title: Hippocampal gene expression profiling across 8 inbred strains: towards understanding the molecular basis of behaviour

status: Public on Aug 07 2006

city: Utrecht

first: Cathy

last: Fernandes

address: Universiteitsweg 100

department: Pharmacology & Anatomy

country: Netherlands

institute: Rudolf Magnus Institute of Neuroscience

summary:
Mouse inbred strains differ in many aspects of their phenotypes, and it is known that gene expression does so too. This gives us an opportunity to isolate the genetic aspect of variation in expression and compare it to other phenotypic variables. We have investigated these issues using an eight-strain expression profile comparison with four replicates per strain on Affymetrix MGU74av2 GeneChips focusing on one well-defined brain tissue (the hippocampus). We identified substantial strain-specific variation in hippocampal gene expression, with more than two hundred genes showing strain differences by a very conservative criterion. Many such genetically driven differences in gene expression are likely to result in functional differences including differences in behaviour. A large panel of inbred strains could be used to identify genes functionally involved in particular phenotypes, similar to genetic correlation. The genetic correlation between expression profiles and function is potentially very powerful, especially given the current large-scale generation of phenotypic data on multiple strains (the Mouse Phenome Project). As an example, the strongest genetic correlation between more than 200 probe sets showing significant differences among our eight inbred strains and a ranking of these strains by aggression phenotype was found for Comt, a gene known to be involved in aggression.
Keywords: mouse, inbred strains, hippocampus, genetic comparison

overall_design: Total hippocampal RNA was extracted from eight inbred strains of mice and pooled within each strain (six mice/pool, one pool/strain). cDNA samples (eight) were prepared from the total hippocampal RNA and cRNA was prepared twice from cDNA. (Samples labelled 1 & 2 for each strain were from the first cRNA synthesis preparation, samples labelled 3 & 4 for each strain were from the second cRNA synthesis preparation).Each set of cRNA samples (16 in total) were then hybridized in duplicate to the Murine Genome U74Av2 Array (Chip A; Affymetrix, Santa Clara, USA). In total, 32 arrays were used; four arrays (two arrays with cRNA sample replicates in duplicate) for each of eight strains.

first: Jose

last: Paya-Cano

first: Frans

last: Sluyter

first: Ursula

last: D'Souza

first: Robert

last: Plomin

first: Leonard

last: Schalkwyk


title: Affymetrix experiments for cross-platform study including site 2 data

status: Public on Jun 01 2006

city: Boston

first: Winston

middle: Patrick

last: Kuo

state: MA

address: 188 Longwood Avenue

department: Genetics

country: USA

institute: Harvard Medical School

summary:
Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and “in-house” platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than “in-house” arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
Keywords: cross platform microarrays

overall_design:
RNA samples used were aliquoted from two pools of samples: C57/B6 adult mouse retina (MR) and Swiss-Webster postnatal day one (P1) mouse cortex (MC). The mouse cortex was used as a reference sample for the dual-dye platforms.Five replicates of each sample were used to assess the degree of variation in the expression data within each platform.

Additionally there were three replicates of each sample to assess the degree of variation in the expression data across different sites (site 2).

middle: P


title: Hippocampal transcript profile in young and middle-aged mice

status: Public on Jun 20 2006

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

country: Canada

institute: University of British Columbia

summary:
We carried out a global survey of age-related changes in mRNA levels in the C57BL/6NIA mouse hippocampus and found a difference in the hippocampal gene expression profile between 2-month-old young mice and 15-month-old middle-aged mice correlated with an age-related cognitive deficit in hippocampal-based explicit memory formation. Middle-aged mice displayed a mild but specific deficit in spatial memory in the Morris water maze.
Keywords: age comparison

overall_design: No technical replicates; 14 biological replicates for 15-month-old mice, 9 biological replicates for 2-month-old mice. Whole hippocampus.

first: Miguel

last: Verbitsky

first: Eric

last: Kandel

first: Conrad

last: Gilliam

first: Amanda

last: Yonan

first: Gael

last: Malleret


title: Hex acts with β-catenin to regulate anterior-posterior

status: Public on Sep 01 2006

city: Edinburgh

first: Joshua

middle: M

last: Brickman

address: King's Buildings, West Mains Rd.

department: Institute for Stem Cell Research

country: United Kingdom

institute: University of  Edinburgh

summary:
In Xenopus, establishment of the anterior-posterior axis involves two key signalling pathways, canonical Wnt and Nodal-related TGF-β. There are also a number of transcription factors that feedback upon these pathways. The homeodomain protein Hex, an early marker of anterior positional information, acts as a transcriptional repressor suppressing induction and propagation of the Spemman organiser while specifying anterior identity. We show that Hex promotes anterior identity by amplifying the activity of canonical Wnt signalling. Hex exerts this activity by inhibiting the expression of Tle-4, a member of the Groucho family of transcriptional co-repressors that we identified as a Hex target in embryonic stem (ES) cells and Xenopus embryos. This Hex-mediated enhancement of Wnt signalling results in the up-regulation of the Nieuwkoop centre genes Siamois and Xnr-3 and the subsequent increased expression of the anterior endodermal marker Cerberus and other mesendodermal genes downstream of Wnt signalling. We also identified Nodal as a Hex target in ES cells. We demonstrate that in Xenopus, the Nodal-related genes Xnr-1 and 2, but not 5 and 6, are regulated directly by Hex. The identification of Nodal-related genes as Hex targets explains the ability of Hex to suppress induction and propagation of the organiser. Together these results support a model in which Hex acts early in development to reinforce a Wnt-mediated, Nieuwkoop-like signal to induce anterior endoderm, and later in this tissue to block further propagation of Nodal-related signals. The ability of Hex to regulate the same targets in both Xenopus and mouse implies this model is conserved.
Keywords: genetic modification

overall_design: Identification of Hex target genes In Xenopus, the establishment of the anterior-posterior axis involves two key signalling pathways, the canonical Wnt and the Nodal-related TGF-β and a number of transcription factors that feedback upon these pathways. The homeodomain protein Hex, an early marker of anterior positional information, is a transcriptional repressor that suppresses the induction and propagation of the Spemman organiser while specifying anterior identity. Using microarray expression profiling we identified mouse Tle-4 as a Hex target in Embryonic Stem (ES) cells and showed that Tle-4 expression is directly regulated by Hex in Xenopus embryos. We also identified Nodal as a Hex target in ES cells. Taken together these results support a model in which Hex acts early in development to reinforce a Wnt-mediated, Nieuwkoop-like signal to induce anterior endoderm and later in this tissue to block further propagation of Nodal-related signals. The ability of Hex to regulate the same targets in both frog and mouse suggests that this model is conserved.

first: Andrea

middle: L

first: Tim

last: Watts

first: Clare

middle: E

last: Gardner

first: Simon

middle: R

last: Tomlinson

first: Geoffrey

last: Johnston


title: Expression data from NOD-scid vs B6-scid pancreas, submandibular glands, & lacrimal glands

status: Public on Jul 07 2006

city: Bronx

first: Rodolfo

last: Chaparro

state: NY

address: 1300 Morris Park Avenue

department: Microbiology and Immunology

institute: Albert Einstein College of Medicine

summary:
Prior to the onset of autoimmune destruction, type 1 diabetic patients and an animal model thereof, the nonobese diabetic (NOD) mouse, show morphological and functional abnormalities in target organs, which may act as inciting events for leukocyte infiltration. To better understand these abnormalities, but without the complications associated with inflammatory infiltrates, we examined genes expressed in autoimmune target tissues (pancreas, submandibular glands, and lacrimal glands) of NOD/scid mice and of autoimmune-resistant C57BL6/scid mice.
Keywords: tissue expression, disease prone versus resistant strain comparison

overall_design: Pancreata (6 weeks old mice), submandibular (9 and 15 weeks), and lacrimal glands (15 weeks) from individual NOD-scid and B6-scid mice were isolated for RNA extraction and hybridization on Affymetrix microarrays.

middle: J

first: Yves

last: Konigshofer

first: Georg

middle: F

last: Beilhack

first: Judith

middle: A

last: Shizuru

first: Hugh

middle: O

last: McDevitt

first: Yueh-hsiu

last: Chien


title: Expression data from mouse E14.5 wt and RUNX2 -/- humeri

status: Public on May 24 2006

city: Berlin

first: Jochen

last: Hecht

address: Ihnestr. 73

department: Mundlos

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary:
We used microarrays to identify genes differentially expressed between mouse RUNX2 -/- and wt embryonic humeri at stage E14.5
Keywords: wildtype versus knockout comparison

overall_design: To minimize the effects of random biological variation, humeri from different preparations were pooled (approximately 75 wildtype and 60 Runx2-/- for each of the two biological replicates).

first: Volkhard

last: Seitz

first: Florian

last: Wagner

first: Asita

middle: C

last: Stiege

first: Stefan

last: Mundlos


title: Expression profile of the testis from Tslc1-/- mice.

status: Public on May 05 2006

city: Tokyo

first: Murakami

last: Yoshinori

address: 5-1-1 Tsukiji Chuo-ku

department: Tumor Suppression and Functional Genomics Project

country: Japan

institute: National Cancer Center Reseach Institute

summary:
TSLC1/IGSF4, an immunoglobulin superfamily molecule, is predominantly expressed in the brain, lung, and testis and plays important roles in epithelial cell adhesion, cancer invasion, and synapse formation.  We generated Tslc1/Igsf4-deficient mice by disrupting exon 1 of the gene and found that Tslc1-/- mice were born with the expected Mendelian ratio but Tslc1-/- male mice were infertile.  In adult Tslc1-/- mice of 11-week of age, the weight of the testis was 90% of that of the Tslc1+/+ mice, and the number of sperm in the semen was approximately 0.01% of it.  Histological analysis revealed that the round spermatids and the pachytene spermatocytes failed to attach to the Sertoli cells in the seminiferous tubules and sloughed off into the lumen with apoptosis in the Tslc1-/- mice.  On the other hand, the spermatogonia and the Sertoli cells, as well as the interstitial cells, were essentially unaffected.  In the Tslc1+/+ mice, TSLC1/IGSF4 expression was observed in the spermatogenic cells from the intermediate spermatogonia to the early pachyten spermatocytes and from step-7 or later spermatids.  These findings suggest that TSLC1/IGSF4 expression is indispensable for the adhesion of spermatocytes and spermatids to Sertoli cells and for their normal differentiation to mature spermatozoa.
Keywords: Tslc1 Igsf4 knock out mice testis

overall_design: The protocol used for the sample preparation and microarray processing is available from Affymetrix (Santa Clara, CA, USA).  Briefly, 3 ug purified RNA, extracted from the testis from Tslc1+/+ and Tslc1-/- mice of 16-week-old, was reverse-transcribed with Superscript II reverse transcriptase (Invitrogen) using the primer T7-dT24 containing a T7 RNA polymerase promoter.  After a second strand of cDNA was synthesized using RNase H, Escherichia coli DNA polymerase, and E. coli DNA ligase, in vitro transcription was carried out on the cDNA to produce biotin-labeled cRNA with a MEGAscript High Yield Transcription Kit (Ambion, Austin, TX, USA) as recommended by the manufacturer.  After the cRNA was linearly amplified with T7 polymerase, the biotinylated cRNA was cleaned with an RNeasy Mini Column (Qiagen), fragmented to 50 to 200 nucleotides, and then hybridized to Mouse Genome U74A ver.2 arrays (Affymetrix).  The stained microarray was scanned with a GeneArray Scanner (Affymetrix), and the signal was calculated with Affymetrix software, Microarray Suite 5.0.  All of the data were scaled with the global scaling method to adjust the target intensity to 1,000.

first: Daisuke

last: Yamada

first: Midori

last: Yoshida

first: Yuko

middle: N

last: Williams

first: Takeshi

last: Fukami

first: Shinji

last: Kikuchi

first: Mari

last: Masuda

first: Tomoko

last: Maruyama

first: Tsutomu

last: Ohta

first: Dai

last: Nakae

first: Akihiko

last: Maekawa

first: Tadaichi

last: Kitamura

first: Yoshinori

last: Murakami


title: Murine intestinal lymphoid tissue infected with Yersinia enterocolitica

status: Public on May 04 2006

city: St. Louis

first: Scott

middle: Allyn

last: Handley

state: MO

address: 660 South Euclid Avenue

department: Molecular Microbiology

institute: Washington University

summary:
To gain a comprehensive view of the host response to pathogens within these tissues, we determined the transcriptional profiles of intestinal lymphatic tissue infected with Y. enterocolitica. Expression analysis using Affymetrix GeneChips revealed a complex host response in the Peyer’s patches (PP) and mesenteric lymph nodes (MLN) following oral infection with Y. enterocolitica.
Keywords: Disease state analysis

overall_design: Peyer's patches and mesenteric lymph nodes were surgically removed from uninfected (control) and infected (experimental) mice at 12 hours, day 2, 4 and 7 post oral infection. Tissue samples from 10 mice per time-point were combined. Total RNA was extracted using the Trizol method prior to total cDNA syntesis, labeling and hybridization to Affymetrix MGU74Av2 GeneChips. Data was processed and analyzed using MAS 5.0 and custom analysis protocols. Samples from Peyer's patches and mesenteric lymph nodes are included in this series.

first: Peter

middle: H

last: Dube

first: Virginia

last: Miller


title: Analysis of the mammary gland transcriptome in wild type C57BL/6J mice

status: Public on Oct 01 2006

city: Davis

first: Juan

middle: F.

last: Medrano

state: CA

address: One Shields Ave

department: Animal Science

institute: University of California

summary:
This study was performed to identify transcripts that are differentially expressed in the mammary gland at 4 stages of developmental (virgin, pregnant, lactating and involution) in wild type C57BL/6J mice.
Keywords: developmental stage

overall_design: Whole mammary glands No4 (inguinal) were obtained from female mice at 4 stages of development: Virgin (puberty, 6 wks of age), Pregnant (14 days of pregnancy), Lactating (day 10 postpartum) and Involution (4 days post weaning of pups). Three biological replicates were obtained from Virgin females and two biological replicates for the three other stages.

first: Micha

last: Ron

first: Jeffrey

last: Gregg


title: Lung Development Timecourse

status: Public on Apr 30 2006

first: Elizabeth

middle: D

last: George

address: 715 Albany St

department: Bioinformatics

institute: Boston University

summary:
Time course study of lung development in normal oxygen and 10% oxygen conditions in order to study the relationship between oxidant stress and gene expression changes in the developing lung around birth.  Comparison to normal liver as control tissue not under oxidant stress.
Keywords: time course

overall_design: 3 mice at each of 5 time points: fetal day 21, 2, 6, 12 and 24 hours after birth.  Lung samples taken from pre- and post-natal mice in normal oxygen conditions.  3 mice at each of first 3 time points: fetal day 21, 2, and 6 hours after birth.  Liver samples from mice in normal oxygen conditions.  Lung samples from mice birthed into 10% oxygen.

first: Martin

last: Joyce-Brady


title: Differential expression in testis in 4 house mouse species

status: Public on Apr 01 2006

city: Thuwal

first: Christian

middle: Robert

last: Voolstra

address: Red Sea Research Center

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary:
RNA from testis from 4 mus musculus species was hybridized on affymetrix gene chip U74Av2. Subspecies-specific differences in expression level were then extracted by conditioning on outcomes to cases where the expression in one subspecies differed significantly from all others but these did not differ significantly among each other.
Keywords: other

first: Bettina

last: Harr

first: Chris

first: Diethard

last: Tautz

first: Sonja

last: Ihle

first: Werner

last: Mueller

first: Francois

last: Bonhomme


title: Expression data from mouse primary visual cortex under different deprivation conditions

city: Cambridge

first: gabriel

last: kreiman

address: 77 Massachusetts Avenue MIT 46-5155

department: BCS

institute: MIT

summary:
Two key paradigms for examining activity-dependent development of primary visual cortex (V1) involve either reduction of activity in both eyes via dark-rearing (DR) or imbalance of activity between the two eyes via monocular deprivation (MD).
Combining DNA microarray analysis with computational approaches, RT-PCR, immunohistochemistry and physiological imaging, we find that DR leads to (i) upregulation of genes subserving synaptic transmission and electrical activity, consistent with a coordinated response of cortical neurons to reduction of visual drive, and (ii) downregulation of parvalbumin, implicating parvalbumin-expressing neurons as underlying the delay in cortical maturation after DR. MD partially activates homeostatic mechanisms but differentially upregulates gene systems related to growth factors and neuronal degeneration, consistent with reorganization of connections after MD. A binding protein of Insulin-like Growth Factor 1 is highly upregulated after MD, and exogenous application of IGF1 prevents the physiological effects of MD on ocular dominance plasticity examined in vivo.
Keywords: multiple comparisons

overall_design: We compared gene expression using Affymetrix microarray chips for normal reared animals, dark-reared animals and monocularly deprived animals

first: Daniela

last: Tropea

first: Gabriel

last: Kreiman

first: Mriganka

last: Sur

first: Sam

last: Horng

first: Hongbo

last: Yu


title: whole brain gene expression pattern

status: Public on Apr 05 2006

city: Aurora

first: Sanjiv

middle: Vijay

last: Bhave

state: CO

address: 12800 E. 19th Avenue

department: Pharmacology

institute: UCDHSC

summary:
We have used commercially available oligonucleotide arrays to measure the relative expression levels of >10,000 genes and ESTs. Recent evidence
suggested certain advantages of performing such expression experiments on two or more different platforms of oligonucleotide arrays.  Here we have used two
oligonucleotide platforms, MG U74Av2.0 arrays from Affymetrix and CodeLink UniSet1 from GE Healthcare, to assess whole brain gene expression patterns in
naive C57BL/6 and DBA/2J mice.  C57BL/6J (n = 5) and DBA/2J (n = 4) male mice, 25-30 g body weight, were obtained from Jackson Laboratories.  Animals were group-housed and quickly sacrificed by CO2 exposure according to a protocol approved by the UCHSC IACUC.
Brains were rapidly removed and stored at -80oC until use. Whole brain was homogenized in lysis buffer using a Polytron, and total RNA was isolated using the RNeasy Midi Kit (Qiagen) following the protocol supplied by the manufacturer.  An additional clean-up of total RNA was carried out using the RNeasy Mini Kit (Qiagen).
Using the protocol supplied by the manufacturer, double-stranded cDNA was synthesized from the total RNA (4 ug of total RNA from an individual mouse brain was used for each array) and was used to obtain biotin-labeled cRNA by an in vitro transcription reaction.  Biotin-labeled cRNA was recovered using the RNeasy kit.  Biotin-labeled cRNA from each mouse was then fragmented and hybridized with two separate (duplicate) CodeLink BioArrays.  The average of the gene expression intensity values for each probe set from these technical replicates was used for data analysis.  The BioArrays were subsequently stained for 30 min with Cy5-Streptavidin and washed prior to scanning. For MG U74Av2 arrays,double-stranded cDNA was synthesized from 5 ug of total RNA, using the protocol supplied by the manufacturer, and used to obtain biotin-labeled cRNA by an in vitro transcription reaction.  Biotin-labeled cRNA was then fragmented and the quality of the fragmented cRNA was assessed using Test2 chips prior to hybridization with the Affymetrix arrays.  Hybridization of the cRNA with the Affymetrix arrays was carried out according to the manufacturer's protocol.  The arrays were stained with streptavidin-phycoerythrin conjugate and scanned by a GeneArray scanner.
Keywords: other

middle: V

first: Paula

last: Hoffman

first: Natalie

last: Lassen

first: Vasilis

last: Vasiliou

first: Richard

last: Deitrich

first: Boris

last: Tabakoff


title: The AIN-centered DCN of delayed-type eyeblink conditioned mice

status: Public on Apr 04 2006

city: Wako-shi

first: Jin-Sung

last: Park

state: Saitama

address: 2-1 Hirosawa

department: BSI

institute: RIKEN

summary:
Anterior interpositus nucleus (AIN) is a proposed site of memory formation of eyeblink conditioning. A large part of the underlying molecular events, however, remains unknown. To elucidate molecular mechanisms, we examined transcriptional changes in the AIN of mice trained with delayed-type eyeblink conditioning

The data are not directly comparable between GSE3651 and GSE3652, given the different experimental time periods and amounts of cRNA used for hybridizations.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Jin

middle: S

first: Shin

middle: I

last: Nishimura

first: Shigeyoshi

last: Itohara


title: Comparison of neural stem cell lines overexpressing Nurr1 to clonal controls

status: Public on May 03 2006

city: Stockholm

first: Kyle

middle: Matthew

last: Sousa

address: Scheeles väg 1 A1 Plan 2

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Molecular Neurobiology

summary:
The orphan nuclear receptor Nurr1 has been shown to be critical for the development of ventral midbrain dopaminergic neurons. Consequently, the development of ES cells overexpressing Nurr1 has raised hope for the development of cell replacement therapies for Parkinson's Disease to replace degenerated dopaminergic neurons.  However, the molecular consequences of Nurr1 on gene expression in these cells remain unknown.  To address this, stable, clonal, c17.2 neural stem cell lines were established that overexpressed the orphan nuclear receptor Nurr1 (clone 42 & clone 48) or parental control cell line (puroB & puroD, respectively).
Keywords: genetic modification

overall_design:
Stable neural stem cell lines were grown in proliferating conditions and matched for further microarray analysis based on their similar proliferation rates:
clone 42(c42) vs. puroB(pB)
clone 42(c48) vs. puroD(pD)

middle: M

first: Helena

last: Mira

first: Anita

last: Hall

first: Lottie

last: Sjostrand

first: Moriake

last: Kusakabe

first: Ernest

last: Arenas


title: Cross-platform study

first: Winston

middle: Patrick

last: Kuo

summary:
Gene expression microarrays have made a profound impact in biomedical research. The diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and in house platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by QRT-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent pre-processing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.

This SuperSeries is composed of the SubSeries listed below.

middle: P

first: Fang

last: Liu

first: Connie

middle: L

last: Cepko

first: Tor-Kristian

last: Jensen

first: Lucila

last: Ohno-Machado

first: Roger

last: Bumgarner

first: Sangdun

last: Choi

first: George

last: Church

first: Roderick

first: JuHan

last: Kim

first: Steve

last: Perrin

first: Paola

last: Ricciardi-Castagnoli

first: Brian

last: Seed

first: Eivind

last: Hovig

first: Claudio

last: Punzo

first: Micheal

last: Lombardi

first: Jasit

last: Sarang

first: Malini

last: Maysuria

last: Serikawa

first: Sun

middle: Y

last: Lee

first: Donald

last: McCrann

first: Jason

last: Kang

first: Jeffrey

last: Shearstone

first: Jocelyn

last: Burke

first: Daniel

first: Xiaowei

last: Wang

first: Glenn

last: Short

first: Mason

last: Freeman

first: Jeff

last: Trimarchi

first: Mark

middle: E

last: Whipple

first: Trent

last: Rector


title: Microarray expression from isolated germ cell types

city: Pullman

first: Lizhong

last: Yang

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

summary:
Analysis of cell-specific expression patterns produced unique and characteristic groups of transcripts that provide greater insight into the activities, biological and chronological, of testicular cell types during the progression of spermatogenesis
Keywords: Cell type comparison

overall_design: Four types of mouse germ cells


title: The AIN-centered DCN of delayed-type eyeblink conditioned mice: 7-d paired and 7-d unpaired training groups

first: Jin-Sung

last: Park

summary:
Anterior interpositus nucleus (AIN) is a proposed site of memory formation of eyeblink conditioning. A large part of the underlying molecular events, however, remains unknown. To elucidate molecular mechanisms, we examined transcriptional changes in the AIN of mice trained with delayed-type eyeblink conditioning
Keywords: 7-d paired training, 7-d unpaired training, delayed-type eyeblink conditioning of mice, anterior interpositus nucleus-centered deep cerebellar nuclei

overall_design: 7-d paired training group: Mice received a surgery for implanting four Teflon-coated stainless-steel wires in their left eyelid and a headstage on their head. After 3days’ recovery, they were trained with paired paradigm of conditioned stimulus (CS) and unconditioned stimulus (US) for 7 days: A 352-ms tone CS (1kHz, 83~85dB) was delivered first and a 100ms periorbital shock US (100kHz square pluses) were delivered with 252ms after the onset of CS, and they co-terminated. In case of 7-d unpaired training group, A CS and a US were delivered in an explicitly unpaired, pseudorandomized manner for 7 days. After the last trial was given, anterior interpositus was immediately sampled in 10 to 30 min from the sacrifice.

first: Shin-ichi

last: Nishimura

first: Shigeyoshi

last: Itohara


title: gene expression profiling of mouse model of Helicobacter-induced gastric cancer

status: Public on Apr 13 2006

city: New York

first: Shigeo

last: Takaishi

address: 1130 St. Nicholas Avenue, ICRC 901A

department: Medicine (Division of Digestive and Liver Disease)

institute: Columbia University, College of Physicians and Surgeons

summary:
We have previously reported human gastrin overexpressing transgenic mice (=INS-GAS mice) and Helicobacter felis (=H.felis) infection synergistically accelerated gastric cancer in mice stomachs.  (Wang et al 2000)  Using this mouse model, we employed microarray analysis of gene expression profiling to identify gastric cancer-specific genes.
Keywords: disease state analysis

overall_design:
30 male INS-GAS mice (FVB/N background) were divided into groups: 15 mice were infected with H.felis at the age of 2-3 months and another 15 mice were not infected. 30 male non-transgenic FVB/N mice were also divided into 2 groups: 15 mice were infected with H.felis at the age of 2-3 months and another 15 mice were not infected. All mice were sacrificed after 6 months of H.felis infection, and total RNAs were extracted from whole stomachs.
    Histological analysis confirmed all of the stomachs in H.felis infected INS-GAS mice (=INSGAS+Hf) had intra-epithelial gastric cancer, and some of them also had invasion into submucosa, but none of them had distant metastatic lesions. Other 3 control groups had following histology in stomachs. (1) non-transgenic mice with H.felis infection (=FVB+Hf): severe intestinal metaplasia and/or mild dysplasia. (2) INS-GAS mice without infection (=INSGAS wt): severe atrophic gastritis and/or mild intestinal metaplasia (3) non-transgenic mice without infection (=FVB wt): normal stomach. Total RNAs extracted from each mouse in 4 different groups were used for microarray analysis of Affymetrix GeneChip.
      Up- or down-regulated genes  in INSGAS+Hf group compared with all 3 control groups (FVB+HF, INSGAS wt and FVB wt) may represent gastric cancer-specific genes.

first: Timothy

middle: C


title: Myc Activation in Beta Cells in vivo

city: Ann Arbor

first: Elizabeth

middle: R

last: Lawlor

state: MI

address: 1600 Huron Parkway, NCRC Bldg 520

institute: University of Michigan

summary:
Deregulated expression of the Myc transcription factor is a frequent causal mutation in human cancer. Thousands of putative Myc target genes have been identified in in vitro studies, indicating that Myc exerts highly pleiotropic effects within cells and tissues. However, the complexity and diversity of Myc gene targets has confounded attempts at identifying which of these genes are the critical targets mediating Myc-driven tumorigenesis in vivo. Acute activation of Myc in a reversibly switchable transgenic model of Myc-mediated β cell tumorigenesis induces rapid tumor onset whereas subsequent Myc de-activation triggers equally rapid tumor regression. Thus, sustained Myc activity is required for tumor maintenance. We have used this reversibly switchable kinetic tumor model in combination with high-density oligonucleotide microarrays to develop an unbiased strategy for identifying candidate Myc-regulated genes responsible for maintenance of Myc-dependent tumors. Consistent with known Myc functions, some Myc-regulated genes are involved in cell growth, cycle and proliferation. In addition, however, many Myc-regulated genes are specific to β cells, indicating that a significant component of Myc action is cell-type specific. Finally, we identify a very restricted cadre of genes whose expression is inversely regulated upon Myc activation-induced tumor progression and de-activation-induced tumor regression. By definition, such genes are candidates for tumor maintenance functions. Combining reversibly switchable, transgenic models of tumor formation and regression with genomic profiling offers a novel strategy with which to deconvolute the complexities of oncogenic signaling pathways in vivo
Keywords: in vivo kinetic analyis myc function

overall_design: Transgenic mice expressing both the MycER and BclXL transgenes under the regulation of an insulin promoter were systemically injected with 4-hydroxytamoxifen to acutely activate MycER. Mice were sacrificed at 2, 4, 8 or 24hrs after injection or at time 0 (untreated control mice). For analysis of the effects of sustained Myc activation mice received daily doses of tamoxifen for 21days. Tumor regression was analysed by isolation of islets 2, 4 or 6 days after cessation of a 21 day course of treatment. All conditions were repeated in triplicate and gene expression levels compared between treated and untreated and activation and regression samples.

first: Gerard

last: Evan

first: Laura

last: Soucek

first: Lamorna

last: Brown-Swigart

first: Ksenya

last: Shchors

first: Carl

middle: U

last: Bialucha


title: microarray profiling of potential calorie restriction mimetics

status: Public on Mar 22 2006

city: Riverside

first: Stephen

middle: R.

last: Spindler

department: Biochemistry

institute: University of California, Riverside

summary:
Mice and diets.  One-month-old male mice of the long-lived B6C3F1 strain were purchased from Harlan (Indianapolis, IN) and maintained as described after weaning (15).  Mice were housed in groups of 4 per cage and fed a non-purified diet, PMI Nutrition International Product #5001 (Purina Mills, Richmond, IN).  At 5 months of age, the mice were individually housed, and randomly assigned to one of two groups, control (CON) or long-term CR (LTCR).  CON mice were fed 93 kcal per week of a defined control diet (AIN-93M, Diet No. F05312, BIO-SERV).  LTCR mice were fed 52.2 kcal per week of a defined CR diet (AIN-93M 40% Restricted, Diet No. F05314, BIO-SERV).  The LTCR mice consumed approximately 40% fewer calories than mice in the CON mice.  The CR diet was enriched so that the CR mice consumed approximately the same amount of protein, vitamins, and minerals per gram body weight as the control mice.  Experimental design.  At 20 months of age, cohorts of mice in the CON group were randomly assigned to one of 7 experimental groups (Fig. 1).  A CON group continued to be fed 93 kcal per week of control diet for 8 weeks.  A CR8 group was fed 77 kcal per week of CR diet for 2 weeks, followed by 52.2 kcal per week of CR diet for 6 weeks.  The remaining dietary groups were fed the control diets containing, respectively, metformin (MET; Sigma, St. Louis, MO), glipizide (GLIP; Sigma), GLIP plus MET (GM), rosiglitazone (ROS; Avandia, SmithKline Beecham) or soy isoflavone extract (SOY; NOVASOY 400, Life Extension Foundation) for 8 weeks at the dosages indicated in Table 1.  The drugs were mixed with powdered control diet and cold-pressed into one gram pellets (BIO-SERV Inc.).  At 0900, all mice were fed 2/7 of the weekly allotment of food on Monday and Wednesday and 3/7 on Friday.  The mice had free access to acidified tap water.  They were fasted for 48 hours and killed by cervical dislocation at 22 months of age.  No signs of pathology were detected in the animals used for the studies reported (n=4 per group).  Organs were removed rapidly, flash frozen, and stored in liquid nitrogen.  The weights of the mice were monitored bi-weekly.  Mouse weights are given in Table 1.
Measurement of specific mRNA levels.  Liver total RNA was isolated as described from livers of pathology-free mice in each group (n=4 per group) (13). mRNA levels were measured using Affymetrix mouse U74Av2 arrays according to standard Affymetrix protocols (Affymetrix).
Probe set expression measurement and normalization.  After hybridization and scanning, raw image files were converted to probe set data (*.CEL files) using Microarray Suite (MAS 5.0). Probe set data from all 32 arrays were simultaneously analyzed with the Robust multichip Average (RMA) method to generate normalized expression measures for each probe set (Fig. 2; Ref. 24)  The data were further filtered to exclude probe data sets that were “Absent” across all 32 arrays according to the MAS 5.0 detection algorithm (1,47).
Keywords = CR mimetics
Keywords = microarray profiling
Keywords = drug discovery
Keywords = gene-expression biomarkers
Keywords: other

first: Joseph

last: Dhahbi

first: Patricia

last: Mote


title: Virus Induced Airway Hyperreactivity and Goblet Cell Metaplasia Phenotypic Extremes (CB6F2/J)

status: Public on Mar 30 2006

first: Anand

middle: Champak

last: Patel

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

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

summary:
Mice representing phenotypic extremes of airway hyperreactivity and goblet cell metaplasia post-Sendai virus infection were identified from a 500 mouse F2 cohort (CB6F2/J).  Whole lung RNA from 3 mice at each extreme was analyzed via microarray for gene expression.  Subsequent pairwise comparisons between arrays allowed the identification of genes differentially expressed with respect to the disease phenotypes (airway hyperreactivity and goblet cell metaplasia).
Keywords: disease state analysis

overall_design: 3 mice at each phenotypic extreme were analyzed.

first: Jeffrey

middle: D

last: Morton

first: Edy

last: Kim

first: Yael

last: Alevy

first: Suzanne

last: Swanson

first: Jennifer

last: Tucker

first: Guaming

last: Huang

first: Eugene

last: Agapov

first: Thomas

last: Phillips

first: John

last: Allard

first: Karim

last: Dabbagh

first: Gary

last: Peltz

first: Michael

middle: J

last: Holtzman


title: Differential expression: associative and nonassociative learning

status: Public on Mar 20 2006

city: Philadelphia

first: Ted

last: Abel

state: PA

address: 415 S. University Ave

department: Biology

institute: University of Pennsylvania

summary:
Hippocamus and amygdala expression was examined in naïve, conditioned stimulus exposed, and fear conditioned mice 30 minutes after behavioral manipulation
Keywords: comparison of 3 groups x 2 brain regions

overall_design: six to 10 replicates were used in each group


title: p300-mediated gene expression during muscle cell survival

status: Public on Mar 01 2006

city: Portland

first: David

last: Kuninger

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Biochemistry and Molecular Biology

institute: Oregon Health & Science University

summary:
Type of experiment:
The primary focus of these studies is to define the transcriptional network regulated by ectopic expression of the transcriptional co-activator protein, p300, in order to define its mechanism(s) of action in promoting muscle cell survival.

Experimental factors:
Our laboratory has generated a murine C2-derived myoblast cell line stably expressing an IGF-II cDNA in antisense orientation (C2AS12 cells).   These cells proliferate normally in serum-rich growth medium but progressively die in low-serum differentiation medium.  Ectopic expression of p300 (a transcriptional co-coactivator with acetyltransferase activity) prevents the progressive cell death induced by serum withdrawal, however, the mechanism of this action is not understood.  Further, over-expression of a mutated form of p300, lacking at protein interaction domain (deltaTAZ2), failed to maintain cell viability although it retains catalytic activity.   Wild-type and mutant p300 are delivered using recombinant adenoviruses (Ad-p300 and Ad-p300deltaTAZ2) and their expression is regulated by a second recombinant adenovirus encoding the tetracycline transactivator protein (Ad-tTA), affording regulated expression of p300 forms (Tet-off system) and providing a control for viral load.

Using these reagents the overall experiment was as follows:  Three parallel series of C2AS12 cells were infected with (1) wt p300 + tTA, (2) p300deltaTAZ2 +tTA, (3) wt p300 +tTA +doxycycline.  Infected cells were grown to confluence followed by transfer to low-serum differentiation medium (T0).   Cell were isolated at this point and following 24 (T24) hours incubation for RNA isolation.  Companion dishes of cells were included for analysis by immunocytochemistry to ensure regulated transgene expression and cell viabilities.
Keywords: time course

overall_design: 6 biological replicates, representing 3 treatment groups, two timepoints and 2 biological outcomes (cell survival with p300wt and apoptotic cell death with p300wt+Dox and p300mut)

first: Peter

last: Rotwein


title: Hoxc13 overexpression in skin

status: Public on Mar 07 2006

city: Charleston

first: Alexander

last: Awgulewitsch

state: SC

address: 173 Ashley Ave

institute: Medical University of South Carolina

summary:
A study of the effects of Hoxc13 overexpression in skin using Hoxc13 transgenic mice (GC13) known to develop severe hair growth defects and alopecia. Total skin from GC13 mice 5 dpn is compared to total skin from normal FVB mice 5 dpn using Affymetrix HG-U74Av2 GeneChips.
Keywords: repeat sample

first: Ron

last: Peterson

first: Christopher

last: Potter

first: Jeremy

last: Barth

first: Nathan

last: Pruett

first: Donna

last: Jacobs

last: Kern

first: William

last: Argraves

last: Sundberg


title: The AIN-centered DCN of delayed-type eyeblink conditioned mice: 3-d paired training and sham negative control groups

first: Jin-Sung

last: Park

summary:
Anterior interpositus nucleus (AIN) is a proposed site of memory formation of eyeblink conditioning. A large part of the underlying molecular events, however, remains unknown. To elucidate molecular mechanisms, we examined transcriptional changes in the AIN of mice trained with delayed-type eyeblink conditioning
Keywords: 3-d paired training, sham negative control, delayed-type eyeblink conditioning of mice, anterior interpositus nucleus-centered deep cerebellar nuclei

overall_design:
3-d paired training group: Mice received a surgery for implanting four Teflon-coated stainless-steel wires in their left eyelid and a headstage on their head. After 3days’ recovery, they were trained with paired paradigm of conditioned stimulus (CS) and unconditioned stimulus (US) for 3days: A 352-ms tone CS (1kHz, 83~85dB) was delivered first and a 100ms periorbital shock US (100kHz square pluses) were delivered with 252ms after the onset of CS, and they co-terminated. After the last trial was given, anterior interpositus was immediately sampled in 10 to 30 min from the sacrifice.

Sham negative control group: Mice received a surgery for implanting four Teflon-coated stainless-steel wires in their left eyelid and a headstage on their head. After recovery, anterior interpositus nucleus-centered deep cerebellar nuclei were immediately sampled in 10 to 30 min from the sacrifice.

~10-15 anterior interpositus-centered deep cerebellar nuclei ipsilateral to the eye implanted with four wires were pooled into the same sham control or training group and subjected to microarray analysis.

first: Shin-ichi

last: Nishimura

first: Shigeyoshi

last: Itohara


title: Mitochondrial biogenesis induced by PGC-1alpha

status: Public on Apr 03 2006

first: Vamsi

middle: K.

last: Mootha

address: 7 Cambridge Center

department: Medical and Population Genetics

institute: Broad Institute

summary:
Microarray time-course of mouse myotubes transduced with the transcriptional co-activator PGC-1alpha, which is known to induce mitochondrial biogenesis in muscle cells.
Keywords: time course

overall_design: Cultured mouse myoblasts (C2C12 cells) were differentiated into myotubes and on day 3 were infected with an adenovirus expressing either green fluorescent protein (GFP) or PGC-1alpha.  Gene expression was measured at three time points (days 0, 1, 2, 3) in biological triplicate.

first: Sarah

last: Calvo


title: Analysis of expression in SOD1 transgenic mouse spinal cord

status: Public on Mar 09 2006

city: Chicago

first: Thomas

last: Lukas

state: IL

address: 303 E. Chicago Ave

department: MPBC

institute: Northwestern University

summary:
mRNA expression in the spinal cords of the G93A-SOD1 familial ALS transgenic mouse model was compared to that in nontransgenic (Normal mouse) and transgenic mice expressing wild-type (WT)SOD1.  Gene Ontology (GO)analysis was used to characterize differences in expression between G93A-SOD1 mouse and nontransgenic mouse spinal cord. Changes in multiple GO categories were found.  Many of these were associated with subsystems involving cell-cell communication and intracellular signal transduction.  Expression profiles of mice expressing WT-SOD1 did not differ from nontransgenic mice.  In contrast, protein profiling using proteomics technology indicated changes in mitochondrial protein expression in the G93A-SOD1 mouse spinal cord that were not found in the mRNA expression analysis.
Keywords: Disease state analysis, time course, transgenic mice

overall_design: Spinal cord mRNA expression was profiled using Affymetrix gene chips.  75-day old animals expressing G93A-SOD1 are presymptomatic, while 110-day animals display tremor and partial paralysis characteristic of ALS.  WT-SOD1 animals exhibit no disease phenotype at 75 or 110 days. Nontransgenic mice at 75 and 110 days served as controls.

first: WeiWei

last: Luo

first: Teepu

last: Siddique

first: Haihong

last: Mao

first: Natalie

last: Cole


title: Transcriptional adaptation to cystic fibrosis transmembrane conductance regulator deficiency

status: Public on Mar 24 2006

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

summary:
Cystic fibrosis, the most commonly inherited lethal pulmonary disorder in Caucasians, is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR). To identify genomic responses to the presence or absence of CFTR in pulmonary tissues in vivo, microarray analyses of lung mRNAs were performed on whole lung tissue from mice lacking (CFTR(-)) or expressing mouse CFTR (CFTR(+)). Whereas the histology of lungs from CFTR(-) and CFTR(+) mice was indistinguishable, statistically significant increases in the relative abundance of 29 and decreases in 25 RNAs were identified by RNA microarray analysis. Of RNAs whose expression was consistently altered by the absence of CFTR, functional classes of genes influencing gene transcription, inflammation, intracellular trafficking, signal transduction, and ion transport were identified. RNAs encoding the transcription factor CCAAT enhancer-binding protein (CEBP) delta and interleukin (IL) 1beta, both known to regulate CFTR expression, were induced, perhaps indicating adaptation to the lack of CFTR. RNAs mediating lung inflammation including calgranulin-S100 family members, IL-1beta and IL-4, were increased. Likewise, expression of several membrane transport proteins that interact directly with CFTR were increased, suggesting that CFTR-protein complexes initiate genomic responses. Absence of CFTR influenced the expression of genes modulating diverse pulmonary cell functions that may ameliorate or contribute to the pathogenesis of CF.
Keywords: Genotype comparison

overall_design: Lungs from sex-matched littermates at 3, 6, and 11 weeks of agewere carefully dissected and the conducting airways and mediastinal structures removed.


title: P104 mouse non-deprived vs. deprived visual cortex

status: Public on Feb 24 2006

city: Boston

first: Marta

last: Majdan

address: 220 Longwood Ave.

department: Neurobiology

institute: Harvard Medical School

summary:
Wild-type (C57Bl6) mice underwent monocular enucleation at P100 and were sacrificed 4 days later at P104. Bilateral (non-deprived and deprived) visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).
Keywords: repeat

overall_design: Gene expression in pooled samples from 3 non-deprived (ipsilateral to monocular enucleation) and 3 deprived (contralateral to monocular enucleation) visual hemispheres was compared.

first: Carla

last: Shatz


title: P46DR (dark reared) mouse non-deprived vs. deprived visual cortex

summary:
Wild-type (C57Bl6) mice were dark reared from birth to P42, then underwent monocular enucleation at P42. They were then placed in a normal light-dark environment for 4 days, after which they were sacrificed (at P46). Visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).
Keywords: repeat

overall_design: Gene expression in pooled samples from 2 non-deprived (ipsilateral to monocular enucleation) and 2 deprived (contralateral to monocular enucleation) visual hemispheres was compared. Note: two additional cross-animal comparisons were made.


title: P18, P24, P46, P104, and P46DR (dark reared) non-deprived vs. deprived visual cortex

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


title: P24 mouse non-deprived vs. deprived visual cortex

summary:
Wild-type (C57Bl6) mice underwent monocular enucleation at P20 and were sacrificed 4 days later at P24. Bilateral (non-deprived and deprived) visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).
Keywords: repeat

overall_design: Gene expression in pooled samples from 4 non-deprived (ipsilateral to monocular enucleation) and 4 deprived (contralateral to monocular enucleation) visual hemispheres was compared.


title: P46 mouse non-deprived vs. deprived visual cortex

summary:
Wild-type (C57Bl6) mice underwent monocular enucleation at P42 and were sacrificed 4 days later at P46. Bilateral (non-deprived and deprived) visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).
Keywords: repeat


title: P18 mouse non-deprived vs. deprived visual cortex

summary:
Wild-type (C57Bl6) mice underwent monocular enucleation at P14 and were sacrificed 4 days later at P18. Bilateral (non-deprived and deprived) visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL).
Keywords: repeat

overall_design: Gene expression in pooled samples from 5 non-deprived (ipsilateral to monocular enucleation) and 5 deprived (contralateral to monocular enucleation) visual hemispheres was compared.


title: Innate vs. adaptive lymphocyte gene expression

status: Public on Jan 31 2006

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

summary:
Three innate (B1-B, NKT, CD8aaT cells) and adaptive (B2-B, CD4T, CD8abT cells) cell-types were sorted by FACS.  Three biological replicates for NKT, CD4T, CD8aaT, CD8abT cells and two biological replicates for B1 and B2 cells were generated and the expression profiles were determined using Affymetrix Mu74Av2 chip.  Comparisons between the sample groups allow the identification of genes differentially expressed between the innate and adaptive cell-types.
Keywords: cell type comparison, innate vs. adaptive

overall_design: 3 biological replicates for NKT, CD4T, CD8aaT, CD8abT cells and 2 biological replicates for B1, B2 cells were analyzed

first: Tetsuya

last: Yamagata

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Interferon-gamma timecourse in IFNg-/- and SOCS1-/-IFNg-/- mouse livers

status: Public on Feb 14 2006

city: Parkville

first: Sam

last: Wormald

state: Victoria

address: 1G Royal Parade

department: Cancer and Haematology

country: Australia

institute: The Walter and Eliza Hall Institute

summary:
Timecourse analysis of Interferon-Gamma (IFNg) signalling in mice deficient for IFNg or both IFNg and Suppressor of Cytokine Signalling-1 (SOCS1).
Keywords: time course expression analysis

overall_design: 8 experimental timepoints (0.5h, 1h, 2h, 4h, 12h, 16h, 24h, 48h), 2 PBS control timepoints (4h and 12h), 1 negative control point (not injected), 2 genotypes (IFNg-/- and SOCS1-/-IFNg-/-), no replicates.

first: Samuel


title: Hypoxic response in wild type and HIF-1alpha null hepatoctyes

status: Public on Jan 28 2006

city: La Jolla

first: Jared

last: Allen

address: 9500 Gilman Drive, 0412

department: Bioengineering

institute: University of California, San Diego

summary:
The primary aim of this study was to evaluate the changes in hepatocyte gene expression under short-term hypoxic conditions in wild type and HIF-1a null cultures.  To this end, hypoxia treated cultures were subjected to incubation with 1% O2/5% CO2/94% N2 at 37° C for eight hours prior to RNA isolation.  Duplicate normoxic controls were established from separate animals wherein cultures were untreated and treated with Adbgal.  Biological triplicates of wild type and HIF-1a null cultures were placed under hypoxic conditions and subsequently processed for microarray analysis.  A total of 10 microarray hybridizations were performed.
Keywords: repeat sample

middle: W

first: Salman

last: Khetani

first: Randall

middle: S

last: Johnson

first: Sangeeta

middle: N

last: Bhatia


title: Oligonucleotide microarray analysis of H-2b AND-TCR-transgenic thymocytes and C57BL/6 thymocytes

city: Chuo-ku

first: Tsutomu

last: Ohta

state: Tokyo

address: 5-1-1 Tsukiji

department: Medical Genomics Center

institute: National Cancer Center Research Institute

summary:
Screening for mouse cDNA that was highly expressed in positive-selector H-2b AND-TCR-transgenic thymocytes using Affymetrix Murine Genome arrays.
Keywords: transgenic  mouse

overall_design: 2 thymocytes, H-2b AND-TCR-transgenic thymocytes and C57BL/6 thymocytes, were analyzed by duplicate hybridization.

first: Takeshi

last: Nitta

first: Mariam

last: Nasreen

first: Takafumi

last: Seike

first: Atsushi

last: Goji

first: Izumi

last: Ohigashi

first: Tadaaki

last: Miyazaki

first: Masamoto

last: Kanno

first: Yousuke

last: Takahama


title: profiling of C/EBP targets

status: Public on Jan 26 2006

city: Los Angeles

first: sigal

last: gery

institute: Cedars-Sinai Medical Center

summary:
The zinc-inducible C/EBP expression vectors pMTa, pMTb, pMTd and pMTe were constructed by cloning the human C/EBPa, C/EBPb, C/EBPd and C/EBPe cDNAs, respectively, into the pMTCB6+ vector. NIH 3T3 cells were transfected with zinc-inducible C/EBP vectors as well as control empty vector using the GenePORTER™ transfection Reagent (GTS Inc.). Multiple polyclonal clones were obtained by selection with G418 (700 mg/ml). Clones were screened by Western blot analysis for C/EBP protein expression following induction for 16 h with ZnSO4 (100 mM). Triplicate clones of NIH 3T3 cells were induced by addition of ZnSO4 (100 mM) for 16 h to the medium. Total RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA). Biotinylated cRNAs were prepared and hybridized to murine MG_74Av2 microarrays (Affymetrix, Santa Clara, CA, USA), which contains >12 000 genes. The probed arrays were scanned with a Hewlett Packard Gene Array scanner. The scanned output image files were analyzed using Affymetrix Microarray Suite version 5.0. To identify genes that were differently expressed between the five-sample sets (empty vector, C/EBPa, C/EBPb, C/EBPd and C/EBPe) class compression analysis were performed using BRBArray Tools (developed by Richard Simon and Amy Peng Lam; http://linus.nci.nih.gov/BRB-ArrayTools.html). Medium normalization was applied to the arrays and the percent absent filter was set at 80% to exclude probe sets that were unreliable. A list of 158 genes with probability of 95% that contain no more then 10% false discoveries was generated. Of these genes, 117 were significant at the 0.001 level of univariate F-test used and the remaining 41 were significant at the 0.027 level.
Keywords: other

first: Sigal

last: Gery

first: Adrian

middle: F

last: Gombart

first: William

last: Yi

first: Chloe

last: Koeffler

first: Wolf

middle: K

last: Hofmann

first: H-Phillip


title: Effects of iFGFR1 activation in the mammary gland

status: Public on Jan 01 2006

city: Houston

first: Kathryn

last: Schwertfeger

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

summary:
This study was performed to identify genes that are regulated following iFGFR1 activation in mammary glands from MMTV-iFGFR1 transgenic mice.
Keywords: time course

overall_design: Mammary gland samples were obtained following 0, 8, 16, and 24 hours of dimerizer treatment.  Four replicates were performed, rep1 and rep2, are technical replicates and the rest are biological replicates.  The non-treated (0 hour) transgenic littermates were used as reference.

first: Jeffrey

middle: M

last: Rosen


title: Gene profiling analysis of mouse splenic DC subpopulations

status: Public on Jan 11 2006

city: baltimore

first: Drew

last: Pardoll

state: MD

address: orleans st

institute: Drew Pardoll

summary:
To characterize differences between BALB/c splenic CD11cintB220+Gr1+ PDCs (plasmacytoid dendritic cells), CD11cintB220+CD49b+ IKDCs (interferon producing killer-dendritic cells), and CD11chighB220- cDCs (conventional dendritic cells), we performed gene expression profile analysis using Affymetrix chips. We FACS-sorted BALB/c spleen DC subpopulations. Comparison of differentially expressed genes between IKDCs and cDCs vividly revealed selective expression of multiple NK-related genes in IKDCs . These included granzymes A, B, K and M, perforin, Fas ligand, and NK receptors such as NKG2A, NKG2D, Ly49 family genes, NKR-P1, NKG7, NKp46 and Mafa (KLRG1). No NK-related genes were highly expressed in the PDCs.
Keywords: Cell type comparison

overall_design: We prepared two biological samples separately for each DC population, and analyzed the expression profiles by comparing to those of cDCs (control sample).

first: Camie

last: Chan

first: Emily

last: Crafton

first: Franck

last: Housseau


title: Expression data from WT, H1c/H1d/H1e triple null ES cells

status: Public on Jan 15 2006

city: Bronx

first: Yuhong

last: Fan

address: 1300 Morris Park Ave., Chanin 402

department: cell biology

institute: Albert Einstein College of Medicine

summary:
Affymetrix expression profiling of wild-type and H1c, H1d, H1e triple null mouse embryonic stem cells revealed that loss of three linker histone subtypes (H1c, H1d and H1e) results in specific changes in gene regulation.
Keywords: cell comparison

overall_design: Affymetrix experiments performed on RNA extracted from wild-type and two H1c/H1d/H1e triple null ES cell lines and data acquired in duplicate.

first: Arthur

middle: I

last: Skoultchi


title: Gene profiling of VP16-CREB transgenic mice

status: Public on Jan 12 2006

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

summary:
Expression of VP16-CREB, a constitutively active form of CREB, in hippocampal neurons of the CA1 region lowers the threshold for eliciting the late, persistent phase of long-term potentiation (L-LTP) in the Schaffer collateral pathway. This VP16-CREB-mediated L-LTP differs from the conventional late phase of LTP in not being dependent on new transcription. This finding suggests that in the transgenic mice the mRNA transcript(s) encoding the protein(s) necessary for this form of L-LTP might already be present in CA1 neurons in the basal condition. We used high-density oligonucleotide arrays to identify the mRNAs differentially expressed in the hippocampus of transgenic and wild-type mice.
Keywords: Genetic modification, time course

overall_design:
To identify the specific gene whose induction in hippocampal neurons correlated with the facilitated L-LTP phenotype, we harvested hippocampal mRNA at time points assessed in our physiological study and carried out a gene expression analysis using oligonucleotide microarrays. To obtain a sufficient quantity of poly(A)-RNA and reduce the effect of the biological variability of the sample, hippocampi from 6 to 10 mice matched for genotype and time of induction were pooled together in each sample. The final data set included genechips for animals on dox (gene Off) and for animals that were one, two, and five weeks after removal of dox (gene On). We also included samples from wild-type mice maintained under identical conditions and from transgenic mice that expressed VP16-CREB for three weeks before turning the transgene off again for two weeks with dox (Rev, gene Off). Since the isolation of mRNA from the whole hippocampus favors genes that are more broadly over-expressed in the hippocampus of transgenic mice and, therefore, may lead to an underestimation of the total complement of genes showing an altered expression in specific hippocampal subregions, we extended our comparison between transgenic and wild-type expression profiles using microdissected CA1 regions. We obtained two samples corresponding to VP16-CREB mice three weeks after induction and one sample corresponding to wild-type mice kept in the same conditions.
These twelve mRNA samples were analyzed using Affymetrix genechips MG-U74v2 setA.

first: Susan

last: Patterson

first: Juan

last: Alarcon

first: Petra

last: Gromova

first: Manuel

last: Mata-Roig

first: Alexei

last: Morozov

first: Eric

last: Kandel


title: GSC RT-PCR amplification of 10 cells (SP & CD8 T cells), single SP cell and single-SP-cell equivalent

status: Public on Jan 02 2006

first: Carlos

middle: Almeida

last: Ramos

address: One Baylor Plaza

department: Center for Cell and Gene Therapy

summary:
GSM48315-GSM48332: Ten cells from C57Bl/6 male mouse bone marrow (SP or CD8 T cells) were sorted into individual wells of 96-well plates. The mRNA of these cells was amplified by the global single cell RT-PCR method and biotinylated targets were generated after optimal digestion with DNAse I.

GSM48333-GSM48344: Single SP cell from C57Bl/6 male mouse bone marrow were sorted into individual wells of 96-well plates. The mRNA of these single cells was amplified by the global single cell RT-PCR method and biotinylated targets were generated after optimal digestion with DNAse I.

GSM48345-GSM48349: Forty bone marrow SP cells from C57Bl/6 male mouse bone marrow, Sca-1 positive and Gr-1 negative, gated on the tip of the SP tail, were sorted into 160 microliters of lysis buffer (40 times the amount used for single cells). 4-microliter aliquots (containing the mRNA equivalent to one single cell) were dispensed into individual wells of 96-well plates. The mRNA contained in each aliquot was amplified by the global single cell RT-PCR method and biotinylated targets were generated after optimal digestion with DNAse I.

Detection of the microarray hybridization signals was done according to the standard Affymetrix protocol (antibody amplified).
Keywords = HSC
Keywords = stem cell
Keywords = SP
Keywords = side population
Keywords = CD8
Keywords = lymphocytes
Keywords = global single cell RT-PCR
Keywords = GSC RT-PCR
Keywords: parallel sample

middle: A

first: Teresa

last: Venezia

first: Yayun

last: Zheng

first: Irma

last: Parra

last: Hilsenbeck

first: Suzanne

last: Fuqua

first: Chad

last: Shaw

first: Margaret

last: Goodell


title: Apoptosis and differentiation commitment:novel insights revealed by gene profiling studies in mouse Embryonic Stem cells

status: Public on Dec 21 2005

city: BORDEAUX

first: Helene

last: BOEUF

country: France

summary:
Mouse embryonic stem (ES) cells remain pluripotent in vitro when grown in presence of Leukaemia Inhibitory Factor (LIF). LIF starvation leads to apoptosis of some of the ES-derived differentiated cells, together with p38a MAP kinase activation. Apoptosis, but not morphological cell differentiation, is blocked by a p38 inhibitor, PD 169316. To further understand the mechanism of action of this compound, we have identified its specific targets by microarray studies. We report on the global expression profiles of genes expressed at three days upon LIF withdrawal (d3) compared to pluripotent cells and of genes whose expression is modulated at d3 under anti-apoptotic conditions. We showed that at d3 without LIF cells express, earlier than anticipated, specialized cell markers and that when the apoptotic process was impaired, expression of differentiation markers was altered. In addition, functional tests revealed properties of anti-apoptotic proteins not to alter cell pluripotency and a novel role for metallothionein 1 gene which prevents apoptosis of early differentiated cells.

Keywords:  mouse ES cells; apoptosis; differentiation; p38; PD169316;
Ca++ binding proteins; Metallothionein; stress-response
Keywords: ordered

first: David

last: Duval

first: Marina

last: Trouillas

first: Christelle

last: Thibault

first: Doulaye

last: Dembele

first: Frederic

last: Diemunsch

first: Beatrice

last: Reinhardt

first: A

last: Mertz

first: Andree

last: Dierich

last: Boeuf


title: Comparison of gene expression profiles of p63 null skin versus wild type skin

status: Public on Dec 10 2005

first: Maranke

last: Koster

address: One Baylor Plaza, Room T707

department: Molecular and Cellular Biology

summary:
In the absence of p63 expression, the epidermis fails to commit to stratification, resulting in aborted skin development.  In this study, gene expression profiles of E18.5 p63 null and wt skin, were compared in an effort to identify genes that are directly or indirectly regulated by p63.
Keywords: Genetically modified mice

overall_design: E18.5 embryos were obtained from matings between p63 heterozygous mice.  RNA was isolated from the skin of two p63 null and two wild type embryos.

first: Soeun

last: Kim

first: Dennis

last: Roop


title: IR-response in Atm-/- and control lymph nodes

status: Public on Dec 20 2005

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary:
The DNA damage response network modulates a wide array of signaling pathways, including DNA repair, cell cycle checkpoints, apoptotic pathways and numerous stress signals. The ATM protein kinase, functionally missing in patients with the human genetic disorder ataxia-telangiectasia (A-T), is a master regulator of this network when the inducing DNA lesions are double strand breaks. The ATM gene is also frequently mutated in sporadic cancers of lymphoid origin. Here, we applied a functional genomics approach that combines gene expression profiling and computational promoter analysis to obtain global dissection of the transcriptional response to ionizing radiation (IR) in murine lymphoid tissue. Cluster analysis revealed six major expression patterns in the data. Prominent among them was a gene cluster that contained dozens of genes whose response to irradiation was Atm-dependent. Computational analysis identified significant enrichment of the binding site signatures of the transcription factors NF-kB and p53 among promoters of these genes, pointing to the major role of these two transcription factors in mediating the Atm-dependent transcriptional response in the irradiated lymphoid tissue. Examination of the response showed that pro- and anti-apoptotic signals were simultaneously induced, with the pro-apoptotic pathway mediated by p53, and the pro-survival pathway by NF-kB. These findings further elucidate the molecular network induced by IR and have implications for cancer management as they suggest that a combined treatment that restores the p53-mediated apoptotic arm while blocking the NF-kB-mediated pro-survival arm could be most successful in increasing the radiosensitivity of lymphoid tumors.
Keywords: ordered

first: Sharon

last: Rashi-Elkeles

first: Nir

last: Weizman

first: Chaim

last: Linhart

first: Ninette

last: Amarglio

first: Giora

last: Sternberg

first: Gideon

last: Rechavi

first: Ari

last: Barzilai

first: Ron

last: Shamir

first: Yosef

last: Shiloh


title: Growth Hormone (GH) Treatment of 3T3-F442A Adipocytes

city: Ann Arbor

first: Jessica

last: Schwartz

address: 1301 Catherine St.

department: Molecular and Integrative Physiology

institute: University of Michigan

summary:
Expression profiling of 3T3-F442A adipocytes treated with growth hormone (GH, 500 nM) or vehicle (DMEM + 1% BSA) control for 30 min., 4 hr., or 48 hr in three independent experiments. Chronic GH treatment induces metabolic changes consistent with insulin resistance in 3T3-F442A adipocytes.
Keywords: time-course

first: Jeffrey

last: Huo

first: Richard

middle: C

last: McEachin

first: David

last: States


title: 3T3 Fibrolasts

status: Public on Dec 09 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
3T3 Fibrobalasts grown in the presence of fibronectin to assess MAP kinase signalling pathways.
Keywords: other

overall_design: this experiment include 2 samples and 2 replicates


title: C2C12 Mouse Skeletal Muscle Cells Grown in Differentiation Medium for 5 Days.

summary:
C2C12 mouse skeletal muscle cells grown in differentiation medium for 5 days.
Keywords: other

overall_design: this experiment include 1 samples and 9 replicates


title: Coordinated regulation of gene expression by Brn3a in developing sensory ganglia

status: Public on Dec 24 2005

first: Eric

last: Turner

address: 9500 Gilman Dr., BSB 2077

department: Psychiatry

institute: University of California San Diego

summary:
Mice lacking the POU-domain transcription factor Brn3a exhibit marked defects in sensory axon growth and abnormal sensory apoptosis. We have determined the regulatory targets of Brn3a in the developing trigeminal ganglion using microarray analysis of Brn3a mutant mice. These results show that Brn3 mediates the coordinated expression of neurotransmitter systems, ion channels, structural components of axons and inter- and intracellular signaling systems. Loss of Brn3a also results in the ectopic expression of transcription factors normally detected in earlier developmental stages and in other areas of the nervous system. Target gene expression is normal in heterozygous mice, consistent with prior work showing that autoregulation by Brn3a results in gene dosage compensation. Detailed examination of the expression of several of these downstream genes reveals that the regulatory role of Brn3a in the trigeminal ganglion appears to be conserved in more posterior sensory ganglia but not in the CNS neurons that express this factor.
Keywords: Gene expression in the developing nervous system

overall_design: Microarrays used to compare the patterns of gene expression in the trigeminal ganglia of Brn3a knockout and wild-type mice.  Embryonic day 13.5 (E13.5) was chosen because at this point in development mutant mice exhibit major defects in sensory axon growth, but have yet to undergo the period of extensive sensory neuron death associated with later stages.

first: Sani

middle: R

last: Eng

first: Jason

last: Lanier

first: Fedtsova

last: Natalia

middle: E


title: IL10 deficiency

status: Public on Dec 31 2005

city: Hannover

first: Andre

last: Bleich

institute: Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School

summary:
Abstract: Interleukin-10-deficient (Il10-/-) mice serve as a model for inflammatory bowel disease (IBD). The severity of colitis strongly depends on the inbred strain carrying the disrupted Il10 gene: C3H/HeJBir (C3) confers disease susceptibility, whereas C57BL/6J (B6) confers resistance. Genome-wide scans with microsatellite markers on segregrating backcross and F2 populations resulted in the detection of ten colitogenic quantitative trait loci (QTL). The aim of this study was to reduce the large number of candidate genes within the QTL intervals by identifying those genes which are located within the candidate gene intervals and which are differentially expressed in the colon of IBD-susceptible and -resistant strains. Using this combination of QTL mapping and microarray analysis, we identified 16 genes which were differentially expressed between B6- and C3-Il10-/- mice and were located within the candidate gene intervals. Three of these genes (Pla2g2a, Gbp1, Cd14) showed prominent differences in expression levels between B6- and C3-Il10-/- as well as between B6 and C3 wildtype mice and were considered to be major candidate genes. Pla2g2a and Gbp1 are known to be polymorphic between C3 and B6 mice. Expression data for Cd14 were confirmed by real-time RT PCR using specified pathogen free and germfree Il10-/- mice. In conclusion, the large number of candidate genes was reduced to three major candidates by using a combination of QTL mapping and microarray analysis. All three genes play an important role in inflammatory processes and immune response.
Material & Methods:
Two independent microarray experiments were performed using SPF mice: 19 for the first experiment (4 C3 WT [GSM39296], 5 C3-Il10-/- [GSM39297], 5 B6 WT [GSM39290], 5 B6-Il10-/- [GSM39291]) and 18 for the second (4 C3 WT [GSM39295], 4 C3-Il10-/- [GSM39294], 5 B6 WT [GSM39288], 5 B6-Il10-/- [GSM39289]). The mice were euthanized by cervical dislocation. Following a ventral midline incision, the colon (including the rectum, but not the anus) was removed and flushed with PBS. Each colon was opened longitudinally with a pair of scissors, further dissected and homogenized using a micropistill in 1.5 ml peqGOLD Trifast FL. RNA was isolated according to the manufacturer´s protocol, and quality was checked using RNA Nano LabChip® technology (Agilent, Böblingen, Germany). For each of the two array experiments, equal amounts (7 micro gram) of RNA were pooled from the four or five animals of each mouse strain, resulting in a total of eight samples.
For biotin-labeled target synthesis starting from 3-5 µg of total RNA, reactions were performed using standard protocols supplied by the manufacturer (Affymetrix; Santa Clara, CA). Briefly, 3-5 µg total RNA were converted to dsDNA using 100 pmol of a T7T23V primer (Eurogentec; Seraing, Belgium) containing a T7 promoter. The cDNA was then used directly in an in-vitro transcription reaction in the presence of biotinylated nucleotides.
The concentration of biotin-labeled cRNA was determined by UV absorbance. In all cases, 12.5 µg of each biotinylated cRNA preparation were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix MG U74Av2 for 16 hours.
Data selection and transformation procedures. For normalization, all array experiments were scaled to a target intensity of 150, otherwise using the default values of the Microarray suite 5.0 (MAS 5.0). Filtering of the results was done as follows: Genes were considered as strong regulated if their fold change was greater than or equal 2 or less than or equal -2, the statistical parameter for a significant change was less than 0.01 (change p-Value for changes called Increased) or greater than 0.99 (change p-Value for changes called Decreased). Additionally, the signal difference of a certain gene was greater than 200. Genes were considered as weak regulated if their fold change was greater than or equal 1.5 or less than or equal -1.5, the statistical parameter for a significant change was less than 0.001 or greater than 0.999 and the signal difference of a certain gene was greater than 40.
Keywords = Inflammatory Bowel Disease
Keywords = IBD
Keywords = interleukin-10
Keywords = microarray
Keywords = mice
Keywords = quantitative trait locus
Keywords = QTL
Keywords = susceptibility
Keywords: parallel sample

first: Robert

last: Geffers

first: Wiebke

last: Hansen

first: Jörg

last: Lauber

first: Jan

last: Buer

first: Hans

last: Hedrich

first: Michael

last: Mähler


title: Gene Expression Analysis of Neural Stem Cells

summary:
Tissue from the telencephalon was isolated from E13.5 BALB/C mouse and allowed to culture as neurospheres in the presence of FGF2. These cultures were assessed for undifferentiated neural stem cells by the expression of Nestin and were found to be ~98% Nestin positive. Comparisons of these nestin positive neural stem cells will be made to R1 ES cells to identify the genes that are important in totipotent, self-renewing ES cells vs. commitment to the multipotent, self-renewing neural stem cell phenotype.
Keywords: other

overall_design: this experiment include 3 samples and 4 replicates


title: Expression Profile of Homogenous Bone Marrow Stromal Stem Cell Clones

summary:
The role of bone marrow stromal cells in angiogenesis and tissue regeneration has previously been assessed by the use of heterogenous populations. This experiment is designed to assess the angiogenic potential of homogenous, well characterized clones and to provide gene expression profiling for these clones.
Keywords: other

overall_design: this experiment include 2 samples and 18 replicates


title: Intermediolateral column, medial, and lateral motoneurons

city: Atlanta

first: Deborah

last: Baro

state: GA

institute: Georgia State University

summary:
Three cell types, intermediolateral column motoneurons, medial motoneurons, and lateral motoneurons were isolated from a single adult spinal cord using laser capture microscopy. Four hundred captures were collected for each cell type. For a given cell type, RNA was extracted from the 400 captures using an Arcturus picopure kit. RNA was split in half and two targets were produced using a double amplification protocol. Each target was hybridized to Affymetrix chips and signals were normalized with R-pack. Inverse logs are provided. Five animals were used in these experiments, and all three cell types were collected from each animal. Thus, for each cell type, there are five biological replicates, and for each biological replicate there are two technical replicates. In all thirty chips were analyzed. Techinical replicates are indicated as Set 1 and Set 2. Animal numbers are indicated by Pair1 through Pair 5.
Keywords: other

first: Shawn

last: Hochman

first: Dapeng

last: Cui


title: Parietal cell gene expression in the presence and absence of gastrin

status: Public on Nov 15 2005

city: ANN ARBOR

first: Linda

last: Samuelson

address: MED SCI II, # 7761, 1150 W. MEDICAL CENTER DRIVE

summary:
Parietal cells were isolated from WT and Gastrin Knockout mice.  Targets from three biological replicates of each were generated and the expression profiles were determined using Affymetrix murine U74Av2 arrays.  Comparisons between the sample groups allow the identification of genes with gastrin responsiveness.
Keywords: repeat

overall_design: 3 WT parietal cell and 3 Gastrin Kncokout parietal cell replicates were analyzed

first: Renu

last: Jain


title: Temporal Analysis of Differentiating Limb Bud Mesenchymal Cell Gene Expression

first: Theodore

last: Perkins

summary:
Comparison of gene expression in differentiating limb bud mesenchymal cells harvested at 0, 1 day and 3 days culture.
Keywords: other

overall_design: this experiment include 3 samples and 27 replicates


title: Gene Expression Study of Mammary Glands Tumours of PEA3-null and Wild-type PEA3 Mice

summary:
Study of differences in gene expression profiles in the mammary glands tumours of PEA3-null and wild-type PEA3 mice induced by the Her2/Neu transgene.
Keywords: other

overall_design: this experiment include 3 samples and 22 replicates


title: Two circadian oscillatory mechanisms in the mouse liver

status: Public on Nov 14 2005

city: Tsukuba

first: Norio

last: Ishida

institute: National Institute of Advanced Industrial Science and Technology

summary:
Genome-wide expression analysis of two circadian oscillatory mechanisms in the mouse liver

To identify the genes of which the circadian expression is regulated by endogenous glucocorticoids, we performed DNA microarray analysis using hepatic RNA from adrenalectomized (ADX) and sham-operated mice. Mice were housed in a 12:12 h light-dark cycle (LD12:12; lights on at zeitgeber time (ZT) 0) for at least two weeks before the day of the experiment. Liver samples were dissected, quickly frozen, and stored in liquid nitrogen. Total RNA was purified from pools of 3 animal tissues collected at each time-point using ISOGEN (Nippon Gene Co., Ltd., Japan). Hybridization to Affymetrix GeneChip (MG-U74Av2) arrays proceeded as described (Oishi K et al., J Biol Chem, 278, 41519-41527, 2003). The average difference (AD) value for each gene was provided by GeneChip software. To identify putative glucocorticoid-regulated circadian genes, we compared AD values between two time points (ZT2 and ZT14) in sham operated and in ADX mice. We applied three criteria to the selection of putative glucocorticoid-regulated circadian genes: (i) the AD value is marked as “present” by the GeneChip software in at least one of two time points, (ii) the AD value exhibits a 2-fold or greater change in sham-operated mice and (iii) the fold change is below 2-fold in ADX mice. We identified 169 genes that fluctuated between day and night in the livers of sham-operated mice. Among these, 100 lost circadian rhythmicity in ADX mice. On the other hand, the circadian expression of clock or clock-related genes such as mPer2 and DBP remained almost totally intact in the liver of ADX mice. The present study showed that the circadian expression of one type of liver genes in the mouse is governed by core components of the circadian clock such as CLOCK and BMAL1, and the other depends on endogenous glucocorticoids.
Keywords: parallel sample

first: Katsutaka

last: Oishi

first: Hidenori

last: Shirai

first: Noriko

last: Amagai

first: Koji

last: Kadota

first: Naoki

last: Ohkura


title: Gene expression profiling of IDO-competent dendritic cells

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
Although much is known on the transcriptional profiles of dendritic cells (DCs) during maturation, the molecular switches critical for the acquisition of a tolerogenic program by DCs are still obscure. In the present study, we explored the gene expression pattern of CD8+ DCs purified from the mouse spleen and treated with interferon (IFN)-gamma. The cytokine, indeed, potentiates the tolerogenic potential of this DC subset via induction of the immunosuppressive tryptophan catabolism mediated by indoleamine 2,3-dioxygenase (IDO). By comparing the expression of the IFN-gamma-modulated genes in IDO+ versus IDO- murine DCs, we found a consistent and selective association of the IDO-competent phenotype with the down-modulation of the Tyrobp gene, encoding the adapter molecule DAP12. IFN-gamma-mediated down-modulation of this gene involved IFN consensus sequence binding protein (ICSBP), a transcription factor also known as IRF-8. While silencing of Tyrobp conferred IDO functional competence on IDO- DCs, silencing of Icsbp1 in IDO+ cells completely abolished IDO expression and function. In parallel, silencing of TYROBP conferred IDO competence on human IDO- DCs while silencing of IRF8 impaired IDO expression and activity in human IDO+ DCs. Therefore, the same small set of molecular switches controls IDO competence in murine and human DCs.
Keywords: Time-course, treatment with agent (IFN-gamma)

overall_design: Labeled cRNA extracted from a a total of 8 samples was hybridized to the Affymetrix GeneChip MG-U74Av2 which contains 12,488 probe sets . The 4 control samples included 2 replicates each of RNA extracted from cells incubated in medium for 4 and 16 hours. Treated samples included 2 replicates each of RNA extracted from cells incubated in IFN-gammas for 4 and 16 hours.

first: Ursula

last: Grohmann

first: Ciriana

last: Orabona

first: Alessandra

last: Luchini


title: Trophoblast stem cells

summary:
Comparison of trophoblast stem cells vs. R1 ES cells.
Keywords: other

overall_design: this experiment include 2 samples and 14 replicates


title: Expression Profile of Untransformed Bone Marrow Stromal Cells from Wild-Type C57Bl/6 Mice.

summary:
These samples, isolated from untransformed marrow stromal cells from wild-type C57Bl/6 mice, serve as a control set. The cells (CD31-, CD34 low/-, CD45-) are from a mixed population of 100% bone marrow stromal cells arising after more than two months in culture and 10-15 passages.
Keywords: other


title: Adult Mouse Brain Gene Expression

status: Public on Nov 11 2005

first: Matthew

last: Zapala

state: CA

address: 10010 N. Torrey Pines Road

department: Genetics

institute: Salk Intitute for Biological Sciences

summary:
The current model to explain the organization of the mammalian nervous system is based on studies of anatomy, embryology, and evolution. To further investigate the molecular organization of the adult mammalian brain, we have built a gene expression-based brain map. We measured gene expression patterns for 24 neural tissues covering the mouse central nervous system and found, surprisingly, that the adult brain bears a transcriptional "imprint" consistent with both embryological origins and classic evolutionary relationships. Embryonic cellular position along the anterior-posterior axis of the neural tube was shown to be closely associated with, and possibly a determinant of, the gene expression patterns in adult structures. We also observed a significant number of embryonic patterning and homeobox genes with region-specific expression in the adult nervous system. The relationships between global expression patterns for different anatomical regions and the nature of the observed region-specific genes suggest that the adult brain retains a degree of overall gene expression established during embryogenesis that is important for regional specificity and the functional relationships between regions in the adult. The complete collection of extensively annotated gene expression data along with data mining and visualization tools have been made available on a publicly accessible web site (www.barlow-lockhartbrainmapnimhgrant.org).
Keywords: multiple strain, multiple tissues

overall_design: Large amount of high-quality, quantitative gene expression data obtained for 24 neural tissues from 3 strains of inbred mice and and 10 body tissues from 5 strains of inbred mice.

first: Carrolee

last: Barlow


title: Comparison of mammary glands of 16 wk old wild type and LH-overexpressing mice

status: Public on Oct 10 2005

city: Cleveland

first: Ruth

last: Keri

address: 2109 Adelbert

department: Pharmacology

institute: Case Western Reserve University

summary:
LH-overexpressing mice display elevated levels of mammogenic hormones and consequently develop spontaneous mammary tumors with a median latency of 41 weeks. Tumors occur in the absence of p53 mutations and in the presence of a seemingly functional p53 signaling pathway. At 16 weeks of age, no histological evidence of tumors is observed in these transgenic mammary glands; however, mammary cells do demonstrate centrosome amplification at this age suggesting that early tumorigenic processes may have occured. Thus comparison of the transcriptome of the mammary glands from 16 week old LH-overexpressing mice to that of wild type mice will provide insight into early events occuring in p53-independent hormone-induced tumorigenesis.
Keywords: disease state analysis

overall_design: Total RNA was isolated from mammary glands of a total of 9 wild type and 9 transgenic mice. RNA from 3 mammary glands was pooled together generating 3 wild type samples and 3 transgenic samples.

first: Erin

middle: L

last: Milliken

first: Melissa

last: Landis

first: Ira

last: Whitten


title: Adult mouse gene expression

status: Public on Oct 23 2005

city: La Jolla

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

summary:
Adult mouse gene expression patterns in common strains
Keywords: mouse strain and brain region comparison

overall_design: six mouse strains and seven brain regions were analyzed

first: Iiris

last: Hovatta

first: David

last: Lockhart


title: Undifferentiated mouse embryonic stem cells, differentiated nestin-positive cells and fibroblast feeder layer.

status: Public on Sep 17 2005

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

summary:
Embryonic stem (ES) cells and ES cell-derived progeny characterized by nestin expression (including neural progenitors) were studied (three independent experiments). The mouse ES cell line R1 was cultured on a feeder layer of mouse embryonic fibroblasts (FL). ES cells were differentiated into nestin-positive cells for 4+8 days and 4+11 days according to the differentiation protocol by Rolletschek et al. (Mechanisms of Development 105, 93-104, 2001).

The study was performed with three independent cell cultures (= triplicates). RNA was prepared from both undifferentiated ES cells and ES cell-derived nestin-positive cells, and from fibroblast feeder cells.
Keywords = ES cell
Keywords = nestin positive cells
Keywords = feeder layer
Keywords: other

first: Anna

last: Wobus

last: Ruau

first: Christine

last: Hacker

first: Nicole

last: Kirchhof

first: Alexandra

last: Rolletschek


title: Macrophage Response to Sendai virus infection.

city: St. Louis

first: Anand

middle: Champak

last: Patel

state: MO

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

department: Pulmonary/Critical Care Medicine

institute: Washington University School of Medicine

summary:
Thus, mouse macrophage cultures were established from PBMCs isolated from wild-type control mice and were inoculated with SeV (Sendai virus) or UV-SeV (UV-inactivated SeV). These microarrays were performed in concert with assays of CCL5 and CCR5 expression, viral replication, and cellular apoptosis. Initial experiments indicated that wild-type mouse macrophages inoculated with SeV exhibit induction of CCL5 mRNA to the highest level of any known mouse gene product, while mRNA levels for CCL5 receptors (CCR5 as well as CCR3 and CCR1) or alternative ligands for these receptors (CCL3 and CCL4) were relatively unchanged by viral infection.
Keywords: Treatment Comparison

overall_design: Macrophages were pooled from mice and subsequently cultured (~3 mice/well).  Each culture well was then subjected to one of two treatments (SeV, or UV-SeV) for 4 days.  Thus, per condition, N = 2 culture wells, with each well independently analyzed by microarray.  No technical replicates were performed, but arrays were evaluated for quality control using the SimpleAffy package (Miller CJ, 2004) in Bioconductor 1.5.

first: Jeffrey

last: Tyner

first: Osamu

last: Uchida

first: Naohiro

last: Kajiwara

first: Edy

middle: Y

last: Kim

first: Mary

middle: P

last: O'Sullivan

first: Michael

last: Walter

first: Reto

last: Schwendener

first: Donald

last: Cook

first: Theodore

last: Danoff

last: Holtzman


title: Soleus muscle

status: Public on Sep 16 2005

city: LUND

first: Ola

middle: Axel

last: Hansson

address: BMC C11

department: Molecular Signalling

institute: Cell and Molecular Biology, Lund University

summary:
Expression analysis in order to elucidatethe role of hormone-sensitive lipase in soleus muscle.
Keywords: other


title: Muscle Satellite Cells: MyoD and p53 genes

status: Public on Sep 07 2005

last: Perkins

summary:
Muscle satellite cells are a self-renewing pool of stem cells that give rise to daughter myogenic precursor cells in adult skeletal muscle. Published and preliminary data indicated that MyoD and p53 genes are involved in satellite cell differentiation. We would like to know what downstream genes of both transcription factors are affected in satellite cell-derived myoblasts (MyoD-/-, p53 -/-).
Keywords: other

overall_design: this experiment include 3 samples and 25 replicates


title: Ezh2 deficiency in double negative thymocytes

status: Public on Sep 01 2005

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
Expression profiles from Rag1 mutant and Rag1/Ezh2 double mutant double negative thymocytes
Keywords = Rag1
Keywords = Ezh2
Keywords = Thymocyte
Keywords: repeat sample

first: I-hsin

last: Su

first: Alexander

last: Tarakhovsky


status: Public on Dec 08 2005

first: Markus

last: Stoffel

address: 1230 York Avenue

department: Metabolic Diseases

institute: Rockefeller University

summary:
Expression profiling of pancreatic islets in Tcf1 knock out mice
Keywords: repeat sample serie

overall_design:
two biological replicates per condition
two conditions: WT and Tcf1 KO mice
Affy MG-U74A and B array

first: Pinar

last: Akpinar


title: BWF1 mice

status: Public on Aug 23 2005

city: Denver

first: Melanie

last: Gubbels

state: CO

institute: University of Colorado Health Sciences Center

summary:
Goal of experiment: Identification of differentially expressed immune genes from male and female BWF1 lupus-prone mice. (Female incidence is higher than male--attempting to find sex hormone regulated genes that may contribute to this difference). Whole spleen was taken from pre-lupus (4 months old) BWF1 (females are lupus-prone) male and female mice.  Preparation of cDNA.  Double-stranded cDNA was synthesized from purified RNA.  The first strand was synthesized by incubating 5 μg of RNA with 100 pg/ml T7-(dT)24 primer (HPLC purified DNA primer sequence: 5’-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGG-(dT)24 -3’ Genset Corp, San Diego, CA) at 70°C for 10 minutes.  Samples were incubated for 1 hour at 42°C with the following mix: 1X first strand buffer, 10 mM dithiothreitol, 500 μM each dNTP, 200 U SuperScript II in diethylpyrocarbonate (DEPC)-treated water up to 20 μl.  Second strand synthesis was performed by incubating the first strand with the following mix for 2 hours at 16°C: 1X second strand reaction buffer, 200 μM dntps, 10 U E. coli DNA ligase, 40 U E coli DNA Polymerase I, 2 U of E. coli RNase H up to 150 μl with DEPC-treated water (all reagents were contained in SuperScript Choice System for cDNA Synthesis, Invitrogen).  A phenol/chloroform extraction was performed on the ds-cDNA preparation before biotin-labeled cRNA was generated.  Synthesis and fragmentation of biotin-labeled cRNA (in vitro transcription). The ENZO BioArrayTM HighYieldTM RNA Transcript Labeling Kit (T7) (Enzo diagnostics, Inc., Farmingdale, NY) was used to produce large amounts of hybridizable biotin-labeled RNA targets by in vitro transcription from the ds-cDNA.  The following mix was incubated at 37°C for 5 hours:  1 μg of ds-cDNA, 1X HY reaction buffer, 1X biotin labeled ribonucleotides, 1X dithiothreitol, 1X T7 RNA Polymerase.  Biotin-labeled cRNA was run over RNeasy spin columns (Qiagen), quantified, and run on an agarose gel to visualize the size distribution of labeled transcripts.  Twenty micrograms of cRNA was incubated with 1X fragmentation buffer for 35 minutes at 94°C.  (5X fragmentation buffer: 200 mM Tris-acetate, pH 8.1, 500 mM KOAc, 150 mM MgOAc).  After fragmentation, the samples were stored at -20°C until the hybridization was performed.  Sample hybridization.  Oligonucleotide microarrays (MGU74v2 A, B, and C GeneChip probe arrays; Affymetrix) were hybridized with labeled cRNA derived from spleens from individual mice.  For each array,15 μg of fragmented cRNA was mixed with a hybridization cocktail consisting of 1X hybridization buffer (2X hybridization buffer: 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween), 0.5 mg/ml acetylated BSA (Invitrogen),  0.1 mg/ml herring sperm DNA (Promega), and water (BioWhittaker) up to 300 μl).  Biotin labeled cRNA transcripts of the E. coli and P1 bacteriophage genes, BioB, bioC, bioD, and cre (GeneChip Eukaryotic Hybridization control kit, Affymetrix) were spiked into each hybridization mix at 1.5, 5, 25, and 100 pM to evaluate sample hybridization efficiency for each array. The hybridization cocktail was heated to 99°C and then 45°C for 5 minutes each before it was centrifuged to remove any insoluble material. The array was equilibrated to room temperature, moistened with 1X hybridization buffer, and incubated for 10 minutes at 45°C with rotation.  After incubation, the buffer solution was removed from the array. The array was filled with 300 μl of the hybridization cocktail, placed in a rotisserie box in a 45°C oven, and incubated for 16 hours while rotating at 60 rpm.  Washing and staining of array.  The hybridization cocktail was removed and the GeneChip Fluidics Station 400 (Affymetrix) with Microarray Suite software (Affymetrix) was used to wash and stain the probe arrays with the following protocol: 10 cycles of 2 mixes/cycle with wash buffer A at 25°C, 4 cycles of 15 mixes/cycle with wash buffer B at 50°C, 30 minute incubation with staining solution at 25°C, 10 cycles of 4 mixes/cycle with wash buffer A at 25°C.  Wash buffer A -- non-stringent wash buffer (6X sodium chloride sodium phosphate + ethylenediaminetetraacetic acid (SSPE), 0.01% Tween-20).  (20X SSPE: 3 M NaCl, 0.2 M NaH2PO4, 0.02 EDTA) (BioWhittaker).  Wash buffer B – stringent wash buffer (100mM MES, 0.1 M [Na+], 0.1% Tween 20).  Staining solution (1X 2-(N-Morpholino)ethanesulfonic Acid (MES) stain buffer, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin (SAPE), and water up to 600 μl). (12X MES stain buffer: 1.22 M MES, 0.89 M [Na+]).  Analysis.  After staining, the probe arrays were scanned using the GeneChip 3000 Scanner (Affymetrix) with Microarray Suite software (Affymetrix).  Technical and assay variation between arrays was corrected for by multiplying or dividing the overall intensity of each array by a scaling factor so that the overall intensity of each array was equivalent to facilitate comparison analysis.
Keywords = BWF1 total spleen
Keywords: repeat sample

first: Brian

last: Kotzin


title: GFAP transgenic mice expression analysis

status: Public on Jul 20 2005

city: Madison

first: Tracy

last: Hagemann

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin, Madison

summary:
Olfactory bulb transcript levels for GFAP transgenic mice compared to wildtype at 3wks and 4mos
Keywords = GFAP
Keywords = Rosenthal fibers
Keywords = Alexander disease
Keywords: other

first: Albee

last: Messing