title: Wilms tumor versus Stratagene Universal Reference

city: Amsterdam

first: Fred

last: van Ruissen

department: Department of Neurogenetics

country: Netherlands

institute: Academic Medical Center

summary:
Gene expression comparison of Wilms tumor RNA versus Stratagene Universal reference RNA
Keywords: repeat sample

first: Jan

last: Ruijter

first: Gerben

last: Schaaf

first: Lida

last: Asgharnegad

first: Danny

last: Zwijnenburg

first: Marcel

last: Kool

first: Frank

last: Baas


title: scien-affy-human-87089

status: Public on Nov 24 2004

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

country: USA

institute: Translational Genomics

summary:
Normal kidney, liver, spleen, and Universal RNA from Stratagene were expression profiled across five centers (UCLA, Duke, TGen, Children's National Medical Center in Washington, DC, and University of Pennsylvania) using the Affymetrix, spotted Operon, Agilent, and Amersham arrays to identify differences in expression between microarray platforms as well as centers.
To compare the four microarray platforms as well as the reproducibility across the centers.
There will be expression differences between the five centers.
The following array types were profiled at the centers:
UCLA: Affymetrix, Amersham, Agilent
TGen: Affymetrix (3000 scanner)
Children's: Affymetrix (2500 scanner)
Duke: Operon Oligo
University of Penn.: Affymetrix
Series_author: Consortium,,Cross Platform
Keywords: other


title: Collagen-GAG Biocompatibility Tests

status: Public on Nov 09 2004

city: Boston

first: Catherine

last: Klapperich

state: MA

address: 44 Cummington St. 7th Floor

department: Biomedical and Manufacturing Engineering

institute: Boston University

summary:
All mRNA was isolated after 8 hours of culture time in each of three culture conditions. (1) TCPS Plate, (2) Collagen-GAG 2 dimensional coated plate and (3) collagen-GAG three dimensional mesh.
Keywords: ordered

middle: M


title: Barrett's esophagus, Barrett's-associated adenocarcinomas and normal esophageal epithelium

status: Public on Nov 18 2004

city: Chicago

first: Nikolai

middle: N.

last: Khodarev

state: IL

address: 5841 South Maryland Avenue

department: Radiation and Cellular Oncology

institute: The University of Chicago

summary:
Samples were obtained from 8 patients with Barrett's associated adenocarcinomas after transhiatal esophagectomy. Samples representative of the normal esophageal epithelium (N), Barrett’s esophagus (B) and esophageal adenocarcinomas (ADC) were obtained from every patient by experienced GI pathologists. RNA were extracted and samples were profiled for detection of genes differentially expressed in B and ADC relative to N and in ADC relative to B.
Keywords: other

first: Eric

last: Kimchi

first: James

last: Park

first: Thomas

last: Darga

first: Maria

last: Kocherginsky

first: Teodore

last: Karrison

first: John

last: Hart

first: Mitchell

middle: C

last: Posner

first: Ralph

middle: R

last: Weichselbaum

middle: N

first: Erick


title: CBCD34-TGFbeta targets

status: Public on Oct 28 2004

city: New York

first: Agnes

last: Viale

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
TGFbeta regulated genes in human umbilical cord blood CD34+ cells
Keywords: other

first: Joseph

last: Scandura

first: Joan

last: Massague

first: Piernicola

last: Boccuni

first: Stephen

last: Nimer


title: Leukemia study / K562 cell line

status: Public on Nov 03 2004

city: Columbus

first: David

middle: Lawrence

last: Newsom

state: OH

department: Human Cancer Genetics

institute: Comprehensive Cancer Center

summary:
K562 cell line mock treated or for 24 hours with one micromolar imatinib.
Keywords: other

first: Herbert

last: Auer

first: Alan

last: Bakaletz

first: Yiwen

last: Liu-Stratton

first: Chandan

last: Sen

middle: E

last: Carter

first: Rabert

middle: A

last: Hegele

first: Jay

middle: P

last: Tiesman

first: Suzanne

last: Torontali

first: Sherry

middle: F

last: Grissom

first: Charles

middle: J

last: Tucker

first: Hinrich

middle: W

last: Gohlmann

first: Ilse

last: Wyangaert

first: Don

last: Baldwin

first: Grace

last: Straszewski

first: Nehad

last: Mohamed

first: Sandya

last: Liyanarachchi

first: Danilo

last: Perrotti

last: Willey

first: Karl

last: Kornacker


title: Melanoma cell lines

status: Public on Oct 19 2004

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary:
5 melanoma cell lines: MelJUSO, A375, 607B, 518A2, Skmel 28
Keywords: other

first: Ichiro

last: Okamoto

first: Hubert

last: Pehamberger


title: Effect of Oxandrolone on Muscle in Duchenne Muscular Dystrophy

status: Public on Oct 15 2004

city: Jacksonville

first: Robert

middle: C.

last: Olney

state: FL

address: 807 Children's Way

department: Pediatrics

institute: Nemours Children's Clinic

summary:
Three subjects with Duchenne muscular dystrophy (8.3, 10.4, and 16.7 years old) were studied. Baseline studies included stable isotope infusion followed by gastrocnemius muscle biopsy to determine myosin heavy chain synthesis rates. RNA was isolated from the muscle biopsy as well. The subjects were then treated for 3 months with oxandrolone (a synthetic anabolic steroid, 0.1 mg/kg/day) and the studies repeated.
Keywords = muscle
Keywords = Duschenne muscular dystrophy
Keywords = oxandrolone
Keywords = androgen
Keywords: parallel sample

first: Prabhakaran

last: Balagopal

first: Dominique

last: Darmaun

first: Edward

last: Mougey

first: Maryanne

last: Dokler

first: Gary

last: Sieck

first: David

last: Hammond


title: Human hematopoietic stem cell engraftment in goat

status: Public on Oct 14 2004

city: Philadelphia

last: Baldwin

state: PA

address: 277 John Morgan, 3620 Hamilton Walk

department: Pathology and Lab Medicine

institute: University of Pennsylvania

summary:
Robust human-goat chimerism was achieved by transplanting human CD34+Lin- cord blood cells into fetal goats. We observed a broad distribution of GFP-marked human cells in non-hematopoietic organs including kidney, muscle, lung, and heart of transplant goats.  Various marker techniques indicated that human genes were expressed in chimeric livers and blood.
Keywords: other

sample_organism:
Homo sapiens
Capra hircus

first: Fanyi

last: Zeng

first: Shu-zhen

last: Huang


title: lung and tonsillar mast cells

status: Public on Oct 20 2004

city: Yokohama

first: Yoshimichi

last: Okayama

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Research Center for Allergy and Immunology

country: Japan

institute: RIKEN Yokohama Institute

summary:
GeneChip Data of human lung mast cells and tonsillar mast cells

Keywords: other

first: Jun-ichi

last: Kashiwakura

first: Hidenori

last: Yokoi

first: Hirohisa

last: Saito


title: PGA_DogLung_regional_MV

city: Baltimore

first: Shwu-Fan

last: Ma

state: MD

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins University

summary:
This series contain unilateral mechanical ventilated canine lung samples.
Keywords: other

first: Brett

last: Simon

first: R

middle: Blaine

last: Easley

first: Dmitry

last: Grigoryev

first: Shui

middle: Q

last: Ye

first: Tera

last: Lavoie

first: Joe

middle: G. N.

last: Garcia


title: Pseudomonas aeruginosa infection of Calu-3 human lung epithelial cells

status: Public on Oct 08 2004

city: Winston-Salem

first: Josyf

last: Mychaleckyj

state: NC

department: Center for Human Genomics

institute: Wake Forest Univ School of Medicine

summary:
This series contains 5 groups of U133A arrays with targets from Calu-3 cell line post-infection with P aeruginosa strains. Calu-3 human lung epithelial cells were seeded onto 6-well plates and grown to about 80% confluency. Epithelial monolayers were infected with 108 CFUs per ml of each bacterial strain for 60 min and then washed extensively with phosphate-buffered saline. The cultures were subsequently incubated in fresh RPMI 1640 medium supplemented with 10% fetal bovine serum and 100 µg/ml gentamicin. After 6 h, total RNA from the cells was prepared with RNAzol and further purified with RNEasy for microarray hybridization. All arrays processed and globally scaled to 500 using MAS 5.
CONTROL (4 arrays) - no infection
FRD1 (4 arrays)
FRD1234 (3 arrays)
FRD440 (4 arrays)
FRD875 (4 arrays)
Keywords = Cystic Fibrosis
Keywords = Pseudomonas aeruginosa
Keywords = CF
Keywords = flagellin
Keywords = alginate
Keywords = lung
Keywords: repeat sample

first: Laura

last: Cobb

first: Daniel

last: Wozniak

first: Yolanda

middle: S

last: López-Boado


title: Leukotriene D4-triggered Transcriptome

status: Public on Aug 20 2004

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

country: Germany

institute: Ludwig Maximilians Universität München

summary:
Human umbilical vein endothelial cells (HUVEC) or the human macrophage cell line, Mono-Mac-6, treated with Leukotriene D4 for 1 hour
Keywords = Leukotriene-Transcriptome
Keywords = Mono-Mac-6
Keywords = HUVEC
Keywords: other


title: dermatomyositis

status: Public on Oct 01 2004

first: Steven

middle: Alan

last: Greenberg

address: 75 Francis Street

department: Neurology

institute: Brigham and Women's Hospital

summary:
muscle biopsies of normal and dermatomyositis patients
Keywords: other

first: Elizabeth

last: Bradshaw

first: Peter

last: Park

first: Travis

last: Burleson

first: Despina

last: Sanoudou

first: Marian

last: Slaney

first: Brice

last: Due

first: Maria

last: Ericsson

first: Rabi

last: Tawil

first: Richard

last: Barohn

first: David

last: Saperstein

first: Hannah

last: Briemberg

first: Kevin

last: O'Connor

first: Lisa

last: Bregoli

first: Geraldine

last: Pinkus

first: Jack

middle: L


title: Isogenic primary tumor/metastasis comparison

status: Public on Sep 01 2004

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

country: Italy

institute: University of Trento

summary:
SW480 and SW620 are colon cancer cells lines derived from a primary tumor and a corresponding metastasis from the same individual. The numbers indicate the three indipendent replicate RNA samples processed. Three different software packages were used in parallel for signal calculation: Affymetrix microarray suite 5.0, DNA-Chip analyzer, and Robust multi-array analyses.
Keywords = metastasis
Keywords = colorectal cancer
Keywords = tumor progression
Keywords: repeat sample

last: Quattrone


title: T-ALL and T-lymphoblastic lymphoma

first: Dong-Joon

last: Min

institute: Mount Sinai School of Medicine

summary:
T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LL) and are often thought to represent a spectrum of a single disease. The malignant cells in T-ALL and T-LL are morphologically indistinguishable, and they share the expression of common cell surface antigens and  cytogenetic characteristics.  However, despite these similarities, differences in the predominant sites of disease in T-ALL and T-LL are observed. To determine if underlying biological distinctions may potentially contribute to some of these differences, we analyzed the global gene expression profiles of malignant T-cell precursors in ten T-ALL and nine T-LL using DNA arrays. Ten additional B-precursor ALL bone marrow samples,  were used in a separate analysis.
Keywords: ordered

last: Raetz

first: Sherrie

last: Perkins

first: Deepa

last: Bhojwani

first: Mary

last: Philip

first: William

last: Carroll


title: COPD Study

status: Public on Aug 08 2004

first: Avrum

last: Spira

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

summary:
Comparison of severely emphysematous tissue removed at lung volume reduction surgery to that of normal or mildly emphysematous lung tissue resected from smokers with nodules suspicious for lung cancer.
Data obtained from the 18 patients with severe emphysema and 12 patients with mild/no emphysema.
Research may provide insights into the pathogenetic mechanisms involved in chronic obstructive pulmonary disease (COPD).
Keywords: other


title: Osmotic Loading of Human Intervertebral Disc Cells

status: Public on Aug 07 2004

city: Durham

first: Lawrence

middle: Martin

last: Boyd

address: 136 Hudson Hall, Box 90281

department: Biomedical Engineering

institute: Duke University

summary:
Human intervertebral disc tissue was obtained from patients (average age 51 yrs) undergoing surgery for lumbar interbody fusion (n=3) or lumbar disc herniation (n=1).  Cells were isolated by sequential pronase-collagenase digestion [3].  Cells were passaged twice in monolayer and suspended at a density of 2 x 106 cells/ml in 1.2% alginate (low viscosity, Sigma Chemical, St Louis, MO) dissolved in 150 mM NaCl.  Alginate beads were formed by dropwise addition of the alginate from a 22 gauge needle into 102 mM CaCl2, followed by 10 minutes of curing, as described previously [13, 27].  Cell-gel beads were incubated in cell culture media consisting of Ham’s F-12 medium (Gibco BRL, Grand Island, NY), supplemented with 10% FBS (HyClone, Logan, UT), 25 μg/ml ascorbic acid (Sigma, St. Louis,  MO), 100 U/ml penicillin, 100 μg/ml streptomycin, and 1 μg/ml Fungizone at 5% CO2  and 37° C.

After 24 h, the cell culture medium was removed via pipette and exchanged for one of three osmotically active solutions, representing iso-osmotic, hyper-osmotic and hypo-osmotic media [12, 23, 34].  The iso-osmotic solution consisted of a defined cell culture medium (Ham’s F-12 with supplements as described above; 293 mOsm/kg H2O).  The hypo-osmotic solution consisted of the same cell culture media diluted with de-ionized water to a final osmolarity of 250 mOsm/kg H2O.  The hyper-osmotic solution consisted of the same cell culture media supplemented with sucrose to a final osmolarity of 450 mOsm/kg H20.  The osmolarity of all solution formulations was determined using a freezing-point osmometer (Advanced Laboratory Wide Range 3W2, Advanced Instrument, Needham Heights, MA) as described previously [12].  Cell-alginate beads were cultured for a 4 hour period under one of these conditions, after which the cells were released from alginate in a dissolving buffer (55 mM Na-citrate and 150 mM NaCl), lysed and stored at –80°C.

Intervertebral disc (IVD) cells experience a broad range of physical stimuli under physiologic conditions, including alterations in their osmotic environment.    In this study, the gene expression profile of human IVD cells was quantified with gene array technology following exposure to varying osmolarity in order to capture the biological responses for a broad set of targets.  A total of 42 genes were identified in IVD cells as significantly changed following culture under hyper-osmotic conditions, while a total of 18 genes were identified as significantly changed under hypo-osmotic conditions.  Gene expression patterns were verified using RT-PCR.  Genes identified in this study include those related to cytoskeleton remodeling and stabilization (ephrin-B2, sarcoglycan beta, IQGAP1), as well as membrane transport (ion transporter SLC21A12, osmolyte tranporter SLC5A3, monocarboxylic acid SLC16A6, and amino acid transporter SLC7A8).  An unexpected finding was the differential regulation of the gene for the neurotrophin brain-derived neurotrophic factor by hyper-osmotic stimuli that may be indicative of a physiological response of IVD cells to physical stimuli important in regulating discogenic pain.
Keywords = intervertebral disc
Keywords = osmotic stimuli
Keywords: other

middle: M

last: Richardson

first: Jun

last: Chen

first: Virginia

middle: B

last: Kraus

first: Lori

last: Setton


title: DNR resistant B-ALL

status: Public on Aug 06 2004

city: Memphis

middle: E

last: Evans

state: TN

address: 332 N. Lauderdale St.

department: Pharmaceutical Sciences

institute: St.Jude Children's Research Hospital

summary:
primary ALL cells (B-lineage) resistant to daunorubicin by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other

first: Amy

last: Holleman

first: Meyling

middle: H

last: Cheok

first: Monique

last: Den Boer

first: Wenjian

last: Yang

first: Karin

last: Kazemier

first: Gritta

last: Janka-Schaub

first: Rob

last: Pieters


title: VCR resistant B-ALL

summary:
primary ALL cells (B-lineage) resistant to vincristine by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other


title: IFN-Gamma keratinocytes

city: El Segundo

first: Anton

last: Petrov

state: CA

institute: BioDiscovery Inc

summary:
An experiment comparing control versus IFN-g treated skin cells (one design factor on two levels). To evaluate the biological and the experimental variability, the following experimental design was planned as shown in Figure 1: "Control" and "IFN-g stimulated" keratinocytes were cultured in triplicate using three individual petri Æ10 culture dishes and RNA was independently extracted from each cultured replicate.  For each RNA sample, cRNA synthesis was performed in triplicate and each cRNA pool was hybridized to an Affymetrix U133 Gene Chip.
Keywords: ordered

first: Robert

last: Mansourian

first: David

last: Mutch

first: Nicolas

last: Antille

first: Jerome

last: Aubert

first: Paul

last: Fogel

first: Jean-Marc

last: Le Goff

first: Julie

last: Moulin

first: Andreas

last: Rytz

first: Johannes

last: Voegel

first: Matthew-Alan

last: Roberts


title: Human bladder smooth muscle cells - effect of stretch in vitro

status: Public on Nov 04 2004

first: Rosalyn

last: Adam

address: 300 Longwood Avenue

department: Urology

institute: Children's Hospital Boston

summary:
The aim of the experiment was to determine the effect of cyclic stretch-relaxation ("stretch") on gene expression patterns in normal diploid human bladder smooth muscle cells. Cells plated on silicone elastomer bottomed 6-well culture dishes were grown to ~80% confluence, serum-depleted for 48h and subjected to cyclic stretch-relaxation at 20% elongation for 4h. Cells seeded in stretch plates but not subjected to stretch served as controls. Total RNA was extracted from both groups of cells, reverse-transcribed, biotin-labeled, fragmented and hybridized to HG-U133A.  Four biological replicates were generated for each treatment group (non-stretched or stretched).
Keywords = bladder
Keywords = smooth muscle cells
Keywords = cyclic stretch-relaxation
Keywords: other

first: Samuel

last: Eaton

first: Carlos

last: Estrada

first: Ashish

last: Nimgaonkar

first: Shu-Ching

last: Shih

first: Lois

last: Smith

first: Isaac

last: Kohane

first: Darius

last: Bagli

first: Michael

middle: R

last: Freeman


title: Essential Thrombocythemia megakaryocytes versus normal megakaryocytes

status: Public on Sep 17 2004

city: Modena

first: Elena

last: Tenedini

department: department of biomedical sciences

institute: University of Modena and Reggio Emilia

summary:
Normal donors BM CD34+ cells were differentiated in thrombopoietin-treated liquid suspension cultures. Briefly, CD34+ cells (80,000 /mL) were resuspended in a serum-free medium in the presence of 100 ng/mL of human recombinant thrombopoietin (TPO; Genzyme, Boston, MA). Every 3 days, viable cells were scored by Trypan blue dye exclusion and cultures were amplified with fresh serum-free medium. Each well was then supplemented with 100 ng/mL TPO. After 14 to 16 days of liquid culture, CD34-derived megakaryocytes (MKs) were purified by means of an anti-CD41a monoclonal antibody (MoAb) (Dako, Milan, Italy) directed against the glycoproteic *IIb-*3 complex and immunobeads (MPC 450 Dynabeads; Dynal, Oslo, Norway), as previously described (27). The purity of MKs was determined for each isolation by indirect immunofluorescence, using an anti-CD41b MoAb which reacts with a different epitope of *IIb-*3 subunit (Immunotech Inc., Westbrook, ME), followed by a goat anti-mouse IgG, covalently linked to fluorescein (Becton Dickinson, San Jose, CA).
Essential Throbocytemia BM CD34+ cells were differentiated in thrombopoietin-treated liquid suspension cultures. Briefly, CD34+ cells (80,000 /mL) were resuspended in a serum-free medium in the presence of 100 ng/mL of human recombinant thrombopoietin (TPO; Genzyme, Boston, MA). Every 3 days, viable cells were scored by Trypan blue dye exclusion and cultures were amplified with fresh serum-free medium. Each well was then supplemented with 100 ng/mL TPO. After 14 to 16 days of liquid culture, CD34-derived megakaryocytes (MKs) were purified by means of an anti-CD41a monoclonal antibody (MoAb) (Dako, Milan, Italy) directed against the glycoproteic *IIb-*3 complex and immunobeads (MPC 450 Dynabeads; Dynal, Oslo, Norway), as previously described (27). The purity of MKs was determined for each isolation by indirect immunofluorescence, using an anti-CD41b MoAb which reacts with a different epitope of *IIb-*3 subunit (Immunotech Inc., Westbrook, ME), followed by a goat anti-mouse IgG, covalently linked to fluorescein (Becton Dickinson, San Jose, CA).
Keywords: other

first: Maria

last: Fagioli

first: Nicola

last: Vianelli

first: Enrico

last: Tagliafico

first: Michela

last: Poli

first: Luigi

last: Gugliotta

first: Giovanni

last: Martinelli

first: Sante

last: Tura

first: Michele

last: Baccarani

first: Sergio

last: Ferrari

first: Lucia

last: Catani


title: Beta-catenin/GFP

status: Public on Aug 11 2004

first: Agnes

last: Viale

institute: Memorial Sloan Kettering Cancer Center

summary:
293 cells,  infected with RCAS-beta-cateninS37A or RCAS-GFP
Keywords = 293cells
Keywords = beta catenin
Keywords: repeat sample

first: Mario

last: Chamorro

first: Harold

last: Varmus


title: Ischemic and Nonischemic CM and NF Hearts

status: Public on Oct 26 2004

first: Michelle

last: Kittleson

address: Carnegie 568, 600 North Wolfe Street

department: Internal Medicine, Division of Cardiology

institute: Johns Hopkins Medical Institutions

summary:
Pre-LVAD and explanted ischemic and nonischemic cardiomyopathy and nonfailing hearts all normalized with RMA
Keywords: other

first: Shui

last: Ye

first: Rafael

middle: A

last: Irizarry

first: Joe

middle: G

last: Garcia

first: Joshua

last: Hare


title: VCR sensitive B-ALL

first: William

last: Evans

summary:
primary ALL cells (B-lineage) sensitive to vincristine by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other

first: Amy

last: Holleman

first: Meyling

last: Cheok

first: Monique

last: Den Boer

first: Wenjian

last: Yang

first: Karin

last: Kazemier

first: Gritta

last: Janka-Schaub

first: Rob

last: Pieters


title: PRED sensitive B-ALL

summary:
primary ALL cells (B-lineage) sensitive to prednisolone by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other


title: PRED resistant B-ALL

summary:
primary ALL cells (B-lineage) resistant to prednisolone by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other


title: ASP sensitive B-ALL

summary:
primary ALL cells (B-lineage) sensitive to L-asparaginase by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other


title: ASP resistant B-ALL

summary:
primary ALL cells (B-lineage) resistant to L-asparaginase by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other


title: De novo kidney transplantation without use of calcineurin inhibitors preserves renal structure and function

status: Public on Sep 23 2004

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary:
Background: Despite significant improvements in short-term kidney transplant survival, comparable increases in 5 and 10-year outcomes have not been achieved. Chronic allograft nephropathy (CAN) is a major cause of late graft loss. Toxic nephropathy and inadequate long-term immunosuppression are possible factors. We performed a randomized prospective trial comparing calcineurin inhibitor (CNI)-free to CNI-based immunosuppression to determine the impact on renal function, structure, and gene expression.

Methods: Sixty-one kidney recipients received mycophenolate mofetil (MMF), and prednisone (P). Randomized patients received concentration-controlled sirolimus or cyclosporine. Two years post-transplant 55 patients underwent renal function studies, 48 (87%) underwent transplant biopsies; all classified by Banff scoring and 41 by DNA microarrays.

Findings:  Comparing sirolimus/MMF/P to cyclosporine/MMF/P at two years, there was a significantly lower serum creatinine (1.35 vs. 1.81 mg/dl; p=0.008), significantly higher Cockroft-Gault glomerular filtration rate (GFR) (80.4 vs. 63.4 cc/min; p=0.008), iothalamate GFR (60.6 vs. 49.2 cc/min; p= 0.018), and Banff 0 (normal) biopsies (66.6 vs. 20.8%; p=0.013).  Regression analysis of calculated GFR’s from 1 to 36 months yielded a positive slope for sirolimus of 3.36 ml/min/year, and a negative slope for cyclosporine of –1.58 ml/min/year (p=0.008). Gene expression profiles of kidney biopsies with higher Banff CAN scores confirmed significant up regulation of genes responsible for immune/inflammation and fibrosis/tissue remodeling.

Interpretation:  At two years the sirolimus-treated patients have better renal transplant function, a diminished prevalence of CAN, and down regulated expression of genes responsible for the progression of CAN. All may provide for an alternative natural history with improved graft survival.
Keywords = Cyclosporine
Keywords = Sirolimus
Keywords = Transplantation
Keywords = DNA microarrays
Keywords = calcineurin inhibitors
Keywords: parallel sample

first: Stuart

last: Flechner

first: Kim

last: Solez

first: Daniel

middle: J

last: Cook

first: Hank

last: Rollin

first: James

middle: T

last: Burke

first: Jennifer

last: Hammond

first: Thomas

middle: C

last: Whisenant

first: Caroline

last: Lanigan

first: Steven

last: Head

last: Salomon


title: DNR sensitive all ALL

first: William

last: Evans

summary:
primary ALL cells (B- and T-lineage) sensitive to daunorubicinby the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other

first: Amy

last: Holleman

last: Cheok


title: EWS-FLI1-transfection of HEK293

status: Public on Oct 07 2004

city: Halle (Saale)

first: Christoph

last: Hutter

state: Sachsen-Anhalt

address: Weinbergweg 22

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

summary:
Response of HEK293-cells after transfection with EWS-FLI1. HEK293 cells were transfected with the expression vector pIRES2-EGFP containing type I EWS-FLI1 or empty control vector. For transient transfection standard DEAE dextran method was used and RNA was isolated 48h post transfection. For stable transfection cells were transfected using FuGENE 6 (Roche, Mannheim, Germany) and cells were selected with 400 ug/mL G418. DNA-microarray analysis was performed using Affymetrix HG-U133A microarrays.(see Staege et al. Cancer Res. 2004)
Keywords = HEK293
Keywords = EWS-FLI1
Keywords = Ewing family tumors
Keywords: other

first: Martin

last: Staege

first: Ingo

last: Neumann

first: Sabine

last: Foja

first: Uwe

last: Hattenhorst

first: Gesine

last: Hansen

first: Danny

last: Afar

first: Stefan

last: Burdach


title: DNR sensitive B-ALL

summary:
primary ALL cells (B-lineage) sensitive to daunorubicin by the MTT in vitro sensitivity assay
Keywords = ALL
Keywords: other

first: Meyling

first: Monique

last: Den Boer

first: Wenjian

last: Yang

first: Karin

last: Kazemier

first: Gritta

last: Janka-Schaub

first: Rob

last: Pieters


title: VCR sensitive all ALL

summary:
primary ALL cells (B- and T-lineage) sensitive to vincristine by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other


title: PRED resistant all ALL

summary:
primary ALL cells (B- and T-lineage) resistant to prednisolone by the MTT in vitro sensitivity assay
Keywords = ALL
Keywords: other


title: DNR resistant all ALL

summary:
primary ALL cells (B- and T-lineage) resistant to daunorubicin by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other


title: VCR resistant all ALL

summary:
primary ALL cells (B- and T-lineage) resistant to vincristine by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other


title: Skeletal muscle sarcopenia

status: Public on Aug 15 2004

city: Boston

first: Susan

last: Kandarian

department: Department of Health Sciences

institute: Boston University

summary:
This series includes the global gene expression profile of the vastus lateralis muscle for 10 young (19-25 years old) and 12 older (70-80 years old) male subjects.
Keywords: other

first: Paul

last: Giresi

first: Joachim

last: Theilhaber

first: Alan

last: Koncarevic

first: Eric

last: Stevenson

first: Roger

last: Fielding

first: Jascha

last: Parkington


title: PRED sensitive all ALL

first: William

last: Evans

summary:
primary ALL cells (B- and T-lineage) sensitive to prednisolone by the MTT in vitro sensitivity assay

Keywords = ALL
Keywords: other

first: Amy

last: Holleman

last: Cheok


title: ASP sensitive all ALL

summary:
primary ALL cells (B- and T-lineage) sensitive to L-asparaginase by the MTT in vitro sensitivity assay
Keywords = ALL
Keywords: other


title: Expression analysis of monocytes in response to interleukins-4 and -13

status: Public on Jul 31 2004

city: Berlin

first: Hartmut

last: Kuhn

address: Monbijoustr. 2

department: University Clinics Charite, Humboldt University

institute: Institute of Biochemistry

summary:
Human peripheral monocytes were icultured in vitro in the absence (control) and presence of interleukins-4 and -13
Keywords: other

first: P

last: Chaitidis

first: R

last: Kuban

first: U

last: Ungethuem

first: H


title: Gene expression profiles of in vitro fertilized bovine embryos in comparison to those of bovine adult tissues

status: Public on Aug 05 2004

city: Austin

first: Wenli

last: Zhou

state: TX

institute: ViaGen, InC

summary:
Affymetrix Human GeneChips are used to profile gene expression of bovine tissues and embryos to identify uniquely expressed genes in bovine in-vitro fertilized embryos by comparing with seven bovine adult tissues through gene clustering
Keywords: other

first: Wan

last: Ji

first: Keqin

last: Gregg

first: Wei

last: Guo

last: Yu

first: Scott

last: Davis

first: Sara


title: Human endothelium exposed to shear stress and pressure

status: Public on Jul 07 2004

city: Göteborg

first: Per-Arne

last: Svensson

country: Sweden

institute: Internal Medicine

summary:
Intact living conduit vessels (umbilical veins) were exposed to normal or high intraluminal pressure, or low or high shear stress in combination with a physiological level of the other force. We used a unique vascular ex vivo perfusion system. After six hours of perfusion endothelial cells were isolated from the stimulated vessels and RNA was extracted. RNA from 16 experiments from each stimulation were pooled and analyzed in duplicate DNA microarrays.
Keywords: repeat sample

first: Maria

last: Andersson

first: Lena

last: Karlsson

first: Sverker

last: Jern


title: Incipient Alzheimer's Disease: Microarray Correlation Analyses

status: Public on Jul 16 2004

city: Lexington

first: Eric

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

summary:
For these data, we analyzed hippocampal gene expression of nine control and 22 AD subjects of varying severity on 31 separate microarrays. We then tested the correlation of each gene's expression with MiniMental Status Examination (MMSE) and neurofibrillary tangle (NFT) scores across all 31 subjects regardless of diagnosis. These tests revealed a major transcriptional response comprising thousands of genes significantly correlated with AD markers. Several hundred of these genes were also correlated with AD markers across only control and incipient AD subjects (MMSE > 20).
Keywords = bioinformatics
Keywords = gene expression
Keywords = memory
Keywords = synaptic plasticity
Keywords = myelin
Keywords = inflamation
Keywords = aging
Keywords = behavior
Keywords = Alzheimer's
Keywords = microarray
Keywords: repeat sample

first: James

middle: W

last: Geddes

first: Kuey-Chu

last: Chen

first: Nada

last: Porter

first: William

last: Markesbery

first: Philip

last: Landfield


title: Gene expession profiles for monoclonal cell lines with high or low levels of store-operated Ca2+ entry.

status: Public on Jun 08 2004

city: Chicago

first: Tatiana

last: Zagranichnaya

institute: The University of Chicago

summary:
This series of microarray experiments monitored the gene expression profiles for monoclonal cell lines (derived from HEK-293 parental cell culture) with high (H1, H15, H24, H36, H39) or low (L3, L28, L29) levels of store-operated Ca2+ entry (SOCE). For selection of clones, HEK-293 cells were loaded with indo-1 and sorted by FACS on the basis of their cyclopiazonic acid (CPA)-stimulated Ca2+ entry. Monoclonal cell lines were selected from the sorted cells and their levels of SOCE confirmed by monitoring thapsigargin-stimulated Ba2+ entry. Total RNA was extracted from cells immediately after removal from their growth environment. RNA was processed and hybridized to the Affymetrix HG-U133A chip. Two parallel hybridizations were done for each RNA preparation from each monoclonal cell line or from the parental HEK-293 cell culture.

Keywords: parallel sample

middle: K

first: Xiaoyan

last: Wu

first: Arpad

last: Danos

first: Mitchel

last: Villereal


title: Caco-2 and T84 cells stimulated with with flagellin, lymphotox beta or TNF alpha

status: Public on Jun 16 2004

city: Epalinges

first: Pascale

last: Anderle

country: Switzerland

institute: ISREC

summary:
14 day old Caco-2 and T84 cells were treated with flagellin, lymphotox beta or TNF alpha, respectively, and their expression profile compared to non-stimulated cells.
Keywords: other

first: Martin

last: Rumbo

first: Frederic

last: Sierro

first: Robert

last: Mansourian

first: Pierre

last: Michetti

first: Matthew-Alan

last: Roberts

first: Jean-Pierre

last: Kraehenbuhl


title: Untreated vs. Camptothecin Treated HeLa cells

status: Public on May 18 2004

city: Cambridge

first: Garrett

last: Frampton

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

summary:
Pharmacogenomic identification of targets for adjuvant therapy with the topoisomerase poison camptothecin.

The response of tumor cells to the unusual form of DNA damage caused by topoisomerase poisons such as camptothecin (CPT) is poorly understood, and knowledge regarding which drugs can be effectively combined with CPT is lacking. To better understand the response of tumor cells to CPT and to identify potential targets for adjuvant therapy, we examined global changes in mRNA abundance in HeLa cells after CPT treatment using Affymetrix U133A GeneChips, which include all annotated human genes (22,283 probe sets). Statistical analysis of the data using a Bayesian/Cyber t test and a modified Benjamini and Hochberg correction for multiple hypotheses testing identified 188 probe sets that are induced and 495 that are repressed 8 h after CPT treatment at a False Discovery Rate of <0.05 and a minimum 3-fold change. This pharmacogenomic approach led us to identify two pathways that are CPT induced: (a) the epidermal growth factor receptor; and (b) nuclear factor-kappaB-regulated antiapoptotic factors. Experiments using HeLa cells in our lab and prior animal model studies performed elsewhere confirm that inhibitors of these respective pathways super-additively enhance CPT's cytotoxicity, suggesting their potential as targets for adjuvant therapy with CPT.

Cancer Res. 2004 Mar 15;64(6):2096-104
Keywords = HeLa
Keywords = Camptothecin
Keywords: ordered

first: Jon

middle: P

last: Carson

first: N

last: Zhang

first: Norman

last: Gerry

first: Marc

last: Lenburg

first: Michael

middle: F

last: Christman


title: Identification of Inhibitors of Auxin Transcriptional Activation via Chemical Genetics in Arabidopsis

status: Public on Jun 23 2004

city: Albany

first: Atsunari

last: Tsuchisaka

address: 800 Buchanan St.

department: Plant Gene Expression Center

institute: University of California, Berkeley / USDA

summary:
Approximately 2.5 mg dry Col-0 seedlings were surface sterilized and stratified for 2 days at 4degreesC in liquid media containing 1.5% sucrose (w/v) before being transferred to light with constant shaking at 100 rpm on an orbital shaker. After 7 days, the seedling clusters were subjected to the treatments for 1 hr followed by total RNA isolation using the RNAqueous kit (Ambion). Each treatment was performed in triplicate or quadruplicate. All labeling (Enzo) and hybridization (Affymetrix) procedures were performed as directed by the manufacturers.  Raw probe intensities output by the Affymetrix MAS software were processed using the RMA algorithm to obtain an expression measure for each gene on each array.
Keywords: repeat sample

first: Joshua

middle: I

last: Armstrong

first: Shiaulou

last: Yuan

first: Joseph

last: Dale

first: Vanessa

middle: N

last: Tanner

first: Athanasios

last: Theologis


title: ASLV vector infected 293t-TVA cells

status: Public on May 19 2004

first: Richard

middle: Steven

last: Mitchell

address: 10010 North Torrey Pines Rd

department: Infectious Disease Laboratory

institute: The Salk Institute

summary:
Human 293T cells engineered to express the TVA receptor (see Mitchell et al., PLoS) infected with an ASLV vector.  RNA isolated 48 hours later.

***PLEASE NOTE***
Series entries GSE1408 & GSE1409 no longer exist. All data discussed in the author's PLoS publication (PubMed ID 15314653) is available under GSE1407 & GSE1410.
***PLEASE NOTE***
Keywords: repeat sample

middle: S

first: Brett

last: Beitzel

first: Astrid

last: Schroder

first: Paul

last: Shinn

first: Huaming

last: Chen

first: Charles

last: Berry

last: Ecker

first: Frederic

middle: D

last: Bushman


title: ASP resistant all ALL

status: Public on Aug 06 2004

first: William

middle: E

last: Evans

institute: St.Jude Children's Research Hospital

summary:
primary ALL cells (B- and T-lineage) resistant to L-asparaginase by the MTT in vitro sensitivity assay
Keywords = ALL
Keywords: other

first: Amy

last: Holleman

first: Meyling

last: Cheok

first: Monique

middle: L

last: Den Boer

first: Wenjian

last: Yang

first: Karin

middle: M

last: Kazemier

first: Gritta

last: Janka-Schaub

first: Rob

last: Pieters


title: Kaposi's sarcoma-associated herpes virus

status: Public on May 08 2004

city: Zurich

first: Jay

middle: Woo

last: Shin

state: Zurich

address: Wolfgang-Paulistrasse 10; HCI H394

department: Institute of Pharmaceutical Sciences

institute: ETH Zurich

summary:
Primary human dermal endothelial cells were infected or NOT infected with isolated Kaposi's sarcoma associated herpes virus for 7 days. Total RNA was isolated using Trireagent and subjected to microarray.
Keywords: other

first: Young

last: Hong

first: Kimberly

last: Foreman

first: Satoshi

last: Hirakawa

first: Christine

last: Curry

first: Dave

middle: R

last: Sage

first: Towia

last: Libermann

first: Bruce

last: Dezube

first: Joyce

last: Fingeroth

first: Michael

last: Detmar

middle: H


title: Ultraviolet induced gene expression in human basal cell culture

status: Public on Apr 17 2004

first: Jeff

last: Shearstone

address: 70 Fargo Street

institute: Acetylon Pharmaceuticals

summary:
This data set was generated as part of Biogen Community Lab's science fair mentorship program. In brief, human basal cells (ATCC: CRL-7761, designation TE 353.Sk) were cultured to 80% confluence. After removing media, cells were treated with a titration of ultraviolet light (Biorad GS GeneLinker, 254 nm energy maximum). Media was then added and cells were grown for 24 hours. Total RNA was harvested using RLT buffer and Qiagen RNeasy kit. 5 ug of total RNA was labeled using standard Affymetrix protocols for Eukaryotic target preparation (GeneChip Expression Analysis Technical Manual Revision 4). GeneChip intensity values were scaled to 2500 RFU.
Keywords = UV
Keywords = ultraviolet
Keywords = basal cell
Keywords: dose response

first: Xu Fang

last: Zou


title: Burn/Trauma Study

status: Public on Apr 24 2004

city: Gainesville

first: Lyle

last: Moldawer

address: 1600 SW Archer Road

department: Surgery

institute: University of Florida College of Medicine

summary:
#G017 Burn/Trauma Study.

This is a Glue Grant Study comparison between gene expression analyses performed in eight trauma/burn subjects using either a buffy coat isolation of whole blood or using the PAXgene system
Keywords: other


title: Simple ambient preservation of human tissues for RNA expression array analysis

status: Public on Apr 09 2004

city: Santa Clara

first: Chunmei

last: Liu

address: 3380 Central Expressway

institute: Affymetrix

summary:
We used quantitative RNA expression profiling on the Affymetrix U133 human expression array to validate quantitative expression results obtained with the tissue preservative RNALater against snap frozen and fresh tissues as a means of routine tissue collection and temporary storage.  By using split samples from a homogenous tissue (uterine myometrium), and including duplicates within each processing group compared, we were able to undertake a formal ANOVA analysis comparing the magnitude of result variation contributed by sample source (different patients), processing protocol (fresh vs. frozen vs. 24 or 72 hours RNALater), and random background (duplicates).   The dataset was randomly permuted to define a baseline pattern of test statistic values against which the observed results could be interpreted.  Ambient storage of tissues for 24 or 72 hours in RNALater did not contribute any systematic shift in quantitative RNA expression results relative to the alternatives of fresh or frozen tissue.
Keywords: parallel sample


title: PMBCs and the effect of exercise

status: Public on Apr 07 2004

city: Orange

first: Peter

last: Connolly

institute: University of California, Irvine

summary:
Analysis of peripheral blood mononuclear cells (PBMCs) separated from whole blood of healthy male subjects
- prior to onset of exercise
- immediately following the end of exercise and
- immediately following 1 hour of recovery from exercise
Keywords: other

first: Vincent

middle: J

last: Caiozzo

first: Frank

last: Zaldivar

first: Dan

last: Nemet

first: She-pin

last: Hung

first: J

middle: Denis

last: Heck

first: G

middle: Wesley

last: Hatfiled

last: Cooper


title: Inflammatory bowel disease (HG-U133A)

status: Public on Apr 20 2004

city: Regensburg

first: Thomas

last: Langmann

address: Franz-Josef-Strauss-Allee 11

department: University of Regensburg

institute: Institute of Human Genetics

summary:
Samples for microarray analysis were derived from terminal ileum and colonic tissues from probands with Crohn´s disease and Ulcerative Colitis and control patients, respectively. IBD tissue biopsies from non-inflamed regions 10 cm distant from pathological areas were selected. To minimize inter-individual differences in gene expression and to enrich for IBD-specific transcriptional events, 2.5 µg of total RNA from terminal ileum and colon transversum from four individuals of each patient and control group were used for pooling. Gene expression profiles were determined using Affymetrix HG-U133A Gene Chips.
Keywords: ordered

first: Christoph

last: Moehle

first: Richard

last: Mauerer

last: Scharl

first: Gerhard

last: Liebisch

first: Alexandra

last: Zahn

first: Wolfgang

last: Stremmel

first: Gerd

last: Schmitz


title: Hemin timecourse 0-72h

status: Public on Apr 05 2004

city: Philadelphia

first: Sankar

last: Addya

address: 233 South 10th Street

department: Kimmel Cancer Center

institute: Thomas Jefferson University Hospital

summary:
K562 cells (duplicate cultures A & B) are treated with 50 micromolar hemin for 0, 6, 12, 24, 48, 72 hours followed by RNA extraction and gene expression profiling on Affymetrix human U133A arrays and analysis by MAS 5.0
Keywords: other

first: Margaret

middle: A

last: Keller

first: Kathleen

last: Delgrosso

first: Christine

last: Ponte

first: Saul

last: Surrey


title: Identification of novel genomic determinants of cellular drug resistance in acute lymphoblastic leukemia.

city: Memphis

first: William

last: Evans

summary:
Cellular drug resistance is associated with an unfavorable prognosis in pediatric acute lymphoblastic leukemia (ALL). To identify genes conferring resistance to antileukemic agents, we analyzed the expression of >12,700 genes in sensitive and resistant ALL cells obtained at diagnosis from 174 patients. This revealed 42, 59, 54 and 22 genes (P≤0.001) that were differentially expressed in B-lineage ALL that was sensitive versus resistant to prednisolone, vincristine, asparaginase or daunorubicin, respectively, with prediction accuracies of 71-76%.  Notably, 149 of the discriminating genes have not been previously associated with resistance to these anticancer agents. These included carbohydrate-metabolism and transcription-associated genes for prednisolone, cytoskeleton and extracellular matrix genes for vincristine, ribosomal protein and translation-associated genes for asparaginase, and RAS signaling and nucleosome remodeling complex genes for daunorubicin. The identification of novel genomic determinants of cellular drug resistance provides new insights for overcoming drug resistance in acute lymphoblastic leukemia.
Keywords = ALL
Keywords: other

first: Amy

last: Holleman

first: Meyling

last: Cheok

first: Monique

last: Den Boer

first: Wenjian

last: Yang

first: Karin

last: Kazemier

first: Gritta

last: Janka-Schaub

first: Rob

last: Pieters


title: Inflammatory bowel disease

first: Thomas

last: Langmann

summary:
Samples for microarray analysis were derived from terminal ileum and colonic tissues from probands with Crohn´s disease and Ulcerative Colitis and control patients, respectively. IBD tissue biopsies from non-inflamed regions 10 cm distant from pathological areas were selected. To minimize inter-individual differences in gene expression and to enrich for IBD-specific transcriptional events, 2.5 µg of total RNA from terminal ileum and colon transversum from four individuals of each patient and control group were used for pooling.
Keywords = IBD
Keywords = Crohn´s disease
Keywords = Ulcerative Colitis
Keywords: other

first: Christoph

last: Moehle

first: Richard

last: Mauerer

first: Michael

last: Scharl

first: Gerhard

last: Liebisch


title: Gene Expression Profile during human CD4+ T cell differentiation

status: Public on Jul 01 2004

city: San Francisco

first: Myeong

last: Lee

department: Gladstone Institute of Virology and Immunology

institute: University of California at San Francisco

summary:
Subpopulations of human fetal thymocyte and circulating naïve T cells were obtained through FACS sorting, including CD3-CD4+CD8- intrathymic T progenitor cells (ITTP), CD3intCD4+CD8+ "double positive" thymocytes (DP), CD3highCD4+CD8- "single positive" thymocytes (SP4), CD3+CD4+CD8-CD45RA+CD62L+ naïve T cells from cord blood (CB4+), and CD3+CD4+CD8-CD45RA+CD62L+ naïve T cells from adult blood (AB4+).
Keywords = Microarray
Keywords = gene expression
Keywords = thymocytes
Keywords = naïve CD4+ T cell
Keywords = recent thymic emigrants
Keywords: other

first: Kristina

last: Hanspers

first: Christopher

last: Barker

first: Abner

middle: P

last: Korn

first: Joseph

last: McCune


title: FCHL study

status: Public on Mar 27 2004

city: Boston

first: Fulvio

last: Morello

address: 77 L. Pasteur Avenue

department: Medicine

institute: Brigham and Women's Hospital

summary:
RNA samples prepared from lymphoblastic cells or cell lines from normal and FCHL (familial combined hyperlipemia) patients
Keywords: other

first: Tjerk

middle: W

last: de Bruin

first: Jerome

last: Rotter

last: Pratt

first: Carla

last: van der Kallen

first: Gary

last: Hladik

first: Victor

last: Dzau

first: Choong-Chin

last: Liew

first: Yii-Der

last: Chen


status: Public on Mar 28 2004

city: New Haven

first: Joel

last: Rozowsky

state: CT

address: 266 Whitney Ave, Bass 437

department: Molecular Biophysics & Biochemistry

institute: Yale University

summary:
Sex Specific Transciption in Human Hypothalamus between 7 male biological samples (2 technical replicates of each) and 5 female biological samples (2 technical replicates of 4 of these).
Keywords = human hypothalamus, sex-specific transcription
Keywords: other

first: John

last: Rinn

first: Ian

last: Laurenzi

first: Petur

last: Petersen

first: Kaiyong

last: Zon

first: Weimin

last: Zhong

first: Mark

last: Gerstein

last: Snyder


title: Gene expression profiling of Rhesus monkey extraocular muscle and its layers (Porter lab)

status: Public on Apr 01 2004

city: Cleveland

first: Sangeeta

last: Khanna

address: 11100 Euclid Avenue

department: Neurology

institute: Case Western Reserve University

summary:
Rhesus monkey extraocular muscle.  Data set includes: (a) whole medial and lateral rectus muscle and (b) global and orbital muscle layers separately microdissected using a Leica LSM.  All samples were expression profiled here using the Affymetrix human U133 A&B arrays.  Data form part of publication: Investigative Ophthalmology and Visual Science 45, 2004.
Keywords = skeletal muscle
Keywords = microarray
Keywords = orbital layer
Keywords = global layer
Keywords: ordered

first: Georgiana

last: Cheng

first: Bendi

last: Gong

first: Michael

last: Mustari

last: Porter


title: IL-1 stimulation of HUVEC

status: Public on Jul 20 2004

city: Vienna

first: Herbert

last: Mayer

address: Brunnerstr 59

institute: Institute of Vascular Biology and Thrombosis Research

summary:
Endothelial cells comprise a key component of the inflammatory response. HUVEC (human umbilical vein endothelial cells) were stimulated with interleukin-1 for 0, 0.5, 1, 2.5 and 6 hours, and analyzed using Affymetrix U133A microarrays, in order to obtain a comprehensive overview of the immediate early to early gene expression profiles. HUVEC were isolated and cultured on gelatine-coated cell culture dishes in M199 medium supplemented with 20% FCS, antibiotics, ECGS (endothelial cell growth supplement) and Heparin as described by Zhang et al., Blood 1996;88:3880-3886. HUVEC were stimulated with 100 U/ml human IL-1 (Biosource) for various periods of time, and total RNA isolated using the RNeasy kit (Qiagen) according to the manufacturer's instructions. Hybridization to one set of human U133A GeneChips (Affymetrix, Santa Clara, CA) and scanning of the arrays was carried out according to manufacturer’s protocols (https://www.affymetrix.com). Briefly, 5 µg of total RNA was used to generate double-stranded cDNA by reverse transcription using a cDNA synthesis kit (Superscript Choice System; Life Technologies, Inc., Rockville, MD) that uses an oligo(dT)24 primer containing a T7 RNA polymerase promoter 3' to the polyT (Geneset, La Jolla, CA), followed by second-strand synthesis. Labeled cRNA was prepared from the double-stranded cDNA by in vitro transcription using T7 RNA polymerase in the presence of biotin-11-CTP and biotin-16-UTP (Enzo, Farmington, NY). The labeled cRNA was purified over RNeasy columns (Qiagen, Valencia, CA). Fifteen µg of cRNA was fragmented at 94°C for 35 minutes in 40 mmol/L of Tris-acetate, pH 8.1, 100 mmol/L of potassium acetate, and 30 mmol/L of magnesium acetate. The cRNA was then used to prepare 300 µl of hybridization cocktail (100 mmol/L MES, 1 mol/L NaCl, 20 mmol/L ethylenediaminetetraacetic acid, 0.01% Tween 20) containing 0.1 mg/ml of herring sperm DNA (Promega, Madison, WI) and 500 µg/ml of acetylated bovine serum albumin (Life Technologies, Inc.). Before hybridization, the cocktails were heated to 94°C for 5 minutes, equilibrated at 45°C for 5 minutes, and then clarified by centrifugation (16,000 x g) at room temperature for 5 minutes. Aliquots of this hybridization cocktail containing 15 µg of fragmented cRNA were hybridized to HU133A arrays (Affymetrix, Santa Clara, CA) at 45°C for 16 hours in a rotisserie oven at 60 rpm. The arrays were washed using non-stringent buffer (6xSSPE: 0.9 M sodium chloride, 0.06 M sodium phosphate, 6 mM EDTA pH 7.4)  at 25°C, followed by stringent buffer (100 mmol/L MES, pH 6.7, 0.1 mol/L NaCl, 0.01% Tween 20) at 50°C. The arrays were stained with streptavidin-phycoerythrin (Molecular Probes, Eugene, OR), washed with 6xSSPE, incubated with biotinylated anti-streptavidin IgG, stained again with streptavidin-phycoerythrin, and washed again with 6xSSPE. The arrays were scanned using the GeneArray scanner (Affymetrix). Image analysis was performed with GeneChip software (Affymetrix, MAS 5.0). Normalization was performed by global scaling, with the arrays scaled to an average intensity of 500.
Keywords: time-course

first: Martin

last: Bilban

first: Vladislav

last: Kurtev

first: Florian

last: Gruber

first: Oswald

last: Wagner

first: Bernd

last: Binder

first: Rainer

last: de Martin


title: Estradiol Treated Breast Cancer Cells Expressing Mutant Estrogen Receptors

status: Public on Mar 24 2004

city: Urbana

first: Joshua

middle: David

last: Stender

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana-Champaign

summary:
MDA-MB-231 Breast Cancer Cells expressing either wild-type estrogen receptor or the mutant estrogen recepor L540Q were treated with estradiol for 1 or 2 hours
Keywords: time-course

first: Benita

last: Katzenellenbogen

first: William

last: Kraus


title: 267B1, PC3M, LNCaP Methylation Profile vs. mRNA Expression Level

status: Public on Mar 21 2004

city: San Diego

first: Yipeng

last: Wang

institute: Vaccine Research Institute of San Diego

type:
Expression profiling by array
Methylation profiling by array

summary:
Two prostate immortalized cell lines, 267B1, RWPE-1, Ml-csv40, and five prostate cancer cell lines, PC3, PC3M, PC3M-Pro4, PC3M-LN4 and LNCaP are included in this experiment. Their methylation profile are detected using human promoter array (v11). mRNA expression level are profiled with Affymetrix U133A Arrays for 267B1 and PC3M.
Keywords: other

last: McClelland


title: Effect of a 4 hour treatment of 100 nM endothelin-1 on human primary lung fibroblasts

status: Public on Mar 12 2004

city: London

first: Andrew

last: Leask

country: United Kingdom

institute: Royal Free and University College Medical School

summary:
primary lung fibroblasts p3 from normal periphery of resected cancer. grown in DMEM 10% FBS, until confluence, then DMEM 0.5% FBS for 18 hours. Media were then changed and incubated for an additional 4 hours in the presence or absence of 100 nM endothelin-1.  Data represent two independent experiments performed on two different occasions.
Keywords: other

first: Xu

last: Shiwen

first: Elisabetta

last: Renzoni

first: George

last: Bou-Gharios

first: Roland

last: du Bois

first: Carol

last: Black

first: David

last: Abraham


status: Public on Mar 19 2004

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues. The resulting data set provides the expression patterns for thousands of predicted genes, as well as known and poorly characterized genes, from mice and humans. We have explored this data set for global trends in gene expression, evaluated commonly used lines of evidence in gene prediction methodologies, and investigated patterns indicative of chromosomal organization of transcription. We describe hundreds of regions of correlated transcription and show that some are subject to both tissue and parental allele-specific expression, suggesting a link between spatial expression and imprinting.
Keywords: different tissues

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: baseline gene expression was taken from various human and mouse tissues

middle: I

last: Su

first: Tim

last: Wiltshire

first: Serge

last: Batalov

first: Hilmar

last: Lapp

first: Keith

last: Ching

last: Block

first: Jie

last: Zhang

first: Richard

last: Soden

first: Mimi

last: Hayakawa

first: Gabriel

last: Kreiman

first: Michael

last: Cooke

middle: B

last: Hogenesch


title: Endothelin-1 (ET-1) treated lung fibroblasts

status: Public on Feb 28 2004

first: Andrew

last: Leask

summary:
Primary lung fibroblasts were grown to confluence in DMEM 10% FBS, serum starved in DMEM 0.5% FBS for 18 hours.  Cells were then treated in the presence or absence of 100 nM ET-1 in the same medium for an additional 4 hours.
Keywords: repeat sample

last: Shiwen

last: Renzoni

last: Bou-Gharios


title: Sindbis survivors

status: Public on May 01 2004

city: Galveston

first: Aaron

middle: M.

last: Domina

address: 301 University Blvd

department: HBCG

institute: University of Texas Medical Branch

summary:
Microarray analysis comparing cells that are resistant to Sindbis virus-induced cell death (clones 9, 43) versus cells that are sensitive to Sindbis virus-induced cell death (WT293)
Keywords = Sindbis alphavirus functinal phenotype
Keywords: repeat sample

first: Andrey

last: Kolokoltsov

first: Olga

last: Kolokoltsova

first: Eryu

last: Wang

first: Scott

middle: C

last: Weaver

first: Stanley

last: Watowich

first: Robert

last: Davey


title: Myometrial cells expressing CREB, CREM alpha, CREM tau2alpha, ATF2 or the ATF2-small gene

status: Public on Feb 21 2004

city: Newcastle upon Tyne

first: Jarrod

last: Bailey

state: Tyne and Wear

address: Leech Building, Medical School

department: School of Surgical and Reproductive Sciences

institute: University of Newcastle upon Tyne

summary:
Human myometrial cells taken from biopsies of pre-menopausal non-cancerous non-pregnant uteri were cultured in complete MEM D-valine medium plus 10% FCS, and stably-transfected with the pcDNA3.1/V5-His TOPO vector (Invitrogen) harbouring either CREB, CREM alpha, CREM tau2alpha, ATF2, ATF2-small gene or a control empty-vector. Total RNA was extracted using TRI-reagent (Sigma) and RNeasy columns (Qiagen), and 10 ug used in target preparation for array hybridization.
Keywords: other

first: G.

middle: N

last: Europe-Finner


title: Inflammatory bowel disease (HG-U133B)

first: Thomas

last: Langmann

summary:
Samples for microarray analysis were derived from terminal ileum and colonic tissues from probands with Crohn´s disease and Ulcerative Colitis and control patients, respectively. IBD tissue biopsies from non-inflamed regions 10 cm distant from pathological areas were selected. To minimize inter-individual differences in gene expression and to enrich for IBD-specific transcriptional events, 2.5 µg of total RNA from terminal ileum and colon transversum from four individuals of each patient and control group were used for pooling. Gene expression profiles were determined using Affymetrix HG-U133B Gene Chips.
Keywords: ordered

first: Christoph

last: Moehle

last: Mauerer

last: Scharl

first: Gerhard

last: Liebisch

first: Alexandra

last: Zahn

first: Wolfgang

last: Stremmel

first: Gerd

last: Schmitz


title: Differentiation of acute myeloid leukemia cells

status: Public on Jan 30 2004

city: Cambridge

first: Ken

last: Ross

state: MA

address: 7 Cambridge Center

department: Cancer Genomics

institute: Broad Institute

summary:
We developed a general approach to small molecule library screening called GE-HTS (Gene Expression-Based High Throughput Screening) in which a gene expression signature is used as a surrogate for cellular states and applied it to the identification of compounds inducing the differentiation of acute myeloid leukemia cells. In screening 1,739 compounds, we identified 8 that reliably induced the differentiation signature, and furthermore yielded functional evidence of bona fide differentiation.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Kimberly

last: Stegmaier

first: Kenneth

first: Sierra

last: Colavito

first: Shawn

last: O'Malley

first: Brent

last: Stockwell

first: Todd

last: Golub


title: Gene Expression-Based High Throughput Screening: APL Treatment with Candidate Compounds

summary:
We developed a general approach to small molecule library screening called GE-HTS (Gene Expression-Based High Throughput Screening) in which a gene expression signature is used as a surrogate for cellular states and applied  it to the identification of compounds inducing the differentiation of acute myeloid leukemia cells. In screening 1,739 compounds, we identified 8 that reliably induced the differentiation signature, and furthermore yielded functional evidence of bona fide differentiation. We tested several of these in duplicate replicates in blasts from a patient with APL. Also included in this data set are a collection of 6 primary patient AML cells, 3 normal neutrophils samples, and 3 normal monocyte samples. This data was used to evaluate whole genome effects of the compounds on APL cells in relation to AML versus normal neutrophils and monocytes.
Keywords = Leukemia
Keywords = APL
Keywords = AML
Keywords = chemical genomics
Keywords: repeat sample

last: O’Malley


title: Amino Acid Conjugated Surfaces and Controls 6 Hours

status: Public on Jan 28 2004

first: Catherine

last: Klapperich

address: 44 Cummington St. 7th Floor

department: Biomedical and Manufacturing Engineering

institute: Boston University

summary:
Amino Acid Conjugated Surfaces and Controls at Time point 6 hours
Keywords: parallel sample

first: Jie

last: Song

first: Carolyn

last: Bettozzi


summary:
Amino Acid Conjugated Surfaces and Controls 32 Hours Time Point
Keywords: parallel sample

last: Bertozzi


title: Gene Expression-Based High Throughput Screening: HL-60 Cell Treatment with Candidate Compounds

summary:
We developed a general approach to small molecule library screening called GE-HTS (Gene Expression-Based High Throughput Screening) in which a gene expression signature is used as a surrogate for cellular states and applied it to the identification of compounds inducing the differentiation of acute myeloid leukemia cells. In screening 1,739 compounds, we prioritized 15 candidate compounds (2 were already confirmed in the literature). We next evaluated the 13 remaining compounds.  Eight reliably induced the differentiation signature, and furthermore yielded functional evidence of bona fide differentiation.

This data set contains HL-60 cells treated in replicates of 3 with the original 13 selected candidates. It also contains 6 untreated, 6 DMSO treated, 3 ATRA treated, 3 PMA treated, and 3 1,25-dihydroxyvitamin D3 treated HL-60 controls. In addition, it contains 3 neutrophil and 3 monocyte samples from distinct normal human donors and 9 primary patient AML samples. This data set was used to evaluate the whole genome effects of the candidate compounds on HL-60 cells.
Keywords = AML
Keywords = leukemia
Keywords = HL-60
Keywords = chemical genomics
Keywords: repeat sample


title: Osteosarcoma TE85 cell tissue culture study

summary:
Amino acid conjugated surfaces and controls at 6 and 32 hours
Keywords: other


title: Effects of cigarette smoke on the human airway epithelial cell transcriptome

status: Public on Jan 27 2004

first: Avrum

last: Spira

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

institute: Boston University Medical Center

summary:
A number of studies have shown that cigarette smoking produces a field defect, such that genetic mutations induced by smoking occur throughout the lung and its intra and extra-pulmonary airways. Based on this concept, we have begun this study, which has as its goal the definition of the normal airway transcriptome, an analysis of how that transcriptome is affected by cigarette smoke, and to explore the reversibility of altered gene expression when smoking has been discontinued. We have obtained brushings from intra-pulmonary airways (the right upper lobe carina) and scrapings from the buccal mucosa, from normal smoking and non-smoking volunteers (including 34 Current Smokers, 23 Never Smokers and 18 Former Smokers). RNA was isolated from these samples and gene expression profiles from intra-pulmonary airway epithelial cells were analyzed using Affymetrix U133A human gene expression arrays. All microarray data from the experiments described above have been stored, preprocessed and analyzed in a relational MySQL database that is accessible through our website at http://pulm.bumc.bu.edu/aged
Keywords = Lung
Keywords = Cancer
Keywords = Airway
Keywords = Epithelium
Keywords = Transcriptome
Keywords = Gene
Keywords = Microarray
Keywords = Bronchi
Keywords: repeat sample

first: Jennifer

last: Beane

first: Vishal

last: Shah

first: Gang

last: Liu

first: Frank

last: Schembri

first: Xuemei

last: Yang

first: John

last: Palma

first: Jerome

last: Brody


title: Normal and Renal Cell Carcinoma Kidney Tissue, Human

status: Public on Nov 25 2003

first: Marc

middle: E.

last: Lenburg

address: 715 Albany Street, E613B

department: Genetics and Genomics

institute: Boston University School of Medicine

summary:
Each total RNA sample is hybridized to two different arrays:  Affymetrix U133A (GPL96) and U133B (GPL97).

For most of the normal tissue samples there is a renal clear cell carcinoma sample from the same patient.  There is no matching tumor sample for normal sample N1.

For most of the renal clear cell carcinoma samples there is a corresponding adjacent normal tissue sample from the same patient.  There are no matching normal tissue samples for C011 or C032.
Keywords = kidney
Keywords = renal
Keywords = RCC
Keywords = carcinoma
Keywords = cancer
Keywords: parallel sample

middle: E

first: Louis

middle: S

last: Liou

first: Norman

last: Gerry

first: Garrett

last: Frampton

first: Herbert

middle: T

last: Cohen

first: Michael

middle: F

last: Christman


title: Osteopontin vs empty vector

status: Public on Jan 07 2004

city: Tampa

first: Gregory

last: Bloom

institute: Moffitt Cancer Center

summary:
Osteopontin tranfected vs empty vector breast cell line
Keywords: parallel sample

first: Amy

last: Cook

first: Ann

last: Chambers


title: Conversion

status: Public on Jan 01 2004

city: Los Angeles

first: Charlie

last: Chen

institute: University of California at Los Angeles

summary:
AR overexpression converts antagonists to weak agonists
Keywords: dose response

first: Derek

last: Welsbie

first: Charles

last: Sawyers


title: Muscle, normal extraocular, profile

status: Public on Dec 31 2003

first: Dominik

last: Fischer

institute: Pennsylvania Muscle Institute

summary:
Molecular definition of human extraocular muscles (EOM). Human EOM were compared with limb (quadriceps femoris) muscle.
Keywords = Eye
Keywords = EOM
Keywords = Muscle
Keywords = DMD
Keywords = Myasthenia Gravis
Keywords: other

first: Manuel

middle: D

first: J

middle: R

last: Gorospe

first: Marina

last: Bakay

first: Daniel

last: Kjellgren

first: Fatima

last: Pedrosa-Domellof

first: Eric

last: Hoffman

first: Tejvir

last: Khurana


title: USF1 haplotype comparison

status: Public on Feb 29 2004

city: Helsinki

first: Massimiliano

last: Gentile

address: Haartmaninkatu 8

department: Biomedicum Bioinformatics Unit

country: Finland

institute: Biomedicum Helsinki

summary:
Comparison of gene expression for individuals affected with FCHL exhibiting the USF1 susceptibility haplotype and FCHL affected indiviuals carrying the protective haplotype
Keywords: ordered

first: Päivi

last: Pajukanta

first: Heidi

last: Lilja

first: Janet

last: Sinsheimer

first: Rita

middle: M

last: Cantor

first: Aldons

middle: J

last: Lusis

first: Leena

last: Peltonen


title: Left ventricular apex samples

status: Public on Jan 18 2004

city: Minneapolis

first: Grindle

last: Suzanne

state: MN

address: Dwan CVRC 289, MMC 508, 420 Delaware Street SE

department: Division of Cardiology

institute: Lillehei Heart Institute

summary:
19 paired human left ventricular apex samples were harvested at the time of implant of a left ventricular assist device (PRE) and at the time of explant (POST). The cohort included patients that were clinically classified as "ischemic" (I) showing evidence of coronary artery disease, "non-ischemic" (N) no evidence of coronary artery disease or "acute Myocardial  infarction" (IM) myocardial infarction within 10 days of the implant. Tissue was processed and hybridized to the Affymetrix HG-U133A chip.
Keywords: other

first: Jennifer

last: Hall

first: Suzanne

last: Grindle

first: Xinqiang

last: Han

first: David

last: Fermin

first: Soon

last: Park

first: Yingjie

last: Chen

first: Robert

last: Bache

first: Ami

last: Mariash

first: Zhanjun

last: Guan

first: Sofia

last: Ormaza

first: Jeanne

last: Thompson

first: Judith

last: Graziano

first: Shireen

last: de Sam Lazaro

first: Schuchong

last: Pan

last: Simari

first: Leslie

last: Miller


title: IMR-90 cells: Tissue Culture Polystyrene Time Course

status: Public on Sep 10 2003

first: Catherine

last: Klapperich

summary:
IMR-90 Human Fibroblasts were seeded onto TCPS dishes.  mRNA was isolated at 1, 2, 4, 8, 12, 24, 48 and 96 hours. This time course was used as a control for gene expression studies on collagen/chondroitin sulfate tissue engineering scaffold materials using the same cell line.
Keywords = tissue culture plates
Keywords: time-course

first: Carolyn

last: Bertozzi


title: IMR-90 cells: Collagen Mesh Time Course

summary:
A series of chips with some repeated measurments. Each chip represents a pool of 4 collagen/chondroitin sulfate tissue engineering scaffold meshes seeded with 1 x 10^6 IMR-90 Human Fibroblasts.

mRNA was isolated at 30 minutes, 1, 2, 4, 8, 12, 24, 48, and 72 hours after seeding.
Keywords = tissue engineering mesh, collagen, chondroitin sulfate, biomaterials design
Keywords: time-course


title: Identification of LEAFY targets during reproductive transition

status: Public on Dec 18 2003

city: Philadelphia

first: Doris

last: Wagner

department: Biology

institute: University of Pennsylvania

summary:
Global analysis of gene expression in 9 day old LEAFY-GR, 35S::LFY or  Landsberg erecta seedlings treated with the steroid dexamethasone and/or the protein synthesis inhibitor cycloheximide.
Keywords: other

first: Dilusha

middle: A

last: William

first: Yanhui

last: Su

first: Michael

last: Smith

first: Meina

last: Lu

first: Don

last: Baldwin


title: Effect of left ventricular assist device support on congestive heart failure patients

status: Public on Sep 01 2003

first: Yingjie

last: Chen

department: Medicine, Cardiovascular Division

institute: University of Minnesota

summary:
Molecular analysis of the effect left ventricular assist device (LVAD) support has on congestive heart failure patients.
Keywords = Congestive heart failure, left ventricular assist device, eNOS, gene, dimethylarginine dimethylaminohydrolase
Keywords: other

first: Soon

last: Park

first: Li

last: Yunfang

first: Emil

last: Missov

first: Xinqiang

last: Han

first: Jennifer

last: Hall

middle: W

first: Robert

last: Bache


title: Gene expression profile analysis of 4-phenylbutyrate treatment of IB3-1 bronchial epithelial cell line

status: Public on Oct 29 2003

city: Baltimore

first: Jerry

last: Wright

address: 725 N. Wolfe St

department: Physiology

institute: Johns Hopkins Medical Institutions

summary:
Most individuals with cystic fibrosis (CF) carry one or two mutations that result in a maturation defect of the full-length CFTR protein.  The deltaF508 mutation results in a mutant protein that is degraded by the proteasome instead of progressing to the apical membrane where it functions as a cyclic AMP-regulated chloride channel.  4 phenylbutyrate modulates heat shock protein expression and promotes trafficking of deltaF508 thus permitting maturation and membrane insertion.  The goal of this study was to gain insight into the genetic mechanism of PBA action through a large-scale analysis of gene expression.  The Affymetrix genome spanning U133 microarray set was used to compare mRNA expression in untreated IB3-1 cell line cultures with cultures treated with 1mM 4-phenylbuyterate for 12 and 24 hr.  IB3-1 deltaF508/W1282X) bronchial epithelial cells were cultured in T75 flasks with gentamicin-free LHC-8 medium.  Cells were fed with 10 ml of media every 2 to 3 days.  After reaching 80% confluence cells were treated with 1 mM PBA.  A T75 flask of confluent IB3-1 cells was rinsed twice with ice cold Hank’s buffer then scraped into 3ml of ice cold TRIzol (Gibco BRL) then rinsed with 3 ml ice cold TRIzol and the mRNA was isolated according to the TRIzol protocol.  A total of 5 control cultures, 3 cultures with 12 hr BPA application and 3 cultures with 24 hr PBA application were processed
Keywords: time-course

first: Pamela

middle: L

last: Zeitlin

first: Liudmila

last: Cebotaru

first: Sandra

last: Guggino

first: William


title: Uterine Fibroid and Normal Myometrial Expression Profiles- U133 Arrays

status: Public on Oct 17 2003

city: Sacramento

first: Jeffrey

last: Gregg

institute: University of California, Davis School of Medicine

summary:
Our study seeks to identify genes differentially expressed between uterine leiomyomas and normal myometrial tissue. This series consists of samples derived from normal myometrium and uterine leiomyomas obtained from fibroid afflicted patients.Total RNA was extracted from samples, converted to biotin-labeled cRNA, hybridized to oligonucleotide arrays, and followed by model based expression analysis.

In order to select differentially expressed genes of interest, dChip model-based expression analysis was employed. Significant genes were identified, utilizing the dChip software, as having an average fold change of > +1.5 or < -1.5 between leiomyoma and normal myometrium and p < 0.05. Under these conditions the 226 genes in the following list were identified.
Keywords: other

first: Paul

last: Hoffman

first: Dawn

last: Milliken

first: Ryan

last: Davis

middle: P


title: Essential Thrombocythemia (ET) vs Normal (baseline) Megakaryocytes

status: Public on Dec 25 2003

city: Modena

first: Enrico

last: Tagliafico

state: MO

address: Via Campi 287

department: Center for Genome Research

institute: University of Modena and Reggio Emilia

summary:
Essential Thrombocythemia (ET) patients, as well as normal donors BM CD34+ cells were differentiated in thrombopoietin-treated liquid suspension cultures. Briefly, CD34+ cells (80,000 /mL) were resuspended in a serum-free medium in the presence of 100 ng/mL of human recombinant thrombopoietin (TPO; Genzyme, Boston, MA). Every 3 days, viable cells were scored by Trypan blue dye exclusion and cultures were amplified with fresh serum-free medium. Each well was then supplemented with 100 ng/mL TPO. After 14 to 16 days of liquid culture, CD34-derived megakaryocytes (MKs) were purified by means of an anti-CD41a monoclonal antibody (MoAb) (Dako, Milan, Italy) directed against the glycoproteic alpha2B-beta3 complex and immunobeads (MPC 450 Dynabeads; Dynal, Oslo, Norway). The purity of MKs was determined for each isolation by indirect immunofluorescence, using an anti-CD41b MoAb which reacts with a different epitope of alpha2B-beta3 subunit (Immunotech Inc., Westbrook, ME), followed by a goat anti-mouse IgG, covalently linked to fluorescein (Becton Dickinson, San Jose, CA).
Keywords: other

first: Elena

last: Tenedini

first: Maria Elena

last: Fagioli

first: Nicola

last: Vianelli

first: Michela

last: Poli

first: Luigi

last: Gugliotta

first: Giovanni

last: Martinelli

first: Sante

last: Tura

first: Michele

last: Baccarani

first: Sergio

last: Ferrari

first: Lucia

last: Catani


title: Normal Muscle - Female , Effect of Age

status: Public on Sep 22 2003

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

summary:
Healthy younger (20-29 yr) and older (65-71 yr) women donated vastus lateralis muscle under standard conditions.
Keywords = muscle
Keywords = aging
Keywords: time-course

first: Charles

last: Thornton

first: Andrew

middle: I

last: Brooks


title: Normal human muscle - U133 arrays

status: Public on Apr 03 2003

summary:
vastus lateralis biopsies were obtained from healthy subjects, either young adults (20-29 yr old) or older (65-75 yr old)
Keywords = muscle
Keywords = aging
Keywords: other

first: J

last: Delehanty

first: N

last: Needler


title: pmr4 vs. wild-type (May, 2003)

status: Public on Aug 15 2003

city: Stanford

first: Shauna

last: Somerville

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution of Washington

summary:
There were two genotypes:
(1)	Columbia-0, wild-type (C)
(2)	 pmr4-1 mutant (P), callose synthase deficient mutant (Vogel and Somerville (2000) Proc. Natl. Acad. Sci., USA 97: 1897).

There were two treatments:
(1)	uninoculated (U)
(2)	3 days after inoculation with the powdery mildew pathogen, Erysiphe cichoracearum, race UCSC (I).

There were four biological replicates, labeled 1, 2, 3 or 4.

Examples of the sample labels are:
CU1 = Columbia-0, uninoculated, replicate 1
CI2 = Columbia-0, 3 days after inoculation with powdery mildew, replicate 2
PU3 = pmr4-1, uninoculated, replicate 3
PI4 = pmr4-1, 3 days after inoculation with powdery mildew, replicate 4.

In total, there were 16 Affymetrix ATH1 GeneChips (2 genotypes x 2 treatments x 4 biological replicates).
Keywords: repeat sample

first: Marc

last: Nishimura

first: Monica

last: Stein

first: Bi-Huei

last: Hou

first: John

last: Vogel

first: Herb

middle: H

last: Edwards


title: DACH1 inhibits TGF-beta signaling through binding Smad4

status: Public on Oct 15 2003

city: Georgetown

first: Kongming

last: Wu

state: DC

address: 3970 Reservoir Rd, NW

department: Lombardi Cancer Center & Department of Oncology

institute: Georgetown University

summary:
The vertebrate homologues of Drosophila dachsund, DACH1 and DACH2, have been implicated as important regulatory genes in development. DACH1 plays a role in retinal and pituitary precursor cell proliferation and DACH2 plays a specific role in myogenesis. DACH proteins contain a domain (DS-domain) that is conserved with the proto-oncogenes Ski and Sno. Since the Ski/Sno proto-oncogenes repress AP-1 and SMAD signaling, we hypothesized that DACH1 might play a similar cellular function. Herein, DACH1 was found to be expressed in breast cancer cell lines and to inhibit TGF-beta induced apoptosis. DACH1 repressed TGF-beta induction of AP-1 and Smad signaling in gene reporter assays and repressed endogenous TGF-beta responsive genes by microarray analyses. DACH1 bound to endogenous NCoR and Smad4 in cultured cells and DACH1 co-localized with NCoR in nuclear dot-like structures. NCoR enhanced DACH1 repression and the repression of TGF-beta-induced AP-1 or Smad-signaling by DACH1 required the DACH1 DS domain. The DS-domain of DACH was sufficient for NCoR-binding at a Smad4-binding site. Smad4 was required for DACH1 repression of Smad signaling. In Smad4 null HTB-134 cells, DACH1 inhibited the activation of SBE-4 reporter activity induced by Smad2 or Smad3 only in the presence of Smad4. DACH1 participates in the negative regulation of TGF-beta signaling by interacting with NCoR and Smad4.
Keywords: other

first: Ying

last: Yang

first: Chenguang

last: Wang

first: Maria

last: Davoli

first: Mark

last: D'Amico

first: Anping

last: Li

first: Kveta

last: Cveklova

first: Zbynek

last: Kozmik

first: Michael

last: Lisanti

first: Robert

middle: G

last: Russell

first: Ales

last: Cvekl

first: Richard

last: Pestell