical Center

summary:
Comparison of autograft and allograft samples from C57Bl/6 femur
Keywords: other

first: Edward

last: Schwarz


title: Cell Culture A and B chips EOM

first: Henry

last: Kaminski

summary:
Standard Affymetrix Protocol
Keywords: time-course

first: John

last: Porter


title: PDGF induction of immediate early genes in NIH3T3 cells

status: Public on Feb 23 2005

city: Grand Rapids

first: Paul

last: Bromann

state: MI

address: 333 Bostwick Avenue, NE

department: Signal Regulation and Cancer

institute: Van Andel Research Institute

summary:
This experiment was performed to identify immediate early genes that were induced by PDGF specifically through Src family kinases (SFKs), MEK1/2, or PI 3-K.
Keywords: repeat sample

first: Hasan

last: Korkaya

first: Craig

middle: P

last: Webb

first: Jeremy

last: Miller

first: Tammy

middle: L

last: Calvin

first: Sara

last: Courtneidge


title: Hepatocellular carcinoma mouse model

status: Public on Jan 07 2005

city: Los Angeles

first: Sonal

middle: Suresh

last: Sheth

address: 10833 Le Conte Avenue

department: Cardiology

institute: UCLA

summary:
Txnip deficient mice with hepatocellular carcinoma
Keywords: repeat sample

middle: S

first: Anatole

last: Ghazalpour

first: Jackie

last: Bodnar

first: Christopher

middle: K

last: Thipphavong

first: Shuichi

last: Tsutsumi

first: Aaron

last: Tward

first: Tatsuhiko

last: Kodama

first: Hiroyuki

last: Aburatani

first: Aldons

last: Lusis


title: IL-21/IL-15 regulation of CD8 T-cells

status: Public on Dec 11 2004

city: Bethesda

last: Brady

state: MD

institute: NCI

summary:
murine naive CD8+ T-cell  samples for control or treated with 100ng/ml of IL-15 and/or IL-21 for 4 hours
Keywords: other

first: Rong

last: Zeng

first: Rosanne

last: Spolski

first: Steven

middle: E

last: Finkelstein

first: SangKon

last: Oh

first: Panu

last: Kovanen

first: Christian

last: Hinrichs

first: Cynthia

middle: A

last: Pise-Masison

first: Michael

middle: F

last: Radonovich

first: Nicholas

last: Restifo

first: Jay

last: Berzofsky

first: Warren

last: Leonard


title: Cardiac muscle, comparisons of wild type and mdx mice, 8 week and 10.5 month (Porter lab)

status: Public on Dec 10 2004

first: Henry

last: Kaminski

summary:
Determination of gene expression changes in cardiac muscle of mdx (dystrophin-deficient) mice at postnatal ages 8 weeks and 10.5 months.  3 independent replicates/age/strain.
Keywords: parallel sample

first: John

middle: D

last: Porter


title: Mouse neuroblastoma Tcof1

status: Public on Nov 11 2004

city: Richmond

first: Timothy

last: York

state: VA

department: Human Genetics

institute: Virginia Commonwealth University

summary:
Genomewide analysis of gene expression associated with Tcof1 in mouse neuroblastoma.  NB N1E-115 cells with wildtype, overexpression, knockdown of Tcof1.
Keywords: ordered

last: Mogass

first: Lin

last: Li

first: Sinitdhorn

last: Rujirabanjerd

first: Rita

last: Shiang


title: Gene expression profiling and localization of Hoechst-effluxing CD45- and CD45+ cells in the Embryonic Mouse Lung

first: Simon

middle: Xun

last: Liang

address: 80 East Concord ST

department: Pulmonary Center

institute: Boston University School of Medicine

summary:
Side population (SP) cells are highly enriched in stem and progenitor cells. CD45+and CD45- SP cells were found at all developmental lung stages with the highest frequency of cells present at embryonic day 17.5 (E17.5), In order to clarify the role of these cells in lung development, we used oligonucleotide microarrays to evaluate their gene expression profiles. To do this, oligonucleotide gene arrays were performed in triplicate on RNA derived from CD45+ and CD45-SP cells,  and CD45+ and CD45- non-SP populations (main population; MP)  isolated from the E17.5 lung.
Keywords: parallel sample

middle: X

first: Ross

last: Summer

first: Xi

last: Sun

first: Alan

last: Fine


title: LGG treatment on YANC

status: Public on Nov 09 2004

city: Chicago

first: Julia

last: Tao

address: 5841 south maryland

department: Medicine

institute: University of Chicago

summary:
YAMC (young adult mouse colon) cells are a conditionally immortalized mouse colonic intestinal epithelial cell line derived from the Immortimouse.Prior to each experiment, cells were plated at a density of 7.5 x 105 cells per p100mm dish.Cells were treated with LGG (the probiotic Lactobacillus GG ) conditioned media overnight, then harvested the following day. RNA were extracted with Trizol and purified with Qiagen kit. Affymetrix microarray chip Mouse 430A containing 19,000 murine genes was run in duplicate(experiment on 7-24-03 and 1-22-04 ). Data were analyzed using Affymetrix Genechip Operating Software (GCOS, Version 1.0) In each case; LGG treatment was compared to mock treatment controls.  Results are expressed as fold change of treated cells as compared to controls, as calculated using GENESPRING software (Version 4.2.1, Silicon Genetics, Mountain View, CA), Statistical analysis was performed using D chip. DNA microarray experiments demonstrate that epithelial cell hsp70 is one of the most highly upregulated genes in response to LGG-CM treatment
Keywords: repeat sample

first: Yun

first: Kenneth

last: Drabik

first: Tonya

last: Waypa

first: Mark

middle: W

last: Musch

last: Alverdy

first: Eugene

middle: B

last: Chang

first: Elaine

middle: O

last: Petrof


title: Murine Müllrian duct Day0 DES

status: Public on Oct 28 2004

city: Okazaki

first: Atsuko

last: Suzuki

state: Aichi

address: Myodaiji, Higashiyama 5-1

department: Center for Integrative Bioscience

institute: National Institutes of Natural Sciences

summary:
Diethylstilbestrol (DES) inhibits the differentiation of female reproductive tracts during fetal and neonatal days . We examined global gene expressions in the  oviduct, uterus and vagina in newborn mice with or without DES. These results suggest understanding the mechanism of the differentiation of female reproductive tracts.
Keywords: ordered

first: Hajime

last: Watanabe

first: Taisen

last: Iguchi


title: EP - GMP

status: Public on Oct 22 2004

city: Berlin-Steglitz

first: Dirk

last: Carstanjen

state: Berlin

address: Krahmer Strasse 6

department: Molecular Genetics

institute: Institute for Molecular Pharmacology

summary:
Mouse erythroid progenitors (EP) in comparison to granulocyte/monocyte - macrophage progenitors (GMP) from 10 - 16 week old C57/Bl6 - S129Ola (mixed genetic background) purified by flow cytometry
Keywords = EP
Keywords = GMP
Keywords = hematopoiesis
Keywords: other

first: Ivan

last: Horak

first: Gregory

last: Terszowski

first: Hans-Reimer

last: Rodewald

first: Jessica

last: Koenigsmann

first: Dido

last: Lenze


title: The effect of intermittent hypoxia on gene expression in the liver of ob/ob mice

status: Public on Oct 27 2004

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

institute: JHU

summary:
All animals were kept in a controlled environment (22-24 °C with a 12 h : 12 h light : dark cycle; lights on at 09.00) on a standard chow diet with free access to water. Five ob/ob mice (sample_ids GSM32865-GSM32869) were placed in the intermittent hypoxia (IH) chamber and subjected to IH for 12 consecutive weeks and compared to pair-fed control exposed to intermittent room (IA) air for 12 weeks in identical chambers (n = 5, sample_ids GSM32860-GSM32864). The IH and IA states were induced during the light phase alternating with 12 h of constant room air during the dark phase. The IH and IA groups were weight-matched daily during the experiment by varying food intake. Weight-matching was conducted in pairs.
The signal intensity fluorescent images produced during samples hybridizations to Affymetrix GeneChip were read using the Agilent Gene Array Scanner and converted into GeneChip Cell files (CEL) using MAS 5.0 software (Affymetrix, Santa Clara, CA). Gene expression values were generated form CEL files using Robust Microarray Analysis (RMA, Bioconductor affy package). Briefly, the rma module of this package was used for background correction, across array normalization, and extraction of the probe level data.
Ref:  Irizarry R, Gautier L, and Cope L, An R package for analyses of Affymetrix oligonucleotide arrays. The Analysis of Gene Expression Data: Methods and Software, ed. G Parmigiani,ES Garrett, RA Irizarry,and SL Zeger. 2003, New York: Springer
Keywords: ordered

first: V

middle: Y

last: Polotsky


title: Boswellia Serrata

status: Public on Oct 20 2004

city: Tucson

first: Pawel

middle: R.

last: Kiela

address: 1501 N. Campbell Ave.

department: Pediatrics

institute: University of Arizona

summary:
Hepatic gene expression analysis in mice fed control diet or diets supplemented with 1% Fraction 1 (haxane) or Fraction 2 (methanol) of Boswellia Serrata
Keywords: other

middle: R

first: Anna

middle: J

last: Midura

first: Nesrin

last: Kuscuoglu

first: Shivanand

last: Jolad

first: Anikó

middle: M

last: Sólyom

first: David

middle: G

last: Besselsen

first: Barbara

last: Timmermann

first: Fayez

last: Ghishan


title: Identification of spinal cord fusimotor neuron-specific genes.Tourtellotte-5R01NS040748-03-2

status: Public on Oct 14 2004

city: Phoenix

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Egr3 is a zinc-finger transcription factor involved in growth and development.  Egr3-deficient mice have severe sensory ataxia due to failed development of muscle spindle stretch receptors.  Sensory and motor neurons that normally innervate spindles are absent in Egr3-deficient mice, presumably as a secondary consequence to the loss of trophic signals produced by spindles during development that are required for innervation and neuron survival.  The molecular mechanisms involving motor neuron fate specification, target derived growth factor dependencies, and specification of target innervation have been difficult to study since select markers for functionally specific motor neurons are very poorly characterized.  A more thorough understanding of the molecular mediators of motor neuron biology will be important to evaluate the efficacy of new strategies devised to thwart neuron death that occurs in a variety of human motor neuronopathies and neuropathies.
To identify genes specifically expressed by spinal cord fusimotor neurons:  Many motor neuron specific genes have been described over the years.  However, none have been described that distinguish fusimotor neurons from skeletomotor neurons despite the fact that they have distinct muscle targets (muscle spindle stretch receptors) and comprise 25-30% of the spinal motor neuron populations.  Since these motor neurons have remarkably different target innervation and function, we hypothesize that they express genes that establish their specific phenotypes during development.
We hypothesize that fusimotor neurons can be distinguished in the spinal cord by characterizing fusimotor neuron specific gene expression.  Once fusimotor neuron specific genes are identified, they will be used as markers to identify fusimotor neurons in complex neuroglial cell populations in vivo and in vitro.  We hypothesize that by characterizing fusimotor neuron specific genes, unique marker molecules will be identified for in vivo and in vitro study of this functionally distinct and important motor neuron subtype.  Moreover, we hypothesize that many of the genes that are specifically expressed by fusimotor neurons will be involved in mechanisms related to their fate specification, target innervation and growth factor dependent biology.
We will use the Affymetrix microarray platform to identify genes that are specifically expressed by fusimotor neurons in mouse spinal cord.  The differential expression analysis will be performed on microdissected segments of spinal cord (L3-L5) from wild type and Egr3-deficient mice.  Postnatal Egr3-deficient mice lack muscle spindles and fusimotor neurons in their spinal cords.  By comparing gene expression from microdissected segments of spinal cord (L3-L5) between wild type and Egr3-deficient mice, we hypothesize that fusimotor neuron selective genes can be identified. We will microdissect L3-L5 segments of spinal cord using precise anatomical landmarks to ensure that comparable spinal cord regions are anlayzed from each animal.  For each microarray experiment, total RNA will be extracted from L3-L5 cords (approximately 2 mm length of spinal cord).  The integrity of each RNA sample will be verified by gel electrophoresis.  The intact RNA samples from mice of similar genotype will be pooled from three (3) 27-day old animals.  The intact cord dissection is easier in young animals (eg: 27-day old) and the phenotype is known to exist at this developmental stage.  The RNA from each animal of a similar genotype will be pooled into a single sample to minimize false positive gene calls that may represent genes related to the specific state of vigilance of a particular animal at the time of sacrifice (eg:  activity dependent genes).  Thus, each of the two RNA samples to be analyzed for a particular microarray experiment will represent RNA from three (3) spinal cords of each genotype.  RNA amplification for probe synthesis should not be necessary since we will provide 7 ug of intact pooled total RNA for each sample.  For statistical analysis, the experiment will be performed twice.  Since the RNA samples are precious, they will be provided to the Array Consortium in two shipments with each of the experiments performed independently.
Keywords: other

first: Warren

last: Tourtellotte


title: Preimplantation mouse embryo development MOE430B

status: Public on Sep 10 2004

city: Philadelphia

first: Richard

middle: M.

last: Schultz

address: 415 S. University Ave.

department: Biology

institute: University of Pennsylvania

summary:
Preimplantation mouse embryo development on Affymetrix MOE430B. Zeng et al (2004) Dev Biol 272:483-496.
Keywords: other

first: Fanyi

last: Zeng

first: Don

last: Baldwin


title: Fibrillin-1 deficient mice

first: Daniel

last: Judge

address: 720 Rutland Avenue

institute: Johns Hopkins University

summary:
Different fibrillin-1 mutant mice
Keywords: other


title: Preimplantation mouse embryo development

status: Public on Sep 13 2004

summary:
Studies using low-resolution methods to assess gene expression during preimplantation mouse development indicate that changes in gene expression either precede or occur concomitantly with the major morphological transitions, that is, conversion of the oocyte to totipotent 2-cell blastomeres, compaction, and blastocyst formation. Using microarrays, we characterized global changes in gene expression and used Expression Analysis Systematic Explorer (EASE) to identify biological and molecular processes that accompany and likely underlie these transitions. The analysis confirmed previously described processes or events, but more important, EASE revealed new insights. Response to DNA damage and DNA repair genes are overrepresented in the oocyte compared to 1-cell through blastocyst stages and may reflect the oocyte's response to selective pressures to insure genomic integrity; fertilization results in changes in the transcript profile in the 1-cell embryo that are far greater than previously recognized; and genome activation during 2-cell stage may not be as global and promiscuous as previously proposed, but rather far more selective, with genes involved in transcription and RNA processing being preferentially expressed. These results validate this hypothesis-generating approach by identifying genes involved in critical biological processes that can be the subject of a more traditional hypothesis-driven approach.
Keywords: other


title: Preimplantation mouse embryo development MOE430A

summary:
Preimplantation mouse embryo development study on Affymetrix MOE430A.  Zeng et al (2004) Dev Biol 272:483-496.
Keywords: other


title: Control and starved myotubes

status: Public on Sep 20 2004

first: Susan

last: Kandarian

department: Department of Health Sciences

institute: Boston University

summary:
C2C12 mouse myoblasts (American Type Culture Collection, Manassas, VA) were maintained in growth medium (DMEM supplemented with 10% Fetal Bovine serum, Invitrogen Corporation, Carlsbad, CA) in 5% CO2. Cells were plated at a density of 40-50% in 100mm dishes. When cells reached ~90% confluency 24 hours later, they were switched to differentiation media (DMEM containing 2% horse serum; GIBCO, Invitrogen Corporation, Carlsbad, CA) which was subsequently changed every 48 hours. All cells were allowed to differentiate for 4 days with feeding every two days (day 0, 2, and 4). Beginning at day 4, control cells were re-fed every 48 hours whereas experimental cells were not re-fed. After an additional 4 days (8 days post differentiation), cells were harvested and total RNA was isolated from control and "starved" (non re-fed cells)
Keywords: repeat sample

first: Eric

last: Stevenson

first: Alan

last: Koncarevic

first: Paul

last: Giresi

first: Robert

last: Jackman

middle: C


title: Comparison of transcriptional changes in Cre infected with Vector infected alpha4-floxed MEFs

status: Public on Sep 01 2004

first: Mei

last: Kong

summary:
To examine the transcriptional changes that occur following alpha4 deletion, RNA microarray analysis was performed using RNA from alpha4-floxed MEFs 48 hours after infection with the Cre-containing or Vector control virus.
Keywords: other

first: Casey

last: Fox

first: James

last: Mu

first: Laura

last: Solt

first: Anne

last: Xu

first: Ryan

last: Cinalli

first: Morris

last: Birnbaum

first: Tullia

last: Lindsten

first: Craig

last: Thompson


title: FACS purified cortical projection neurons

status: Public on Jan 19 2005

first: Bradley

last: Molyneaux

department: MGH-HMS Center For Nervous System Repair

institute: Harvard Medical School

summary:
3 subtypes of cortical projection neurons were purified by fluorescence-activated cell sorting at 4 different stages of development from mouse cortex.  A detailed description of the data set is described in Arlotta, P et al (2005).

Keywords = corticospinal motor neuron callosal corticotectal cortex development FACS

first: Paola

last: Arlotta

first: Jeffrey

last: Macklis


title: LPS effects on macrophages

status: Public on Jun 05 2004

city: Brisbane

first: Rachael

middle: Zoe

last: Murray

country: Australia

institute: IMB

summary:
RAW264.7 murine macrophages treated with LPS
Keywords: time-course

middle: Z


title: IL10-/-DC + 0,SEA,LPS,SEA/LPS 6H

status: Public on May 14 2004

first: Colleen

last: Kane

address: 3610 Hamilton Walk

department: Department of Pathobiology

summary:
IL10-/-DC pulsed for 6h with 0, SEA, LPS, or co-pulsed with SEA/LPS together to compare changes in LPS-induced gene expression mediated by SEA (Schistosome soluble egg antigen)
Keywords: other

first: Jie

last: Sun

first: Edward

last: Pearce


title: Sex Specific Transciption in Mouse Tissues

status: Public on Mar 28 2004

city: New Haven

first: Joel

last: Rozowsky

state: CT

address: 266 Whitney Ave, Bass 437

department: Molecular Biophysics & Biochemistry

institute: Yale University

summary:
Sex Specific Transciption in Mouse Hypothalamus, Liver, Kidney, Ovary and Testis. For each somatic tissue there are 3 biological samples from different pools comprised of 10 animals for each sex each with a technical replicate. For each of the reproductive tissues there are 3 biological samples from different pools comprised of 10 animals with a technical replicate for each.
Keywords = Mouse sex-specific transcription, gonad specific gene expression
Keywords: other

first: John

middle: L

last: Rinn

middle: S

first: Ian

last: Laurenzi

first: Petur

last: Petersen

first: Kaiyong

last: Zon

first: Weimin

last: Zhong

first: Mark

last: Gerstein

first: Michael

middle: P

last: Snyder


title: CstF-64 Influenced Gene Expression

status: Public on Jan 01 2005

city: Pittsburgh

first: Milcarek

last: Christine

address: 200 Lothrop St. BST E1009

department: Immunology

institute: University Of Pittsburgh

summary:
Triplicate samples of RAW 264.7 murine macrophages either untreated, stimulated with 100 ng/ml LPS for 18 hours, or constituitively over-expressing CstF-64  were analyzed by microarray using Affymetrix murine gene chip 430A.
Keywords = RAW 264.7 macrophages
Keywords = LPS
Keywords = CstF-64
Keywords: repeat sample

first: Scott

middle: A

last: Shell

first: Sidney

last: Morris

first: Christine

last: Milcarek


title: Genes regulated by Egr3 in primary myotubes. Tourtellotte-5R01NS040748-03

status: Public on Nov 24 2004

first: Winnie

last: Liang

summary:
Muscle spindles are skeletal muscle stretch receptors that mediate axial and limb position sensation (proprioception) to the central nervous system.  Defective proprioception, often characterized by gait ataxia and poor coordination, is present in a variety of human sensory and motor neuropathies having diverse etiologies. Spindles contain specialized intrafusal muscle fibers that are induced during development by sensory innervation.  The molecular events mediating the morphogenetic induction process are poorly characterized but depend upon neuregulins and their cognate ErbB receptor signaling.  Recently, we demonstrated that the transcription factor Egr3 is induced and regulated by intrafusal muscle fiber sensory innervation during spindle induction.  Moreover, Egr3-deficient mice have impaired spindle morphogenesis and profound gait ataxia.  Thus, Egr3 mediated transcription is critical for muscle stretch receptor development and potentially for myotube fate specification.
Egr3 may mediate spindle morphogenesis induced by Neuregulin/ErbB signaling after myotubes are contacted by sensory axons during development.  As a starting point for understanding the specific role for Egr3 in this process, we will use a genome wide expression analysis to identify genes regulated (either directly or indirectly) by Egr3 in primary myotubes.  It is not practical to examine Egr3 mediated gene expression directly within spindles since they comprise less than 0.1% of the muscle mass.  Therefore, gene expression analysis will be examined in primary myotubes grown in vitro.  Primary myoblasts isolated from mice and differentiated in vitro are biochemically most similar to extrafusal muscle fibers which do not express Egr3.  To identify genes regulated by Egr3 in myotubes, gene expression in myotubes enforced to express full length Egr3 will be compared to gene expression in myotubes enforced to express truncated (transcriptionally inactive) Egr3.
Egr3-deficient mice lack muscle spindles and have profound proprioceptive deficits.  Egr3 is specifically expressed in a subset of developing primary myotubes after innervation by sensory axons.  Spindle induction is dependent upon sensory/myotube contact which involves sensory axon produced neuregulin and ErbB receptor signaling in the myotube.  Shortly after or during induction, Egr3 expression is upregulated and maintained in the nascent myotube/spindle as one of the earliest molecular events know to occur during spindle morphogenesis.  We hypothesize that Egr3 mediated transcription is critical for engaging gene programs specific to and essential for, muscle spindle formation.  Moreover, Egr3 may be involved in fate specification of myotubes that develop into biochemically and physiologically distinct intrafusal muscle fibers within spindles.  To date, the target genes regulated by Egr3 during spindle morphogenesis have not been characterized.
Myoblasts from wild type newborn mice will be isolated and purified.  Myoblasts will be plated on collagen coated plates and differentiated in vitro for 7 days.  During in vitro differentiation, myoblasts fuse to form multinucleated myotubes that exhibit contractile properties.  Egr3 is not expressed in myotubes in vitro, which is consistent with their similarity to extrafusal muscle fibers that also do not express Egr3 in vivo.  Only intrafusal fibers of muscle spindles express high levels of Egr3 in this muscle fiber context.  Adenoviruses that express full length Egr3 (Egr3wt; transcriptionally active) and truncated Egr3 (Egr3tr; transcriptionally inactive) have been generated and characterized in our laboratory.  After 7 days of in vitro differentiation, primary myotubes will be infected with either Egr3wt or Egr3tr adenoviruses.  100% infection is routinely obtained which is confirmed by coexpression of enhanced green fluorescent protein (EGFP).  Care will be taken to minimize viral induced toxicity of the myotubes after infection.  Myotubes are maintained after infection for 24 hours, after which total RNA is extracted from the cell lysates.  The two RNA samples will be used for microarray analysis to identify genes that are upregulated and downregulated by Egr3 in the myotube cellular context.  We will repeat the infection, RNA isolation and microarray analysis three times to minimize identifying false positive differentially expressed genes. Differentially expressed genes will be confirmed using real-time PCR.  Interesting differentially expressed genes will be examined by in situ hybridization to determine if they are specifically expressed in wild type spindles.  Since the identified differentially expressed genes will represent both indirect and direct target genes, we will perform Chromatin Immunoprecipitation (ChIP) from Egr3wt infected myotubes and screen the ChIP DNA library by PCR to determine which gene promoters are directly bound by Egr3.
Keywords: other

first: Warren

last: Tourtellotte


title: AKT_Prostate_RAD001_v_PLACEBO

status: Public on May 17 2004

city: Durham

first: Phillip

middle: George

last: Febbo

state: NC

address: 2175 CIEMAS, 101 Science Drive

department: Medicine, Molecular Genetics and Microbiology

institute: Duke Institute for Genome Sciences and Policy

summary:
Transgenic (Probasin driven Myr-AKT)or wild-type littermates were treated with RAD001 or placebo and sacrificed at 12 and 48 hours following the beginning of treatment
Keywords = AKT Prostate RAD001 mTOR PIN
Keywords: time-course

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