title: Effects of ethanol on poly IC gene induction

status: Public on Apr 15 2004

city: Shreveport

first: Stephen

middle: B.

last: Pruett

state: LA

address: 1501 Kings Hwy.

department: Dept. Cellular Biology & Anatomy

institute: LSU Health Sciences Center

summary:
Experiment on the effects of ethanol (acute oral) on induction of genes by polyinosinic polycytidylic acid (poly IC). Microarray methodology follows: cDNA for each sample was synthesized from 8.5 µg total RNA using a Superscript cDNA Synthesis Kit (Invitrogen, Carlsbad, CA) in combination with a T7-(dT)24 primer. Following phenol-chloroform extraction of the cDNA, biotinylated cRNA was transcribed in vitro using the BioArray HighYield RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA). Twenty micrograms of purified cRNA was fragmented by incubation in fragmentation buffer (200 mM Tris-acetate, pH 8.1, 500 mM potassium acetate, 150 mM magnesium acetate) at 94°C for 35 minutes and chilled on ice. Fifteen micrograms of fragmented biotin-labeled cRNA was hybridized to the Murine Genome U74Av2 Array (Affymetrix, Santa Clara, CA), interrogating a total of 12,488 murine gene cDNA probes, for 16 hr at 45°C with constant rotation (60 rpm). The arrays were washed and then stained for 10 min at 25°C with 10 µg/mL streptavidin-R phycoerythrin (Vector Laboratories, Burlingame, CA) followed by 3 µg/mL biotinylated goat anti-streptavidin antibody (Vector Laboratories) for 10 minutes at 25°C. Arrays were then stained once again with streptavidin-R phycoerythrin for 10 min at 25°C. After washing and staining, the arrays were scanned using an Agilent GeneArray Scanner (Agilent Technologies) at 570 nm. Pixel intensities were measured, expression signals were analyzed and features extracted using a commercial software package (Microarray Suite ver 5.0, Affymetrix). Data mining and statistical analyses were performed with Data Mining Tool ver 3.0 (Affymetrix) algorithms. Arrays were globally scaled to a target intensity value of 2,500 in order to compare individual experiments. The absolute call (present, marginal, absent) of 12,488 gene expressions in each sample, as well as the direction of change, and fold change of gene expressions between samples were identified using the above-mentioned software.
Keywords: other

middle: B

first: Carlton

last: Schwab

first: Qiang

last: Zhang

first: Ruping

last: Fan


title: Erythroid Progenitor Cell Gene Expression Profiles

status: Public on May 02 2004

city: Scarborough

first: Diya

email: WOJCHD@mmc.org , diya@northwestern.edu

state: ME

address: 81 Research Drive

department: Molecular Medicine

country: USA

institute: Maine Medical Center Research Institute

summary:
A]  DESCRIPTION - GENE EXPRESSION PROFILES were analyzed (via Affymetrix MG-U74Av2 arrays) at three distinct stages of late erythroid progenitor cell development. Stages correspond to Kit(+)/EpoR-high/CD71(+)/Ter119(-) proerythroblasts [stage I]; Kit-low/EpoR(+)/CD71-high/Ter119(+) polychromatophilic erythroblasts [stage II]; and Kit(-)/EpoR-low/CD71-low/Ter119-high/lowFALS normoblasts [stage III]. Primary splenic (pro)erythroblasts were prepared at 80, 100 and 120 hours post thiamphenicol dosing, and were purified by MACS using a transgenic erythroid-restricted “EE” tag. For each stage, duplicate hybridizations were performed. GSM3371 and GSM3372 are results from stage I hybridizations; GSM3373 and GSM3374 are results for stage II; and GSM3375 and GSM3376 are results for stage III. The order of listed genes is organized based first on average p-value among all six hybridizations in ascending order, and second on fold-increases in expression levels from stage I to stage II (descending order).

B] METHOD DETAILS (as a supplement to Zhang et al., submitted) B1-B6 below:

B.1/ ERYTHROID PROGENITOR CELL PREPARATIONS: Thiamphenicol (TAP) (Sigma, St. Louis, MO) was administered on day 1 to 8-week old Gata1-“EE” mice [1] (15 mg per gram weight in 0.4 mL of water) as a subcutaneous implant in Spectra Por 2 tubing (Spectrum, Houston, TX) [2]. On days 2 through 4, mice were phlebotomized (80mL blood per day), and TAP implants were removed on day 6. Splenocytes were prepared at 80, 100, or 120 hours post TAP withdrawal by disruption of spleens in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 2% fetal bovine serum (FBS) and 0.1 U/mL Epo. Cells were passed through a 70 um strainer (Falcon, Franklin Lakes, NJ), collected at 300 x g for 10 minutes, resuspended in 1 mL of phosphate-buffered saline (PBS, 140 mM NaCl, 2.7 mM KCl, 8.1 mM Na2HPO4, 1.2 mM KH2PO4, pH 7.4), exposed for 2 minutes to 9 mL of 0.8% NH4Cl, 0.01 mM Na2EDTA buffered at pH 7.5 with KHCO3. Cells then were collected through 50% FBS in PBS, and washed in DMEM.
B.2/ MACS: Splenocytes (3x10^8 cells per 3 spleens per preparation) in 3 mL of 5mM Na2EDTA, 0.5 % BSA in PBS, pH 7.2 (PBE) were incubated for 5 minutes at 15°C with murine IgG Fc fragment (5 μg per mL) (Pierce, Rockford, IL), and pre-absorbed for 20 minutes at 15°C with anti-mouse IgG2a+2b magnetic microbeads (100 μL per mL) (Miltenyi, Bergisch Gladbach, Germany). Samples were passed through a magnetized MACS-LS column (non-specific adsorption) and unbound cells were collected, washed and resuspended (at 1 x 10^8 cells per mL) in 3 mL of PBE buffer. Cells then were incubated at 15°C for 15 minutes with monoclonal antibody EGFR.1 (5 μg per mL) (PharMingen, San Diego, CA), washed in 20 mL of 2°C PBE buffer, resuspended in PBE at 1 x 10^8 cells per mL, and incubated for 20 minutes at 15°C with anti-mouse IgG2a+2b magnetic microbeads (200 μL per mL). Bead-tagged (pro)erythroblasts were washed in 2°C PBE buffer, resuspended in 3 mL PBE, and applied to a MACS-LS column. Columns were washed six times with 3 mL of PBE, and EE-positive cells were recovered in 5 mL of PBE buffer. Overall, 6 x 10^6 stage I, II and III (pro)erythroblasts were purified from 12, 4, and 3 mice, respectively.
B.3/ RNA ISOLATION AND ANALYSIS: Purified (pro)erythroblasts (6 x 10^6 cells) were lysed in 1 mL Trizol reagent (Life Technologies, Gaithersburg, MD). Chloroform (0.2 mL) was added and samples were vortexed and microcentrifuged at 7,500 rpm for 15 minutes at 4°C. The aqueous phase (approximately 0.5 mL) was recovered, and extracted using 0.5 mL of Trizol LS reagent plus 0.1 mL of chloroform. From the recovered epi-phase (750 μL), RNA was precipitated using isopropanol (750 μL), collected (10 minutes at 4°C, 12,000 rpm), washed with 80% ethanol, air-dried, and dissolved in 35 μl of 70°C DEPC-treated water. In Northern blotting, RNA samples were electrophoresed in 6% formaldehyde 1.2% agarose gels, blotted to Nytran membranes (Schleicher and Schuell, Keene, NH), and fixed (312 nm radiation for 3 minutes; 2 hours at 80°C under vacuum). In hybridizations, Redivue deoxyadenosine 5'-(α-32P)-triphosphate labeled probes were prepared by random priming (Prime-a-Gene System, Promega, Madison, WI) using 25 ng of the following cDNA fragments: murine Epo receptor, 880 bp Bgl II to Xba I fragment of pUC19ER-DpI3K [3]; murine beta-major globin, 1,100 bp Bgl II to Xba I fragment of pGEM7-betamaj-globin [4]; murine Kit, 1,500 bp BamH I to Nhe I fragment of pRep4DEB-cKit [5]; murine Gata-1, Xho I fragment of pBluescript-GATA-1 [6]; 32P-labeled probes were isolated using Sephadex G-50 microcolumns (Pharmacia Biotech, Piscataway, NJ). Hybridizations were for 4 hours at 68°C using 2 × 10^6 cpm of probe per mL in QuickHyb solution (Stratagene, La Jolla, CA). Membranes were exposed to X-OMAT AR film (Kodak, Rochester, NY) and were assayed quantitatively by phosphor imaging (Storm 860 system, Molecular Dynamics, Sunnyvale, CA).
B.4/ BIOTIN-cRNA PREPARATION, AND ARRAY HYBRIDIZATIONS: First-strand cDNA was synthesized with a T7-oligo (dT) 24 primer (5'-GGC CAG TGA ATT GTA ATA CGA CTC ACT ATA GGG AGG CGG-(dT) 24-3') (Geneset, La Jolla CA) and Superscript II reverse transcriptase (Invitrogen, Carsbad, CA) (1 hour, 42°C). DNA polymerase I (cat# 18010-017, Invitrogen) and RNase H (cat# 18021-041, Invitrogen) were used in second strand syntheses (2 hours, 16°C). Products were extracted in Tris-phenol: chloroform: isoamyl (25:24:1) using a phase-lock gel (cat# 175850, Eppendorf 5-prime, Boulder, CO). Precipitation was with 0.5 volumes of 7.5M NH4Ac, 5 μg of glycogen and 2.5 volumes of -20°C absolute ethanol. Double stranded -cDNA (1 μg in 10 µl DEPC-treated water) was used per T7 RNA pol transcription (Enzo BioArray High Yield biotin-UTP and -CTP RNA Labeling Kit) (cat# 42655, Farmingdale, NY). Products were purified using QIAGEN RNeasy columns (cat# 72104) (Valencia, CA). For each sample (16 μg total RNA) approximately 60 μg of purified biotin-labeled cRNA was recovered. Labeled cRNA was fragmented for 35 min at 94°C in 500 mM potassium acetate (C2H3KO2), 150 mM magnesium acetate (C4H6MgO4), 200 mM Tris-acetate (C4H11NO3 • CH3COOH), pH 8.1. Each sample (diluted 1:10 in hybridization buffer) was first hybridized to a Test2 Genechip to confirm full-length transcript representation. Replicate hybridizations were to Affymetrix murine U74Av2 arrays, and data were analyzed using Affymetrix Genechip 5.1 software.
B.5/ ANALYSES OF PROFILING OUTCOMES: Transcripts expressed (detected) at each stage were identified based on a detection p-value of <0.05 in one replicate, and <0.1 in the other. 3'/5' ratios of housekeeping genes confirmed uniform biotin cRNA syntheses. Pair-wise comparisons among stages included 4659 transcripts detected in at least one stage, and employed averages of log expression values from duplicate hybridizations for each gene. In these comparisons, modulation is defined by vertical distances from a regression (no-modulation) trendline. For the above 4659 detected transcripts, mean expression values were normalized to account for chip/sample variability by subtracting the stage mean, and dividing by the stage standard deviation. The three normalized values of each gene (one for each stage) then were standardized by subtracting the gene mean and dividing by the gene standard deviation. Non-modulated genes (less than two-fold change) then were removed from further consideration. Clustering of the resulting data was performed by K-means (S+ package), a partitioning algorithm that pursues a minimum of the within-clusters sums of squares (WSS, which measures square Euclidean distances between cluster points and the cluster average within each cluster) [7]. Principal component analysis (PCA) was used to visualize K-means clustering results. PCA is a common method for reduction of dimensionality. Wh
Keywords: ordered

first: Don

middle: M

last: Wojchowski


title: prefrontal cortex (ctrl vs transgenic synaptic AChE)

status: Public on May 01 2004

city: Jerusalem

first: Eran

last: Meshorer

state: Israel

address: Givat Ram

department: Biological Chemistry

country: Israel

institute: Life Sciences

summary:
total prefrontal cortex RNA in female FVB/N mice (control) versus transgenic female mice overexpressing the human synaptic AChE
Keywords: other

first: Hermona

last: Soreq


title: Triple treatment R6/2 mice

status: Public on Jun 01 2004

city: Cardiff

first: Lesley

last: Jones

address: Heath Park

department: Psychological Medicine

country: United Kingdom

institute: Cardiff University School of Medicine

summary:
Huntington’s disease is a genetic disease caused by a single mutation. It is characterised by progressive movement, emotional and cognitive deficits. R6/2 transgenic mice carrying the Huntington’s disease mutation have a progressive neurological phenotype, including deterioration in cognitive function. The mechanism underlying the cognitive deficits in R6/2 mice is unknown, but dysregulated gene expression, reduced neurotransmitter levels and abnormal synaptic function are present before the cognitive decline becomes pronounced. Our goal here was to ameliorate the cognitive phenotype in R6/2 mice using a combination drug therapy (tacrine, moclobemide and creatine) aimed boosting neurotransmitter levels in the brain. Treatment from 5 weeks of age prevented deterioration in two different cognitive tasks until at least 12 weeks. However, motor deterioration continued unabated. Microarray analysis of global gene expression revealed that many genes significantly up- or down-regulated in untreated R6/2 mice had returned towards normal levels after treatment. Thus dysregulated gene expression was reversed by the combination treatment in the R6/2 mice and probably underlies the observed improvements in cognitive function. Our study shows that cognitive decline caused by a genetic mutation can be slowed by a combination drug treatment, and gives hope that cognitive symptoms in HD can be treated.
Keywords = HD
Keywords = Huntingtin
Keywords = cognitive disorder
Keywords = R6/2
Keywords = transgenic mice
Keywords = gene expression
Keywords = microarray
Keywords: ordered

first: A

middle: J

last: Morton

first: Mark

last: Hunt

first: Angela

middle: K

last: Hodges

first: Paul

middle: D

last: Lewis

last: Dunnett


title: P18 knockout

city: Memphis

first: Jiewu

last: Liu

state: TN

address: 332 N. Lauderdale St.

department: Department of Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P18. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample

first: Qian

last: Huang

first: Wei

first: Kyeogmi

last: Cheon

first: Jason

last: Higdon

first: Cheng

last: Cheng

first: Jian

last: Zuo


title: Rp1 knockout mice retinal development

summary:
Mice were a mixed background between 129/SvEv and C57BL/6.
Rp1 knockout mice (Rp1-/-) and wildtype littermates examined.
At P7, P10, P14, P18 and P21, mice were sacrificed and retinas removed.
Each RNA sample included a pool of neural retinas from 3-4 mice.
Retinas were all collected at 1-2 pm.
Keywords: other


title: Profiling of aggressive vs benign pancreatic infiltrates in the BDC2.5 Tg model of Type I diabetes

status: Public on Apr 17 2004

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
This study was performed to understand what controls the aggressivity of the pancreatic infiltrate during type-I diabetes development. We used the BDC2.5 transgenic mouse model. Samples were obtained at the age of onset of insultis. Depending on their genetic background, mice transgenic for the BDC2.5 T cell receptor present very different forms of insulitis. The NOD genetic background leads to a benign insulitis whereas the C57Bl/6-H2g7/g7 leads to an aggressive insulitis. We first studied how antigen-specific T cells are affected by these differences by obtaining the transcriptional profiles of BDC2.5 T cells from pancreas and pancreatic lymph nodes. We also compared the gene expression profiles of the entire leukocyte population present in the pancreatic lesion.
Keywords: other

first: Laurent

last: Poirot

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: P10 knockout

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P10. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample


title: P18 wildtype

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P18. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample


title: P7 knockout

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P7. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample


title: P21 wildtype

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P21. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample


title: P21 knockout

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P21. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample


title: P14 wildtype

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P14. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample


title: P10 wildtype

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P10. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample


title: P7 wildtype

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. Triplicates of RNA samples from Rp1+/+ neural retinas for hybridization were collected at P7. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample

first: Qiang


title: Hair follicle stem cell gene profile

status: Public on Apr 01 2004

city: Philadelphia

first: George

last: Cotsarelis

state: PA

address: M8 Stellar Chance Laboratories, 422 Curie Blvd

department: Dermatology

institute: University of Pennsylvania School of Medicine

summary:
Mouse keratinocytes were isolated from K15-EGFP transgenic mice for FACS sorting. RNA samples from EGFP-high and alpha-6 integrin positive cells (hair follicle stem cells) and from EGFP negative and alpha-6 integrin positive cells were used for Microarray analysis.
Keywords = stem cells
Keywords = hair follicle
Keywords = epidermis
Keywords = alopecia
Keywords: ordered

first: Yaping

first: Rebecca

last: Morris

first: Lee

last: Marles

first: Zaixin

last: Yang

first: Carol

last: Trempus

first: Shulan

last: Li

first: Jamie

last: Lin

first: Janet

last: Sawicki


title: Zfp145 spermatogonia

status: Public on May 21 2004

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
Expression analysis of spermatogonia in a wild type or Zfp145 knock out background
Keywords: parallel sample

first: Jose

middle: A

last: Costoya

first: Pier Paolo

last: Pandolfi


title: C3H10T1/2 Adipogenesis: Effects of EGF and TCDD

status: Public on Mar 25 2004

city: Madison

first: Paul

last: Hanlon

state: WI

institute: University of Wisconsin

summary:
Confluent C3H10T1/2 cells stimulated to differentiate using IDMB (1uM BRL49653, 1uM Dexamethasone, 0.5uM IBMX, 10ug/mL Insulin).  Expression was examined 24 hours after IDMB treatment.  Additionally, the effects of addition of TCDD 48 hours prior to IDMB treatment, and EGF addition concurrent with IDMB treatment were examined.
Keywords = Adipogenesis
Keywords = TCDD
Keywords = EGF
Keywords: repeat sample

middle: R

first: Colin

last: Jefcoate


title: Molecular profiles of dystrophin-deficient and normal murine muscle

status: Public on Apr 12 2004

first: Judith

last: Haslett

summary:
Expression profiles of six skeletal muscle types in mdx, mdx5cv and wildtype mice.
Keywords: other

middle: N

first: Alvin

middle: T

last: Kho

first: Mei

last: Han

first: Despina

last: Sanoudou

first: Jay

last: Volinski

first: Alan

middle: H

last: Beggs

first: Isaac

middle: S

last: Kohane

first: Louis

last: Kunkel

first: Issac


title: Insulin-like growth factor 1 (IGF1) heart study

status: Public on Mar 24 2004

city: Cambridge

first: Martina

last: Schinke

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

institute: Harvard University

summary:
IGF1 and IGF1 receptors (IGF1R) are present in the adult heart and have been shown to be essential for myocardial performance. Insulin-like growth factor 1 (IGF1) is produced in numerous tissues particularly by the liver in response to growth hormone stimulation and is an important factor in the regulation of post-natal growth and development. We have generated and characterized transgenic mice over-expressing the IGF1R. We crossed IGF1R transgenic mice with dominant negative (dn)PI3K (p110) and with constitutively active (ca)PI3K(p110) transgenic mice. Expression profiling was performed on the ventricles of IGF1R, IGF1R-caPI3K, IGF1R-dnPI3K, caPI3K, dnPI3K transgenic female mice at 3 months of age. Non-transgenic littermates were used as controls.
Keywords = http://cardiogenomics.med.harvard.edu/groups/proj1/pages/igfr1_home.html
Keywords: other

first: Julie

last: McMullen

first: Tetsuo

last: Shioi

first: Weei-Yuarn

last: Huang

first: Li

last: Zhang

first: Oleg

last: Tarnavski

first: Egbert

last: Bisping

first: Sekwon

last: Kong

first: Megan

middle: C

last: Sherwood

first: Jeffrey

last: Brown

first: Lauren

middle: E

last: Riggi

first: Peter

last: Kang

first: Seigo

last: Izumo


title: Chronic Rosiglitazone Mouse Aorta

status: Public on Mar 19 2004

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

summary:
To better understand what genes are regulated by PPAR gamma, an experimental dataset was generated by microarray analysis, in duplicate, of pooled aortic mRNA isolated from adult male mice (C57BL/6J strain) treated for 21 days with a PPAR gamma agonist (rosiglitazone) or vehicle.
Keywords: other


title: NCSC-SC development

status: Public on Feb 21 2004

city: Zurich

first: Ned

last: Mantei

department: Institute for Cell Biology

country: Switzerland

institute: Swiss Federal Institute of Technology

summary:
Time course of early development of peripheral nerve, from embryonic day 9.5 to postnatal day 0.
Origin of samples: mouse embryos expressing green fluorescent protein (GFP) in neural crest stem cells and later glial cells under the control of the proteolipid protein gene (Plp) promoter. At E9.5 the trunk region was dissected out. At E12, E14, E16, E18 and P0 the sciatic nerve was taken. GFP-expressing cells were isolated by FACS sorting. Three or 4 separate batches of embryos analyzed at each stage.
Keywords: time-course

first: Johanna

last: Buchstaller

first: Lukas

last: Sommer

first: Matthias

last: Bodmer

first: Reinhard

last: Hoffmann

first: Ueli

last: Suter


title: Laminin binding/non-binding germ cells

status: Public on Mar 16 2004

first: Nikolaus

last: Schultz

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

summary:
Comparison of laminin binding and laminin non-binding germ cells
Keywords: other

first: F

middle: Kent

last: Hamra

first: Karen

last: Chapman

first: Dana

last: Grellhesl

first: Jennifer

last: Cronkhite

first: Robert

last: Hammer

first: David

middle: L

last: Garbers


title: Diaphram, comparison of wild type and mdx mice, 7 to 112 Days (Porter lab)

status: Public on Feb 10 2004

city: Cleveland

middle: J.

last: Kaminski

state: OH

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

summary:
Determination of gene expression changes in extraocular muscle of mdx (dystrophin-deficient) mice at postnatal ages 7, 14, 23, 28, 56, and 112 days.  3 independent replicates/age/strain. Data form part of publication: Human Molecular Genetics 13:257-269, 2004.
Keywords = microarray
Keywords = muscle
Keywords: time-course

first: John

last: Porter


title: P14 knockout

first: Jiewu

last: Liu

summary:
Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). Triplicates of RNA samples from Rp1-/- neural retinas for hybridization were collected at P14. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.
Keywords: repeat sample

first: Qian

last: Huang

first: Wei

first: Kyeogmi

last: Cheon

first: Jason

last: Higdon

first: Cheng

last: Cheng

first: Jian

last: Zuo


title: Leg muscle mdx and control

status: Public on Feb 05 2004

first: Henry

summary:
Leg muscle mdx and control: 7,14,23 day
Keywords: other


title: Extraocular muscle, comparison of wild type and mdx mice, 14 to 112 Days (Porter lab)

status: Public on Feb 04 2004

summary:
Determination of gene expression changes in extraocular muscle of mdx (dystrophin-deficient) mice at postnatal ages 14, 28, 56, and 112 days.  3 independent replicates/age/strain.
Keywords = microarray
Keywords = muscle
Keywords: time-course


title: Murine Testis Developmental Time Course

status: Public on Feb 01 2004

city: Pullman

first: James

last: Shima

state: WA

address: 531 Fulmer Hall/POB 644660

department: School of Molecular Biosciences

institute: Washington State University

summary:
Murine testis developmental time course created from tissue  samples collected from birth through adulthood and hybridized to MGU74v2 A, B, and C chips in duplicate
Keywords: time-course


title: Hindlimb muscle, comparison of wild type and mdx mice, 7 to 112 Day (Porter lab)

summary:
Determination of gene expression changes in hindlimb muscle (gastrocnemius/soleus) of mdx (dystrophin-deficient) mice at postnatal ages 7, 14, 23, 28, 56, and 112.
Keywords: time-course

first: JOhn


title: Erythroid Differentiation: G1E Model

last: Welch

address: 34th & Civic Center Blvd.

department: Division of Hematology

institute: Children's Hospital of Philadelphia

summary:
G1E cells are a Gata-1 erythroid-committed cell line derived from targeted disruption of Gata-1 in embryonic stem cells. The ER4 subclone contains an inducible form of Gata-1 (Gata-1-ER, Gata-1 fused to the estradiol receptor ligand binding domain). We performed transcriptome analysis using this cell line. Estradiol was added to culture medium triggering synchronous and homogenous differentiation. At various time points, RNA was sampled and analyzed using the Affymetrix MG-U74Av2 platform. Three biological replicas (A,B, and C) were performed. The thirty hour time course corresponds to development from the late BFU-E stage through the orthochromatic erythroblast stage.
Keywords = Gata1
Keywords = erythroid
Keywords = mouse
Keywords: time-course

first: Lewis

last: Chodosh

first: Mitchell

last: Weiss


title: Control vs CF Small Intestine

status: Public on Jan 26 2004

city: Kansas City

last: De Lisle

state: KS

address: 3901 Rainbow Blvd

department: Anatomy & Cell Biology

institute: Univ Kansas Med Ctr

summary:
Total RNA was prepared from the entire small intestines of 40 day old Control and CFTR null mice (2 males and 1 female of each genotype), congenic on the black6 background, using TRIzol reagent. Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.
Keywords: parallel sample

first: Oxana

last: Norkina

first: Simran

last: Kaur

first: Donna

last: Ziemer


title: Myogenic differentiation_Achip

status: Public on Jan 24 2004

first: Kinga

middle: Katarzyna

last: Tomczak

address: 300 Longwood Avenue

department: Genomics Program and Division of Genetics

institute: Children's Hospital Boston

summary:
In this study, Affymetrix MG_U74Av2 and MG_U74Cv2 GeneChips were used to analyze gene expression over a 12 day time course in C2C12 myoblasts induced to differentiate in vitro.  Triplicate cultures were studied during cell proliferation (days -2 and -1), at cell cycle withdrawal (day 0) and during myogenic fusion and maturation of multinucleated myotubes (days 2, 4, 6, 8, 10).  The manuscript associated to this work is Tomczak et al., FASEB J., 2003 Dec 19.  Additionally, the supplementary data can be found on our homepage at http://www.chb-genomics.org/beggslab/
Keywords = C2C12 myoblasts
Keywords = myogenesis
Keywords: time-course

first: Voichita

last: Marinescu

first: Marco

middle: F

last: Ramoni

first: Despina

last: Sanoudou

first: Federica

last: Montanaro

first: Mei

last: Han

first: Louis

last: Kunkel

first: Isaac

last: Kohane

first: Alan

last: Beggs


title: Examining the effects of tTA expression in mouse hearts

status: Public on Jan 23 2004

city: Claremont

first: Alexander

last: Zambon

state: CA

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

summary:
This study was conducted using affymetrix microarrays. We were interested in determining the effects of tTA expression in the hearts of FVBN mice. We compared expression to wild type mice.
Keywords: other


title: MastomysMouseMucosa

status: Public on Jan 07 2004

city: New Haven

first: Mark

last: Kidd

state: CT

address: 333 Cedar Street

department: Surgery

institute: Yale University School of Medicine

summary:
Analysis of gene expression in gastric mucosa from Mastomys treated for different time periods with Loxtidine
Keywords = ECL Mastomys Affymetrix Hyperplasia Neoplasia
Keywords: repeat sample

first: Toshinori

last: Hinoue

first: Kevin

last: Lye

first: Yi

last: Wen

first: Irvin

middle: M

last: Modlin


title: Wild-type vs. Rb-/- Prostate Epithelial Cell Lines

status: Public on Jan 05 2004

city: Ann Arbor

first: Michael

middle: Thomas

last: McCabe

state: MI

address: 1500 E. Medical Center Drive

department: Urology

institute: University of Michigan

summary:
Comparison of control wild-type and Rb-/- prostate epithelial cell lines under untreated and serum-free conditions
Keywords = prostate
Keywords = epithelial
Keywords: other

last: Day


title: DNA methylation and histone deacetylation in neural stem cells

status: Public on Jan 04 2004

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

summary:
Neurosphere cultures were established from individually isolated E 14.5 forebrains of mouse embryos that carry a bcl2 transgene. Single-cell suspensions were prepared, seeded at 1x105 cells/ml and treated for two days with 150 nM Trichostatin A (TSA; histone deacetylase inhibitor), 500 nM 5-Aza-2’-deoxycytidine (AzaC; demethylating agent) or both compounds, or left untreated. Two independent experiments were performed.
Keywords: other


title: CF vs control Pancreas

status: Public on Mar 29 2004

first: Robert

last: De Lisle

summary:
Total RNA was prepared using TRIzol reagent from the pancreata of eight week old male mice.  The genotypes were Control: gastrin+/-, CFTR+/+; and CF: gastrin+/-, CFTR-/-.  All mice were on 95% black6, 5% 129Sv background.  Mice were fed Peptamen from age 10 days to prevent intestinal obstruction.
Keywords: parallel sample

first: Simran

last: Kaur

first: Donna

last: Ziemer

first: Oxana

last: Norkina

first: Linda

last: Samuelson


title: Gene expression analysis of the developing cortex

status: Public on Mar 27 2004

city: Kodaira

first: Nobuo

last: Funatsu

state: Tokyo

address: 4-1-1 Ogawahigashi

department: Cellular Biology

country: Japan

institute: National Institute of Neuroscience, NCNP

summary:
The mammalian neocortex develops layer organizations with regional differences represented by expression of multiple genes at embryonic stages. These genes could play important roles in the formation of areal cyto-architecture, yet, the number of genes identified so far is not sufficient to explain such intricate processes. Here we collected five regions; the medial, dorsal, lateral, rostral, and occipital, from the dissected E16.5 mouse cerebral cortex and performed extensive gene expression analysis using the Affymetrix U74Av2 array.
Keywords = mouse
Keywords = cortex
Keywords = development
Keywords = regional
Keywords = gene expression
Keywords = medial
Keywords = dorsal
Keywords = lateral
Keywords = rostral
Keywords = occipital
Keywords: ordered

first: Takayoshi

last: Inoue

first: Shun

last: Nakamura


title: Mesangioblast clone comparison

status: Public on Dec 25 2003

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

summary:
Mouse dorsal aorta from E9.5 mouse embryos (C57BL6) was grown as an explant culture as described elsewhere (De Angelis et al., 1999). After 5 days the explant was dissociated into a single cell suspension, and plated at limiting dilution on a feeder layer of Mitomycin C-treated primary embryonic mouse fibroblasts, in 96 multiwell plates in complete medium, RPMI 20% Fetal Calf Serum. After 1 week, mesangioblast clones appeared approximately 2-4% of the wells. When the clones had grown to approximately 103 cells they were passed on gelatin-coated dishes, and further expanded. Clones D16 and D351 were used for microarray analysis.
Keywords: other

first: Silvia

last: Brunelli

first: Fernanda

last: De Angelis

first: Rossana

last: Tonlorenzi

last: Baesso

first: Sergio

last: Ferrari

first: Irene

last: Bozzoni

first: Stefano

first: Giulio

last: Cossu


title: Nrf2 Knockout vs. Wildtype mice

status: Public on Dec 16 2003

first: Jiang

last: Li

address: 777 Highland Ave.

department: School of Pharmacy

institute: University of Wisconsin Madison

summary:
In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the liver (GSE864) and spleen (GSE865) of Nrf2 knockout and wildtype mice at 5 months of age.

This SuperSeries is composed of the SubSeries listed below.

first: Thor

last: Stein

first: Jeffrey

last: Johnson


title: Mesangioblast clone comparison- U74A


title: Nrf2 Knockout vs. Wildtype mice, spleen sample

summary:
In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the spleen of Nrf2 knockout and wildtype female mice at 5 month age.
Total RNAs from two Nrf2 knockout or wildtype littermates were analyzed separately. There are two replicates (GSM 13470, 13472) for the female Nrf2 wildtype group and two replicates (GSM 13467, 13469) for the female Nrf2 knockout group.

Keywords: parallel sample


title: Nrf2 Knockout vs. Wildtype mice, liver sample

summary:
In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the liver of Nrf2 knockout and wildtype mice at 5 month age.
Total RNAs from two Nrf2 knockout or wildtype littermates were analyzed separately. There are two replicates (GSM 13431, 13435) for the female Nrf2 wildtype group, two replicates (GSM 13439, 13441) for the male Nrf2 wildtype group, two replicates (GSM 13436, 13437) for the female Nrf2 knockout group, and two replicates (GSM 13438, 13440) for the male Nrf2 knockout group.
Keywords: parallel sample


title: Genomic profile of the mouse intestine

status: Public on Dec 04 2003

city: Epalinges

first: Pascale

last: Anderle

institute: ISREC

summary:
8 week-old male Hsd:ICR(CD-1) mice were fed ad libitum a standard chow (Harlan Teklad diet 2018S) and housed in groups of five. Animals were then divided into 3 pools (n=10) and sacrificed. The small intestine was extracted and divided into three sections, where the first 2-3 cm after the stomach comprised the duodenum, the middle third the jejunum, and the section before the ileo-ceco-colic junction comprised the ileum. Colon was not divided into proximal and distal sections and was treated as a single intestinal section.
Keywords: other

first: David

last: Mutch

first: Muriel

last: Fiaux

first: Robert

last: Mansourian

first: Karine

last: Vidal

first: Walter

last: Wahli

first: Gary

last: Williamson

first: Matthew-Alan

last: Roberts


title: Mouse model of myocardial infarction

status: Public on Oct 24 2003

first: Martina

last: Schinke

institute: Harvard University

summary:
This dataset is a time series (1 hour [h], 4 hours, 24 hours, 48 hours, 1 week [w], and 8 weeks) intended to compare normal functioning left ventricles [lv + lv2] with infarcted [ilv] and non-infarcted left ventricles [nilv]. Ilv samples are taken from the region between the LAD artery and the apex on a mouse with myocardial infarction. Lv2 samples are from the same region in a sham operated mouse. Nilv samples are taken from the region above the infartion and the left ventricle [lv] samples mimic that region in a sham mouse. The lv and lv2 samples can be compared as both are from normal functioning hearts. For more information visit http://cardiogenomics.med.harvard.edu/groups/proj1/pages/mi_home.html
Keywords: other

last: Brown

first: Seigo

last: Izumo


title: Neurospheres of WT and BMI-1 KO

status: Public on Oct 14 2003

first: Toshihide

last: Iwashita

department: Internal Medicine

summary:
The cRNA derived from Brain and Gut neurospheres of wild type and BMI-1 knockout mice were hybridized to Affymetrix mouse ver 2 Chips A, B and C. In case of brain neurospheres, the cRNA were generated by one round RNA amplification (conventional method). In contrast, the cRNA of Gut neurospheres were generated by two round RNA amplifications.
Keywords: parallel sample

first: Anna

middle: V

last: Molofsky

first: Ricardo

last: Pardal

first: In-Kyung

last: Park

first: Michael

last: Clarke

first: Sean

middle: J

last: Morrison


title: Gene expression of transplanted hearts

city: Meguro-ku

first: Yuichi

last: Matsui

address: Komaba 4-6-1

department: Biology

institute: University of Tokyo

summary:
C57/BL6 to C57/BL6
Balb/c to C57/BL6
Balb/c to C57/BL6 with anti CD80/86 mAb

Identificaton of gene expression profile in tolerizing murine cardiac allograft by co-stimulatory blockade.

The induction of specific tolerance would be the ultimate achievement in transplant immunology, but the precise mechanisms of immunological tolerance remain largely unknown. Here, we investigated global gene expression analysis in tolerizing murine cardiac allografts by means of oligonucleotide microarrays. Tolerance induction was achieved in cardiac allografts from BALB/c to C57BL/6 mice by daily intraperitoneal injection of anti-CD80 and CD86 mAbs. Comparative analysis revealed 64 genes to be induced more extensively in the tolerizing than in the syngeneic isografts, and 16 genes than in the rejecting allografts. Two genes were specifically upregulated in the tolerizing allografts. In the tolerizing allografts there were induced marked expressions of a number of genes for proinflammatory factors, including interferon-gamma inducible cytokines and chemokines, as well as apoptosis-related genes which were also upregulated in the rejecting allografts. Moreover, these gene expression patterns continued to be upregulated more than 70 days post transplant. These results provide evidence that immunological tolerance can be induced and maintained in the presence of prominent proinflammatory gene expression in vivo.
Keywords: other

first: Y

first: A

last: Saiura

last: Sugawara

first: M

last: Sata

first: K

last: Naruse

first: H

last: Yagita

first: T

last: Kohro

first: C

last: Mataki

last: Izumi

last: Yamaguchi

last: Minami

last: Sakihama

first: S

last: Ihara

last: Aburatani

last: Hamakubo

last: Kodama

last: Makuuchi


title: Time course of aortic gene expression

status: Public on Sep 19 2003

city: Philadelphia

first: Radu

middle: Daniel

last: Rudic

address: 421 Curie Boulevard

department: Center of Experimental Therapeutics

institute: University of Pennsylvania

summary:
After 2 week acclimation to 12 hr/12 hr light/dark regimen, c57/Bl6 mice were subjected to a 36 hour period of constant darkness. Aortae were subsequently harvested at 4 hour intervals to 48 hours.  Duplicate microarrays were hybridized with biotin-labeled probes derived from aorta tissue (6 pooled aortae/timepoint).
Keywords: time-course

middle: D

first: Peter

last: McNamara

first: Satchidananda

last: Panda

first: John

last: Hogenesch

first: Garret

last: FitzGerald


title: Heart failure in TNF-alpha transgenic mice

status: Public on Nov 09 2003

first: Zhong

last: Tang

address: 1025 Walnut Street

department: Medicine

institute: Thomas Jefferson University

summary:
Cardiac-specific TNF-alpha transgenic mice are an excellent model to study the pathologenesis of heart failure. Affymetrix U74V2A was used to analyze the gene expression profile of  male and female wildtype FVB and TNF-alpha transgenic mice at the time point of compensated hypertrophy  and dilated heart failure. 3 week, 13 week and 40 week samples examined.
Keywords: other

first: Z

last: Feldman

first: Arthur


title: CD8+ memory T cells

status: Public on Jul 25 2003

city: Denver

first: Brad

last: Swanson

state: CO

institute: National Jewish Medical and Research Center/HHMI

summary:
Expression profiles of in vitro generated CD8+ central memory (CM) and effector/effector memory (E/EM) T cells on Affymetrix GeneChip Murine Genome U74 Version 2 Set MG-U74A, MG-U74B, and MG-U74C. T cells were generated from female P14 T cell receptor transgenic mice on the C57Bl/6 genetic background.
Keywords: other

first: Vanessa

last: Ott

last: Cambier

last: Kappler

first: Philippa

last: Marrack

first: Bradley


title: Affymetrix of DC's from wildtype B6, CIITA-/-, and Iab-/- mice

city: Chapel Hill

first: Athena

last: Wong

state: NC

department: Microbiology and Immunology

institute: Lineberger Cancer Center

summary:
Triplicates preparations of RNA from day 10 DC's.  Experiment is described in Wong et al 2003 Nat. Immunol.
Keywords: equivalent probe


title: Spermatogenesis

status: Public on Oct 02 2003

city: New York

first: Nikolaus

last: Schultz

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

summary:
A multitude of genes expressed solely in meiotic or postmeiotic spermatogenic cells offers a myriad of contraceptive targets.

Understanding mammalian spermatozoan development and the events surrounding fertilization has grown slowly, in part because of uncertainty about the number and identity of the cellular components involved. Determination of those transcripts expressed specifically by germ cells should provide an inclusive list of probable critical proteins. Here, total mouse testis transcript profiles were trimmed of transcripts found in cultures enriched in Sertoli or interstitial cells to yield a germ cell-enriched transcript profile. Monitoring of changes of this profile in the developing testis identified 1,652 genes whose transcript abundance increased markedly coincident with the onset of meiosis. Remarkably, 351 of these genes ( approximately 20%) appear to be expressed only in the male germline. Germ cell-specific transcripts are much less common earlier in testis development. Further analysis of the UniGene EST database coupled with quantitative PCR indicates that approximately 4% of the mouse genome is dedicated to expression in postmeiotic male germ cells. Most or many of the protein products of these transcripts are probably retained in mature spermatozoa. Targeted disruption of 19 of these genes has indicated that a majority have roles critical for normal fertility. Thus, we find an astonishing number of genes expressed specifically by male germ cells late in development. This extensive group provides a plethora of potential targets for germ cell-directed contraception and a staggering number of candidate proteins that could be critical for fertilization.
Keywords: other

first: N

first: F

middle: K

last: Hamra

first: D

last: Garbers

first: David


title: Effect of LAMR1-TP1. 092603MCM6

status: Public on Dec 30 2003

city: Suita, Osaka

first: Yoshihiro

last: Asano

institute: Osaka Univ.

summary:
Infected neonatal mouse cardiomyocyte

COMMENT:  Submitter has not provided GEO with full dataset as described in Nat Genet. 2004 Feb;36(2):123-30.
Keywords: parallel sample


title: Cardiac hypertrophy related to the phosphoinositide 3-kinase signaling pathway

status: Public on Jul 24 2003

city: Cambridge

first: Martina

last: Schinke

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

summary:
The insulin/IGF-IRS-PI3K-Akt pathway is highly conserved in evolution. To test whether this signaling cascade determines organ size in vertebrates, we have recently created mouse lines transgenic for constitutively active (caPI3K) and dominant-negative forms of PI3K (dnPI3K) (Shioi et al., 2000). Transgene expression is driven by the cardiac-specific a -myosin heavy chain (MHC) promoter. Both transgenic lines are characterized by moderate but highly consistent changes in heart size, despite the fact that body weight and the size of other organs are completely normal. caPI3K transgenic animals have hearts 20% larger than those of wild type littermates, whereas dnPI3K mice have hearts that are 17% smaller. The observed changes in heart size correlate with an appropriate increase or decrease in the size of transgenic cardiomyocytes. These hearts do not have cardiomyopathic changes, since the contractile function of transgenic hearts is normal, and signs of necrosis, apoptosis, or interstitial fibrosis are absent (see Physiology). These data suggest an autonomous role for PI3K in cell size regulation. Our goal is now to determine how activation of this system translates into changes in cell size by identifying the trigger and components of this signaling cascade.

Heterozygous caPI3K (constitutively active PI3K) and dnPI3K (dominant-negative PI3K) transgenic female mice (5-14 months) compared with non-transgenic littermates. Transgene expression driven by the a -myosin heavy chain (a -MHC) promoter.
Keywords: other

first: Jeffrey

last: Brown

first: Seigo

last: Izumo


title: Murine dermal burn wound

status: Public on Jun 23 2003

city: Gainesville

first: Robert

middle: Joseph

last: Feezor

state: FL

address: 1600 SW Archer Road, Room 6116

institute: University of Florida

summary:
Investigation into murine dermal burn wound.
Mouse thermal injury induced, and skin excised at 0 hours, 2 hours, 3 days and 14 days post-injury.
Keywords: other

first: Heather

middle: N

last: Paddock

first: Henry

last: Baker

first: Juan

last: Varela

first: Lyle

last: Moldawer

first: Gregory

middle: W

last: Mozingo


title: 48h EC/IC/C mouse

status: Public on Aug 18 2003

city: La Jolla

first: Richard

middle: Louis

last: Lieber

address: 9500 Gilman Drive

department: Orthopaedics and Bioengineering

institute: University of California

summary:
Mice were subjected to 50 eccentric contractions (EC) or 50 isometric contractions (IC) using a non-invasive model, and then sacrificed 48 hours later. RNA from the tibialis anterior of 4 animals were pooled and then split into two groups for hybridization onto two separate Affymetrix MGU74Av2 chips. Control samples were contralateral to the exercised legs, and were only subjected to enough contractions to measure isometric torque.

Eccentric contractions (ECs), in which a muscle is forced to lengthen while activated, result in muscle injury and, eventually, muscle strengthening and prevention of further injury. Although the mechanical basis of eccentric contraction-induced injury has been studied in detail, muscle's biological response is less well characterized. This study presents the development of a minimally-invasive model of EC injury in the mouse, follows the time course of torque recovery after an injurious bout of ECs, and uses Affymetrix microarrays to compare the gene expression profile 48 hours after ECs to both isometrically stimulated muscles and contralateral muscles. Torque dropped by about 55% immediately after the exercise bout, and recovered to initial levels 7 days later. 36 known genes were upregulated after ECs compared to contralateral and isometrically stimulated muscles, including five muscle specific genes: muscle LIM protein (MLP), Muscle Ankyrin Repeat Proteins (MARP 1 and 2; also known as cardiac ankyrin repeat protein and Arpp/Ankrd2, respectively), Xin, and Myosin Binding Protein H. The time courses of MLP and MARP expression after the injury bout (determined by quantitative real-time polymerase chain reaction) indicate that these genes are rapidly induced, reaching a peak expression level of 6-11 times contralateral values 12-24 hours after the EC bout and returning to baseline within 72 hours. Very little gene induction was seen after either isometric activation or passive stretch, indicating that the MLP and MARP genes may play an important and specific role in the biological response of muscle to EC-induced injury.
Keywords = mouse tibialis anterior eccentric isometric contraction muscle
Keywords: other

first: Ilona

middle: A

last: Barash


title: Splenic Dendritic Cell Subsets

status: Public on Jun 09 2003

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary:
The functional relationships and properties of different sub-types of dendritic cells (DC) remain largely undefined. We used a global gene profiling approach to determine gene expression patterns among murine splenic CD11c high DC subsets in an effort to better characterise these cells.
Keywords: equivalent probe

first: A

last: Edwards

first: S

last: Tomlinson

first: O

last: Schulz

last: Sher

first: C

last: Reis E Sousa


title: Epithelium transition profile

status: Public on Sep 12 2003

city: Notre Dame

first: Matthew

last: Feldman

state: IN

address: 251 Nieuwland Science Hall

department: Chemistry and Biochemistry

institute: University of Notre Dame

summary:
Transcriptional Profiling of the Transition from Normal Intestinal Epithelia to Adenomas and Carcinomas in the APC(Min/+) Mouse.

Samples used in analysis:
* GSM6191-GSM6196 (WT): Ilea epithelial cells from C57/BL6 wild-type samples
* GSM6197-GSM6201 (Adenoma): Epithelial cells from crypts of adenomas of APC(Min/+) mice
* GSM6202-GSM6206 (Carcinoma): Epithelial cells from crypts of carcinomas of APC(Min/+) mice

Using a PixCell IIe instrument (Arcturus), ~30,000 laser firings per sample were used to collect cells of interest. RNA was extracted from captured cells by PicoPure (Arcturus) technique, followed by 2 rounds of RiboAmp amplification (Arcturus), with incorporation of biotinylated nucleotides (Enzo) in the IVT of round 2. All protocols were as per manufacturers instructions. 15ug of labeled cRNA from individual samples were hybridized to respective MG_U74Av2 chips (Affymetrix) and washed/stained using the standard EukGEWS2v4 protocol (Affymetrix). Chips were scanned and analyzed using MAS 5 (Affymetrix) and data scaled to TI=500.

Pairwise comparisons using the Mann-Whitney test were performed in DMT 3 (Affymetrix), comparing:
* WT vs Adenoma (n=6 x n=5; 83.3% concordance)
* WT vs Carcinoma (n=5 x n=5; 84% concordance)
* Adenoma vs Carcinoma (n=5 x n=5; 84% concordance)

This resulted in the identification of differentially expressed transcripts. Fold changes were calculated from signal-log-ratios. Identified transcripts were clustered based on functional information which was publicly available at time of analysis, obtained through the NetAffx web portal (Affymetrix).
Keywords = colon cancer
Keywords = gene expression
Keywords = DNA microarrays
Keywords = beta-catenin
Keywords = familial adenomatous polyposis
Keywords: ordered

first: Nicholas

last: Paoni

first: Linda

middle: S

last: Gutierrez

first: Victoria

last: Ploplis

first: Francis

last: Castellino


title: Naive, EAE placebo-treated and EAE 1,25(OH)2D3-treated groups

status: Public on Dec 01 2003

city: Madison

first: Karen

middle: Marie

last: Spach

address: 433 Babcock Drive

department: Nutritional Sciences / Biochemistry

institute: University of Wisconsin-Madison

summary:
B10.PL mice with severe (stage 2.5-3) experimental autoimmune encephalomyelitis were treated with placebo or 200 ng 1,25(OH)2D3.  Six hours later, the spinal cords were harvested and mRNA was extracted for microarray analysis.  Naive mice serve as controls.  Individual samples were hybridized to individual microarrays.
Keywords = Experimental autoimmune encephalomyelitis
Keywords = multiple sclerosis
Keywords = 1
Keywords = 25(OH)2D3
Keywords: repeat sample

first: Laura

middle: B

last: Pedersen

first: Faye

middle: E

last: Nashold

first: Brian

last: Yandell

first: Tsuyoshi

last: Kayo

first: Tomas

last: Prolla

first: Colleen

last: Hayes


title: Effect of SOCS3 on the transcriptional response of bone marrow-derived macrophages to IL-6

status: Public on Apr 17 2003

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

summary:
Effects of SOCS3 on the transcriptional response of bone marrow-derived macrophages to IL-6.

Fetal liver cells from SOCS3+/+ or SOCS3-/- embryos were used to reconstitute recipient mice. Donor derived bone marrow from these mice was differentiated to macrophages.  Macrophages were either unstimulated, or stimulated for 100 or 400 minutes with 10 ng/ml IL-6.
Keywords = macrophage, SOCS3, IL-6, interferon
Keywords: repeat sample

first: R

last: Pauleau

first: E

last: Parganas

first: Y

last: Takahashi

first: J

last: Mages

last: Ihle

last: Rutschman

first: P

last: Murray


title: Diet induced changes in mouse liver

status: Public on Apr 05 2003

city: Galveston

first: Allan

last: Brasier

address: 301 Univ. Blvd

institute: University Texas Medical Branch

summary:
Examination of gene expression profiles from liver of C57BL/6 mice and LDL receptor deficient mice fed on either a low fat diet or a high fat Western-style diet for 12 weeks.  Three replicates of each condition analyzed.
Keywords = LDL receptor deficiency, high fat diet, atherosclerosis, liver
Keywords: repeat sample

first: Adrian

last: Recinos


title: Hypothalamus response to LPS and restraint stress

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
The paraventricular hypothalamic nucleus (PVH) is a key site for integrating neuroendocrine, autonomic, and behavioral adjustments to diverse homeostatic challenges, including "physiological" (e.g., infection or hemorrhage) and "emotional" [e.g., restraint (RST) or footshock] stresses. Both types of challenges ultimately converge to activate common response systems represented in PVH, including the hypothalamo-pituitary-adrenal axis and the sympathoadrenal system. Oligonucleotide microarrays (U74A; Affymetrix, Santa Clara, CA) were used to compare and contrast gene expression profiles in the PVH elicited at 1 and 3 hr after acute exposure to representative physiological [intraperitoneal injection of 10 microg lipopolysaccharide (LPS)] and emotional (30 min RST) stressors. In general, the two challenges recruited relatively few genes in common, with the degree of overlap varying across functional classes of genes. The greatest degree of commonality was seen among signaling molecules and neuropeptides, whereas transcription factors upregulated by RST and LPS were largely distinct. Unexpectedly, RST induced a number of immune-related molecules, which were not regulated by LPS. Hybridization histochemical analyses localized a subset of responsive transcripts to the PVH and/or immediately adjoining regions. Immunerelated molecules in particular distributed broadly to vascular and other barrier-associated cell types. These global transcriptional profiles inform the search for early (transcription factors) and late (target genes) mechanisms in the modulation of PVH, and generalized CNS, responses to categorically distinct stressors.
Keywords: other

first: T

last: Reyes

last: Sawchenko


title: Circadian rhythm in Clock mutant and Cry deficient mice

status: Public on Nov 08 2003

city: Tsukuba

first: Norio

last: Ishida

institute: National Institute of Advanced Industrial Science and Technology

summary:
Molecular analysis of circadian rhythm in mice. Liver tissue of wildtype, Clock mutant and Cry deficient C57BL/6  8- to 10-week-old male mice examined.
Keywords = circadian rhythm
Keywords: other

first: K

last: Ooishi

last: Miyazaki

last: Kadota

last: Kikuno

last: Nagase

first: G

last: Atsumi

first: N

last: Ohkura

last: Azama

first: M

last: Mesaki

first: S

last: Yukimasa

first: H

last: Kobayashi

first: C

last: Iitaka

last: Umehara

last: Horikoshi

last: Kudo

last: Shimizu

last: Yano

last: Monden

last: Machida

last: Matsuda

last: Horie

last: Todo

first: Katsutaka

first: Koyomi

first: Koji

first: Reiko

first: Takahiro

first: Gen-ichi

first: Naoki

first: Takashi

first: Miho

first: Shima

first: Hisato

first: Chisato

first: Masami

first: Yoshihisa

first: Masahiko

first: Morito

first: Kazuhiko

first: Juzo

first: Shuichi

first: Takeshi


title: S-DG

status: Public on Feb 27 2003

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

institute: California Institute of Technology

summary:
S: Shock alone. Young male C57BL/6J mice were placed into the novel context 2 hours prior to receiving the training paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals remained in the training chamber for 1 hour after the last shock. RNA was extracted was extracted 1hr, 2hr, 4hr, and 6hr after the last shock treatment.
Keywords: time-course

first: Jonathan

middle: M

last: Levenson

first: Sun-Young

last: Lee

first: Yun Anna

last: Cao

first: Kim

last: Worley

first: Hui

last: Zheng

first: Melvin

middle: I

last: Simon

first: David

last: Sweatt


title: Murine inner medullary collecting duct cells response to aldosterone

status: Public on May 22 2003

first: Michelle

middle: L.

last: Gumz

address: 1600 SW Archer Rd

department: Biochemistry and Molecular Biology

summary:
Murine inner medullary collecting duct cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations.

The mineralocorticoid aldosterone is a major regulator of Na+ and acid-base balance and control of blood pressure. Although the long-term effects of aldosterone have been extensively studied, the early aldosterone-responsive genes remain largely unknown. Using DNA array technology, we have characterized changes in gene expression after 1 h of exposure to aldosterone in a mouse inner medullary collecting duct cell line, mIMCD-3. Results from three independent microarray experiments revealed that the expression of many transcripts was affected by aldosterone treatment. Northern blot analysis confirmed the upregulation of four distinct transcripts identified by the microarray analysis, namely, the serum and glucose-regulated kinase sgk, connective tissue growth factor, period homolog, and preproendothelin. Immunoblot analysis for preproendothelin demonstrated increased protein expression. Following the levels of the four transcripts over time showed that each had a unique pattern of expression, suggesting that the cellular response to aldosterone is complex. The results presented here represent a novel list of early aldosterone-responsive transcripts and provide new avenues for elucidating the mechanism of acute aldosterone action in the kidney.
Keywords: other

first: M

middle: L

middle: P

last: Popp

first: C

last: Wingo

first: B

last: Cain


title: IFNg-/- and conditional Socs3-/- mice: cytokine treatments

status: Public on Apr 10 2003

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:
Changes in mouse liver mRNA profiles following intraperitoneal cytokine injection.
Either interferon-gamma-/-, albumin-cre(-) Socs3(w/fl) mice, or albumin-cre(+) Socs3(-/fl) mice were injected with either phosphate-buffered saline, interferon-gamma, or interfeukin-6, and livers taken after 4h.
Keywords = Socs3, interferon gamma, interleukin-6, il6, liver, suppressor of cytokine signalling 3
Keywords: repeat sample

first: Ben

last: Croker

first: Doug

last: Hilton


title: S-CA1


title: Integrated stress response

status: Public on Oct 07 2003

first: Heather

middle: P.

last: Harding

state: NY

address: 540 First Ave

department: Pharmacology

institute: NYU School of Medicine

summary:
Comparison of genes induced during activation of the Integrated Stress Response by tunicamycin or following AP20187 induced dimerization of a Fv2E-PERK chimera in wildtype cells and cells carrying mutations in key ISR signaling molecules.
Keywords: other

first: P

middle: D

last: Lu

last: Jousse

first: S

middle: J

last: Marciniak

first: Y

last: Zhang

first: I

last: Novoa

first: D

last: Scheuner

first: R

last: Kaufman

last: Ron

first: H


title: effect of +/- mutations in ES cells

status: Public on Sep 28 2003

city: Troy

first: Derek

last: Symula

institute: Wadsworth Center Genomics Institute

summary:
effect of +/- mutations in ES cells
Keywords: other


title: 2nd C+S-DG

first: Sangdun

last: Choi

summary:
C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1hr, 2hr, 4hr, and 6hr after the last shock treatment.
Keywords: time-course

first: Jonathan

last: Levenson

first: Sun-Young

last: Lee

first: Yun Anna

last: Cao

first: Kim

last: Worley

first: Hui

last: Zheng

first: Melvin

last: Simon

first: David

last: Sweatt


title: 3rd C+S-DG


title: 1st C+S-DG


title: 2nd C+S-CA1


title: 1st C+S-CA1


title: 3rd C-DG

summary:
C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 1hr, 2hr, 4hr, and 6hr after experimental mice received their last shock treatment.
Keywords: time-course


title: Hypogonadal mice and testosterone proprionate treatment

status: Public on May 28 2003

city: Pullman

first: Patricia

middle: Imele

last: Sadate-Ngatchou

department: School of Molecular Biosciences

institute: Washington State University

summary:
Analysis of the transcriptome of testes of hypogonadal mice that had been pretreated with testosterone proprionate for 2 weeks then submitted to testosterone withdrawal.
Keywords = testis, hypogonadal mice, testosterone
Keywords: other

last: Pouchnik

first: M

last: Griswold


title: 1st C-DG


title: 2nd C-CA1


title: 3rd C+S-CA1


title: Spleen

status: Public on Mar 06 2003

summary:
Spleen total RNA (Catalog #64044-1) was purchased from Clontech and used as the starting material.
Keywords: repeat sample

first: Jong-Woo

last: Kim

first: Mi Sook

last: Chang


title: 1st C-CA1


title: 6hr C+S-DG

summary:
C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 6 hour after the last shock treatment. All three sample treatments are identical but prepared separately.
Keywords: repeat sample


title: Liver

summary:
Liver total RNA (Catalog #64042-1) was purchased from Clontech and used as the starting material.
Keywords: repeat sample


title: 6hr C-DG

summary:
C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 6hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.
Keywords: repeat sample


title: 4hr C-DG

summary:
C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 4hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.
Keywords: repeat sample


title: 1hr C+S-DG

summary:
C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 1 hour after the last shock treatment. All three sample treatments are identical but prepared separately.
Keywords: repeat sample


title: 2hr C-DG

summary:
C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 2hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.
Keywords: repeat sample


title: 1hr C-DG

summary:
C: Control. Young male C57BL/6J mice were handled by experimenter. No other treatment administered. RNA from control mice were extracted 1hr after experimental mice received their last shock treatment. All three sample treatments are identical but prepared separately.
Keywords: repeat sample


title: 6hr C-CA1


title: 2hr C+S-CA1

summary:
C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 2 hour after the last shock treatment. All three sample treatments are identical but prepared separately.
Keywords: repeat sample


title: 1hr C+S-CA1


title: 6hr C+S-CA1


title: 2nd C-DG


title: 3rd C-CA1


title: OVX/P4/6h/UTX 129 WT vs. Hoxa-10-/-

status: Public on Dec 10 2002

city: Boston

first: Richard

last: Maas

state: MA

address: 20 Shattuck St, Room 1019A

department: Medicine/Division of Genetics

institute: Brigham and Women's Hospital/Harvard Medical School

summary:
Female mice used were SvJ/129, 10-16 weeks of age; Hoxa-10+/+ and Hoxa-10-/- littermates were used in parallel experiments.
14 days after ovariectomy, mice were injected subcutaneously with
progesterone dissolved in sesame oil (Sigma; 0.2mg/0.1mL/mouse),
followed by sacrifice and removal of uterine horns at 6 hours after
injection.  8 uterine horns from 4 mice were pooled to form one
sample.  Total RNA preparation, cRNA labeling and hybridization were
performed according to recommendations by Affymetrix.
The 6 samples were obtained and processed in two batches: (1: GSM3047 and GSM3041), and (2: GSM3048, GSM3049, GSM3042, and GSM3043).
Keywords: other

first: Mylene

middle: W

last: Yao

first: Hyunjung

last: Lim

first: Daniel

last: Schust

first: Sung

last: Choe

first: Anna

last: Farago

first: Yueyun

last: Ding

first: Sebastien

last: Michaud

first: George

last: Church


title: 2hr C-CA1

status: Public on Feb 26 2003

first: Sangdun

last: Choi

first: Jonathan

last: Levenson

first: Sun-Young

last: Lee

first: Yun Anna

last: Cao

first: Kim

last: Worley

last: Zheng


title: OVX/P4/UTX 129/SvImJ WT A

summary:
Female mice used were 129/SvImJ wildtype (Jackson Lab), 10-16 weeks
of age.  14 days after ovariectomy, mice were injected
subcutaneously with progesterone dissolved in sesame oil (Sigma;
0.2mg/0.1mL/mouse), followed by sacrifice and removal of uterine
horns at various times after injection.  8 uterine horns from 4 mice were
pooled to form one sample.  Total RNA preparation, cRNA labeling and
hybridization were performed according to recommendations by
Affymetrix.
Keywords: time-course


title: 4hr C-CA1

first: Hui

first: Melvin

last: Simon

first: David

last: Sweatt


title: 4hr C+S-DG

summary:
C + S: Context + Shock. Young male C57BL/6J mice were exposed to a contextual fear conditioning paradigm that consisted of: Placement into a novel spatial context for 2 min. After 2 min, a 1 sec (0.5 mA) shock was administered through a floor grid. The 2 min-1 sec shock paradigm was repeated for a total of 3 shocks. 1 min after the last shock, animals were removed to their homecage. RNA was extracted was extracted 4 hour after the last shock treatment. All three sample treatments are identical but prepared separately.
Keywords: repeat sample


title: OVX/oil/6h/UTX 129 WT vs. Hoxa-10-/-

first: Richard

last: Maas

summary:
Female mice used were SvJ/129, 10-16 weeks of age; Hoxa-10+/+ and Hoxa-10-/- littermates were used in parallel experiments.  14 days after ovariectomy, mice were injected with sesame oil
(Sigma; 0.1mL/mouse), followed by sacrifice and removal of uterine
horns at 6 hours after injection.  8 uterine horns from 4 mice were
pooled to form one sample.  Total RNA preparation, cRNA labeling and
hybridization were performed according to recommendations by
Affymetrix.  All 6 samples were collected and processed in parallel.
Keywords: other

first: Hyunhung

first: Sebastein


title: 1hr C-CA1


title: wild type and aire -/- murine meduallary thymic epithelial cells

status: Public on Sep 19 2002

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary:
Mice used were B6/129 F2's, 3-5 weeks of age, either wild type or with both copies of the autoimmune regulator gene (aire, GenBank #AF079536) disrupted.  Thymi from five of these mice of both sexes were removed and pooled. After collagenase/dispase digestion, density gradient fractionation, and fluorescent antibody staining, cells with the phenotype CD45-, G8.8+, CDR1int and B7.1hi were FACS-sorted and total RNA was made from them. RNA was twice-amplified using a T7 polymerase-based method.
Keywords: ordered


title: 2hr C+S-DG


title: OVX/P4/UTX 129/SvImJ WT B

first: Mylene

last: Yao

first: Hyunjung

last: Lim

first: Daniel

first: Sung


title: Hippocampus replicate samples

status: Public on May 28 2002

city: Memphis

first: Lu

last: Lu

state: TN

address: 855 Monroe Avenue

department: Center of Genomics and Bioinformatics

institute: University of Tennessee Health Science Center

summary:
Hippocampus gene expression experiments
Keywords: parallel sample


title: 4hr C+S-CA1

first: Sangdun


title: Exercised Induced Hypertrophy

status: Public on Aug 02 2002

first: Martina

last: Schinke

institute: Harvard University

summary:
The Affymetrix GeneChip MgU74Av2 was used to analyze expression profiles of mice that had cardiac hypertrophy induced by swimming training.  More information of this model can be obtained at
http://cardiogenomics.med.harvard.edu/groups/proj1/pages/swim_home.html
Keywords = exercise induced hypertrophy, cardiac
Keywords: time-course

first: Lauren

last: Riggi

first: Iuan

last: Chen

first: Seigo

last: Izumo


title: Brain after ischemia and antioxidant

status: Public on Jun 26 2002

city: Denver

first: Russell

last: Bowler

address: 1400 Jackson Street, K736a

institute: National Jewish Medical and Research Center

summary:
A catalytic antioxidant (AEOL 10150) attenuates expression of inflammatory genes in stroke.

White and grey matter in the distribution on the middle cerebral artery 6 hours after administration of the saline/catalytic antioxidant AEOL 10150 and ischemia/reperfusion of the MCAO; pooled mRNA from 6 brains.
Keywords = stroke, antioxidant
Keywords: repeat sample

first: Huaxin

last: Sheng

first: Jan

last: Enghild

first: Robert

last: Pearlstein

last: Warner

first: James

last: Crapo