title: freij-affy-human-91666

status: Public on Mar 08 2006

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Diffuse infiltrating gliomas are the most common primary brain malignancy found in adults, and Glioblastoma multiforme, the highest grade glioma, is associated with a median survival of 7 months. Transcriptional profiling has been applied to 85 gliomas from 74 patients to elucidate glioma biology, prognosticate survival, and define tumor sub-classes. These studies reveal that transcriptional profiling of gliomas is more accurate at predicting survival than traditional pathologic grading, and that gliomas characteristically express coordinately regulated genes of one of four molecular signatures: neurogenesis, synaptic transmission, mitotic, or extra-cellular matrix. Elucidation of these survival associated molecular signatures will aid in tumor prognostication and define targets for future directed therapy.
Evaluate a large number of diffuse infiltrating gliomas through transcriptional profiling.
Glioma tumor sub-classes may be identified through large scale gene expression studies.
All patients undergoing surgical treatment at the University of California, Los Angeles for primary brain cancers between 1996 and 2003 were invited to participate in this Institutional Review Board approved study. 74 of the patients participating in this broad protocol were analyzed as part of this study if their initial tumor was diagnosed as a grade III (n=24) or IV (n=50) glioma of any histologic type on initial surgical treatment and fresh frozen material was obtained. Only grade III and IV gliomas were included in this study as the distinction between these grades is subtle and prone to misclassification. The time in days elapsed from resection to the day of death, or if the patient has remained alive, to the current day was recorded for all samples studied. Patient ages at diagnosis varied from 18 to 82 years. There were 46 females and 28 males. Probes were prepared using standard Affymetrix protocols, and hybridized to Affymetrix HG-U133A and HG-U133B arrays.
Keywords: disease state analysis

first: Stanley

middle: F

last: Nelson


title: Airway Epithelial Gene Expression Diagnostic for the Evaluation of Smokers with Suspect Lung Cancer

status: Public on Feb 27 2006

city: Boston

first: Avrum

last: Spira

state: MA

address: 715 Albany Street, R304

department: Pulmonary and Critical Care Medicine

country: USA

institute: Boston University Medical Center

summary:
RNA was obtained from histologically normal bronchial epithelium of smokers during time of clinical bronchoscopy from relatively accessible airway tissue. Gene expression data from smokers with lung cancer was compared with samples from smokers without lung cancer. This allowed us to generate a diagnostic gene expression profile that could distinguish the two classes. This profile could provide additional clinical benefit in diagnosing cancer amongst smokers with suspect lung cancer.
Keywords: Disease state analysis

overall_design:
79 total arrays run on total RNA obtained from Bronchial Epithelium of Smokers with Lung Cancer
73 total arrays run on total RNA obtained from Bronchial Epithelium of Smokers without Lung Cancer
23 of these samples were then filtered for quality control reasons


title: Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis

status: Public on Feb 16 2006

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

summary:
Background: Histologic grade in breast cancer provides clinically important prognostic information. However, 30%-60% of tumors are classified as histologic grade 2. This grade is associated with an intermediate risk of recurrence and is thus not informative for clinical decision making. We examined whether histologic grade was associated with gene expression profi les of breast cancers and whether such profi les could be used to improve histologic grading.

Methods: We analyzed microarray data from 189 invasive breast carcinomas and from three published gene expression datasets from breast  carcinomas. We identified differentially expressed genes in a training set of 64 estrogen receptor (ER)-positive tumor samples by comparing expression profiles between histologic grade 3 tumors and histologic grade 1 tumors and used the expression of these genes to define the gene expression grade index. Data from 597 independent tumors were used to evaluate the association between relapse-free survival and the gene expression grade index in a Kaplan-Meier analysis. All statistical tests were two-sided.

Results: We identified 97 genes in our training set that were associated with histologic grade; most of these genes were involved in cell cycle regulation and proliferation. In validation datasets, the gene expression grade index was strongly associated with histologic grade 1 and 3 status; however, among histologic grade 2 tumors, the index spanned the values for histologic grade 1-3 tumors. Among patients with histologic grade 2 tumors, a high gene expression grade index was associated with a higher risk of recurrence than a low gene expression grade index (hazard ratio = 3.61, 95% confidence interval = 2.25 to 5.78; P<.001, log-rank test).

Conclusions: Gene expression grade index appeared to reclassify patients with histologic grade 2 tumors into two groups with high versus low risks of recurrence. This approach may improve the accuracy of tumor grading and thus its prognostic value.

NB: The patients coming from Uppsala Hospital have been also used in other studies as in GSE3494. You can find the common set of patients in removing the abbreviation "UPP_" from the sample names and compare the results with the "INDEX (ID)" from the GSE3494 series.
Keywords: disease state analysis

overall_design:
64 microarray experiments from primary breast tumors used as training set to identify genes differentially expressed in grade 1 and 3.

129 microarray experiments from primary breast tumors of untreated patients used as validation set to validate the list of genes and its correlation with survival.

No replicate, no reference sample.

Supplementary file GSE2990_suppl_info.txt added Dec 20, 2006.

first: Christos

last: Sotiriou

first: Pratyaksha

last: Wirapati

first: Sherene

last: Loi

first: Adrian

last: Harris

first: Jonas

last: Bergh

first: Johanna

last: Smeds

first: Pierre

last: Farmer

first: Vivianne

last: Praz

first: Marc

last: Buyse

first: Martine

last: Piccart

first: Mauro

last: Delorenzi

first: Christine

last: Desmedt

first: Denis

last: Larsimont

first: Fatima

last: Cardoso

first: Hans

last: Peterse

first: Dimitry

last: Nuyten

last: Van de Vijver


title: Anticancer drug clustering in lung cancer based on gene expression profiles and sensitivity database

status: Public on Feb 10 2006

city: Tokyo

first: Akihiko

last: Gemma

address: Bumkyo-ku

country: Japan

institute: Nippon Medical School

summary:
Anticancer drug clustering in lung cancer based on gene expression profiles.
We performed gene expression analysis in lung cancer cell lines. (used: Affymetrix GeneChip Human Genome U133 Array Set HG-U133A).
We also examines the sensitivity of these cell lines to commonly used anti-cancer agents (docetaxel, paclitaxel, gemcitabine, vinorelbine, 5-FU, SN38, cisplatin, and carboplatin) via MTT assay.
We related the cytoxic activity of each of these agents to corresponding expression pattern in each of the cell lines using modified NCI program.
Keywords: cytotoxicity, lung cancer, anticancer drugs


title: Changes in Expression of Genes Involved in Apoptosis in Activated Human T-Cells in Response to Modeled  Microgravity

status: Public on Feb 09 2006

city: Houston

first: Diana

last: Risin

state: TX

address: 2101 NASA Parkway

department: Space Medicine

institute: NASA/JSC

summary:
The purpose of this study was to search for microgravity-sensitive genes, specifically for apoptotic genes influenced by the microgravity environment and other genes related to immune response.
Keywords: stress response

overall_design:
Two-group design with paired samples, i.e., one 1G and one MMG culture came from the same donor.  Therefore, 6 samples came from 3 different donors.
Donor 1 :GSM96146,GSM96147
Donor 2: GSM96148, GSM96149
Donor 3: GSM96150,GSM96151

Total RNA was submitted to, and then labeled, hybridized and data generated by the Baylor College Medicine Microarray Core Facility (333E One Baylor Plaza, Houston, TX 77030).


title: Expression profiling of human endomyocardial biopsies before, during and after cardiac allograft rejection

status: Public on Mar 02 2006

city: Gothenburg

first: Per-Arne

last: Svensson

department: Department of molecular and clinical medicine

country: Sweden

institute: institute of medicine

summary:
Cardiac allograft rejection remains a significant clinical problem in the early phase after heart transplantation and requires frequent surveillance with endomyocardial biopsy.
Endomyocardial tissue samples were obtained in connection with clinical biopsies from twenty consecutive heart transplant patients followed for six months. A rejection episode was observed in 14 patients and biopsies obtained before, during and after the episode were identified. Endomyocardial RNA, from three patients, matching these three points in time were analysed with DNA microarray.
Keywords: time course

overall_design:
Three subjects (subject number 1,8 and 12)
Three timepoints (Before, during and after an rejection episode)

first: Kristjan

last: Karason

first: Margareta

last: Jernås

first: Daniel

middle: A

last: Hägg


title: PTHrP-responsive genes in breast cancer

status: Public on Feb 25 2006

city: Halle (Saale)

first: Juergen

last: Dittmer

department: Clinic of Gynecology

country: Germany

institute: University of Halle

summary:
Parathyroid hormone-related protein (PTHrP) is overexpressed in many cancer types. This secretory protein can induce hypercalcaemia of malignancy by mimicking the action of calcium-regulating parathyroid hormone (PTH). PTHrP may also be involved in the regulation of migration, invasion, proliferation and apoptosis. It can either stimulate signal cascades, such as the cAMP pathway, or act on not yet defined targets in the nucleus. In this study, we analyzed the effect of PTHrP-specific siRNA on gene expression in MDA-MB-231 breast cancer cells. MDA-MB-231 cells were either transfected with the PTHrP-specific siRNA (siPTHrP) or a control siRNA (siLuc). Differences in gene expression pattern in siPTHrP- vs. siLuc-treated cells were measured by microarray analysis. More than 200 differentially expressed genes were found. Some of these genes have important functions in carcinogenesis.
Keywords: siRNA knock-down analysis

overall_design: Three independent transfection experiments were performed. Cells were transfected with siPTHrP or siLuc by electroporation, grown for three days and harvested for isolation of total RNA. RNAs were subjected to microarray analysis. The RNAs of experiment 1 are designated as siLuc 1 and siPTHrP 1, those of experiment 2 as siLuc 2 and siPTHrP 2 etc.. To identify siPTHrP-responsive genes, the siPTHrP- and siLuc-RNAs of the same experiment were compared.

first: Pearl

last: Campbell


title: Genomic Strategies Identify the Antitumor Agent Apratoxin A as a Potent Antagonist of FGF Signaling and STAT3 Activation

status: Public on Feb 08 2006

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
Total RNA was extracted from apratoxin A or vehicle treated HT29 cells using the RNeasy Mini Kit (Qiagen).  Probe values from CEL files were condensed to probe sets using Rosetta Resolver software.  Resolver ANOVA analysis was then performed between groups.
Keywords: time course and dose

overall_design: 2 doses were compared to vehicle at 3 time points.  Each time point had its own vehicle control

first: Hendrik

last: Luesch

first: Sumit

middle: K

last: Chanda

first: R

middle: M

last: Raya

first: Anthony

middle: P

last: Orth

first: J

last: Belmonte

first: Peter

middle: G

last: Schultz


title: Genomic and expression profiling identifies Syk as a possible therapeutic target in mantle cell lymphoma

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via Vela 6

department: Experimental Oncology

country: Switzerland

institute: Institute of Southern Switzerland

type:
Expression profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Among B-cell lymphomas mantle cell lymphoma (MCL) has the worst prognosis. By using a combination of genomic and expression profiling (Affymetrix GeneChip Mapping 10k Xba131 and U133 set), we analysed 26 MCL samples to identify genes relevant to MCL pathogenesis and that could represent new therapeutic targets. Recurrent genomic deletions and gains were detected. Genes were identified as overexpressed in regions of DNA gain on 3q, 6p, 8q, 9q, 16p and 18q, including the cancer genes BCL2 and MYC. Among the transcripts with high correlation between DNA and RNA, we identified SYK, a tyrosine kinase involved in B-cell receptor signalling. SYK was amplified at DNA level, as validated by fluorescence in situ hybridisation (FISH) analysis, and overexpressed at both RNA and protein levels in the JeKo-1 cell line. Low-level amplification, with protein overexpression of Syk was demonstrated by FISH in a small subset of clinical samples. After treatment with low doses of the Syk inhibitor piceatannol, cell proliferation arrest and apoptosis were induced in the cell line overexpressing Syk, while cells expressing low levels of Syk were much less sensitive. A combination of genomic and expression profiling suggested Syk inhibition as a new therapeutic strategy to be explored in lymphomas.
Keywords: cell type comparison

overall_design:
Expression profiling: Four untreated human cell lines were analyzed. No replications except for REC.
Genomic profiling: 26 MCL samples (22 patients, 4 cell lines) were analyzed. No replications except for REC

first: Andrea

last: Rinaldi

first: Ivo

last: Kwee


title: Targets of cytostatic drugs in HT1080 fibrosarcoma

status: Public on Feb 04 2006

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
HT1080 fibrosarcoma cells were treated with cytostatic drugs and analysed on Affymetrix microarray to identify genes and pathways regulated by these compounds.  The array images were processed using Affymetrix MAS 5.0 software. and normalized by global scaling or scaled to a polyA+ spike mask
Keywords = Cytostatic drugs
Keywords = Actinomycin D
Keywords = Doxorubicin
Keywords = Vincristine
Keywords = apoptosis
Keywords: ordered

first: M

last: Lehnhardt

first: C

last: Kuhnen

first: L

last: Schnoor

first: S

last: Roehrs

first: H

middle: H

last: Homann

middle: U

last: Steinau

first: A

last: Daigeler

first: O

last: Mueller


title: kitam-affy-droso-176167

status: Public on Jan 13 2006

first: Winnie

last: Liang

summary:
Disruption of learning and memory can occur for a number of reasons including chronic alcohol abuse, head injury, anoxia, and various neurodegenerative disorders such as Alzheimer’s disease.  An understanding of the basic mechanisms underlying learning and memory is essential for prevention and treatment of such brain disorders.  Recent studies unequivocally demonstrated the astonishing similarities in the basic mechanisms of learning and memory between divergent species, indicating that studies of experimentally tractable model organisms with relatively simpler nervous systems are likely to produce valuable information that will facilitate our understanding of learning and memory in higher organisms.  We are studying the experience-dependent modification in Drosophila male courtship as a physiologically relevant model of learning and memory.  The genome-scale gene-profiling analysis in this model system should provide us the basic information about learning-induced changes in gene expression, which will be the foundation of our future studies to identify genes and genetic pathways specifically involved in the formation of long-term memory.
The proposed gene-profiling experiment is designed to identify candidate genes and genetic pathways involved in the formation of long-term memory in the Drosophila courtship conditioning.  The specific aims of this project are to: 1) compare gene expression profiles between the naïve and trained wild type males using the GeneChip Drosophila Genome 2.0 Arrays and identify genes that are up- or down-regulated in the fly head immediately or 24-hr after the male fly is exposed to the condition where the long-term courtship memory is established (i.e., paired with a mated female for 7 hrs), 2) carry out the same analysis for the per null mutant males, 3) compare the identified genes between  the 0 and 24-hr after training as well as the wild type and per mutant males, 4) identify candidate genes which might be involved in the long-term memory formation either upstream or downstream of per, 5) classify the candidate genes according to their putative cellular function and discern the possible genetic pathways necessary for the long-term memory formation.
When a male fly is presented with a previously mated female, he will initially court her vigorously but his courtship activity is reduced over time.  Subsequently, when paired with a virgin female, the male will display a reduced amount of courtship compared with naïve males with no prior courtship experience.  This modification of courtship is called “courtship conditioning”.  We found that this type of courtship memory lasts at least 5 days when a male is trained with a mated female for 7 hrs.  We have also found that the period gene (per) that is involved in circadian rhythm regulation plays a critical role in the formation of long-term, but not short-term, courtship memory.  Our hypotheses are 1) the long-lasting memory in 7 h-trained males is accompanied with characteristic temporal changes in gene expression in the brain, 2) per mutant males are defective in regulation of critical genes involved in long-term courtship memory, 3) the memory–related changes in gene expression can be detected by comparing total head transcript levels between trained and naïve as well as the wild type and the per mutant males using the Affymetrix microarray.
Two fly strains, a wild type Oregon R (OR) and a null mutant allele of per (per01) with the OR background for the second and third chromosomes, will be used.  Virgin males and females will be collected without anesthesia within 6 hrs after eclosion and maintained individually in vials until experiments.  Mated wild type females will be prepared by crossing to the wild type males the night before they are used for conditioning males.  All flies will be raised at 25oC in a 12 h light/12 h dark cycle and the following behavioral experiments will be carried out during daytime.  For courtship conditioning, a 3 day-old virgin male (either OR or per01) will be placed with a mated OR female in a conditioning chamber (15 mm x 5 mm in depth) containing fly food.  As a control, a virgin male will be introduced into another conditioning chamber without a mated female.  Seven hours after the male is introduced into the chamber, he will be anesthetized under CO2 gas or transferred to a new vial.  For the anesthetized male, the head will be immediately excised and frozen with liquid nitrogen.  The male fly transferred to a new vial will be decapitated 24 hrs after the end of the 7-hr training.  Approximately thirty fly heads will be pooled for each of the 8-genotype/treatment groups, i.e., Oregon R 0-hr and 24-hr after conditioning, per01 0-hr and 24-hr after conditioning, in addition to the corresponding four naïve controls.  Total RNA will be extracted from the pooled heads using the TRIzol Reagent (Life Technologies) followed by an RNeasy (Qiagen) cleanup step and a DNAase I digestion step.  After purification, the RNA will be resuspended in DEPC water and the absorbance will be checked at 260 and 280 nm for determination of sample purity and concentration.  The GeneChip Drosophila Genome 2.0 Arrays will be used to quantify the levels of transcripts in each sample.
Keywords: other

first: Toshihiro

last: Kitamoto


title: Letrozole-, Anastrozole- and Tamoxifen-Responsive Genes in MCF-7aro Cells

status: Public on Feb 02 2006

city: Duarte

first: Shiuan

last: Chen

address: 1500 E Duarte Rd

department: Surgical Research

institute: City of Hope

summary:
Anti-estrogens and aromatase inhibitors are important drugs in the treatment of estrogen-dependent breast cancer.  In order to investigate the effects of these drugs on gene expression in breast cancer cells, we treated estrogen receptor-positive MCF-7 cells, stably transfected with the aromatase gene (known as MCF-7aro cells), with testosterone, 17β-estradiol, two aromatase inhibitors (letrozole and anastrozole), and an anti-estrogen (tamoxifen).  Microarray analyses using Affymetrix Human Genome U133A GeneChips were carried out using total RNA isolated from the control and treated cells.  When comparing the effect of each inhibitor on gene expression we observe that letrozole and anastrozole are more similar in terms of the genes they affect, compared to treatment with tamoxifen.  The results of this study provide us with a better understanding of the actions of both aromatase inhibitors and anti-estrogens at the molecular level.  We believe that the results of this study serve as the first step in identifying unique expression patterns following drug treatment, and that this will ultimately be useful in customizing patient treatment strategies for estrogen-dependent breast cancer.

The data presented here have been processed using the R-Project Bioconductor statistical tools package using the affy library.  The following were applied:  RMA background correction, pmonly probe-level correction, quantile normalization, avgdiff summary method.  Raw data is provided in the form of .CEL files.
Keywords = estrogen-dependent breast cancer
Keywords = aromatase
Keywords: other

first: Toru

last: Itoh

first: Kim

last: Karlsberg

first: Ikuko

last: Kijima

first: Yate-Ching

last: Yuan

first: David

last: Smith

first: Jingjing

last: Ye


title: Profiling of three different ER+ breast cancer cell lines grown in the presence and absence of estrogen.

status: Public on Jan 15 2006

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
Three human ER+ breast cancer cell lines--MCF-7, T47-D, BT-474--grown with or without estradiol (E2).
Keywords: Cell Line Comparison

overall_design: We analyzed biological duplicates of each cell line grown in the presence or absence of estrogen, 12 arrays in all.

first: Jimmy

last: Rae

first: Marc

last: Lippman


title: Arabidopsis plants with altered levels of alternative oxidase

status: Public on Jan 31 2006

city: East Lansing

first: Jianping

last: Yu

state: MI

address: Michigan State University

department: Plant Research Laboratory

institute: Michigan State University

summary:
In higher plants, various developmental and environmental conditions enhance expression of the mitochondrial alternative oxidase (AOX). In this work transgenic Arabidopsis thaliana plants were generated that either overexpress AOX or inhibit its synthesis. Gene expression following antimycin A treatment, which inhibits the cytochrome pathway in mitochondria, was studied in an AOX overexpressor line. The role of AOX in regulation of reactive oxygen species (ROS) in leaves was studied in the transgenic lines. The transgenic lines were also used to investigate the mitochondria-chloroplasts interaction in assays performed at three-times growth light. For most of the parameters measured AOX antisense lines and WT plants showed a very similar response whereas AOX sense lines differed in several aspects. An unexpected result was that AOX overexpressors had higher cellular ATP/ADP ratios as compared to WT and antisense lines. This was linked to decreased photosynthetic CO2-assimilation and O2-evolution, closed PSII reaction centers and altered Calvin cycle metabolite contents. We conclude that increased mitochondrial AOX capacity can lead to a drain of electrons from the chloroplasts causing an unfavorable redox status and thereby inhibit photosynthesis.
Keywords: Genetic modification

overall_design: Wild type Arabidopsis thaliana gl1 and two transgenic lines are studied. One transgenic line, S5, accumulates high levels of alternaitve oxidase in leaves constitutively. The other transgenic line, A1-1, can not accululate the protein in leaves even under stress conditions. Transcript profiling was performed in three replicates using leaf RNA from 5 week old plants grown under non-stress conditions.

first: Lee

last: McIntosh

first: Roxy

last: Nickels

first: Per

last: Gardestrom


title: Expression changes induced by transmigration in human neutrophils

status: Public on Jan 01 2006

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

summary:
Human volunteers were exposed to endotoxin by bronchoscopic instillation, airspace and circulating neutrophils were isolated 16 hours later and compared to circulating neutrophils obtained prior to endotoxin exposure, and to circulating neutrophils exposed to endotoxin in vitro.
Keywords = pulmonary inflammantion
Keywords = acute lung injury
Keywords = acute respiratory distress syndrome
Keywords: parallel sample

first: Jerry

last: Nick

first: Katie

last: Poch

first: Malcolm

last: Woolum

first: Brian

middle: W

last: Fouty

first: James

last: O'Brien

first: Michael

last: Gruber

first: Martin

last: Zamora

first: Daiva

last: Svetkauskaite

first: Don

last: Richter

first: Qianbin

last: He

first: Jong

middle: S

last: Park

first: Katherine

last: Overdier

first: Edward

last: Abraham

first: Mark

last: Geraci


title: Omega-6 fatty acids, arachidonic acid (AA) activates PI3K signaling and induces gene expression in prostate cancer

city: Bethesda

first: Jim

last: Boonyaratanakornkit

state: MD

address: 50 South Dr, Bldg 50, Rm 6513

department: LID

institute: NIH - NIAID

summary:
Essential fatty acids (FA) are not only energy-rich molecules; they are also an important component of the membrane bilayer and recently have been implicated in induction of fatty acid synthase (FAS) and other genes.  Using gene chip analysis, we have found that arachidonic acid (AA), an omega-6 fatty acid, induced 11 genes that are regulated by NFkappaB.  We verified gene induction by omega-6 fatty acids including COX2, IKBA, NFKB, GMCSF, IL1B, CXCL1, TNFA, IL6, LTA, IL8, PPARG, and ICAM1 using qRTPCR.  PGE2 synthesis was increased within 5min of addition of AA.  Analysis of upstream signal transduction showed that within 5min of FA addition, phophatidylinositol 3-kinase (PI3K) was significantly activated followed by activation of Akt at 30min.  ERK1 and 2, p38, and SAPK/JNK were not phosphorylated after omega-6 FA addition.  Thirty minutes after FA addition, we found a significant 3-fold increase in translocation of NFkappaB transcription factor to the nucleus.  Addition of non-steroidal anti-inflammatory drug (NSAID) caused a decrease in cox-2 protein synthesis, PGE2 synthesis as well as inhibition of PI3K activation.  We have previously shown that AA induced proliferation is also blocked (P<0.001) by PI3K inhibitor LY294002.  LY294002 also significantly inhibited the AA induced gene expression of COX2, IL1B, GMCSF, and ICAM1.  Taken together, the data suggests that AA via conversion to PGE2 plays an important role in stimulation of growth related genes and proliferation via PI3K signaling and NFkappaB translocation to the nucleus.
Keywords: Time course of Prostate Cancer Activation by Arachidonic Acid

overall_design: PC-3 prostate cancer cells were incubated with 5 µg/mL AA in RPMI containing 0.25 mg/mL albumin for 2hr.  Control cells were treated with albumin alone and remained unactivated.  Total RNA was isolated and relative gene expression was analyzed by Affymetrix gene arrays and then verified by qRTPCR.  Microarrays for untreated and treated samples were done in quadruplicates.

first: Millie

last: Hughes-Fulford

first: Chai-Fei

last: Li

middle: B

first: Sina

last: Sayyah


title: RNA changes induced by LEAFY COTYLEDON2 activity in Arabidopsis seedlings

status: Public on Jan 04 2006

city: Davis

first: Siobhan

last: Braybrook

address: 1 Shields Ave

department: Plant Biology

institute: University of California, Davis

summary:
LEAFY COTYLEDON2 activity was induced via a LEC2-Glucocorticoid Receptor fusion protein in Arabidopsis seedlings.
Keywords: Ordered

overall_design:
Transgenic plants carrying a 35S:LEC2-Glucocorticoid Receptor transgene were used for LEC2 induction.  Activity was induced in 8 day old seedlings for 1 or 4 hours with Dexamethasone application.  Controls include uninduced transgenic plants and non-transgenic plants treated with Dex.
Two biological replicates per treatment.

first: Sandra

middle: L

last: Stone

first: SooMin

first: Ahnthu

middle: Q

last: Bui

first: Brandon

last: Le

first: Robert

last: Fischer

last: Goldberg

first: John

middle: J

last: Harada


title: Lymphe node vs. Tonsil

status: Public on Dec 31 2005

city: Mannheim

first: Alexei

last: Gratchev

department: Department of Dermatology

institute: Medical Centre Mannheim, University of Heidelberg

summary:
Lymph node vs. tonsil
Keywords: repeat sample

first: Jan-Henning

last: Martens

first: Julia

last: Kzhyshkowska

first: Martin

last: Falkowski-Hansen

first: Kai

last: Schledzewski

first: Ulrich

last: Mansmann

first: Christina

last: Schmuttermaier

first: Edgar

last: Dippel

first: Wolfgang

last: Koenen

first: Frank

last: Riedel

first: Sergij

last: Goerdt


title: The effect of FH mutations on fibroid expression profile, normal myometrium vs. FH-mutant fibroids.

status: Public on Dec 20 2005

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

summary:
A series of gene expression measurements of uterine fibroids with mutated fumarate hydratase (FH) gene and normal myometrium.

Keywords: other

first: Patrick

last: Pollard

first: Heli

last: Lehtonen

first: Päivi

last: Laiho

first: Jari

last: Sjöberg

first: Arto

last: Leminen

first: Kristiina

last: Aittomäki

first: Johanna

last: Arola

first: Mogens

last: Kruhoffer

first: Torben

last: Ørntoft

first: Ian

last: Tomlinson

first: Maija

last: Kiuru

first: Diego

last: Arango

first: Lauri

last: Aaltonen


title: The effect of FH mutations on fibroid expression profile 2.

summary:
A series of gene expression measurements of normal myometrium and uterine fibroids with mutated or wild-type fumarate hydratase (FH) gene.

Keywords: other


title: The effect of FH mutations on fibroid expression profile

summary:
A series of gene expression measurements of uterine fibroids with mutated or wild-type fumarate hydratase (FH) gene.
Keywords: other


title: Lin-, CD38-, CD34+ Hematopoietic Stem Cells.

status: Public on Dec 09 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
Lin-, CD38-, CD34+ hematopoietic stem cells.
Keywords: other

overall_design: this experiment include 1 samples and 6 replicates


title: Suqamous Cell Carcinoma of Head and Neck

status: Public on Dec 14 2005

city: Little Rock

first: Radhakrishnan

last: Nagarajan

state: AR

address: 4301 W Markham, Slot 781, Room: 3234

department: Department of Biostatistics

institute: University of Arkansas for Medical Sciences

summary:
Gene Expression Analysis of Squamous Cell Carcinoma of Head and Neck
Keywords: parallel sample

first: Ehab

last: Hanna


title: Molecular Signatures Orchestrating fate of Human Hematopoietic Stem Cells Originating From Different Stages of Ontogeny

status: Public on Jan 17 2006

summary:
Investigation of human hematopoietic stem cells gene expression patterns originating from different stages of ontogeny including fetal blood, cord blood, bone marrow, and mobilized peripheral blood in Lin-CD34+CD38- versus Lin-CD34+CD38+ populations.
Keywords: other

overall_design: this experiment include 7 samples and 42 replicates


title: SSEA4 sorted I-6 Human ES cells

summary:
Human ES cell line I-6 was cultured in standard conditions to maintain an undifferentiated, self renewing phenotype. The cells were sorted based upon their expression of SSEA4, which is a marker of the undifferentiated, self renewing phenotype
Keywords: other

overall_design: this experiment include 2 samples and 12 replicates


title: Comparison of Hutchinson–Gilford Progeria Syndrome fibroblast cell lines to control fibroblast cell lines

city: Boston

first: Sangeeta

last: English

address: 300 Longwood Avenue

institute: Children's Hospital

summary:
Hutchinson–Gilford progeria syndrome (HGPS) is a rare genetic disease with widespread phenotypic features resembling premature aging. HGPS was recently shown to be caused by dominant mutations in the LMNA gene, resulting in the in-frame deletion of 50 amino acids near the carboxyl terminus of the encoded lamin A protein. Children with this disease typically succumb to myocardial infarction or stroke caused by severe atherosclerosis at an average age of 13 years. To elucidate further the molecular
pathogenesis of this disease, we compared the gene expression patterns of three HGPS fibroblast cell lines heterozygous for the LMNA mutation with three normal, age-matched cell lines. We defined a set of 361 genes (1.1% of the approximately 33 000 genes analyzed) that showed at least a 2-fold, statistically significant change. The most prominent categories encode transcription factors and extracellular matrix proteins, many of which are known to function in the tissues severely affected in HGPS. The most affected gene, MEOX2/GAX, is a homeobox transcription factor implicated as a negative regulator of mesodermal tissue proliferation. Thus, at the gene expression level, HGPS shows the hallmarks of a developmental disorder affecting mesodermal and mesenchymal cell lineages. The identification of a large number of genes implicated in atherosclerosis is especially valuable, because it provides clues to pathological processes that can now be investigated in HGPS patients or animal models.
Keywords: microarrays, Hutchinson–Gilford progeria syndrome, HGPS

overall_design: Three fibroblast cell lines derived from HGPS patients were compared to three control fibroblast cell lines using Affymetrix HG-U133A and HG-133B probe arrays. Triplicates were used for each cell line. Total RNA was used in the analysis. Quantitation was done by MAS 5.0 software (Affymetrix).

first: Antonei

last: Csoka

first: Carl

last: Simkevich

first: David

last: Ginzinger

first: Atul

last: Butte

first: Gerald

last: Schatten

first: Frank

last: Rothman

first: John

last: Sedivy


title: Gene Expression in Cord Blood Derived Lineage Negative and Positive Hematopoeitic Stem Cells After 4 Days in Culture.

summary:
Gene expression of cord blood derived lineage negative and lineage positive hematopoeitic stem cells was studied by collecting samples following 4 days of culture in Stem span medium. For comparison, samples were also collected following both a mock and fresh medium exchange.
Keywords: other

overall_design: this experiment include 4 samples and 20 replicates


summary:
Comparison of muscle stem cell preplates and myoblasts.
Keywords: other

overall_design: this experiment include 2 samples and 2 replicates


title: Characterization and isolation of stem cell enriched human hair follicle bulge cells

status: Public on Dec 06 2005

first: Jonathan

last: Vogel

address: Bldg. 10 / Room 12N260

department: Dermatology

institute: National Cancer Institute; NIH

summary:
The human hair follicle bulge is an important niche for keratinocyte stem cells (KSC).  Elucidation of human bulge cell biology could be facilitated by analysis of global gene expression profiles and identification of unique cell surface markers.  The lack of distinctive bulge morphology in human hair follicles has hampered studies of bulge cells and KSC.  In this study, we determined the distribution of label-retaining cells to carefully define the human anagen bulge. Using navigated-laser capture microdissection, bulge cells and outer root sheath cells from other follicle regions were obtained and analyzed with cDNA microarrays.  Gene transcripts encoding inhibitors of WNT and Activin/BMP signaling were over-represented in the bulge while genes responsible for cell proliferation were under-represented, consistent with quiescent non-cycling KSC in anagen follicles.  Positive markers for bulge cells included CD200, PHLDA1, follistatin, and frizzled homolog 1 while CD24, 34, 71 and 146 were preferentially expressed by non-bulge keratinocytes. Importantly, CD200+ cells (CD200hi24lo34lo71lo146lo) obtained from hair follicle suspensions demonstrated high colony forming efficiency in clonogenic assays, indicating successful enrichment of living human bulge stem cells.
Keywords: Affymetrix micrarray analysis of human hair follicles

overall_design: In this study, we developed methods to precisely identify the anatomical location of the human bulge region, and then collected bulge ORS cells by navigated-LCM (N-LCM).  The global gene expression profile of bulge ORS cells was determined by microarray analysis and compared to that of other defined ORS cell subpopulations to identify genes that were differentially expressed in the bulge area. By combining positive and negative selection markers identified on bulge cells by microarray analysis and confirmed by immunohistochemistry, we enriched living human bulge cells and assessed their biological behavior in an in vitro colony forming keratinocyte stem cell assay. This report describes the systematic transcriptional profiling of human bulge cells and the first demonstration of directed enrichment of putative human hair follicle stem cells.

first: Manabu

last: Ohyama

first: Atsushi

last: Terunuma

first: Christine

last: Tock

first: Michael

last: Redonovich

first: Cynthia

last: Pise-Masison

first: Steven

last: Hopping

middle: N

last: Brady

first: Mark

middle: C

last: Udey


title: Prognostic gene signatures can be measured with samples stored in RNAlater

first: Jack

last: Yu

address: 3210 Merryfield Row

institute: Veridex, LLC

summary:
A number of breast or colon specific genes predictive of the relapse status were used in comparing the outcome from matched fresh frozen and stored in RNAlater preservative.
Keywords: disease state analysis

overall_design: 31 pairs of matched breast and 21 pairs of matched colon primary tumors either fresh frozen or stored in RNAlater preservative


title: Association b/w gene expression profile & tumor invasion in OSCC

status: Public on Dec 01 2005

city: Newark

first: Gokce

last: Toruner

state: NJ

address: 225 Warren Street W410Q

department: Center for Human and Molecular Genetics

institute: UMDNJ-NJ Medical School

summary:
There are limited studies attempting to correlate the expression changes in oral squamous cell carcinoma with clinically relevant variables. We determined the gene expression profile of 16 tumor and 4 normal tissues from 16 patients by means of Affymetrix Hu133A GeneChips. The hybridized RNA was isolated from cells obtained with laser capture microdissection, then was amplified and labeled using T7 polymerase-based in vitro transcription. The expression of 53 genes was found to differ significantly (33 upregulated, 20 downregulated) in normal versus tumor tissues under two independent statistical methods. The expression changes in four selected genes (LGALS1, MMP1, LAGY, and KRT4) were confirmed with reverse transcriptase polymerase chain reaction. Two-dimensional hierarchical clustering of the 53 genes resulted in the samples clustering according to the extent of tumor infiltration: normal epithelial tissue, tumors less than or equal to 4 cm in dimension, and tumors more than 4 cm in dimension (P=0.0014). The same pattern of clustering was also observed for the 20 downregulated genes. We did not observe any associations with lymph node metastasis (P=0.097).

Keywords: TNM,Tumor-node-metastasis LCM,Laser capture microdissection OSCC,Oral squamous cell Carcinoma

overall_design: We performed microarray analysis using RNA from OSCC cells obtained with LCM from 16 patients and compared these results with 4 control squamous cell epithelium samples.We identified expression profiles of differentially expressed genes between normal and tumor tissues and found that tumor invasiveness of a tumor is highly correlated with its gene expression profile.

middle: A

first: Celal

last: Ulger

first: Mualla

last: Alkan

first: Anthony

middle: T

last: Galante

first: Joseph

last: Rinaggio

first: Randall

last: Wilk

first: Bin

last: Tian

first: Patricia

last: Soteropoulos

first: Meera

last: Hameed

first: Marvin

last: Schwalb

first: James

last: Dermody


title: Human immune cell transcriptome

status: Public on Jan 10 2006

city: Darlinghurst

first: Charles

middle: Reay

last: Mackay

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute for Medical Research

summary:
In the present study we used Affymetrix oligonucleotide microarrays to produce gene transcription profiles for the major leukocyte types in humans. This comprehensive dataset enabled us to not only establish which genes were expressed in each leukocyte type, but also which genes were expressed in each subset after activation. The used of a comprehensive dataset of gene profiles from all the major human leukocyte subsets enabled a novel and powerful means for identification of genes associated with single leukocyte subsets, or different immune paradigms.
Keywords: Cell type comparison

overall_design: Different leukocyte subsets were either isolated or differentiated from human blood to obtain consistently >95% pure populations. Gene profiles for activated effector cells such as macrophages, neutrophils and mast cells were also generated. In most cases, microarray analyses were perform on samples from 2 independent donors.

middle: R

first: Kate

last: Jeffrey

first: Sue

last: Liu

first: Tatyana

last: Chtanova

first: Mary

last: Sisavanh

first: Rebecca

last: Newton

first: Sabine

last: Zimmer


title: Carbon fixation (endogenous sugar) and light-dependent gene expression

city: Potsdam-Golm

first: Oliver

middle: E

last: Bläsing

address: Am Mühlenberg 1

department: Abt. Stitt

summary:
Internal sugar and light specific dependent regulation of leaf gene expression was addressed by changing [CO2] to lower than compensation point [CO2] in combination with light or prolonged darkness. Plants were grown on soil in a 12/12 h light/dark rhythm at 20°C day and night and under normal [CO2]. 5 weeks after germination, the above-ground rosettes of the non-flowering plants were harvested, 12 plants per sample. Plants were harvested 4hrs after the end of night (i) under low (< 50 ppm) [CO2] and 150 µE fluorescent light , (ii) under normal [CO2] and light, and, (iii) under low [CO2] and prolonged darkness. The low [CO2] treatment started 30 min before the end of night and stopped with harvesting.
Keywords: repeat

overall_design: 2 biological replicates of plants under 3 treatments (4hrs low CO2+light, 4hrs low CO2+prolonged darkness, and 4hrs normal CO2+light).

first: Mark

last: Stitt


title: Role of Smad7 in Hematopoietic (M-O7e) and Non-Hematopoietic (PG13) Stem Cells

first: Theodore

last: Perkins

summary:
Smad7 is a member of the TGF-B superfamily that plays a signigicant role in fate determination of hematopoietic stem cells. This experiment compares expression between megakaryotic and fibroblast cell lines that have been transduced with either Smad7 recombinant retroviral vector or retroviral vector alone.
Keywords: other

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: this experiment include 4 samples and 30 replicates


title: Diurnal gene expression in Arabidopsis thaliana Col-0 rosette leaves

summary:
How do the transcript levels of leaf-expressed genes change in a normal day-night cycle? The interest is in genes that are regulated by the circadian clock and the diurnal component (i.e. light, metabolite changes). Plants were grown on soil in a 12/12 h light/dark rythm at 20°C day and night. 5 weeks after germination the rosettes of the non-flowering plants were harvested, 15 plants per sample. Plants were harvested at 6 timepoints every 4 hours beginning with the end of the night (still in darkness).
Keywords: repeat

overall_design: 3 biological replicates of the diurnal time series (6 times) were analyzed that were separately grown


title: Effects of a 6h-long treatment with 90 mM sucrose to 4-d old, dark grown Arabidopsis seedlings

status: Public on Dec 03 2005

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

summary:
Dark grown Arabidopsis seedlings (Columbia gl1) were grown in the dark at 23°C for 4 days before adding 90 mM sucrose for 6h.
Keywords: Response to nutrients; sugar sensing

overall_design:
Arabidopsis thaliana ecotype Columbia glabra (gl1-1) was used in this study. Seeds were sterilized with diluted bleach (10 min incubation in 1.7% sodium hypochlorite, rinsing and washing thoroughly in sterile water), and incubated in 2.5 ml liquid growing medium [Murashige-Skoog (MS) half strength solution] in 6-well plates (fully aerobic, with shaking). Plates were incubated in the darkness at 4°C for 2 days and finally transferred to 23°C for 4 days before the sugar treatments (with 90 mM sucrose, lasting 6h). Two independent, replicated experiments were performed for sucrose treatments. Each independent experiment consisted of four replicated seedlings cultures, pooled after RNA extraction.
AIR EXPERIMENT 1: Control without added sucrose
AIR EXPERIMENT 2: Control without added sucrose
Sucrose 90 mM, 6h treatment in the dark, Biological Replicate 1
Sucrose 90 mM, 6h treatment in the dark, Biological Replicate 2

first: Silvia

last: Gonzali

first: Elena

last: Loreti

first: Cinzia

last: Solfanelli

first: Giacomo

last: Novi

first: Amedeo

last: Alpi


title: Egr-1 induced gene expression changes in HUVECs

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

summary:
The target genes of the transcription factor early growth response-1 (EGR-1) were studied in human umbilical vein endothelial cells (HUVEC). Densely cultured HUVEC were infected with recombinant adenoviruses expressing EGR-1 or empty control viruses at a MOI of 100. RNA was isolated from the cells at the time points 16 h, 24 h and 48 h post infection. Control cells without infection were cultured in parallel and harvested at the 24 h time point. Total RNA was isolated using TRIzol (InVitrogen) and Alater (Ambion) reagents and cDNA synthesis, hybridization and microarray analysis using U133 GeneChips performed according to the Affymetrix manual. Gene expression changes were calculated as the ratio of EGR-1 or control virus (CV) infected cells to non-infected control cells.
Keywords: time-course

first: Jirí

last: Pomyje

first: Erhard

last: Hofer


title: FM95-14 Fetal Myoblast Differentiation Time Series

summary:
Fetal myoblasts represent an important source of myogenic stem cells. Analysis of undifferentiated myoblasts and comparison to their cognate differentiated progeny will allow the ascertainment of genes that are important for maintaining myogenic stem cells.
Fetal myoblasts (undifferentiated, time 0hr) will be compared to myoblasts cells allowed to differentiate by the removal of the SKBM-2 medium + growth factors and feeding with DMEM + 2.5% Horse serum. Time course : 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 3 days, 4 days, 7 days
Keywords: other

overall_design: this experiment include 10 samples and 60 replicates


title: Diurnal gene expression in rosette leaves of the phosphoglucomutase mutant (Col-0)

summary:
How do transcript levels of leaf-expressed genes change in a normal day-night cycle of the phosphoglucomutase (pgm) mutant? The interest is in genes that are regulated by the circadian clock and the diurnal component (i.e. light, metabolite changes). Plants were grown on soil in a 12/12 h light/dark rhythm at 20°C day and night. 5 weeks after germination the rosettes of the non-flowering plants were harvested, 15 plants per sample. Plants were harvested in series at 6 times every 4 hours, beginning with the end of the night (still in darkness).
Keywords: repeat

overall_design: A diurnal time series (8 times) was analyzed.


title: Effect of Retinoic Acid on Gene Expression in Human Conjunctival Epithelial Cell Line

first: Ilene

middle: K

last: Gipson

address: 20 Staniford ST

institute: Schepens Eye Research Institute

summary:
Purpose. How vitamin A contributes to the maintenance of the wet-surfaced phenotype at the ocular surface is not well understood. We sought to identify vitamin A responsive genes in ocular surface epithelia using gene microarray analysis of cultures of a human conjunctival epithelial cell line (HCjE) grown with all-trans-retinoic acid (RA). The analysis showed that the membrane-associated mucin MUC16 was induced by RA and that secretory phospholipase A2 Group IIA (sPLA2-IIA), the gene most upregulated by RA, was induced earlier. Since eicosanoids, metabolites of arachidonic acid, which is produced by sPLA2 catalysis of membrane phospholipids, have been demonstrated to affect mucin production, we sought to determine if the sPLA2 induction in HCjE cells was associated with RA induction of MUC16.
Methods. HCjE cells were cultured with or without RA for 3, 6, 24 and 48 hours. Complementary RNA prepared from RNA of the HCjE cells was hybridized to human gene chips (HG-U133A; Affymetrix) and analyzed using Rosetta Resolver software. Microarray data on mucin expression were validated by real-time PCR. To investigate whether sPLA2 is associated with RA-induced MUC16 upregulation, HCjE cells were incubated with RA and the broad spectrum PLA2 inhibitor, aristolochic acid (ArA) or the specific sPLA2-IIA inhibitor LY315920, followed by analysis of MUC16 mRNA and protein by real-time PCR and Western blot analysis.
Results. After RA addition, 28 transcripts were upregulated and 6 downregulated by over 2.0-fold (p < 0.01) at both 3 and 6 hours (early phase). Eighty gene transcripts were upregulated and 45 downregulated at both 24 and 48 hours (late phase). Group IIA sPLA2, significantly upregulated by 24 hours, and MUC16 were the most upregulated RNAs by RA at 48 hours. sPLA2 upregulation by RA was confirmed by Western blot analysis. When HCjE cells were incubated with RA plus ArA or specific inhibitor of sPLA2-IIA, LY315920, the RA-induced MUC16 mRNA was significantly reduced (p < 0.01).
Conclusion. The retinoic acid-associated upregulation of membrane-associated mucin MUC16 at late phase appears to be through sPLA2-IIA. Upregulation of this hydrophilic membrane-associated mucin may be one of the important mechanisms by which vitamin A facilitates maintenance of the wet-surfaced phenotype on the ocular surface.
Keywords: time course

overall_design: Time course of retinoic acid treatment of human conjunctival epithelial cells: 0 (control), 3, 6, 12, 24, and 48 hours. 2 samples per time point.

first: Yuichi

last: Hori

first: Sandra

last: Spurr-Michaud

first: Cindy Leigh

last: Russo

first: Pablo

last: Argueso


title: Global gene expression analysis of human glioma (Hs 683) cell lines exposed to candoxin

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

summary:
Total RNA was isolated from candoxin-treated (n = 3 flasks of each time points - 12hrs, 24hrs and 48hrs) and untreated control (n = 3) cells using RNeasy® mini kit.The preparation and processing of labeled, fragmented cRNA for oligonucleotide mcroarray hybridization has been performed according to the manufacturer’s protocols described in the technical manual (Affymetrix, Santa Clara, CA).
Keywords: time-course

first: Arjunan

last: Pachiappan

first: Manikandan

last: Jayapal

first: Ponnabmalam

last: Gopalakrishnakone

first: Jayapal

last: Manikandan


title: Auxin-mediated gene expression in WT, iaa17, axr3 and iaa5iaa6iaa19 mutants

city: Albany

first: Yoko

last: Okushima

address: 800 Buchanan St.

department: Plant and Microbial Biology

institute: Plant Gene Expression Center, U. C. Berkeley

summary:
Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5�M IAA) for 2 h. Columbia (WT), IAA17 loss of function mutant allele (iaa17-2), IAA17 gain of function mutant allele (axr3-1) and iaa5 iaa6 iaa19 triple loss of function mutant allele (i5i6i19) were used for this study. Each experimental condition has three true replicates for a total of 24 hybridizations. Data
Keywords: parallel sample

first: Athanasios

last: Theologis


title: Auxin-mediated gene expression

summary:
Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h.

This SuperSeries is composed of the SubSeries listed below.

first: Y

first: A


title: Glucocorticoid Induced Changes in Gene Expression in Human Lens Epithelial Cells

status: Public on Nov 14 2005

first: Vanita

last: Gupta

address: 185 South Orange Ave

department: Biochemistry & Molecular Biology

institute: UMDNJ

summary:
Prolonged use of glucocorticoids can lead to the formation of a cataract, however the mechanism is not known. We recently reported the presence of the functional glucocorticoid receptor in immortalized cultured mammalian lens epithelial cells (Gupta & Wagner, Invest Ophthalmol Vis Sci 2003), but the short term biological effect of glucocorticoid action in lens epithelial cells is not known. This study seeks to  examine glucocorticoid induced changes in global gene expression in LECs. RNA isolated from HLE B-3 cells, treated with Dex or Veh for 4 or 16 hours, was used to analyze global changes in gene expression by microarray hybridization. Microarray studies at 2 time periods demonstrate that glucocorticoids modulate gene expression in immortalized human LECs, reveal novel changes in gene expression, and confirms an endogenous genomic lens glucocorticoid response.
Keywords: treatment response

overall_design: HLE B-3 cells were treated with 1uM dexamethasone or vehicle for 4 or 16 hours in triplicate. Total RNA was converted to cRNA and hybridized to Affymetrix HUM_133A genechips. Images were acquired using the Affymetrix GeneArray scanner. Data was extracted using Affymetrix Microarray Suite 5.0.

first: Anthony

last: Galante

first: Patricia

last: Soteropoulos

first: B

last: Wagner


title: Ovarian Cancer Dataset

status: Public on Nov 07 2005

city: Durham

first: Joseph

middle: R.

last: Nevins

state: NC

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

summary:
Signatures of Oncogenic Pathway Deregulation in Human Cancers.
The ability to define cancer subtypes, recurrence of disease, and response to specific therapies using DNA microarray-based gene expression signatures has been demonstrated in multiple studies. Such data is also of substantial importance to the analysis of cellular signaling pathways central to the oncogenic process. With this focus, we have developed a series of gene expression signatures that reliably reflect the activation status of several oncogenic pathways. When evaluated in several large collections of human cancers, these gene expression signatures identify patterns of pathway deregulation in tumors, and clinically relevant associations with disease outcomes. Combining signature-based predictions across several pathways identifies coordinated patterns of pathway deregulation that distinguish between specific cancers and tumor sub-types. Clustering tumors based on pathway signatures further defines prognosis in respective patient subsets, demonstrating that patterns of oncogenic pathway deregulation underlie the development of the oncogenic phenotype and reflect the biology and outcome of specific cancers. Furthermore, predictions of pathway deregulation in cancer cell lines are shown to coincide with sensitivity to therapeutic agents that target components of the pathway, underscoring the potential for such pathway prediction to guide the use of targeted therapeutics.
Keywords: other

overall_design: RNA was extracted from frozen tissue of ovarian tumors for gene array analysis


title: Comparative microarray between normal and essential thrombocythemia platelets

status: Public on Nov 23 2005

city: Stony Brook

first: Wadie

last: Bahou

state: NY

department: Hematology

institute: Stony Brook University

summary:
Human blood platelets have important, regulatory functions in diverse hemostatic and pathological disorders, including vascular remodeling, inflammation, and wound repair. Microarray analysis was used to study the molecular basis of essential thrombocythemia, a myeloproliferative disorder with quantitative and qualitative platelet defects associated with cardiovascular and thrombohemorrhagic symptoms, not infrequently neurological. A platelet-expressed gene (HSD17B3) encoding type 3 17beta-hydroxysteroid dehydrogenase (previously characterized as a testis-specific enzyme catalyzing the final step in gonadal synthesis of testosterone) was selectively down-regulated in ET platelets, with reciprocal induction of the type 12 enzyme (HSD17B12). Functional 17beta-HSD3 activity corresponding to approximately 10% of that found in murine testis was demonstrated in normal platelets. The induction of HSD17B12 in ET platelets was unassociated with a concomitant increase in androgen biosynthesis, suggesting distinct functions and/or substrate specificities of the types 3 and 12 enzymes. Application of a molecular assay distinguished ET from normal platelets in 20 consecutive patients (p < 0.0001). These data provide the first evidence that distinct subtypes of steroidogenic 17beta-HSDs are functionally present in human blood platelets, and that the expression patterns of HSD17B3 and HSD17B12 are associated with an uncommon platelet disorder manifest by quantitative and qualitative platelet defects.
Keywords: other

first: Dmitri

middle: V

last: Gnatenko

first: Lisa

last: Cupit

first: Emily

last: Huang

first: Anilkumar

last: Dhundale

first: Peter

last: Perrotta

middle: F


title: Gene expression of pseudopalisading cells in human glioblastoma

status: Public on Nov 11 2005

city: Charlestown

first: Shumin

last: Dong

department: Pathology and Neurosurgical services

institute: Massachusetts General Hospital

summary:
By comparing to common tumor cells, genes were differencially expressed in pseudopalisading cells in human glioblastoma
Keywords: parallel sample

first: Catherine

last: Nutt

first: Rebecca

last: Betensky

first: Anat

middle: O

last: Stemmer-Rachamimov

first: Nicholas

last: Denko

first: Keith

last: Ligon

first: David

middle: H

last: Rowitch

last: Louis


title: Colon cancer progression-polysomal difference

status: Public on Nov 08 2005

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

institute: University of Trento

summary:
Two colon cancer cell lines are under study. SW480 and SW620. The first one is derived from primary cancer, SW620 are from lymphnode metastatic sites. they both comes from the sampe patient. Polisomal RNA fractions from the two isogenic colon cancer cells lines was purified by sucrose gradient and hybridized on affymetrix hgu133a chips. this study is complementary to the series  GSE1323 were total RNA was used instead. Comparison between the polysomal fraction chips and the total RNA chips is performed and the analysis proposed in a paper from the authors (at the moment in preparation).
Keywords: other

last: Quattrone

first: Raffaele

last: Fronza


title: Circadian gene expression in the primate adrenal gland

status: Public on Nov 02 2005

city: Beaverton

first: Dario

last: Lemos

state: OR

institute: Oregon National Primate Research Center

summary:
Circadian regulation of gene expression in central and peripheral tissue has been studied in mice. The biomedical implications of this findings led us to the development of a model in which to study the circadian mechanisms underlying primate physiology.
The objective of this experiment has been to identify genes that are circadianly regulated in the monkey (macaca mulatta) adrenal gland.
We analyzed the data using three filters: the first one for presence in at least three out of six time points (presence call=P, P value<0.05). The second one for high amplitude oscillations, using the coefficient of variation with a cutt of value of 0.2 (selecting probesets above that value). The last one for circadian expression, calculating the correlation of each curve to cosine curves of 24h periodicity and defined phases with increments of 10 minutes from 0 to 24h.
After two filtrations, the probesets obtained were identified using gene ID, PubMed accession number, and description, and clustered into well-known pathways.
Identification of clock genes was used as an internal control for the determination of phase distribution of the transcripts across the day.
Part of the array data has been validated by sq PCR, real time-PCR and immunohistochemistry, with succesful results.
This study provides evidences for circadian mechanisms of gene expression in primate tissue, in vivo.
Keywords = primate
Keywords = circadian rhythm
Keywords = adrenal gland
Keywords: time-course

first: Jodi

last: Downs

first: Henryk

last: Urbanski


title: Effect of myocardin mis-expression in human skeletal myoblasts

status: Public on Oct 27 2005

city: Dallas

first: G. C. Teg

last: Pipes

address: 6000 Harry Hines Blvd

department: MBO

institute: University of Texas Southwestern Medical Center at Dallas

summary:
transcriptional effects of mis-expression of full length (935) myocardin in growing human skeletal myoblasts
Keywords: mis-expression of transcriptional co-activator

overall_design: Compare transcriptional profiles of Ad-myocardin infected SKM5 cells with that of Ad-B-gal infected cells

first: GCTeg

first: Teresa

last: Gallardo

first: Chun-hong

last: Zhu

first: Woodring

last: Wright

first: Daniel

last: Garry

first: Eric

last: Olson


title: Gene expression profile of small airway epithelium of normal non-smokers and normal smokers

status: Public on Oct 30 2005

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary:
The earliest morphologic evidence of changes in the airways associated with chronic cigarette smoking is in the small airways. To help understand how smoking modifies small airway structure and function, we developed a strategy using fiberoptic bronchoscopy and brushing to sample the human small airway (10th-12th order) bronchial epithelium to assess gene expression (Affymetrix HG-U133A array) in phenotypically normal smokers (n=6, 24 ± 4 pack-yr) compared to matched non-smokers (n=5). Compared to samples from the large (2nd to 3rd order) bronchi, the small airway samples had a higher proportion of ciliated cells, but less basal, undifferentiated, and secretory cells. The small, but not large, airway samples included Clara cells, a cell found only in the small airway epithelium, and the small, but not the large, airway epithelium expressed genes for the surfactant apoproteins. Despite the fact that the smokers were phenotypically normal, analysis of the small airway epithelium of the smokers compared to the non-smokers demonstrated up- and -down-regulation of genes in multiple categories relevant to the pathogenesis of chronic obstructive lung disease (COPD), including genes coding for cytokines/innate immunity, apoptosis, pro-fibrosis, mucin, responses to oxidants and xenobiotics, antiproteases and general cellular processes. In the context that COPD starts in the small airways, these changes in gene expression in the small airway epithelium in phenotypically normal smokers are candidates for the development of therapeutic strategies to prevent the onset of COPD.
Keywords: response to cigarette smoking

overall_design:
6 smokers
5 non-smokers
no replicates

first: Ben

middle: G

last: Harvey

first: Adriana

last: Heguy

first: Ronald

last: Crystal


title: NT2 DMSO vs. RA

status: Public on Oct 18 2005

city: Urbana

first: Michael

last: Spinella

state: IL

address: 2001 South Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois

summary:
NT2 cells were treated with DMSO (control) or 10uM Retinoic Acid (RA).  Total RNA was isolated using TriReagent, and subsequent cleanup with RNeasy columns (Qiagen) according to the manufacturer's directions.  Hybridizations were performed according to Affymetrix guidelines using the Human HG-U133A chip containing 22,500 unique genetic elements.  Double-stranded cDNA was synthesized using Superscript II RT (Invitrogen).  In vitro transcription labeling was performed with biotin labeled nucleotides using the Bioarray High Yield RNA Labeling Kit (ENZO).  20 ul of labeled RNA per sample was added to the hybridization cocktail, with a total of 15 ug hybridized to the chip (16 hours, 45C).  RMA analysis was performed using Gene Traffic software (Iobion), where raw data for each hybridization was normalized, background corrected and filtered for signal intensity of 50 or greater in at least one comparison.
Keywords: other

first: Joanna

middle: S

last: Kerley-Hamilton


title: SLR/IAA14-dependent auxin induced lateral root initiation

status: Public on Nov 01 2005

city: Ghent

first: Steffen

last: Vanneste

address: Technologiepark 927

department: Plant Systems Biology

country: Belgium

institute: VIB-University of Ghent

summary:
Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation.
Keywords: time-course wild type vs mutant comparison

overall_design: Seedlings of both wild type (Col-0) and the lateral root defective mutant (slr-1) were germinated on MS medium supplemented with 10μM NPA (=auxin transport inhibitor). Three days after germination, such seedlings were transferred to MS supplemented with 10μM NAA for 0h, 2h and 6h respectively. The segment between root meristem and root-hypocotyl junction was harvested from about 1500 seedling per time point. All treatments were repeated biologically. 5.8 μg total RNA was used for the preparation of biotinylated cRNA. Labeled RNA was hybridised to ATH1 Affymetrix chips. The resulting data was MAS5.0 normalised.

first: Bert

last: De Rybel

first: Gerrit

last: Beemster

first: Karin

last: Ljung

first: Ive

last: De Smet

first: Gert

last: Van Isterdael

first: Mirande

last: Naudts

first: Ryusuke

last: Iida

first: Wilhelm

last: Gruissem

first: Masao

last: Tasaka

first: Dirk

last: Inz�

first: Hidehiro

last: Fukaki

first: Tom

last: Beeckman


title: Gene induction by low pH in oesophageal cells

status: Public on Oct 04 2005

city: Dublin 8

first: Shane

middle: P

last: Duggan

state: dublin

address: James st hospital,

department: Clinical Medicine

country: Ireland

institute: Institute of Molecular Medicine

summary:
Differential gene expression analysis of oesophageal cells stimulated with a low pH environment. Study designed to identify pathways involved in progression of gastro-oesophageal reflux disease through Barrett's oesophagus to adenocarcinoma. Identified many subsets of genes with involvement in pathogenesis.
Keywords = GORD
Keywords = Barrett's Oesophagus
Keywords = Oesopageal Adenocarcinoma.
Keywords: time-course

first: William

last: Gallagher

first: Edward

last: Fox

first: Mohammed

last: Abdel-latif

first: John

last: Reynolds

first: Dermot

last: Kelleher


title: Plasma Cells in Muscle in Inclusion Body Myositis and Polymyositis

status: Public on Oct 01 2005

city: Boston

first: Steven

middle: Alan

last: Greenberg

state: MA

address: 75 Francis Street

department: Neurology

institute: Brigham and Women's Hospital

summary:
Microarray data from muscle biopsy specimens from subjects with inclusion body myositis, polymyositis, and normals
Keywords: Research study

overall_design: Microarray experiments

first: Elizabeth

middle: M

last: Bradshaw

first: Jack

middle: L

last: Pinkus

first: Geraldine

first: Travis

last: Burleson

first: Brice

last: Due

first: Lisa

last: Bregoli

first: Kevin

last: O'Connor

first: Anthony

last: Amato


title: Auxin mediated gene expression in WT and arf2-6 mutant

status: Public on Oct 19 2005

first: Yoko

last: Okushima

state: CA

summary:
Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Columbia (WT) and Auxin response factor 2 (ARF2) T-DNA insertion mutant (arf2-6 ) were used for this study. Each experimental condition has three true replicates for a total of 12 hybridizations.

Data analysis:
Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The data files containing the probe level intensities (cell files) were used for background correction and normalization using the log2 scale robust multi-array analysis (RMA) procedure (Irizarry et al., 2003). The “R” environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2 converted expression intensity data within Microsoft Excel 98. Based on preliminary analysis, a hybridization signal less than 5.64385619 (= log2 50) was considered as background; all signals less than 5.64385619 were converted to 5.64385619 prior to further analysis.

Keywords = Auxin
Keywords = Auxin response factor
Keywords: other

first: Athanasios

last: Theologis


title: Target genes of the transcription factors HNF1beta and HNF1alpha in the human embryonic kidney cell line HEK293

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
Hepatocyte nuclear factor 1beta (HNF1beta, TCF2) is a tissue-specific transcription factor whose mutation in humans leads to renal cysts, genital malformations, pancreas atrophy and maturity onset diabetes of the young (MODY5). Furthermore, HNF1beta overexpression has been observed in clear cell cancer of the ovary. To identify potential HNF1beta target genes whose activity may be deregulated in human patients we established a human embryonic kidney cell line (HEK293) expressing HNF1beta conditionally. Using Flp recombinase we introduced wildtype or mutated HNF1beta at a defined chromosomal position allowing a most reproducible induction of the HNF1beta derivatives upon tetracycline addition. By oligonucleotide microarrays we identified 25 HNF1beta regulated genes. By an identical approach we identified that the closely related transcription factor HNF1alpha (TCF1) affects only nine genes in HEK293 cells and thus is a less efficient factor in these kidney cells. The HNF1beta target genes dipeptidyl peptidase 4 (DPP4), angiotensin converting enzyme 2 (ACE2) and osteopontin (SPP1) are most likely direct target genes, as they contain functional HNF1 binding sites in their promoter region. Since nine of the potential HNF1beta target genes are deregulated in clear cell carcinoma of the ovary, we propose that HNF1beta overexpression in the ovarian cancer participates in the altered expression pattern
Keywords: cnditional expression

overall_design: Two different clones (biological replicates) were analyzed per transcription factor or mutant. By tetracyclin addition the expression of the transcription factors was induced for 24 hours prior to RNA extraction and array analysis.

first: Sabine

last: Senkel

first: Belen

last: Lucas

first: Gerhart

middle: U

last: Ryffel


title: Auxin mediated gene expression in WT, arf7, arf19 and arf7 arf19 mutants

summary:
RNA samples were extracted from liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h.

Lines used for this study:
Columbia wild-type
nph4-1(arf7) single mutant
arf19-1 single mutant
nph4-1 arf19-1 double mutant

Treatment:
Control (EtOH)
Auxin treated (5µM IAA)
Keywords = Auxin
Keywords = Auxin response factor
Keywords: parallel sample


title: Comparison of PBMCs in Inflammatory Bowel Disease

status: Public on Sep 26 2005

city: Collegeville

first: Michael

middle: E.

last: Burczynski

state: PA

address: 500 Arcola Road

department: Pharmacogenomic Biomarkers

institute: Wyeth

summary:
Comparison of PBMC transcriptional profiles in healthy subjects, patients with Crohn's Disease, and patients with Ulcerative Colitis
Keywords: Disease state

first: Ron

last: Peterson

first: Natalie

middle: C

last: Twine

first: Krystyna

middle: A

last: Zuberek

first: Brendan

middle: J

last: Brodeur

first: Lori

last: Casciotti

first: Vasu

last: Maganti

first: Padma

last: Reddy

first: Andrew

last: Strahs

first: Fred

last: Immermann

first: Walter

last: Spinelli

first: Ulrich

last: Schwertschlag

first: Anna

last: Slager

first: Monette

last: Cotreau

last: Dorner


title: Prostate cancer - comparison of androgen-dependent and -independent microdissected primary tumor

city: Bethesda

first: Carolyn

middle: J. M.

last: Best

address: 37 Convent Drive

institute: NCI, NIH

summary:
Affymetrix U133A comparison of two groups (10 samples each): untreated (androgen-dependent) primary prostate cancer (Gleasons 5-9) and androgen-independent primary prostate cancer.  All samples were microdissected for tumor cells only.
Keywords = advanced prostate cancer
Keywords = androgen-independence
Keywords = laser capture microdissection
Keywords = RNA amplification
Keywords: other

first: CAROLYN


title: Laparoscopic Donor Nephrectomy Gene Expression Profiling Compared to Healthy Control Kidneys

status: Public on Sep 14 2005

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

summary:
We compared gene expression profiles from six donor kidneys prior to surgical manipulation to six kidneys removed after laparoscopic donor nephrectomy (LDN) and several hours of CO2 pneumoperitoneum.  Biopsies were obtained from renal cortex and hybridized to Affymetrix HG-U133A GeneChips.  For control kidneys we identified 1380 genes present on all 6 samples that had a signal intensity greater than 1000.  Functional classification of these revealed genes for cellular signaling (201; 15%), regulation of transcription (156; 11%), cellular transport (144; 10%) and cellular metabolism (111; 8%).  A class comparison between the controls and LDN kidneys yielded 865 differentially expressed genes.  Functional classification of the 502 genes differentially up-regulated in LDN kidneys identified associations with apoptosis, cell adhesion, cell signaling, regulation of cell growth/proliferation, immune/inflammation, ischemia/stress response and proteolysis/peptidolysis. These data demonstrate an altered renal transcriptome induced by several hours of CO2 pneumoperitoneum and laparoscopic surgery characterized by up-regulation of ischemia and injury associated genes.
Keywords: Comparative Expression

overall_design:
Twelve healthy adult kidney donors signed a consent form, and were approved for donation according to the usual evaluation and practice of the Cleveland Clinic Renal Transplant Program.  To avoid potentially significant differences in gene expression based on race and/or ethnicity, only white recipients were selected.  The patients were divided into two groups; six controls from open donor nephrectomy and six from LDN.  Demographic information included age, gender, race, HLA type, and renal function data including serum creatinine (mg/dL), GFR measured by iothalamate clearance (cc/min.), and urine protein excretion (mg/24 hr).  Each patient was given general anesthesia and had a diuresis induced with saline, mannitol, and furosemide.  The controls had an extraperitoneal flank incision made, and with only minimal manipulation of the kidney two subcapsular core renal biopsies were obtained using a 15-gauge spring-loaded needle.  For the LDN cases two core renal biopsies were obtained using the same needles after the kidneys underwent 2 to 3 hours of C02 pneumoperitoneum. Study biopsies went immediately into 1.5 mL of RNALater (Ambion, Austin, TX), and were stored at –80 0C until they were processed.
     Biopsy specimens were homogenized in 1 mL of Trizol (Invitrogen, Carlsbad, CA); total RNA was purified using an RNeasy column (Qiagen, Valencia, CA); and quality confirmed with an Agilent 2100 BioAnalyzer (Palo Alto, CA).  Standard Affymetrix GeneChip (Santa Clara, CA) protocols were used, and labelled samples were hybridized to HG-U133A GeneChip arrays containing 22,283 probe sets representing over 14,500 human genes.  Data was analyzed using Signal intensities generated using GeneChip Operating System version 1.0 and were subsequently analysed  by Robust Multichip Average Express (RMA Express) using all Affymetrix .CEL files as a training set.  BRB ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html) was used to perform class comparisons (significance level of p < 0.005), and create dendrograms.  We used NetAffyx (www.affymetrix.com) to annotate the differentially expressed genes according to biological function based on the Gene Ontology database.  A Heatmap was created using Cluster and TreeView software

first: Stuart

last: Flechner

first: Jihad

last: Kaouk

first: Charles

last: Modlin

first: David

last: Goldfarb

first: Daniel

last: Cook

first: Steven

middle: R

last: Head

last: Salomon


title: Gene induction during differentiation of human pulmonary type II cells in vitro

status: Public on Sep 21 2005

city: San Francisco

first: Philip

last: Ballard

address: 513 Parnassus St

department: Neonatology

institute: UCSF

summary:
Studies of human fetal lung in explant culture and in isolated epithelial cells have demonstrated that both glucocorticoids and cyclic AMP promote differentiated alveolar type II cell phenotype as assessed by ultrastructural morphology and surfactant production.  This project profiles changes in gene expression associated with hormone induced differentiation.   Undifferentiated human fetal lung (13-20 wk) epithelial cells were cultured in serum-free medium (control) or with dexamethasone/8-Bromo cyclic AMP/isobutylmethylxanthine (DCI) to promote type II cell differentiation.  RNA from five sets of experiments (10 samples) was evaluated using the U133A Affymetrix GeneChip set.
Keywords: Hormone treatment

overall_design: Cells were isolated from 13 individual lungs and the cells from each were cultured in the absence (control) and presence of DCI dexamethasone (10 nM)/8-Br-cyclic AMP (0.1 mM)/isobutylxanthine for 72 h.  RNA was isolated from the control and treated cells of each prep.  For the 5 sets of microarray experiments (10 total chips, 2 for each control and treated pair), RNA from 2 of the cell preps was analysed as individual microarray comparisons.  RNA from 11 cell preps was pooled for the other 3 experiments (4, 4, and 3 cell preps) to provide control and DCI-treated RNA pools.

first: Kelly

last: Wade

first: Susan

last: Guttentag

first: Linda

middle: W

last: Gonzales

first: Kathryn

last: Maschhoff

first: John

first: Venkaturi

last: Kolla


title: Classification of carcinoma in situ lesions in human bladder cancer

status: Public on Sep 19 2005

city: Aarhus N

first: Lars

last: Dyrskjot

address: Brendstrupgaardsvej

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University Hospital, Skejby

summary:
The presence of carcinoma in situ (CIS) lesions in the urinary bladder is associated with a high risk of disease progression to a muscle invasive stage. In this study, we used microarray expression profiling to examine the gene expression patterns in superficial transitional cell carcinoma (sTCC) with surrounding CIS (13 patients), without surrounding CIS lesions (15 patients), and in muscle invasive carcinomas (mTCC; 13 patients). Hierarchical cluster analysis separated the sTCC samples according to the presence or absence of CIS in the surrounding urothelium. We identified a few gene clusters that contained genes with similar expression levels in transitional cell carcinoma (TCC) with surrounding CIS and invasive TCC. However, no close relationship between TCC with adjacent CIS and invasive TCC was observed using hierarchical cluster analysis. Expression profiling of a series of biopsies from normal urothelium and urothelium with CIS lesions from the same urinary bladder revealed that the gene expression found in sTCC with surrounding CIS is found also in CIS biopsies as well as in histologically normal samples adjacent to the CIS lesions. Furthermore, we also identified similar gene expression changes in mTCC samples. We used a supervised learning approach to build a 16-gene molecular CIS classifier. The classifier was able to classify sTCC samples according to the presence or absence of surrounding CIS with a high accuracy. This study demonstrates that a CIS gene expression signature is present not only in CIS biopsies but also in sTCC, mTCC, and, remarkably, in histologically normal urothelium from bladders with CIS. Identification of this expression signature could provide guidance for the selection of therapy and follow-up regimen in patients with early stage bladder cancer.
Keywords: Tissue group comparisons (+-CIS)

overall_design: See publication

last: Dyrskjøt

first: Mogens

last: Kruhøffer

first: Thomas

last: Thykjaer

first: Niels

last: Marcussen

first: Jens

last: Jensen

first: Klaus

last: Møller

first: Torben

middle: F

last: Ørntoft


title: Gene expression profiling of CD34+ hematopoietic cells expanded in a collagen I matrix

city: Dresden

first: Martin

last: Bornhaeuser

address: Fetscherstrasse 74

department: Med. Klinik und Poliklinik

institute: Universitätsklinikum Carl Gustav Carus

summary:
CD34+ hematopoietic stem/progenitor cells (HSC) reside in the bone marrow in close vicinity to the endosteal bone surface, surrounded by osteoblasts, stromal cells and various extracellular matrix molecules. We utilized a bioartificial matrix containing fibrillar collagen I, the major matrix component of bone, as scaffold for ex vivo expansion of HSCs. CD34+ HSCs were isolated from umbilical cord blood and cultivated within reconstituted collagen I fibrils in presence of FLT3-ligand, SCF and IL-3. After seven days of culture cell number, colony-forming units and gene expression profile of the cultured cells were assessed. Although the total expansion factor of CD34+ cells was slightly lower when cells were cultivated in the collagen I gel, the frequency of colony-forming units (CFU-C) increased compared to control suspension cultures. Gene expression analysis with microarray chip technology revealed the upregulation of more than 50 genes in presence of collagen I. Among them, genes for several growth factors, cytokines and chemokines (e.g. interleukin 8, MIP1-α) could be confirmed by quantitative PCR. Furthermore, increased expression of the negative cell-cycle regulator BTG2/TIS21 and an inhibitor of MAP kinase pathway, DUSP2, underline the regulatory role of the extracellular matrix. Together, these data show that the expansion of CD34+ cord blood cells in a culture system containing a three-dimensional collagen I matrix induces a qualitative change in the gene expression profile of cultivated HSCs.
Keywords: hematopoietic stem/progenitor cells, collagen I, gene expression

first: Joachim

last: Oswald

first: Christine

last: Steudel

first: Katrin

last: Salchert

first: Birgitte

last: Joergensen

first: Christian

last: Thiede

first: Gerhard

last: Ehninger

last: Bornhäuser


title: Human blood expression for Huntington's disease versus control

status: Public on Sep 13 2005

first: Dimitri

last: Krainc

address: Building 114, 16th St.

institute: MassGeneral Institute for Neurodegeneration

summary:
Affymetrix U133A expression levels for 12 symptomatic and 5 presymptomatic Huntington's disease patients versus 14 healthy controls.
Keywords: other


title: CCSK

status: Public on Sep 22 2005

city: Chicago

first: Elizabeth

middle: Jones

last: Perlman

address: 2300 Children's Plaza, Box 17

department: Pathology

institute: Children's Memorial Hospital

summary:
Clear cell sarcoma of the kidney (CCSK), the second most common renal tumor in children, poses significant diagnostic challenges.  No diagnostic positive markers are available, and the pathogenesis of CCSK remains an enigma.  To address these challenges, the gene expression patterns of fourteen CCSKs were compared to fifteen Wilms tumors (WT) and three fetal kidney samples using oligonucleotide arrays.
Keywords: other

first: Colleen

last: Tsui

first: Donna

last: Kersey

first: Chiang-Ching

last: Huang

first: Chiler

last: Hasan

first: Yong

last: Zeng

first: David

last: Walterhouse


title: Molecular classification of multiple myeloma

status: Public on Sep 01 2005

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

summary:
PURPOSE. The deregulation of CCND1, CCND2 and CCND3 genes represents a common event in multiple myeloma (MM). The recently proposed TC classification grouped MM patients into five classes on the basis of their cyclins D expression profiles and the presence of the main translocations involving the immunoglobulin heavy-chain locus (IGH) at 14q32. In this study, we provide a molecular characterization of the identified TC groups. MATERIALS AND METHODS. The gene expression profiles of purified plasma cells from 50 MM cases were used to stratify the samples into the five TC classes and identify their transcriptional fingerprints. The cyclin D expression data were validated by means of real-time quantitative PCR analysis; fluorescence in-situ hybridization was used to investigate the cyclin D loci arrangements, and to detect the main IGH translocations and the chromosome 13q deletion. RESULTS. Class-prediction analysis identified 112 probe sets as characterizing the TC1, TC2, TC4 and TC5 groups, whereas the TC3 samples showed heterogeneous phenotypes and no marker genes. The TC2 group, which showed extra copies of the CCND1 locus and no IGH translocations or the chromosome 13q deletion, was characterized by the overexpression of genes involved in protein biosynthesis at translational level. A meta-analysis of published datasets validated the identified gene expression signatures. CONCLUSIONS. Our data contribute to the understanding of the molecular and biological features of distinct MM subtypes. The identification of a distinctive gene expression pattern in TC2 patients may improve risk stratification and indicate novel therapeutic targets.
Keywords: other

overall_design: This series of microarray experiments contains the gene expression profiles of purified plasma cells (PCs) obtained from 50 newly diagnosed multiple myeloma (MM). PCs were purified from bone marrow specimens, after red blood cell lysis with 0.86% ammonium chloride, using CD138 immunomagnetic microbeads. The purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases. 5 micrograms of total RNA was processed and hybridized to the Affymetrix HG-U133A chip following the manufacturer's instructions.

first: Silvio

last: Bicciato

first: Michela

last: Mattioli

first: Sonia

last: Fabris

first: Daniela

last: Intini

first: Donata

last: Verdelli

last: Baldini

first: Fortunato

last: Morabito

first: Vincenzo

last: Callea

first: Luigia

last: Lombardi

first: Antonino

last: Neri


title: Embryonic Skeletal Myoblasts

city: Ottawa

first: Theodore

last: Perkins

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

summary:
Skeletal muscle cells (myoblasts - human fetal cells from 17 week old embryo)
Keywords: other

overall_design: this experiment include 1 samples and 6 replicates


title: Squamous Lung Cancer, Paired Samples

status: Public on Sep 09 2005

city: Davis

first: Shinichiro

last: Wachi

address: 1 Shields Avenue

department: Internal Medicine

institute: University of California, Davis

summary:
Gene expression profile of squamous lung cancer cells are used to identify genes that are differentially regulated.
Keywords: Cell type comparison

overall_design: Each pair of samples represent a single patient with squamous lung cancer.  One is derived from the cancer cells, and the other is from the normal cells.  Five patients, with two arrays for each patients.

first: Ken

last: Yoneda

first: Reen

last: Wu


title: Vastus lateralis biopsies from healthy trained and sedentary males

city: Irvine

first: Shlomit

last: Radom-Aizik

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

summary:
Needle biopsies were obtained from the vastus lateralis muscle of 6 healthy, sedentary, 67±2.5 year-old males before and after 3 months of training.
Keywords: other

first: Shlomo

last: Hayek

first: Iris

last: Shahar

first: Naftali

last: Kaminski

first: Issahar

last: Ben-Dov


title: C2C12 myoblast vs myotube

status: Public on Sep 07 2005

summary:
Comparison of undifferentiated C2C12 myoblast to 4 day differentiated myotubes.
Keywords: other

overall_design: this experiment include 2 samples and 6 replicates


title: Colon cancer profiling

status: Public on Aug 26 2005

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

institute: Jichi Medical University

type:
Expression profiling by array
Methylation profiling by array

summary:
Expression profile was obtained for GeneChip probe sets among colon cancer specimens with or without the methylation of MLH1 promoter.
Keywords: other


title: Profile of cultured skin substitute relative to constituent keratinocytes and fibroblasts and in relation to normal skin

status: Public on Aug 29 2005

city: Cincinnati

first: Bruce

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

summary:
Cultured skin substitutes, prepared using keratinocytes, fibroblasts and biopolymers, can facilitate closure of massive burn wounds by increasing the availability of autologous tissue for grafting.  However, because they contain only two cell types, skin substitutes cannot replace all of the functions of native human skin. To better understand the physiological and molecular differences between cultured skin substitutes and native skin, we undertook a comprehensive analysis of gene expression in native skin, cultured keratinocytes, cultured fibroblasts, and skin substitutes using Affymetrix gene chip microarrays.

Goals:  Our analysis focused on identifying gene signatures that were highly characteristic of each cell and tissue type, and those that are regulated by the formation of cultured skin substitute from the individual components.

Normalization: We used a normalization and referencing strategy that consisted of BioConductor/RMA Express RMA processing of the entire series of cel files followed by a per gene normalization in which the median value of expression for each gene was derived from the cultured samples only, and this was used as a reference for all samples including the cultured skin substitute.  This approach allowed for the identification of genes that were higher and lower-expressed in the cultured skin relative to the individual cell types that were also expressed strongly or weakly in normal skin relative to the median value established by the three cell types.

Results Summary:We identified six major clusters of coordinately regulated genes that were the most differentially expressed between groups.  These clusters correspond to biomarker pools representing expression signatures for native skin, fibroblasts, keratinocytes, and cultured skin.  The expression analysis revealed that entire clusters of genes were  either up-regulated or down-regulated upon combination of fibroblasts and keratinocytes in cultured skin grafts.  Further, several categories of genes were overexpressed in cultured skin substitutes compared with native skin, including genes associated with hyperproliferative skin or activated keratinocytes. The observed pattern of expression indicates that cultured skin substitutes in vitro, which display a well-differentiated epidermal layer, exhibit skin-like differentiation relative to gene expression patterns in the individual cells.  This consists of both the activation of normal skin signature genes and the suppression of keratinocyte and fibroblast signatures.  There is also a signature consistent with a hyperproliferative phenotype similar to wounded native skin.
Keywords: Cell interaction and co-culture response expression profile

overall_design: The sample series consists of native human skin (NHS) samples isolated from female donors undergoing reduction mammoplasty (breast skin) or abdominoplasty (abdomen skin).  Skin samples from donors that were used to establish cultures of fibroblasts (CF) and keratinocytes (CK) were assigned donor numbers in the order they were processed in the laboratory, for example: 633, 634, etc.  An additional human skin sample (C-1-Ref) was used only to make RNA as a standard control, and was therefore not assigned a donor number.  Cultured skin substitutes (CSS) were prepared using isogenic CF and CK from each donor, and were cultured for 2 weeks in vitro to permit development of a stratified and cornified epidermal layer (confirmed by histology).  For microarray analysis, RNA was isolated from intact NHS, from CF and CK in monolayer cultures, and from CSS.  Samples are labeled indicating the sample type and donor number; for example, "CF633" represents cultured fibroblasts from donor 633.  To control for variation between individuals, four donors (= biological replicates) were used for each sample type: NHS, CF, CK, and CSS. Efforts were made to have complete sets of 4 samples from each donor, but intact RNA was not obtainable from 2 of the NHS samples (donors 634 and 651); these were replaced with NHS RNA from similar donors (donors C-1-Ref and 636).  To check the fidelity of the microarray analysis, 2 of the RNA samples (CK639 and CSS651) were analyzed in duplicate (= technical replicates)


title: Influence of cyclical mechanical strain on global gene expression in human lamina cribrosa cells in vitro

status: Public on Aug 21 2005

city: Dublin

first: Ruaidhri

middle: Patrick

last: Kirwan

state: Leinster

address: Belfield

department: Conway Institute of Biomolecular and Biomedical Research & School of Medicine and Medical Science

institute: University College Dublin

summary:
The mechanical effect of raised intraocular pressure is a recognised stimulus for optic neuropathy in primary open angle glaucoma (POAG). Characteristic extra-cellular matrix (ECM) remodelling accompanies axonal damage in the lamina cribrosa (LC) of the optic nerve head in POAG. Glial cells in the lamina cribrosa may play a role in this process but the precise cellular responses to mechanical forces in this region are unknown. The authors examined global gene expression profiles in lamina cribrosa cells exposed to cyclical mechanical stretch, with an emphasis on ECM genes.
Keywords: microarray, ECM, glaucoma, mechanical stretch, lamina cribrosa

overall_design:
n=3 stretch and static control experiments.
RNA pooled from each experiment and hybridised to individual experiment and control arrays.

first: Cecilia

middle: H

last: Fenerty

first: John

last: Crean'

first: Robert

last: Wordinger

first: Abbot

last: Clark

first: Colm

last: O'Brien


title: Novel genes associated with malignant melanoma but not benign melanocytic lesions

status: Public on Aug 25 2005

city: San Diego

first: Tim

last: Jatkoe

institute: Veridex

summary:
A number of melanoma specific genes were identified to differentiate clinical relevant tissue samples containing benign from malignant melanocytes.
Keywords: disease state analysis

overall_design: 7 normal skin, 18 nevi and 45 melanoma samples