title: KLF4 Time Course

status: Public on Aug 13 2005

city: Atlanta

first: Vincent

middle: W.

last: Yang

state: GA

address: 201 Whitehead Research Building 615 Michael Street

department: Digestive Diseases Division

institute: Emory University

summary:
 A stably transfected inducible system for KLF4 was established in RKO cells as previously described (Chen et al., 2001; Chen et al., 2003).  This cell line, called EcR-RKO/KLF4, contains stably transfected receptors for the insect hormone, ecdysone (EcR), and a full-length mouse KLF4 cDNA driven by a promoter that responds to ecdysone and its analogue, ponasterone A.  Cells were treated with 5 µM ponasterone A (PA), for various time durations.  To control for the experiment, the vehicle, ethanol, was added for the same periods of time.
Keywords: Time course

overall_design: RNA was extracted from EcR-RKO/KLF4 cells treated with ponasterone A or vehicle control for 0, 1, 2, 4, 6, 8, 12, and 24 hr, using Trizol (Invitrogen).   RNA from each time point labeled with biotin using the Enzo BioArrayTM HighYieldTM RNA Transcript Labeling kit (T7), and hybridized to Affymetrix commercial HU133A chips. Hybridization was done using the GeneChip® Fluidics Station according the Affymetrix single stain protocol. The data were scanned and analyzed by an Affymetrix GeneChip® Fluidics Station 400 scanner and Affymetrix Microarray Suite 2.

first: Erika

last: Whitney

first: Xinming

last: Chen


title: TGF-beta regulated gene transcription and protein expression in human GFAP-negative lamina cribrosa cells

status: Public on Aug 05 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

country: Ireland

institute: University College Dublin

summary:
Primary open angle glaucoma (POAG) is a progressive optic neuropathy, which is a major cause of worldwide visual impairment and blindness. Pathological hallmarks of the glaucomatous optic nerve head include retinal ganglion cell axon loss and extracellular matrix (ECM) remodeling of the lamina cribrosa layer. TGF-beta is an important pro-fibrotic modulator of ECM metabolism, whose levels are elevated in human POAG lamina cribrosa tissue compared with non-glaucomatous controls.  We treated human lamina cribrosa (LC) cells with TGF-beta1 (10ng/ml) for 24 hours in order to examine differential gene expression patterns in repsonse to this cytokine.  In particular we focused on ECM and fibrotic genes.  We found that TGF-beta1 induces expression and release of ECM components in LC cells, which may be important in regulating matrix remodeling in the lamina cribrosa. In disease states such as POAG, the LC cell may represent an important pro-fibrotic cell type and an attractive target for novel therapeutic strategies.
Keywords: other

first: Ruaidhrí

middle: P

first: Martin

middle: O

last: Leonard

first: Madeline

last: Murphy

first: Abbot

middle: F

last: Clark

first: Colm

middle: J

last: O'Brien


title: Expression Profiling of pheochromocytomas of various genetic origins

status: Public on Aug 12 2005

city: San Antonio

first: Patricia

middle: L.

last: Dahia

state: TX

address: 7703 Floyd Curl Dr MC7880

department: Medicine/Cel&Struct Biology

country: USA

institute: UTHSCSA

summary:
Pheochromocytomas are neural crest-derived tumors that arise from inherited or sporadic mutations in at least six independent genes: RET, VHL, NF1, and subunits B, C and D of succinate dehydrogenase (SDH). The proteins encoded by these multiple genes regulate distinct functions. To identify molecular interactions between the distinct pathways we performed expression profiling of a large cohort of pheochromocytomas. We show here a functional link between tumors  with VHL mutations and those with disruption of the genes encoding for succinate  dehydrogenase (SDH) subunits B (SDHB) and D (SDHD). A transcription profile of reduced oxidoreductase is detected in all three of these tumor types, together with an  angiogenesis/hypoxia profile typical of VHL dysfunction. The oxidoreductase defect, not  previously detected in VHL-null tumors, is explained by suppression of the SDHB protein, a  component of mitochondrial complex II. The decrease in SDHB is also noted in tumors with  SDHD mutations. Gain-of-function and loss-of-function analyses show that the link between  hypoxia signals (via VHL) and mitochondrial signals (via SDH) is mediated by HIF1?. These  findings explain the shared features of pheochromocytomas with VHL and SDH mutations and  suggest an additional mechanism for increased HIF1? activity in tumors.
Keywords: disease state analysis: Primary sporadic and hereditary pheochromocytomas and paragangliomas

overall_design: We performed comparative analysis of expression profiling of 76 Pheochromocytomas and paragangliomas with a variety of mutations representatives of distinct pheochromocytoma susceptibility syndromes,sporadic tumors and familial tumors without an identifiable mutation. Six tumors were processed in duplicate.

middle: L

first: Ken

middle: N

last: Ross

first: Matthew

middle: E

last: Wright

first: César

middle: Y

last: Hayashida

first: Sandro

last: Santagata

first: Marta

last: Barontini

first: Andrew

last: Kung

first: Gabriela

last: Sanso

first: James

last: Powers

first: Arthur

middle: S

last: Tischler

first: Richard

last: Hodin

first: Shannon

last: Heitritter

first: Francis

last: Moore Jr.

first: Robert

last: Dluhy

first: JulieAnn

last: Sosa

first: I.

last: Tolgay Ocal

first: Diana

last: Benn

first: Deborah

last: Marsh

first: Bruce

middle: G

last: Robinson

first: Katherine

last: Schneider

first: Judy

last: Garber

first: Seth

middle: M

last: Arum

first: Márta

last: Korbonits

first: Ashley

last: Grossman

first: Pascal

last: Pigny

first: Sérgio

last: Toledo

first: Vania

last: Nosé

first: Cheng

last: Li

first: Charles

middle: D

last: Stiles


title: Arabidopsis Pollination Study

status: Public on Aug 06 2005

city: Chicago

first: Daphne

last: Preuss

state: IL

address: 1103 E. 57th Street

department: Molecular Genetics and Cell Biology

institute: The University of Chicago

summary:
Microarray experiments were used to build a profile of candidate stigma genes that facilitate early pollination events.  Of over 24,000 genes probed, we identified 11,403 genes expressed in stigma tissue, 317 of these that are stigma specific (not expressed in control tissues).
Keywords: Comparative hybridization

overall_design: Expression profiles of stigma, ovary and seedling tissues were studied and contrasted. Four samples each of seedling and ovary were used; and three stigma samples.

last: Swanson

first: Terry

last: Clark


title: ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome

status: Public on Oct 01 2005

city: Riverside

first: Jian-Kang

last: Zhu

state: CA

address: 2150 Batchelor Hall

department: Botany and Plant Sciences

institute: University of California

summary:
To understand the gene network that controls plant tolerance to cold stress, we carried out a near full genome transcript expression profiling in Arabidopsis using Affymetrix GeneChips that contain approximately 24,000 genes.  For microarray analysis, Arabidopsis seedlings were cold treated at 0 C for 0 h, 3 h, 6 h, and 24 h.  A total of 939 genes were statistically determined to be cold-regulated with 655 being up-regulated and 284 down-regulated.  A large number of the early cold-responsive genes encode transcription factors that likely control late-responsive genes, which implies a multitude of transcriptional cascades.  In addition, many genes involved in post-transcriptional and chromatin level regulation were also cold regulated suggesting their involvement in cold responsive gene regulation.  A number of genes important for the biosynthesis or signaling of plant hormones, such as abscisic acid, gibberellic acid and auxin, are regulated by cold stress, which is of potential importance in coordinating cold tolerance with growth and development.  We compared the cold-responsive transcriptomes of wild type and ice1, a mutant defective in an upstream transcription factor required for chilling and freezing tolerance.  The transcript levels of many cold-responsive genes were altered in the ice1 mutant not only during cold stress conditions, but also before cold treatments.  Our study provides a global picture of the Arabidopsis cold-responsive transcriptome and its control by ICE1, and thus will be valuable for understanding gene regulation under cold stress and the molecular mechanisms of cold tolerance.
Keywords: Cold Stress response

overall_design: Two replicates for each time point of 0 hours, 3 hours, 6 hours and 24 hours of cold treatment for the wildtype (control) and ice1 (mutant).

first: Byeong-ha

last: Lee

first: David

last: Henderson


title: Two week Storage and Rehydration of HEK 293 Cells at Ambient Temperature

status: Public on Aug 01 2005

city: Blacksburg

first: Richard

middle: F.

last: Helm

state: VA

address: West Campus Drive

department: Biochemistry, Fralin Biotechnology Center

institute: Virginia Polytechnic Institute and State University

summary:
This series represents the rehydration series of the human 293h media depleted storage on agarose / rehydration condition course analysis. Samples include Control Monolayer,  0 hr desiccation, 0 hr rehydration, 6 hr rehydration, 24 hr rehydration, and 72 hr rehydration.
Keywords = 293h cells
Keywords = desiccation
Keywords = rehydration
Keywords = spheroid
Keywords = stabilization
Keywords = ambient temperature
Keywords: other

first: Graham

last: Jack

first: M

middle: C

last: Cabrera

first: James

last: Garst

first: Andrew

middle: I

last: Brooks

first: Stephen

last: Slaughter

first: Malcolm

middle: A

last: Potts


title: Soy peptide up-regulates tumor suppressor and other chemopreventive genes in prostate epithelial cells

status: Public on Jul 26 2005

city: Davis

first: Kevin

last: Dawson

address: 2795 Second Street, Suite 400

department: CCM

institute: UC Davis

summary:
Numerous studies have identified certain components of soybean as having anticancer properties. Lunasin, a unique 43-amino acid soybean peptide, has been shown to suppress carcinogenesis in mammalian cells and mouse models. It has been hypothesized that lunasin modulates changes in chromatin organization by modifying histone tails, thereby, resulting in the expression of chemopreventive genes. In this report, microarray analysis was used to reveal a novel property of lunasin – its ability to up-regulate tumor suppressor and other chemopreventive genes in prostate epithelial cells. The effects of exogenous lunasin on the comprehensive gene expression profiles revealed that a total of 123 genes had a greater than twofold change in expression in the lunasin-treated cells as compared to the mock-treated cells. Of these genes, 121 genes were up-regulated in normal RWPE-1 cells and only two genes were up-regulated in malignant RWPE-2 epithelial cells. The genes up-regulated in RWPE-1 cells include those involved in tumor suppression, apoptosis, and the control of cell division. The results shed new light on lunasin’s previously observed chemopreventive properties. We propose that lunasin prevents cancer in vitro and in small animal models by up-regulating the expression of genes that prevent the onset of the disease.
Keywords: treatment with lunasin soy peptide

overall_design: Four microarrays were analyzed. Two samples are RWPE1 human non-tumorigenic prostate epithelial cells and the other two samples are the genetically identical RWPE2 prostate epithelial cancer cells. In each cell line, one of the samples was treated with lunasin at 2 microM for 24 hr.

first: Mark

last: Magbanua

first: Liping

last: Huang

first: Alfredo

last: Galvez

first: Wasyl

last: Malyj

first: Benito

last: de Lumen

first: Raymond

last: Rodriguez


title: Expression profile of pancreatic ductal cells

status: Public on Jul 06 2005

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

country: Japan

institute: Jichi Medical University

summary:
RNA was purified from pancreatic ductal cells, and was subjected to microarray experiments with HGU133 A&B arrays.
Keywords: other


title: Long-Term Storage of Human Cells at Ambient Temperature

summary:
This series represents the complete series of the human 293h media depleted storage on agarose / rehydration condition course analysis. Samples include Control, monolayer; Control, monolayer/full recovery, antibiotics; Spheroid, no storage; two week storage/0hr recovery; two week storage/full recovery;  four week storage/0hr recovery; six week storage/0hr recovery.
Keywords = 293h cells
Keywords = desiccation
Keywords = rehydration
Keywords = spheroid
Keywords = stabilization
Keywords = ambient temperature
Keywords: other

first: E

last: Mead

first: Andrea

last: DeSantis

first: Jody

last: Jervis

first: Jung

middle: H

last: Yoon


title: wesle-affy-droso-91201

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Neurogenesis in all animals is dependent on the function of different Notch receptors and their ligands. Drosophila is an excellent system to understand the principles and mechanisms governing this conserved process. Since the different Notch receptors and their ligands are expressed and function in the same cells, or overlapping stages of neurogenesis, and since there is extensive feedback regulation between them, it is very difficult to identify the target genes of each receptor or ligand in vivo. We have developed an excellent model system based on Drosophila cultured Schneider (S2) cells that faithfully represents in vivo activities. We propose microarray analysis with this system to identify the suite of putative target genes that are independently regulated by each protein in our study. We also expect to gather information about the signaling pathways used by the different receptors and their ligands, and develop hypotheses for testing during neurogenesis in vivo. These efforts will contribute significantly towards achieving the Specific Objectives of the grant parent (R01 NS043122, ‘Different Notch Receptors in Drosophila Development’).

To determine the sets of genes regulated by NFull, NDCterm, and Delta through microarray analyses of RNA extracted from S2 cells expressing these proteins that were treated or not treated with S2 cells expressing their ligand or receptor.

Neurogenesis in Drosophila initiates within clusters of cells that have acquired the potential to become neuronal cells. The action of the full-length Notch receptor, NFull, and the ligand Delta make the majority of these cells to differentiate the epidermis. The action of a truncated Notch receptor, NDCterm, and Delta make the remaining cells to differentiate the nervous system. We have recently shown that Delta also has activities independent of Notch receptors that promote neurogenesis. We will test the hypothesis that NFull would promote expression of epidermal differentiation genes while NDCterm and Delta that would promote expression of neuronal differentiation genes. We will also test the hypothesis that genes regulated by NDCterm and Delta would be the same or would complement each other’s activities.

We request the Microarray Consortium to process our samples and help us analyze the data. We will select a set of genes for validation by northern blotting or QPCR on similar samples of RNA from S2 cells and in vivo materials. We have available in the lab fly stocks carrying mutants (nulls) alleles or inducible transgenes for all the proteins used in this microarray experiment. Funds from the parent grant will be used for these in vitro and in vivo validation experiments. This project proposal is a part of the Supplementary Proposal approved by NIH/NINDS. Project proposals covering other parts, the effects on secreted ligands of Scabrous and Wingless, will be submitted when we have ready the RNAs from these experiments.
Keywords: other

overall_design:
S2 cells or S2 cell lines expressing NFull, NDCterm, Delta, and Delta lacking the intracellular domain (DlDI) were mixed and allowed to interact for 45 minutes. RNAs were extracted from these samples and quantified. Six RNA samples were extracted from the following treatments (the cell types mixed are separated by a slash).

(1) S2-NFull/S2; (2) S2-NFull/S2-Dl; (3) S2/S2; (4) S2/S2-Dl; (5) S-NFull/S2-DlDI; (6) S2/S2- DlDI; (7) S2/S2-NDCterm; (8) S2- NDCterm /S2-Dl.

Two independent samples were pooled to yield triplicates for each treatment. Genes responding to the activities of different proteins can be identified using the following contrasts or comparisons. Contrasts/comparison is indicated by versus (vs).

1. Genes responding to NFull treated with Delta: [S2-NFull/S2 vs S2-NFull/S2-Dl] - [S2/S2 vs S2-Dl]- [S2/S2-NFull vs S2-NFull/S2-DlDI] - [S2/S2 vs S2/S2- DlDI]

2. Genes responding to NDCterm treated with Delta: [S2-NDCterm/S2 vs S2-NDCterm/S2-Dl] - [S2/S2 vs S2/S2-Dl]

3. Genes responding to Delta: [S2/S2-Dl vs S2/S2] - [S2/S2 vs S2/S2- DlDI]

4. Genes responding to Delta treated with NFull: [S2-NFull/S2-Dl vs S2-NFull/S2- DlDI] - [S2/S2 vs S2/S2- DlDI]  -[S2/S2-Dl vs S2/S2]

first: Cedric

last: Wesley


title: gene expression study of blood monocytes

status: Public on Jul 01 2005

city: Omaha

first: Yaozhong

last: Liu

state: NE

address: 601 N 30th Street, Suite 6730

department: Osteoporosis Research Center

institute: Creighton University

summary:
Monocytes were isolated from 30 ml of whole blood from each of 19 women, 10 with high BMD and 9 with low BMD, using monocyte negative isolation kit from Dynal Biotech Inc. Total RNA was extracted from monocytes using Qiagen RNeasy Mini Kit. Targets were produced for each subject using standard Affymetrix procedures from about 4ug of total RNA. Hybridization was made for each subject. Comparison was performed between 10 high BMD and 9 low BMD subjects.

Keywords = microarray
Keywords = monocyte
Keywords = osteoporosis
Keywords = HDC
Keywords = CCR3
Keywords = GCR
Keywords: other

first: Yao-Zhong

first: Volodymyr

last: Dvornyk

first: Lu

last: Yan

first: Hui

last: Shen

first: Joan

last: Lappe

first: Robert

middle: R

last: Recker

first: Hong-Wen

last: Deng


title: Gene expression profile of normal v early MDS v non-MDS anemia bone marrow CD34 cells

city: Oxford

first: Alexander

last: Sternberg

state: Oxon

address: Headley Way

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatherall Institute of Molecular Medicine

summary:
Early, low risk IPSS (International Prognostic Scoring System) myelodysplasia (MDS) is a heterogeneous disorder where the molecular and cellular haematopoietic defects are poorly understood. To gain insight into this condition, we analyzed gene expression profiles of marrow CD34+ progenitor cells from normal karyotype, low blast count MDS patients, age-matched controls and patients with non-MDS anaemia. The aim of the study was to further understanding of the cellular defect in MDS and to identify biomarkers of disease
Keywords: Disease v normal

overall_design: Bone marrow (BM) CD34 cells were purified from patients with MDS, non-MDS anemia and from normal donors. Total RNA was extracted from Tri-reagent and quality verified on by capillary electrophoresis (Agilent). RNA was amplified by the Affymetrix small sample protocol. cRNA was hybridised to Affymetrix U133A chips under standard conditions. Initial data was analysed in MAS 5.0

first: Sally

last: Killick

first: Edwin

last: Massey

first: Paresh

last: Vyas

first: Kim

last: Clipsham


title: CALM-AF10 T-ALL

city: Paris

first: Eric

last: DELABESSE

address: 149-161, rue de Sèvres

department: Department of Haematology

country: France

institute: Hôpital Necker

summary:
Comparison of a series of 6 CALM-AF10 positive T-ALL to a series of 17 CALM-AF10 negative T-ALL
Keywords: ordered

last: Delabesse

first: Wim

last: Dik

first: Wajih

last: Brahim

first: Charlene

last: Braun

first: Vahid

last: Asnafi

first: Nicole

last: Dastugue

first: Olivier

last: Bernard

first: Jacques

last: Van Dongen

first: Anton

middle: W

last: Langerak

first: Elizabeth

last: MacIntyre


title: SK-MEL-2 cells treated with Ad-E2F-1, Ad-E2F-1 plus doxorubicn or Ad-LacZ plus doxorubicin

status: Public on Jun 03 2005

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

department: Surgery

institute: University of Louisville

summary:
SK-MEL-2 cells treated with Ad-E2F-1 (MOI 2), Ad-E2F-1 (MOI 2)plus doxorubicin 0.1uM, or Ad-LacZ (MOI 2) plus doxorubicin 0.1uM
Keywords: ordered

first: Maria

middle: T

last: Bowling

first: Yanbin

last: Dong

first: Heshan

last: Zhou

first: Kelly

last: McMasters


title: Auxin induction in wild type and arf6 arf8 flowers

status: Public on Jun 30 2005

city: Chapel Hill

first: Christine

last: Ellis

state: NC

address: 121 Coker Hall

institute: University of North Carolina at Chapel Hill

summary:
The aim of this study was to examine the roles of Auxin Response Factors (ARFs) in flower gene expression. Flowers from arf6 arf8 plants undergo a developmental arrest at approximately stage 12, just prior to flower opening. Wild-type, ARF6/arf6 arf8/arf8, and arf6 arf8 plants were treated with 10 uM indole-3-acetic acid for thirty minutes to identify genes that respond rapidly to auxin in an ARF6/ARF8-dependent manner.
Keywords: auxin response; comparison of wild type and arf6 arf8 mutants

overall_design: Wild-type, ARF6/arf6 arf8/arf8, and arf6 arf8 plants were sprayed with 10 mM indole-3-acetic acid in 1% methanol, 0.05% Tween-20. Thirty minutes after treatment, flowers (stage 1-14) were collected, frozen in liquid nitrogen, and used for RNA extraction.

first: Punita

last: Nagpal

first: Jason

last: Reed


title: HEK293 cells overexpressing wild type HNF4a2 or mutant forms HNF4a2 C106R or HNF4a2 R154X

status: Public on Jul 21 2005

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

summary:
Analysis of gene expression in human embryonic kidney cells HEK293 overexpressing the transcription factors HNF4a2 or mutant forms HNF4a2 C106R and HNF4a2 R154X, which were introduced by FRT/FLP recombination. The analysis was performed 24 hours following 1µg/ml tetracycline treatment to induce the expression of the genes. Results identify HNF4a regulated genes in kidney cells being several of these genes deregulated in renal cell carcinoma.
Keywords = HEK293 embryonic kidney cells
Keywords = HNF4a2
Keywords = tetracycline
Keywords = FRT
Keywords: ordered

first: Belen

last: Lucas

first: Karen

last: Grigo

first: Silke

last: Erdmann

first: Jörn

last: Lausen

first: Gerhart

middle: U

last: Ryffel


title: Auxin Response Factor mediated flower gene expression

summary:
The aim of this study was to examine the contribution of ARF6 and ARF8 to flower gene expression. Flowers from arf6 arf8 plants undergo a developmental arrest at approximately stage 12, just prior to flower opening. Flowers from wild-type, ARF6/arf6 arf8/arf8, and arf6 arf8 plants were separated into stage 1-10 flowers, stage 11+12 flowers, and stage 13-14 flowers to define the developmental stages at which ARF6 and ARF8 are required for gene expression.
Keywords: comparison of wild type and arf6 arf8 mutants

overall_design: Flowers from wild-type, ARF6/arf6 arf8/arf8, and arf6 arf8 plants were separated into stage 1-10 flowers, stage 11+12 flowers, and stage 13-14 flowers, frozen in liquid nitrogen, and used for RNA extraction.


title: EORTC 10994 clinical trial

status: Public on Jun 01 2005

city: Bordeaux

first: Richard

last: Iggo

address: 229 cours de l'Argonne

department: Bergonie Cancer Institute

institute: University of Bordeaux

summary:
EORTC 10994 is a phase III clinical trial comparing FEC with ET in patients with large operable, locally advanced or inflammatory breast cancer (www.eortc.be). Frozen biopsies were taken at randomisation. RNA was extracted from 100um thickness of 14G core needle biopsies. Adjacent sections were tested by H&E to confirm >20% tumour cell content. 100 ng total RNA per chip were amplified using the Affymetrix small sample protocol (IVT then Enzo). 49 tumours were tested on Affymetrix U133A chips. The CEL files were quantile normalised together using rma. Clinical response data are not available yet.
Keywords = Apocrine carcinoma
Keywords = breast cancer


title: Adipocyte Differentiation

city: Cambridge

first: Garrett

last: Frampton

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Instute - MIT

summary:
Fat tissue was resected during gastric bypass surgery for management of obesity.  All subjects had fasted at least 10 hours before surgery. Subjects with malignancies were excluded. No subjects were taking thiazolidinediones or steroids. None had fasting plasma glucose levels over 120 mg/ dl. One half to 10 g of abdominal subcutaneous (external to the fascia superficialis), mesenteric, and greater omental fat were obtained from each subject. The tissue was collected in Hank’s balanced salt solution with bicarbonate, penicillin, and gentamicin.  Fat tissue was minced and then digested in HBSS containing 1 mg/ml collagenase and 7.5% fetal bovine serum in a 37*C shaking water bath until fragments were no longer visible and the digest had a milky appearance. Digests were filtered and centrifuged at 800xG for 10 min. The digests were treated with an erythrocyte lysis buffer.  Cells were plated in 1:1 Dulbecco’s modified Eagle’s medium:Ham’s F12 that contained 10% fetal bovine serum and antibiotics at a density of 4 x 104 cells/cm2. After 18 hours cultures were trypsinized until 95% of cells were detached (leaving endothelial cells and macrophages behind) and re-plated. Macrophages were rare (less than 5 per 106 cells, as assessed by phase contrast microscopy) in the re-plated cultures, irrespective of fat depot origin. Plating medium was changed every 2 days until confluence. For differentiation, preadipocytes were treated for 30 days with plating medium (without serum) enriched with 100 nM dexamethasone, 500 nM human insulin, 200 pM triiodothyronine, 0.5 *M rosiglitazone, antibiotics, and 540 *M methylisobutylxanthine (removed after 2 days). Higher rosiglitazone and insulin concentrations did not further enhance differentiation. Medium was changed every 2 days. For the final 2 days, differentiation medium was removed and cells were cultured in plating medium without serum. Undifferentiated preadipocytes were maintained in plating medium until confluence, when serum was removed for 2 days.  For telomerase-expressing clones, preadipocytes were isolated and when cells had undergone 7 population doublings, they were transduced with a retrovirus containing the plasmid, pBABE-hTERT-Hygro. This vector expresses the human telomerase reverse transcriptase component (hTERT) driven by the Moloney murine leukemia virus long terminal repeat promoter and a hygromycin resistance sequence driven by the SV40 promoter. The 3 abdominal subcutaneous and 3 omental stably transduced, hygromycin-resistant clones capable of achieving confluence fastest were selected from 38 subcutaneous and 42 omental clones. Telomerase activity in these clones was verified using a PCR-based telomere repeat amplification protocol.  RNA was isolated from preadipocytes by the Trizol method.  RNA samples were labeled using the standard one-cycle Affymetrix GeneChip Eukaryotic Target Labeling Assay for Expression Analysis.  Samples were hybridized for 16 hours at 45 ºC and 60 rpm, washed and stained according to the standard Affymetrix Antibody Amplification for Eukaryotic Targets protocol, and scanned at 488 nm.  Images were quantified and linearly scaled using Affymetrix GeneChip Operating Software 1.1 using default analysis settings.
Keywords = adipocyte
Keywords = subcutaneous
Keywords = mesenteric
Keywords = omental
Keywords: repeat sample

first: Tamara

last: Tchkonia

first: Marc

last: Lenburg

first: Nino

last: Giorgadze

first: Alon

last: Sabban

last: Pritshkalava

first: Mark

last: Cartwright

first: Norman

middle: P

last: Gerry

first: R-Armour

last: Forse

first: Opher

last: Gileadi

first: James

middle: L

last: Kirkland

last: Pirtskhalava

first: R


title: Response of PPARs to ligands

status: Public on May 31 2005

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

institute: LSBM, RCAST

summary:
HepG2 tet-off hPPARs treated with ligands
Keywords: parallel sample


title: Chitin Oligomer Experiment

city: Tuscaloosa

first: Katrina

last: Ramonell

state: AL

address: 411 Hackberry Lane, Box 870344

department: Biological Sciences

institute: University of Alabama

summary:
Using the ATH1 Affymetrix microarrays consisting of about 23,000 genes, we examined the response of Arabidopsis seedlings to chito-tetramers, chito-octamers and hydrolyzed chitin after 30 min of treatment.
Keywords = chitin
Keywords = defense
Keywords = elicitor
Keywords = mutant
Keywords = powdery mildew
Keywords = Erysiphe cichoracearum
Keywords: ordered

first: Marta

last: Berrocal-Lobo

first: Serry

last: Koh

first: Jinrong

last: Wan

first: Herb

last: Edwards

first: Gary

last: Stacey

first: Shauna

last: Somerville


title: Gene expression of human soft tissue sarcoma

city: Boston

first: Namali

last: Fernando

department: Surgical Oncology

institute: Massachusetts General Hospital

summary:
Gene expression profiles of 39 human sarcoma samples (GSM 52571-GSM52609) and 15 control samples (GSM52556-GSM52570) were assessed using Affymetrix HG U133A oligonucleotide arrays.
Keywords: other

first: Sam

last: Yoon

first: Niel

last: Segal

first: Sandra

last: Ryeom

first: Kara

last: Detwiller

first: Patricia

last: D'Amore


title: FoxM1 siRNA profiles

first: Diane

last: Wonsey

institute: Wyeth Research

summary:
BT-20 breast cancer cells were exposed to a mock transfection, GFP siRNA, or FoxM1 siRNA.  Each condition was performed in triplicate, and RNA was collected after 48hrs.
Keywords: parallel sample


title: OCI/AML2 ATRA AND VPA GENE EXPRESSION

status: Public on May 17 2005

city: Toronto

first: Mark

last: Minden

country: Canada

institute: Princess Margaret Hospital

summary:
Purpose: Treatment of acute promyelocytic leukemia (APL) with the retinoid, all trans retinoic acid (ATRA), along with standard chemotherapy has significantly improved survival compared to chemotherapy alone1. ATRA mediates its benefit in APL by overcoming the transcriptional block mediated by PML-RAR-alpha fusion oncoprotein, thereby, restoring expression of retinoid response genes2. The therapeutic benefits observed with ATRA treatment in APL have not been achieved in the other more common sub-types of acute myeloblastic leukemia (AML)3. This likely reflects the recruitment of histone deacetylase complexes by other recurrent chromosomal translocations in AML cells4. In this experiment, we evaluated if treatment of the AML cell line, OCI/AML-2, with the histone deacetylase inhibitor, valproic acid (VPA), would alter the expression of sub-sets of genes by itself or in conjunction with ATRA that have been shown to be modulated by ATRA in APL2.
Keywords: other

overall_design:
Methods: OCI/AML-2 cells were cultured at 37°C and 5% CO2 in alpha-MEM growth media supplemented with antibiotics and 10% fetal calf serum (HyClone, UT, USA). The drugs, ATRA and VPA, were obtained from Sigma-Aldrich Canada Ltd. (ON, CAN) and were re-suspended in 100% ethanol. OCI/AML-2 cells were treated with ATRA as a single 10-6 M dose and VPA was dosed at 0.6mM every 8 hours over 24 hours. The following four treatment combinations were evaluated: i) controls (solvent only) ii) ATRA iii) VPA iv) ATRA + VPA.
Suspension cells were pelleted at 300 g 24 h after initial drug exposure. Total RNA was isolated using an RNeasy kit (Qiagen Inc., Canada) and stored at –70°C in DEPC-H2O. Total RNA was then further concentrated to 2.5µg/µL by ethanol precipitation overnight at –20°C in 0.3M sodium acetate pH 5.2 (Sigma-Aldrich Canada Ltd.).
GeneChip experiments were carried out by the Microarray Facility, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON. A total of 20µg of total RNA was used to generate biotin labeled cRNA probes according to Affymetrix’s recommended protocol using a labeling kit from EnzoBiochem, Inc. (NY, USA). A total of 15µg of the biotin labeled cRNA was hybridized onto the human U133A Affymetrix GeneChip. The GeneChip was washed as per the Affymetrix EukGE-ws2v4 protocol available at (https://www.affymetrix.com/site/login/login.affx). The GeneChip was scanned using a GeneArray 2500 scanner (Agilent, CA, USA) and hybridization intensity was obtained and detection p value and signal were calculated using MAS 5.0 software. Target signal was set to 150 for scaling for all of the experiments. The output chp file was exported to text file and used for further analysis with the Multiple experiment viewer (MeV) version 2.2 available from the Institute for Genomic Research at http://www.tigr.org/. Signal intensities obtained from the OCI/AML-2 cells treated with ATRA, VPA, or ATRA + VPA were compared to untreated OCI/AML-2 controls. Only genes that were identified as present (P) and displayed more than two fold change in signal intensity compared to untreated cells (controls) were carried forward for further analysis. Gene expression experiments were normalized using total intensity, median centered and log(2) transformed to give equal weight to expression values relative to the median for analysis. Unsupervised hierarchical clustering was performed using average linkage and Pearson correlation as a measure of distance.
Results: Relatively few genes were regulated by ATRA treatment in OCI/AML-2 cells. However, treatment of OCI/AML-2 cells with VPA altered the expression of genes that encode for proteins involved with regulation of cell cycle, interferon response, apoptosis and differentiation. Examples of genes depressed by VPA, but not ATRA, involved regulators of cell cycle, cyclin A2 and MYC. The combination of ATRA + VPA further suppressed expression of these genes. Genes such as IRF1, neutrophilic cytosolic factor, ICAM3 and C/EBP-beta increased in response to ATRA in OCI/AML-2 cells whereas VPA did not alter their expression over untreated OCI/AML-2 cells. However the combination of ATRA + VPA further enhanced the expression of these genes. Examples of genes induced by VPA that were not affected by ATRA in OCI/AML-2 cells include cell surface markers CD9, and MHC class II, promoters/enhancers of apoptosis such as MAPK kinase, interferon responsive genes, and caspase 7, and negative regulators of cell cycle like p21 and p19. The addition of ATRA to VPA increased the expression of some, but not all of these genes. It would appear that VPA dramatically affects the gene expression pattern of OCI/AML-2 cells, and modulates the expression of a set of genes, similar to those modulated by ATRA in APL cells2.
References
1. Tallman MS, Andersen JW, Schiffer CA, Appelbaum FR, Feusner JH, Ogden A, Shepherd L,

Willman C, Bloomfield CD, Rowe JM, Wiernik PH. All-trans-retinoic acid in acute

promyelocytic leukemia. N Engl J Med 1997; 337(15):1021-1028.

2. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES,

Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods

and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 1999;

96(6):2907-2912.

3. Estey EH, Thall PF, Pierce S, Cortes J, Beran M, Kantarjian H, Keating MJ, Andreeff

M, Freireich E. Randomized phase II study of fludarabine + cytosine arabinoside +

idarubicin +/- all-trans retinoic acid +/- granulocyte colony- stimulating factor in poor

prognosis newly diagnosed acute myeloid leukemia and myelodysplastic syndrome.

Blood 1999; 93(8):2478-2484

4. Gelmetti V, Zhang J, Fanelli M, Minucci S, Pelicci PG, Lazar MA. Aberrant

recruitment of the nuclear receptor corepressor-histone deacetylase complex by the acute

myeloid leukemia fusion partner ETO. Mol Cell Biol 1998; 18(12):7185-7191.

first: M

last: Trus

first: L

last: Yang

first: F

last: Suarez Saiz

last: Bordeleau

first: I

last: Jurisica


title: Differential gene expression in pituitary adenomas by oligonucleotide array analysis

status: Public on May 23 2005

city: London

first: Damian

last: Morris

department: Endocrinology

institute: St. Bartholomew’s and the Royal London School of Medicine and Dentistry

summary:
This series includes the four major subtypes of pituitary adenomas and normal post-mortem pituitary tissue

Data Transformation
Using Affymetrix Microarray Suite 5.0 global scaling was applied to the quantification data to adjust the average recorded to a target intensity of 100. Data were then exported into the bioinformatics software GeneSpring 6.0 (Silicon Genetics, Redwood City, CA) for further analysis. Data normalization was performed to scale the data so that the average intensity value on each array was 1 by dividing each expression value by the median of the expression levels on each chip. The individual gene expression levels for each of the 4 pituitary adenoma subtype arrays was divided by the expression level in the normal pituitary array. Thus, the data are presented as relative to the expression in normal pituitary tissue. Filtering was then performed to identify genes over-expressed or under-expressed at least 2.0 fold in tumours compared to normal pituitary.

TABLE 1:
The genes / ESTs differentially overexpressed >= 2-fold in at least one pituitary adenoma subtype compared to normal pituitary. Negative values represent underexpression. Where genes are represented by more than one probe set, individual probe data sets are given.

TABLE 2:
The genes / ESTs differentially underexpressed >= 2-fold in at least one pituitary adenoma subtype compared to normal pituitary. Negative values represent underexpression. Where genes are represented by more than one probe set, individual probe data sets are given.

Keywords = pituitary tumor
Keywords: other

first: Madalina

last: Musat

first: Sandor

last: Czirjak

first: Zoltan

last: Hanzely

first: Debra

last: Lillington

first: Marta

last: Korbonits

first: Ashley

middle: B

last: Grossman


title: Changes in transcript abundance and association with large polysomes in response to hypoxia stress

city: Riverside

first: Cristina

last: Branco-Price

address: 2215 batchelor Hall

institute: University of California, Riverside

summary:
7d-old WT ler seedlings were submitted to 12h of non-stress (air) or hypoxia-stress treatment under low light conditions (45 uM m-2 s-2), and Total and Large Polysome RNA from both treatments were extracted and hybridized against Affymetrix genome chips. Values were used to evaluate changes in transcript abundance and transcript association with large polysomal complexes.

TABLE 1 - Comparison between transcript abundance in non-stress and hypoxia-stress conditions.

TABLE 2 - Comparison between transcript abundance in large polysome complexes (5 or more ribosomes per mRNA) in non-stress and 12 hypoxia-stress conditions.

TABLE 3 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under non-stress conditions. Raw data (not normalized)

TABLE 4 - Proportion of total transcript that is associated with large polysome complexes (polysome loading) under 12h of hypoxia-stress. Raw data (not normalized)

Keywords: time-course

first: Riki

last: Kawaguchi

first: Ricardo

last: Ferreira

first: Julia

last: bailey-Serres


title: Oncogene-induced senescence

status: Public on May 15 2005

city: Madrid

first: Manuel

last: Collado

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: Spanish Cancer Research Center

summary:
This experiment was designed to study oncogene-induced senescence (OIS). To this end we generated a series of cell lines derived from normal human diploid fibroblasts IMR90 forced to express the catalytic subunit of telomerase (hTERT). This cells were then subjected to further manipulation by orderly introducing defined genetic elements by retroviral transduction. The first cell line generated was ITV, which was obtained from the original cell line (IMR90 with hTERT) after introducing an empty vector. Subsequently, we introduced Mek:ER, which is a switchable version of the Mek kinase, a relevant downstream effector of Ras signaling during Ras-induced senescence, to generate ITM cells. We further modified this cell line by introducing SV40 small-t antigen (ST), papillomavirus oncoproteins E6 and E7 (E6/E7) or the combination of both (E6/E7 and ST). In this manner, we obtained ITMST, ITME6E7 and ITME6E7ST respectively.

This cellular system allow us to have a representation of the different steps into neoplastic transformation. ITM and ITMST cells respond to Mek activation by inducing OIS. ITME6E7 and ITME6E7ST cells do not enter OIS after Mek activation. Mek activation is achieved by treating all cell cultures with 4-hydroxytamoxifen (4OHT) at 100 nM, in the absence of serum, and for 3 days. The gene expression profile of ITV cells served as a reference for all the expression values obtained with the rest of the cell lines.

Thus, we ended up with the expression profiles of two cell lines representing oncogene-induced senescence (ITM and ITMST), and two cell lines representing bypass of oncogene-induced senescence, plus a reference profile provided by ITV, the cell line from which all the other cell lines were derived.

Our final goal was to identify markers of the oncogene-induced senescence response by comparing the expression profiles of the cell lines entering OIS after Mek activation (that is, after 4OHT treatment) with the ones bypassing this response.
Keywords: other

first: Jesus

last: Gil

first: Alejo

last: Efeyan

first: Carmen

last: Guerra

first: Alberto

middle: J

last: Schuhmacher

last: Barradas

last: Benguria

first: Angel

last: Zaballos

first: Juana

last: Flores

first: Mariano

last: Barbacid

first: David

last: Beach

last: Serrano


title: NIH/NIAID Neutrophil Response to A. phagocytophilum

city: Hamilton

first: Frank

middle: R.

last: DeLeo

state: MT

address: 903 South 4th Street

department: Laboratory of Human Bacterial Pathogenesis

summary:
Polymorphonuclear leukocytes (PMNs) were obtained from healthy individuals in accordance with protocols approved by the Institutional Review Board for Human Subjects at the University of Minnesota and the National Institute of Allergy and Infectious Diseases.

PMNs (107) were combined on ice with live S. aureus (108) or with live or heat-killed A. phagocytophilum (bacteria isolated from 5x106 infected HL60 cells for a ratio of 1 infected HL60 cell: 2 PMNs, ~ 5-20 A. phagocytophilum: PMN) in wells of a 12-well tissue culture plate (pre-coated with 20% autologous normal human serum). Unstimulated control assays received either buffer (for S. aureus comparisons) or clarified HL60 lysate (for A. phagocytophilum comparisons).

Plates were centrifuged at 350 x g for 8 min at 4oC to synchronize phagocytosis and incubated at 37 deg. C in a CO2 incubator for the indicated times. At the indicated times, tissue culture medium was aspirated from the plate and PMNs were lysed directly with RLT buffer (Qiagen, Valencia, CA). Purification of PMN RNA and subsequent preparation of labeled cRNA target was performed as described in Methods.

Labeling of samples, hybridization of cRNA with HU133A oligonucleotide arrays (Affymetrix, Santa Clara, CA), and scanning were performed according to standard Affymetrix protocols ( http://www.affymetrix.com/pdf/expression_manual.pdf ).

Experiments were performed in triplicate, using PMNs from three healthy individuals for each treatment.
Keywords = HUMAN NEUTROPHILS BACTERIAL APOPTOSIS GENE REGULATION
Keywords: ordered

first: Dori

last: Borjesson

first: Adeline

last: Whitney

first: Scott

last: Kobayashi

first: Jovanka

last: Voyich

first: Cynthia

last: Argue


title: cMyb and vMyb in MCF7 cells

status: Public on Jun 14 2005

city: Albuquerque

middle: A.

last: Ness

state: NM

department: Internal Medicine

institute: U. of New Mexico HSC

summary:
The transcriptional activities of c-Myb and its oncogenic variant v-Myb were compared by expressing them in human MCF7 cells using recombinant adenovirus vectors. A hybrid construct, 3Mutc, which is a variant of c-Myb harboring three v-Myb-derived DNA binding domain mutations was also analyzed.  All the samples were compared to cells infected with a control adenovirus.  The results showed that v-Myb, which differs from c-Myb only by N- and C-terminal deletions and eleven amino acid substitutions, has a qualitatively different transcriptional activity.
Keywords: repeat

overall_design: 2 replicates of each type were analyzed. Replicates were performed independently, more than a week apart.

first: Fan

last: Liu

first: Wanli

last: Lei

first: John

last: O'Rourke


title: HUVEC gene profile after TNF-stimulation

status: Public on May 12 2005

city: Hannover

first: Dorothee

last: Viemann

state: Deutschland

address: Carl-Neuberg-Straße 1

department: Department of Pediatric Pulmonology, Allergy and Neonatology

institute: Hannover Medical School

summary:
HUVEC were left untreated or stimulated for 5h with 2 ng/ml TNF. Comparsion of the gene profiles revealed TNF-mediated gene expression changes in HUVEC.
Keywords: parallel sample

first: Matthias

last: Goebeler

first: Sybille

last: Schmid

first: Kerstin

last: Klimmek

first: Clemens

last: Sorg

first: Johannes

last: Roth


title: Trisomy 21 and TS13

status: Public on May 10 2005

city: Baltimore

first: Jonathan

last: Pevsner

state: MD

address: 707 N. Broadway

department: Neurology

institute: Kennedy Krieger Institute

summary:
Gene expression was measured in trisomy 21 and trisomy 13 human fetal samples. For TS21, regions assayed were cerebrum, cerebellum, heart, and cerebrum-derived astrocyte cell lines.
Keywords = trisomy 21
Keywords = Down syndrome
Keywords = aneuploidy
Keywords = brain
Keywords = heart
Keywords = trisomy 13
Keywords: other

first: Rong

last: Mao


title: Effects of hTERT overexpression on gene expression profiles in CD4+ T lymphocytes

status: Public on May 02 2005

first: Ludger

last: Klein-Hitpass

summary:
Analysis of gene expression by Affymetrix microarray in a CD4+ T lymphocyte clone transduced with hTERT-GFP vector after after 44 and 80 population doublings (PDs). The untransduced (32 PDs) and GFP-control vector transduced (47 PDs) T cell clone populations served as controls.
Keywords: ordered

first: A

last: Roeth

first: G

middle: M

last: Baerlocher

first: M

last: Schertzer

first: E

last: Chavez

first: U

last: Duehrsen

first: P

last: Lansdorp


title: A549 teatement with MGd

status: Public on May 01 2005

city: Los Angeles

first: Mazen

last: Karaman

address: 2250 Alcazar St IGM/CSC 240

department: Institute for Genetic Medicine

institute: University of Southern California

summary:
Human lung cancer (A549) cells were treated 50uM of the metal cation-containing chemotherapeutic drug motexafin gadolinium (MGd) for 4, 12, and 24 hrs and expression compared to control cells (treated with 5% mannitol for the same length of time)
Keywords: dose response

first: Darren

last: Magda

first: Philip

last: Lecane

first: Richard

last: Miller

first: Cheryl

last: Lepp

first: Dale

last: Miles

first: Mimi

last: Mesfin

middle: E

last: Biaglow

first: Vincent

middle: V

last: Ho

first: Danny

last: Chawannakul

first: Shailender

last: Nagpal

first: Joseph

middle: G

last: Hacia


title: Small RNA biogenesis mutants

status: Public on May 09 2005

city: Corvallis

first: Edwards

last: Allen

state: OR

address: 3021 Ag Life Sciences Building

department: Botany and Plant Pathology

institute: Oregon State University

summary:
Inflorescence stages 1 to 12 from mutants involved in Arabidopsis small RNA metabolism. Three biological replicates of each mutant comprising at least 9 independent plants were harvested, and the expression profiles were determined using Affymetrix ATH1 arrays.  Comparisons among the sample groups allow the identification of genes regulated by small RNAs (microRNAs and siRNAs).
Keywords: other

first: Zhixin

last: Xie

first: Adam

last: Gustafson

first: James

middle: C

last: Carrington


title: Transcriptional profiling of 293T cells treated with 2µM camptothecin compared to untreated cells

city: La Jolla

first: Bettina

last: Groschel

address: 10010 North Torrey Pines Road

department: Infectious Disease

institute: The Salk Institute

summary:
Total RNA from untreated 293T cells (2 samples) and 293T cells treated with 2µM camptothecin for 48h (2 samples) was isolated using RNeasy Midi Kit (QIAGEN, Valencia) followed by gene expression profiling on Affymetrix human U133A arrays and analysis by MAS 5.1.
Keywords = 293T cells
Keywords = camptothecin
Keywords: parallel sample

first: Frederic

middle: D

last: Bushman


title: GFP or spotted-dick RNAi treated S2 cells

status: Public on May 06 2005

first: Andrew

middle: Robin

last: Page

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

summary:
Drosophila S2 cells treated with either GFP or spottes-dick dsRNA and incubated for 5 days. There are three replicates for each condition.
Keywords = Spotted-dick
Keywords: other

first: Andras

last: Kovaks

first: Peter

last: Deak

first: Tibor

last: Torok

first: Istvan

last: Kiss

first: Paulo

last: Dario

first: Cristina

last: Bastos

first: Pedro

last: Batista

first: Rui

last: Gomes

first: Hiro

last: Ohkura

first: Steven

last: Russell

first: David

last: Glover


title: Atypical Ductal Hyperplasia

status: Public on Apr 06 2005

city: Washington

first: Indira

last: Poola

state: DC

address: 520 W Street, NW

department: Biochemistry and MOlecular Biology

institute: Howard University College of Medicine

summary:
Fresh Atypical ductal hyperplasia (ADH) tissue collected from breast of a women who either (1) had no prior history of breast cancer and had not developed breast cancer in five years after diagnosis, (2) had cancer before ADH, or had cancer at the time as ADH or developed cancer after ADH diagnosis
Keywords: other

first: Robert

last: DeWitty

first: Josephine

last: Marshallack

first: Rakesh

last: Bhatnagar

first: Jessy

last: Abraham

first: LaSalle

last: Laffalle

first: Chandramouli

middle: VR

last: Gadisetty


title: Platform Comparison Study

status: Public on Apr 13 2005

first: rafael

last: irizarry

institute: Johns Hopkins University

summary:
Microarray technology is a powerful tool able to measure RNA expression for thousands of genes at once. Various studies have been published comparing competing platforms with mixed results: some find agreement, others do not. As the number of researchers starting to use microarrays and the number of cross platform meta-analysis studies rapidly increase, appropriate platform assessments become more important.
Here we present results from a comparison study that offers important improvements over those previously described in the literature. In particular, we notice that none of the previously published papers consider differences between labs. For this paper, a consortium of ten labs from the DC and Baltimore area was formed to compare three heavily used platforms using identical RNA samples.  Each lab was given identical RNA samples (A1 and B1) which were processed according to what each lab considered best practice. Five of the labs used Affymetrix GeneChips, three used two-color spotted cDNA arrays, and two used two-color long oligo arrays. Samples 1 and 2 represent unique mixtures of total RNA from four knockout cell lines: PEX1, PEX6, PEX7, and PEX12. Each of the four cell lines is deficient for one of four PEX genes (required for peroxisome biogenesis/mutations cause peroxisome biogenesis disorders).  Appropriate statistical analysis demonstrates that relatively large differences exist between labs using the same platform, but that the results from the best performing labs agree rather well.
Keywords: other

first: Rafael

middle: A

last: Irizarry


title: JEG3 vs BeWo

status: Public on May 30 2005

city: Madison

middle: W

last: Burleigh

state: WI

address: 1220 Capital Court

institute: Wisconsin National Primate Research Center

summary:
In this experiment we compared total RNA from two commonly used choriocarcinoma cell lines, JEG3 and BeWo, to identify differentially expressed transcripts.
Keywords: other

first: Christina

last: Kendziorski

first: Yong

last: Choi

first: Kreg

last: Grindle

first: Rick

last: Grendell

first: Ronald

last: Magness

first: Thaddeus

last: Golos

middle: R


title: WTv.AOXantisense

status: Public on Apr 04 2005

city: Durham

first: Ann

middle: L.

last: Umbach

department: Biology Department/DCMB Group

institute: Duke University

summary:
Leaf transcriptome comparison of untransformed Col-0 Arabidopsis plants with plants transformed to be anti-sense for AtAOX1a (alternative oxidase).  Two “bio-replicates” were sampled, for a total of four microarray chips—Col-0 and anti-sense leaf tissue from a first planting (samples GSM45208 and GSM45231, respectively), and from a second planting made one week later (samples GSM45209 and GSM45278, respectively).  See sample descriptions for growth conditions and microarray procedure.
Keywords = alternative oxidase
Keywords = plant mitochondria
Keywords = respiration
Keywords = leaves
Keywords: repeat sample

first: Fabio

last: Fiorani

first: James

middle: N

last: Siedow


title: Expression Proflies of Human Normal tissues

status: Public on Apr 03 2005

city: Evanston

first: Xijin

last: Ge

state: IL

address: 1001 University Place

department: Center for Functional Genomics

institute: ENH Research Institute

summary:
We performed expression profiling of 36 types of normal human tissues and identified 2,503 tissue-specific genes. We then systematically studied the expression of these genes in cancers by re-analyzing a large collection of published DNA microarray datasets. Our study shows that integration of each gene's breadth of expression (BOE) in normal tissues is important for biological interpretation of the expression profiles of cancers in terms of tumor differentiation, cell lineage and metastasis.
Twenty five total RNA specimens were purchased from Clontech (Palo Alto, CA), Ambion (Austin, TX) and Strategene (La Jolla, CA). We tried to cover as many tissue types as possible by using pooled RNA samples. In order to define breadth-of-expression (BOE) accurately at a reasonable cost, we tried to cover as many tissue types as possible by using pooled RNA samples. Each specimen represents a human organ. We used RNA samples pooled from 2 to 84 donors to avoid differences at the individual level.
Keywords = Normal human tissues
Keywords = Tissue-specificity

Detailed sample information and Affymetrix .CEL files are available at http://www.genome.rcast.u-tokyo.ac.jp/normal/

Publication:Ge X et al., Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues.

Genomics. 2005 Aug;86(2):127-141.
PMID: 15950434
Keywords: other

first: Shogo

last: Yamamoto

first: Shuichi

last: Tsutsumi

first: Yutaka

last: Midorikawa

first: Siego

last: Ihara

first: SanMing

last: Wang

first: Hiroyuki

last: Aburatani


title: HIV wtNDK, HIV m7NDK

city: New York

first: Veronique

last: Bourdon

state: NY

department: Human Genetics

institute: Memorial Sloan Kettering Cancer Center

summary:
Arrays analyses of CEM non infected and CEM infected by HIV wtNDK or  HIV m7NDK (mutant). The arrays used were done at AECOM (ET arrays) and by affymetrix. They were hybridized with RNA of the cell lines infected or not. The analyses done as in bourdon et al. Cancer Res. 2002 Nov 1;62(21):6218-23, and with genesis.
Keywords: parallel sample

first: Alejandra

last: Borjabad

first: veronique


title: Human Mesenchymal stem cell

status: Public on Apr 07 2005

first: Agnes

last: Viale

address: 1275 York Avenue

department: Molecular Biology

summary:
Comparisons of expression profils of human undiferentiated ES cells and Mesenchymal ES cells
Keywords: other

first: Tiziano

last: Barberi

first: Studer

last: Lorenz

first: Lorenz

last: Studer


title: Control (IBS) & Ulcerative colitis (UC) subjects

status: Public on Apr 01 2005

city: Copenhagen

first: Jorgen

last: Olsen

address: Blegdamsvej 3

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary:
IBS: Patients who have undergone a diagnostic program for gastrointestinal symptoms and where the diagnosis irritable bowel syndrome was reached.

UC: Patients with well-diagnosed ulcerative colitis
Keywords: other

first: Jakob

middle: B

last: Seidelin

first: Morten

last: Hansen

first: Lene

middle: T

last: Kirkeby

first: Ole

middle: H

last: Nielsen

first: Jesper

last: Troelsen


title: chemotherapy cross-resistance and treatment response in childhood acute lymphoblastic leukemia

city: Memphis

first: William

last: Evans

state: TN

address: 332 N. Lauderdale St.

department: Pharmaceutical Sciences

institute: St.Jude Children's Research Hospital

summary:
Acute lymphoblastic leukemia (ALL) can be cured with combination chemotherapy in over 75% of children, but the cause of treatment failure in the remaining patients is unknown. We determined the sensitivity of ALL cells to individual antileukemic agents in 441 patients, and used a genome-wide approach to identify 45 genes differentially expressed in ALL exhibiting cross-resistance to prednisolone, vincristine, asparaginase and daunorubicin. We also identified a distinct phenotype of discordant resistance to asparaginase and vincristine and 139 genes whose expression was associated with this novel phenotype. The expression of these genes discriminated treatment outcome in two independent patient populations, identifying a subset of patients with a markedly inferior outcome (37%±13% 5-year DFS).
Keywords = Acute lymphoblastic leukemia
Keywords = cross-resistance
Keywords: other

first: Sanne

last: Lugthart

first: Meyling

last: Cheok

first: Monique

middle: L

last: den Boer

first: Wenjian

last: Yang

first: Amy

last: Holleman

first: Cheng

last: Cheng

first: Chin-Hon

last: Pui

first: Mary

last: Relling

first: Gritta

last: Janka-Schaub

first: Rob

last: Pieters


title: VSV7day

status: Public on Mar 29 2005

city: Rochester

first: Chin-Yi

last: Chu

address: 75 Elmwood Avenue

department: Environmental Medicine

institute: University of Rochester

summary:
Infected and Uninfected with VSV
Keywords: repeat sample

first: David

last: Volsky

first: Andew

middle: I

last: Brooks

first: Seon-yeong

last: Kim

first: Jinliang

last: Li

first: Galina

last: Bentsman


title: Endothelial cells and atorvastatin

city: Little Rock

first: Marjan

last: Boerma

state: AR

address: 4301 West Markham, Slot 725

institute: University of Arkansas for Medical Sciences

summary:
Rationale: Immortalized cells may exhibit important differences relative to their primary cell counterparts. Microarrays were used compare primary human umbilical vein endothelial cells (HUVECs) and the immortalized HUVEC cell line EA.hy926, in their response to inhibition of the mevalonate pathway by a HMG-CoA reductase inhibitor (atorvastatin). The effects of atorvastatin were reversed by the addition of mevalonate, to subtract non-specific changes in gene expression.
Methods: Confluent cell cultures of HUVECs and EA.hy926 cells (two independent experiments in each cell type) were incubated with 1) statin-free media; 2) 10 microM atorvastatin; 3) 500 microM mevalonate; or 4) a combination of 10 microM atorvastatin and 500 microM mevalonate. All cells were harvested at 24 h. Total RNA was isolated using Trizol reagent (Invitrogen). cDNA was prepared from 10 microgram total RNA using a double-stranded cDNA synthesis kit (Life Technologies) with a T7-dT24 primer for first-strand synthesis. cRNA was synthesized from cDNA and biotinylated using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). Twenty microgram of cRNA was fragmented by heating at 94°C for 35 min in fragmentation buffer, containing 40 mM Tris-acetate, pH 8.1, 125 mM KOAc, 30 mM MgOAc. Fifteen micrgram of fragmented cRNA, together with control cRNAs and grid alignment oligonucleotides, were hybridized overnight to GeneChip Human Genome U133A 2.0 arrays (Affymetrix) at 45°C under constant rotation. Arrays were washed and incubated with an anti-streptavidin antibody. Fluorescent signals were measured using an Agilent Gene Array Laser Scanner and analyzed with MicroArray Suite 5.0 (Affymetrix). Microarrays were scaled using default settings.
Keywords: other

first: Gregory

last: Burton

first: Junru

last: Wang

first: Louis

middle: M

last: Fink

first: Robert

middle: E

last: McGehee Jr.

first: Martin

last: Hauer-Jensen


title: Comparison of atrial tissue of patients with atrial fibrillation and sinus rhythm with ventricular gene expression

status: Public on May 13 2005

city: Munich

first: Andreas

middle: S.

last: Barth

address: Marchioninistr. 15

department: Department of Cardiology

institute: University of Munich (LMU), Grosshadern

summary:
GSE2240 contains two different experimental subsets:

1) Comparison of atrial and ventricular gene expression (atrial tissue of patients with sinus rhythm vs. human left ventricular non-failing myocardium)

The purpose of our investigation was to identify the transcriptional basis for ultrastructural and functional specialization of human atria and ventricles. Using exploratory microarray analysis (Affymetrix U133A+B), we detected 11,740 transcripts expressed in human heart, representing the most comprehensive report of the human myocardial transcriptome to date. Variation in gene expression between atria and ventricles accounted for the largest differences in this data set, as 3.300 and 2.974 transcripts showed higher expression in atria and ventricles, respectively. Functional classification based on Gene Ontology identified chamber-specific patterns of gene expression and provided molecular insights into the regional specialization of cardiomyocytes, correlating important functional pathways to transcriptional activity: Ventricular myocytes preferentially express genes satisfying contractile and energetic requirements, while atrial myocytes exhibit specific transcriptional activities related to neurohumoral function. In addition, several pro-fibrotic and apoptotic pathways were concentrated in atrial myocardium, substantiating the higher susceptibility of atria to programmed cell death and extracellular matrix remodelling observed in human and experimental animal models of heart failure. Differences in transcriptional profiles of atrial and ventricular myocardium thus provide molecular insights into myocardial cell diversity and distinct region-specific adaptations to physiological and pathophysiological conditions (Barth AS et al., Eur J Physiol, 2005).

2) Comparison of atrial gene expression in patients with permanent atrial fibrillation and sinus rhythm.

Atrial fibrillation is associated with increased expression of ventricular myosin isoforms in atrial myocardium, regarded as part of a dedifferentiation process. Whether re-expression of ventricular isoforms in atrial fibrillation is restricted to transcripts encoding for contractile proteins is unknown. Therefore, this study compares atrial mRNA expression in patients with permanent atrial fibrillation to atrial mRNA expression of patients with sinus rhythm as well as to ventricular gene expression using Affymetrix U133 arrays. In atrial myocardium, we identified 1.434 genes deregulated in atrial fibrillation, the majority of which, including key elements of calcium-dependent signaling pathways, displayed down-regulation. Functional classification based on Gene Ontology provided the specific gene sets of the interdependent processes of structural, contractile and electrophysiological remodeling. In addition, we demonstrate for the first time a prominent up-regulation of transcripts involved in metabolic activities, suggesting an adaptive response to an increased metabolic demand in fibrillating atrial myocardium. Ventricular-predominant genes were five times more likely to be up-regulated in atrial fibrillation (174 genes up-regulated, 35 genes down-regulated), while atrial-specific transcripts were predominantly down-regulated (56 genes up-regulated, 564 genes down-regulated). Overall, in atrial myocardium, functional classes of genes characteristic of ventricular myocardium were found to be up-regulated (e.g. metabolic processes) while functional classes predominantly expressed in atrial myocardium were down-regulated in atrial fibrillation (e.g. signal transduction and cell communication). Therefore, dedifferentiation with adoption of a ventricular-like signature is a general feature of the fibrillating atrium, uncovering the transcriptional response pattern in pmAF (Barth AS et al., Circ Res, 2005).
Keywords = human myocardium
Keywords = atrial fibrillation
Keywords = sinus rhythm
Keywords = left ventricular gene expression
Keywords: other

middle: S

first: Sylvia

last: Merk

first: Elisabeth

last: Arnoldi

first: Ludwig

last: Zwermann

first: Patrick

last: Kloos

first: Mathias

last: Gebauer

first: Klaus

last: Steinmeyer

first: Markus

last: Bleich

first: Stefan

last: Kääb

last: Hinterseer

first: Heike

last: Kartmann

first: Eckart

last: Kreuzer

last: Dugas

first: Gerhard

last: Steinbeck

first: Michael

last: Näbauer


title: HMEC gene profile after TNF-stimulation

first: Dorothee

last: Viemann

institute: Hannover Medical School

summary:
HMEC cultures were left untreated or stimulated for 5h with 2 ng/ml TNF. Comparison of the gene expression profiles revealed the TNF-mediated gene expression changes.
Keywords: parallel sample

first: Matthias

last: Goebeler

first: Sybille

last: Schmid

first: Ursula

last: Nordhues

first: Kerstin

last: Klimmek

first: Clemens

last: Sorg

first: Johannes

last: Roth


title: Human Hematopoietic Stem Cell (HSC) and Progenitor Cell (HPC) Expression Profilies

status: Public on May 19 2005

city: Minneapolis

first: Craig

last: Eckfeldt

state: MN

address: 420 Delaware St. SE, MMC 806

department: Stem Cell Institute

institute: University of Minnesota

summary:
The global gene expression profiles of human umbilical cord blood and adult bone marrow CD34+CD33-CD38-Rho(lo)c-kit+ cells, enriched for hematopoietic stem/progenitor cells (HSC) with CD34+CD33-CD38-Rho(hi) cells, enriched in committed hematopoietic progenitor cells (HPC), were compared to identify candidate regulators of HSC self-renewal versus differentiation fate decisions.
Keywords: parallel sample

first: Eric

last: Mendenhall

first: Catherine

last: Flynn

first: Tzu-Fei

last: Wang

first: Suzanne

last: Grindle

first: Stephen

middle: C

last: Ekker

last: Verfaillie

last: Pickart


title: Leu Effect on Cultured Human Liver Cell Lines

status: Public on Mar 11 2005

city: Jacksonville

first: Yan

middle: W.

last: Asmann

state: FL

address: 4500 San Pablo Road South

institute: Mayo Clinic

summary:
The transcript profiles were measured using total RNAs from low (0.1mM) and high (2.0mM) treated THLE-3 cells across 5 time points.
Keywords: time-course

first: John

last: Carpenter

first: K

last: Nair


title: Cross-platform reproducibility of oligonucleotide microarray expression profiles

status: Public on Mar 01 2005

city: Heidelberg

first: Joerg

last: Schlingemann

address: Technologiepark III, Im Neuenheimer Feld 280

department: Molecular Biology (B060)

institute: German Cancer Research Center (DKFZ)

summary:
Both spotted long oligonucleotide arrays (GPL1384) and Affymetrix GeneChip arrays (GPL96) were used to analyze gene expression in six human head and neck squamous cell carinoma samples versus control samples or lymph node metastases of the same patients. Hybridizations of HG-U133A GeneChip arrays were performed using standard Affymetrix protocols and equipment. Before hybridization on DKFZ Operon 27k long oligonucleotide arrays, 2 µg RNA were amplified by one round of linear isothermal RNA amplification, followed by Cy-dUTP incorporation using Klenow fragment. Hybridizations were performed for 16 h at 42 °C in a GeneTAC Hybridization Station (Genomic Solutions) using UltraHyb hybridization buffer (Ambion). Hybridized microarrays were scanned at 5 µm resolution on a GenePix 4000B microarray scanner (Axon Instruments). Raw signal intensities from both platforms were normalized applying variance stabilization (W. Huber et al., Bioinformatics 18 Suppl 1, 2002). Expression ratios were compared for those genes represented in both array platforms.
Keywords: parallel sample

first: Negusse

last: Habtemichael

first: Carina

last: Ittrich

first: Axel

last: Benner

first: Meinhard

last: Hahn

first: Roland

last: Stauber

first: Peter

last: Lichter

first: Heidi

last: Kramer


title: Transcriptional Profiling of Untreated, HIV-1 Vector-Infected and TNFalpha-treated Jurkat T cells

first: Mary

last: Lewinski

state: CA

institute: The Salk Institute

summary:
Jurkat T cells (in triplicate per treatment group) were left untreated in culture, infected with VSV-G-pseudotyped HIV-based vector (which transduces Tat and eGFP) or treated with TNFalpha.
Keywords: parallel sample

middle: K

first: Dwayne

last: Bisgrove

first: Paul

last: Shinn

first: Huaming

last: Chen

first: Christian

last: Hoffmann

first: Sridhar

last: Hannenhalli

last: Verdin

first: Charles

last: Berry

first: Joseph

last: Ecker

first: Frederic

middle: D

last: Bushman


title: Metal and Gene Expression

status: Public on Feb 28 2005

first: Yuh-Chin

middle: Tony

last: Huang

state: NC

address: Erwin Rd

department: Medicine

institute: Duke University Medical Center

summary:
Human bronchial epithelial cells were treated with vehicle (control), VOSO4 (V, 50 uM) or ZnSO4 (Zn, 50 uM) for 4 hours.
Keywords: other

first: Zhuowei

last: Li

first: Robert

last: Devlin

first: Jackie

last: Stonehuerner


title: Breast cancer relapse free survival

status: Public on Feb 23 2005

city: San Diego

first: Tim

last: Jatkoe

institute: Veridex

summary:
This series represents 180 lymph-node negative relapse free patients and 106 lymph-node negate patients that developed a distant metastasis.
Please see attached patient clinical parameters sheet for more information.
Keywords: other


title: Arabidopsis polysome microarray

status: Public on Feb 12 2005

city: Riverside

first: Julia

last: Bailey-Serres

address: Batchelor Hall

department: Center for Plant Cell Biology

institute: University of California Riverside

summary:
Microarray experiment with polysomal and non-polysomal RNAs extracted under non-stress and mild-dehydration stress.
Keywords = translation
Keywords = ribosome loading
Keywords = polysome
Keywords = dehyrdation
Keywords: other

first: Riki

last: Kawaguchi


title: Prediction of lymphatic metastasis from primary squamous cell carcinoma of the oral cavity

status: Public on Feb 19 2005

city: Philadelphia

first: Rebekah

last: O'Donnell

state: PA

department: Pathology

institute: Children's Hospital of Philadelphia

summary:
Metastasis via the lymphatics is a major risk factor in squamous cell carcinoma of the oral cavity (OSCC). We sought to determine whether the presence of metastasis in the regional lymph node could be predicted by a gene expression signature of the primary tumor. A total of 18 OSCCs were characterized for gene expression by hybridizing RNA to Affymetrix U133A gene chips. Genes with differential expression were identified using a permutation technique and verified by quantitative RT-PCR and immunohistochemistry. A predictive rule was built using a support vector machine, and the accuracy of the rule was evaluated using crossvalidation on the original data set and prediction of an independent set of four patients. Metastatic primary tumors could be differentiated from nonmetastatic primary tumors by a signature gene set of 116 genes. This signature gene set correctly predicted the four independent patients as well as associating five lymph node metastases from the original patient set with the metastatic primary tumor group. We concluded that lymph node metastasis could be predicted by gene expression profiles of primary oral cavity squamous cell carcinomas. The presence of a gene expression signature for lymph node metastasis indicates that clinical testing to assess risk for lymph node metastasis should be possible.
Keywords = oral carcinoma lymphatic metastasis predict
Keywords: repeat sample

first: Michael

last: Kupferman

first: S. Jack

last: Wei

first: Sunil

last: Singhal

first: Randal

last: Weber

first: Bert

last: O'Malley Jr.

first: Yi

last: Cheng

last: Putt

last: Feldman

first: Barry

last: Ziober

first: Ruth

middle: J

last: Muschel


title: Anti-prolif. effect of E2 in breast cancer cells that re-exp. ERalpha is mediated by aberr. regulat. of cell cycle genes

status: Public on Feb 09 2005

city: Sharnbrook

first: Fei Ling

last: Lim

state: Bedfordshire

address: Colworth Science Park

institute: Unilever

summary:
Gene expression changes caused by estrogen treatment of breast cancer cells that re-express ERalpha was investigated by infecting ER-negative MDA-MB-231 breast cancer cells for 24 h with recombinant adenovirus encoding full-length human ERalpha (Ad-ERalpha) or control vector (Ad-LacZ), and treating them with 0·01% ethanol (vehicle control) or 10-8 M 17beta-estradiol (E2). After 48 h of treatment, total RNA was isolated and used for transcript profiling on Affymetrix GeneChips. Three independent biological replicates of this experiment were carried out.
Keywords: ordered

first: Jonathan

middle: g

last: Moggs

first: Tracey

middle: c

last: Murphy

first: David

middle: j

last: Moore

last: Stuckey

first: Kate

last: Antrobus

first: Ian

last: Kimber

first: George

last: Orphanides


title: Plasma cell dyscrasias expression profiles associated with distinct IGH translocations in multiple myeloma

status: Public on Feb 08 2005

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary:
This series of microarray experiments contains the gene expression profiles of purified plasma cells (PCs) obtained from 7 monoclonal gammopathy of undetermined significance (MGUS), 39 newly diagnosed multiple myeloma (MM) and 6 plasma-cell leukaemia (PCL) patients. PCs were purified from bone marrow Seriess, 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. After scanning, the images were processed using Affymetrix MicroArray Suite (MAS) 5.0 software to generate gene expression intensity values. Arrays normalization was performed using MAS 5.0 "global scaling" procedure, which normalizes the signals of different experiments to the same target intensity (TGT=100).
Keywords: other

first: Michela

last: Mattioli

first: Sonia

last: Fabris

last: Baldini

first: Fortunato

last: Morabito

first: Silvio

last: Bicciato

first: Donata

last: Verdelli

first: Intini

last: Daniela

first: Lucia

last: Nobili

first: Lilla

last: Cro

first: Giancarlo

last: Pruneri

first: Vincenzo

last: Callea

first: Caterina

last: Stelitano

first: Anna Teresa

last: Maiolo

first: Luigia

last: Lombardi

first: Antonino

last: Neri


title: Differential Gene Expression in Pulmonary Artery Endothelial Cells Exposed to Sickle Cell Plasma

city: Boston

first: Paola

last: Sebastiani

state: MA

institute: Boston University

summary:
Clinical variability in sickle cell disease (SCD) suggests a role for extra-erythrocytic factors in the pathogenesis of vasoocclusion. We hypothesized that one potential factor, endothelial dysfunction, results from induction of phenotypic changes by circulating factors in SCD patients. The database reports gene expression in cultured human pulmonary artery endothelial cells (HPAEC) exposed to plasma from: a) sickle acute chest syndrome (ACS) patients (samples ; b) SCD patients at steady-state and c) normal volunteers using microarrays (U133A-B GeneChip Affymetrix).
Keywords: other

first: Elizabeth

last: Klings

first: Surinder

last: Safaya

first: Adeboye

last: Adewoe

first: Adam

last: Odhiambo

first: Garret

last: Frampton

first: Marc

last: Lenburg

first: Martin

last: Steinberg

first: Harrison

middle: W

last: Farber


title: Carious versus healthy pulp gene expression

status: Public on Mar 30 2005

city: Birmingham

first: Paul

last: Cooper

state: West Midlands

address: St Chads Queensway

department: School of Dentistry

institute: The University of Birmingham

summary:
Duplicate analysis of pooled healthy and carious pulpal tissue gene expression using Affymetrix HG_U133A arrays
Keywords: repeat sample

first: Julia

last: McLachlan

first: Anthony

last: Smith

first: Iwona

last: Bujalska

middle: R


title: D4-ME effects

status: Public on Jan 26 2005

city: Toronto

first: Daniel

last: Kirouac

state: Ontario

department: Biomaterials and Biomedical Engineering

institute: University of Toronto

summary:
Umbilical cord blood-derived mononuclear cells were lineage depleted using a StemSep column and cultured in serum-free liquid suspension culture with cytokines SCF, FL, and Tpo.  After four days in culture (d4), cultured cells were split into 2 groups; one subjected to media exchange and one subjected to a mock exchange, and cultured for an additional day.

RNA was extracted and analyzed on an oligonucleotide microarray from day 4 cultured cells (d4), day 4-derived sorted lin+ cells (lin+), day 4 cells which were placed in fresh media for 24-hours (d5-E) and day 4 cells which were subjected to a mock media dilution/exchange and left for 24-hours (d5-NE)

Total cellular mRNA was collected by lysing cells in 500 μl Trizol Reagent (Invitrogen, Groningen, The Netherlands) for 5 min followed by addition of 100 μl chloroform. After centrifugation at 12,000 g for 15 min, the aqueous phase was collected and mixed with isopropanol to precipitate the mRNA. The mRNA pellet was then obtained by centrifugation at 12,000 g for 10 min, washed in 70% ethanol and re-suspended in sterile water. mRNA concentration was then determined using a mQuant plate reader (Biotek Instruments, Winooski, VT).

Subsequent sample preparation and hybridization was conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA). Because of the limited numbers of cells that could be collected from each experiment, the Two-Cycle Target Labeling technique was used which first translates RNA into cDNA using a T7-oligo(dT) polymerase primer. The cDNA was then subjected to in vitro transcription during which biotin labeled nucleotides are incorporated into the resultant cRNA. The cRNA was then fragmented and hybridized to the Affymetrix HU133 chip set. All samples were obtained in triplicate and sent to the Ontario Genomics Innovation Centre (Ottawa Health Research Institute, Ottawa, Canada) for analysis.

Keywords: parallel sample

first: Gerard

last: Madlambayan

first: Peter

last: Zandstra


title: Filaria induced monocyte dysfunction and its reversal following treatment

status: Public on Jan 12 2005

city: Bethesda

first: Roshanak

middle: T

last: Semnani

state: MD

address: Center Drive

department: LPD

institute: NIAID

summary:
To assess the function of peripheral blood derived monocytes in patently infected filaria patients (either Wuchereria bancrofti, Mansonella perstans, or both), we investigated the cytokine production and gene expression profile of these cells in filaria infected patients and compared them with those from uninfected normal blood bank donors. Monocytes from infected individuals were studded with intracellular microfilarial antigens. In addition, Staphylococcus aureus Cowan I bacteria (SAC)/IFN γ activated monocytes from the infected individuals produced less IL 8, Exodus II, MIP 1a, MIP 1b, eotaxin, RANTES, IL 1a, and MIP 3b compared with normal patients. Microarray analysis of ex vivo isolated monocytes demonstrated that multiple genes involved in signal transduction, apoptosis, and adhesion were expressed to a greater degree in filaria infected patient monocytes compared with those of uninfected normal individuals. Eight months following treatment with a single dose of ivermectin/albendazole, monocytes of W. bancrofti infected individuals were capable of producing more IL 8, IL 1a, MIP 1a, and IL 10 in response to SAC/IFN γ compared with their pretreatment levels. Further, when monocyte global expression was compared before and after treatment of the W. bancrofti, there was a marked increase in mRNA expression of genes associated with protein metabolism, and in HSP most particularly, compared with pretreatment expression. These data suggest that the function and gene expression of monocytes in filaria infected patients are altered; however, this dysfunction can be reveresed to a degree following treatment with a single dose of ivermection/albendazole.

Keywords: other


title: HOXA5 transcriptional targets

status: Public on Feb 05 2005

city: Baltimore

first: Hexin

last: Chen

institute: Johns Hopkins University

summary:
HOXA5 inducible cell line Hs578T was established and cultured as described previously (MCB 2004. 24:924-935). 2×106 cells were seeded onto a 10-cm cell culture dish at 24h before induction. Two batches of RNA from HOXA5-inducible cells (0 h, 6 h and 9 h) were purified for repeating the microarray hybridization experiments once using Affymatrix Chips.Total RNA was extracted using TRIzol reagent (Gibco BRL, Life Technologies, Grand Island, NY) and purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).
Keywords: time-course

first: Ethel

last: Rubin

first: Huiping

last: Zhang

first: Seung

last: Chung

first: Charles

last: Jie

last: Garrett

first: Shyam

last: Biswal

first: Saraswati

last: Sukumar


title: Mitochondrial disorders

status: Public on Jan 22 2005

city: Milan

first: Marco

last: Crimi

address: Via F. Sforza, 35

department: Dept. of Neuroscience

institute: University of Milan

summary:
Extremely variable clinic and genetic features characterize Mitochondrial Encephalomyopathy Disorders (MED). Pathogenic mitochondrial DNA (mtDNA) defects can be divided into large-scale rearrangements and single point mutations. Clinical manifestations become evident when a threshold percentage of the total mtDNA is mutated. In some MED, the "mutant load" in an affected tissue is directly related to the severity of the phenotype. However, the clinical phenotype is not simply a direct consequence of the relative abundance of mutated mtDNA. Other factors, such as nuclear background, can contribute to the disease process, resulting in a wide range of phenotypes caused by the same mutation. Using Affymetrix oligonucleotide cDNA microarrays (HG-U133A), we studied the gene expression profile of muscle tissue biopsies obtained from 12 MED patients (4 common 4977-bp deleted mtDNA and 8 A3243G: 4 PEO and 4 MELAS phenotypes) compared with age-matched healthy individuals.
Keywords = mtDNA mutation
Keywords = muscle biopsy
Keywords = human
Keywords = mitochondrial disease
Keywords: other

first: Giacomo

middle: P

last: Comi


city: Salamanca

first: Norma

middle: Carmen

last: Gutierrez

department: Hematology

institute: University Hospital

summary:
Gene expression profile of acute myeloid leukemia.

Bone marrow (BM) samples from 43 adult patients with newly de novo diagnosed AML.All samples contained more than 80% blast cells.
Total RNA was extracted using Trizol reagent (Life Technologies, Gaithersburg, MD) and purified with RNeasy Mini Kit (Quiagen, Valencia, CA). The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
The labeled RNA was then fragmented and hybridazed to HU-133A oligonucleotide array (Affymetrix, Santa Clara, CA), which contained 22,283 probe sets, according to Affymetrix protocols. The arrays were scanned using Gene Array Scanner (Affymetrix).
Keywords = expression profile
Keywords = myeloid leukemia
Keywords = microarrays
Keywords: other

last: Gutiérrez

first: Ricardo

last: López-Pérez

first: Jesús

middle: M

last: Hernández

first: Isabel

last: Isidro

first: Belén

last: González

first: Manuel

last: Delgado

first: Encarna

last: Fermiñán

first: Juan

middle: L

last: García

first: Lourdes

last: Vazquez

first: Marcos

middle: F

last: San Miguel


title: Transcript Profiling of Arabidopsis Plant Life Cycle

status: Public on Jan 01 2005

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary:
This series contain all stages Arabidopsis plant development.  Stages of development includes unfertilized ovule, 24-Hr post-fertilization seed, globular stage seed, cotyledon stage seed, mature green seed, post-mature green seed, post-germination seedling, rosette leaf, root, stem, and floral bud.
Keywords = Arabidopsis
Keywords = Seed development
Keywords = seedling
Keywords = germination
Keywords = leaf
Keywords = root
Keywords = stem
Keywords = floral bud
Keywords: ordered

first: Brandon

middle: H

last: Le

first: Anhthu

middle: Q

last: Bui

first: Julie

last: Pelletier

first: Linda

last: Kwong

first: Jack

last: Okamuro

first: Robert

last: Fischer

first: Gary

middle: N

last: Drews

first: John

last: Harada

middle: B


title: Gene expression changes induced by K-ras oncogene in the human pancreatic duct epithelial cell line (H6c7)

status: Public on Jan 11 2005

first: Ming-Sound

last: Tsao

institute: Ontario Cancer Institute/ Princess Margaret Hospital

summary:
k-ras oncogene was transduced into the HPV16-E6E7 immortalized normal human pancreatic duct epithelial cell line (H6c7) to generate a stable K-ras oncogene-expressing cell line (H6c7-Kr). The gene expression profile of the H6c7-Kr cells was compared to that of H6c7 cells. We have excluded (subtracted) genes that were deregulated by transduction of the construct used for K-ras oncogene expression.
Keywords: parallel sample

first: Jiaying

last: Qian

first: Wendy

last: Zhang


title: Effects of anoxia and sucrose on seedling growth

status: Public on Jan 10 2005

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

institute: Sant'Anna School of Advanced Studies

summary:
Arabidopsis thaliana ecotype Columbia glabra were grown for 4 days in the dark without added sucrose. Samples were subsequently kept for 6h either [1] under aerobic conditions, [2] under anoxia in absence of sucrose or [3] under anoxia in presence of sucrose.
Keywords: other

first: Elena

last: Loreti

first: Alessandra

last: Poggi

first: Giacomo

last: Novi

first: Amedeo

last: Alpi


title: Lens Epithelial Cells and Lens Cortical Fiber Cells

status: Public on Feb 15 2005

city: Rochester

last: Hawse

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary:
Total RNA was isolated from three separate populations of human lens epithelial cells and three matching populations of lens cortical fiber cells. All samples were analyzed on separate microarrays.
Keywords: repeat sample

first: Candida

last: DeAmicis-Tress

first: Tracy

last: Cowell

first: Marc

last: Kantorow


title: Marrow-derived Mesenchymal stem cells(2004/12/24)

status: Public on Dec 28 2004

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

institute: National Center for Child Health and Development

summary:
Primary culture of marrow-derived mesenchymal cells vs marrow-derived MSCs with a prolonged life span vs MSCs with a prolonged life span after neuronal induction.

Keywords: repeat sample

first: Kenji

last: Matsumoto

first: Hirohisa

last: Saito

first: Taro

last: Uyama


title: Theca cell gene expression

status: Public on Jan 04 2005

first: Jennifer

middle: Rebecca

last: Wood

address: 421 Curie Blvd

department: Center for Research on Reproduction and Women's Health

institute: University of Pennsylvania

summary:
Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder that affects 5-10% of reproductive aged women.  The hallmark characteristic of PCOS is increased ovarian androgen synthesis.  Previous studies by our laboratory demonstrated that increased androgen synthesis is a stable biochemical phenotype of PCOS theca cells which are the primary source of ovarian androgen production.  The increase in theca cell steroidogenesis was due to an increase in expression of several steroidogenic enzymes including CYP17 and CYP11A but not StAR.  Interestingly, the anti-epileptic drug valproic acid induces increased theca cell androgen synthesis and increased CYP17 and CYP11A mRNA levels. In this study we have characterized the gene expression profiles of theca cells obtained from normal or polycystic ovaries which were maintained in the absence (UNT) or presence (VPA) of valproic acid.  The data identifed new candidate genes and novel signaling pathways which may contribute to the manifestation of PCOS phenotypes including increased androgen production.  The experiments in this study were carried using the Affymetrix U133A and U133B oligonucleotide chips.
Keywords: other

first: Velen

last: Nelson-Degrave

first: Erik

last: Jansen

first: Jan

last: McAllister

first: Sietse

last: Mosselman

first: Jerome

last: Strauss


title: Caco-2 cells cocultured with E.coli Nissle 1917

status: Public on Mar 02 2005

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary:
Confluent Caco-2 cells cultured over 6 hours non-treated with E.coli Nissle 1917
(GSM40938 and GSM40941).

Confluent Caco-2 cells cocultured over 6 hours with E.coli Nissle 1917 (GSM40881 and GSM40937).
Keywords: parallel sample

first: Sya

last: Ukena

first: Astrid

last: Westendorf

first: Wiebke

last: Hansen

first: Manfred

last: Rohde

first: Sina

last: Coldewey

first: Sebastian

last: Suerbaum

last: Buer

first: Florian

last: Gunzer


title: LCCS vs control comparison

status: Public on Dec 31 2004

city: Helsinki

first: Niklas

last: Pakkasjärvi

address: Haartmaninkatu 8

department: Dept. of Molecular Medicine

country: Finland

institute: National Public Health Institute

summary:
Collection of data from ´mRNA obtained from the spinal cord of hree human fetuses suffering from Lethal Congenital Contracture Syndrome and two age-matched human fetuses aborted to unrelated causes.
Keywords: ordered


title: Gene Expression Profile of Primary Effusion Lymphoma

status: Public on Jan 16 2005

city: New York

first: wen

last: fan

address: 1300 York Ave

department: Pathology and Laboratory Medicine

institute: Weill Medical College of Cornell University

summary:
Primary effusion lymphomas (PELs) are specifically associated with KSHV/HHV-8 infection, and most frequently occur in HIV-positive individuals as lymphomatous effusions in the serous cavities without a detectable solid tumor mass. Most PELs have concomitant EBV infection, suggesting that EBV is an important pathogenetic co-factor, although other as yet unidentified cofactors, such as cellular genetic alterations, are also likely to play a role. Lymphomatous effusions that lack KSHV also occur; these are frequently EBV-associated in the setting of HIV infection.  Here we used gene expression profile analysis to determine the viral impact on cellular gene expression and the pathogenesis of these lymphomatous effusions.
We used the Affymetrix HG-U133A microarray to analyze the gene expression profile of these effusion lymphomas (three virologic groups: KSHV-positive EBV-positive PELs, KSHV-positive EBV-negative PELs and KSHV-negative EBV-positive lymphomatous effusions). Nine cell lines derived from patients with lymphomatous effusions (three from each virologic group and each cell line was done in duplicates.) and three PEL patient samples were used in the study. Our results suggest that KSHV-positive PELs are very different from KSHV-negative lymphomatous effusions, and the genes that are differentially expressed include apoptosis regulators, cell cycle regulators, transcriptional factors and signal transduction regulators. KSHV clearly plays a dominant role in the phenotype of PEL. Within the KSHV-positive PELs, two subgroups can be identified, which were correlated with their EBV viral status. Among these genes (45 gene probes), four were regulators of the MAP kinase pathway that were up-regulated in the KSHV-positive, EBV-negative PELs, suggesting that in the absence of EBV, events that lead to the activation of the MAP kinase pathway may act as a cofactor for the development of PEL. Next we determined whether we could predict the viral status of the three primary patient cases of PEL based on the 45 gene probes that were differentially expressed in KSHV-positive cell lines according to EBV status (pt. 1: KSHV-positive, EBV-positive; Pt. 2: KSHV-positive, low proportion of EBV-positive; pt. 3: KSHV-positive EBV-negative), and we could.
Samples:
KSHV-positive EBV-positive cell lines: BC-1, BC-2, BC-5
KSHV-positive EBV-negative cell lines: BC-3, BCBL-1, PEL-5
KSHV-negative EBV-positive cell lines: IBL4, SM1, BCKN-1
pt. 1: KSHV-positive, EBV-positive
pt. 2: KSHV-positive, EBV-positive (low number of positive cells)
pt. 3: KSHV-positive, EBV-negative

Keywords: other

first: Wen

last: Fan

first: Darya

last: Bubman

first: Amy

last: Chadburn

first: William

middle: J

last: Harrington Jr.

first: Ethel

last: Cesarman

first: Daniel

last: Knowles


title: Transcriptional Response of Human Microglial Cells to Interferon-gamma

status: Public on Dec 25 2004

city: Minneapolis

middle: Bryan

last: Rock

institute: University of Minnesota

summary:
Microglial cells are resident macrophages in the central nervous system (CNS) and play a pivotal role in the innate and adaptive immune responses against microbial infections. The immune functions of microglia are regulated by a milieu of cytokines including interferon (IFN)-gamma. We here performed a series of experiments to acertain the transcriptional profile of human fetal microglial cells at 1, 6, and 24 h after IFN-gamma treatment.  Primary human microglial cells were either untreated or treated with 200u/ml IFN-gamma.  Affymetrix U133A chips were utilized.  Four different tissue samples (B18, O, W, and Y20) were analyzed at the three time points.
Keywords = Microglia
Keywords = Interferon-gamma
Keywords: time-course

first: Shuxian

last: Hu

first: Archana

last: Deshpande

first: Shirin

last: Munir

first: Barbara

last: May

first: Phillip

middle: K

last: Peterson

first: Vivek

last: Kapur


title: control-ethanol liver RNA

status: Public on Dec 22 2004

city: Davis

first: Farah

last: ESfandiari

institute: University of California davis

summary:
cRNAs were hybridized with HumU133A oligo arrays (Affymetrix, Santa Clara, CA) which contain 22,283 probe sets. Preliminary studies indicated that Affymetrix Human GeneChips detected more than 60% of pig liver transcripts. All Affymetrix data were filtered for those genes with fluorescent intensity value of less than 100. Genes whose expressions in livers from the folate deficient and ethanol fed groups were either increased or decreased by 2-fold or more (p<0.05) compared to those in livers from the control group were considered significantly changed. GeneChip cRNA probes used in GeneChip expressions were obtained by following a protocol from the manufacturer. First strand cDNA was synthesized by reverse transcription of 8 μg total RNA with superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and T7-oligo (dT) 24 primer (Genset Oligos, Boulder, CO), followed by second strand cDNA  synthesis. Biotin-labeled cRNA probes were generated by reverse transcription of double stranded cDNA using BioArray High yield RNA transcript labeling kit (ENZO Life Sciences, Inc., Farmingdale, NY). The cRNA probes were purified from unincorporated nucleotides by RNeasy mini column (QIAGEN, Valencia, CA), fragmented and hybridized overnight at 680 C to the Human GeneChip array (HG U133A, Affymetrix).
Keywords: parallel sample

last: Esfandiari

first: Jesus

middle: A

last: Villanueva

first: Donna

last: Wong

first: Samual

last: French

first: Charles

last: Halsted


title: HCV_Core_Study

status: Public on Dec 15 2004

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
Gene expression in HepG2 cell line
Keywords: other

first: Hau

last: Nguyen

first: Satya

last: Dandekar


title: Human Lung Transplant - BAL

status: Public on Nov 30 2004

first: Jeff

last: Lande

address: 420 Washington Avenue SE

department: Medicine

summary:
Bronchoalveolar lavage samples collected from lung transplant recipients.  Numeric portion of sample name is an arbitrary patient ID and AxBx number indicates the perivascular (A) and bronchiolar (B) scores from biopsies collected on the same day as the BAL fluid was collected.  Several patients have more than one sample in this series and can be determined by patient number followed by a lower case letter.  Acute rejection state is determined by the combined A and B score - specifically, a combined AB score of 2 or greater is considered an acute rejection.
Keywords = Bronchoalveolar lavage
Keywords = lung transplant
Keywords: other

first: Vincent

last: Gimino

first: Jeffrey

middle: D

first: Todd

last: Berryman

first: Richard

last: King

first: Marshall

middle: I

last: Hertz