title: MCF10A cells in 3-D culture for 15 h after treatment with BRCA1-RNAi vs Luc-RNAi adenovirus

first: Wen-Hwa

last: Lee

summary:
BRCA1 exerts transcriptional repression through interaction with CtIP in the C-terminal BRCT domain and ZBRK1 in the central domain. A dozen of genes including angiopoietin-1 (ANG1), a secreted angiogenic factor, are co-repressed by BRCA1 and CtIP based on microarray analysis of mammary epithelial cells in 3-D culture. BRCA1, CtIP and ZBRK1 form a complex that coordinately represses ANG1 expression via a ZBRK1 recognition site in ANG1 promoter. Impairment of this complex upregulates ANG1, which stabilizes endothelial cells forming capillary-like network structure. Consistently, Brca1-deficient mouse mammary tumors exhibit accelerated growth, pronounced vascularization and overexpressed ANG1. These results suggest, besides its role in maintaining genomic stability, BRCA1 directly regulates the expression of angiogenic factors to modulate the tumor microenvironment.
Keywords: MCF10A, human mammary epithelial cells, 3-D Matrigel, 15 h, BRCA1-RNAi

overall_design: MCF10A cells seeded at 5x105 cells/60mm plate were infected with adenoviral luciferase- or BRCA1-RNAi in duplicate at 20 MOI for 24h. Infected cells were re-seeded at 5x105 cells in a 60mm plate pre-coated with Growth Factor Reduced Matrigel and covered with the growth medium containing 2% Matrigel at 37°C for 15h. RNA was extracted and quality assessed. cDNA synthesized from the harvested RNA was biotin-labeled, hybridized onto Affymetrix HG U133 PLUS 2.0 array (54,676 genes) and stained with streptavidin-phycoerythrin. The hybridized array was analyzed using GeneChip® Scanner 3000 and GCOS 1.2 software (Affymetrix) at the UCI Microarray Core service.


title: Prostate cell specific expression

status: Public on Apr 28 2006

city: Seattle

first: Asa

last: Oudes

state: WA

address: 401 Terry Ave. N

country: USA

institute: Rosetta Biosoftware

summary:
Luminal, basal, stromal, and endothelial cells were MACS sorted from whole tissue.  Targets from five biological replicates of each were generated and the expression profiles were determined using Affymetrix U133 Plus 2.0 arrays.  These data represent cell specific transcriptomes.
Keywords: repeat

overall_design: 5 biological replicates for each sort were analyzed (20 chips)

middle: J

first: Alvin

middle: Y

last: Liu


title: Expression data of glioma samples from Henry Ford Hospital

status: Public on Apr 10 2006

city: Bethesda

first: Howard

last: Fine

state: MD

address: 9030 Old Georgetown Rd

department: Neurological Disorders and Stroke

institute: National Cancer Institute

summary:
mRNA expression data were collected from patients with brain tumor to improve diagnostic of gliomas on molecular level.
Keywords: survey

overall_design: 23 samples from epilepsy patients are used as  non-tumor samples. 157 tumor samples include 26 astrocytomas, 50 oligodendrogliomas and 81 glioblastomas.

middle: A

first: Jean-Claude

last: Zenklusen

first: Yuri

last: Kotliarov

first: Tom

last: Mikkelsen

first: Mark

middle: L

last: Rosenblum


title: Astrocyte and Hela cell response to hypoxia

status: Public on Mar 16 2006

city: New York

first: Sarah

last: Mense

state: NY

address: 722 West 168th Street

department: Environmental Health Sciences

institute: Columbia University

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

overall_design: Refer to individual Series


title: Comparison of gene expression profiles across the normal human body

status: Public on Mar 30 2006

city: San Diego

first: Richard

middle: B

last: Roth

state: CA

address: 12790 El Camino Real

department: Molecular Medicine

institute: Neurocrine Biosciences, Inc.

summary:
Normal human tissue samples from ten post-mortem donors were processed to generate total RNA, which was subsequently analyzed for gene expression using Affymetrix U133 plus 2.0 arrays.  Donor information: Donor 1 - 25 year old male; donor 2 - 38 year old male; donor 3 - 39 year old female; donor 4 - 30 year old male; donor 5 - 35 year old male; donor 6 - 52 year old male; donor 7 - 50 year old female; donor 8 - 48 year old female; donor 9 - 53 year old female; donor 10 - 23 year old female
Keywords: normal human tissue comparison

overall_design: Comparison of normal human tissues; 65 tissues represented, including 20 distinct regions of the CNS


title: Gene Expression Profiles of Multiple Myeloma  (N=65) Before Treatment

status: Public on Apr 15 2006

city: Little Rock

first: Shaughnessy

middle: Jr.

last: John

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

summary:
Samples in this series are pre-treatment bone marrow aspirates from multiple myeloma patients
Keywords: other

overall_design: Samples in this series are: CD-138-selected plasma cells from bone marrow of newly diagnosed multiple myeloma patients susequently treated with Total Therapy

first: John

middle: D

last: Shaughnessy


title: Ectopic expression of Foxp3 and UBD in Th cells

status: Public on May 30 2006

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

summary:
Expression analysis revealed that UBD is a down-stream element of Foxp3 in human activated regulatory CD4+ T cells (Treg).
Keywords: genetic modification

overall_design: Comparison of expression profiles measured in naturally occuring regulatory T-cells (Treg), Foxp3 and UBD transformed Th cells versus their controls with respect to the observed regulatory phenotype.

first: R

first: M

last: Probst-Kepper

first: F

last: Ocklenburg


title: Affymetrix U133Plus2.0 data sets of Human Myeloma Cellline JJN3 with non-specific, scrambled shRNA or CKS1B shRNA

status: Public on Mar 31 2006

summary:
This series represents Affymetrix U133Plus2.0 data sets of JJN3 transduced with levivirus expressing non-specific scrambled shRNA or CKS1B shRNA
Keywords: JJN3 CKS1B shRNA

first: Fenghuang

last: Zhan

first: Ichiro

last: Hanamura

first: Bart

middle: E

last: Burington

first: Peter

last: Stewart

first: Jeffrey

last: Sawyer

first: Erming

last: Tian

first: Yongsheng

last: Huang

first: Elias

last: Anaissie

first: Joshua

last: Epstein

first: Athanasios

last: Fassas

first: M.

last: Cuttler-Fox

first: Klaus

last: Hollmig

first: Erik

last: Rasmussen

first: Frits

last: Van Rhee

first: Ronald

last: Walker

first: Shmuel

last: Yaccoby

first: Maurizio

last: Zangari

first: Guido

last: Tricot

last: Crowley

last: Barlogie


title: Whole-genome expression profiling of melanoma progression.

status: Public on Apr 01 2006

city: Pittsburgh

first: Dorothea

last: Becker

state: PA

address: 5117 Centre Avenue

department: Department of Pathology

institute: University of Pittsburgh

summary:
To gain insights into the genetic profile of every stage of the melanoma progression pathway, and to determine to what extent these profiles are similar or distinct, we performed whole-genome expression profiling of tissue specimens representing normal skin, benign and atypical nevi, and early and advanced-stage melanomas. The results of this study provide first-time evidence that significant molecular changes occur distinctly at the border of/transition from melanoma in situ to primary melanoma, and that genes involved in mitotic cell cycle regulation and cell proliferation constitute the two leading categories of genes associated with these changes.
Keywords: Stage comparative analysis

overall_design: Biopsy specimens representing normal skin, nevi, early and advanced stage melanomas, a melanoma cell line, and short-term cultures of human melanocytes and keratinocytes were subjected to whole-genome expression profiling.

first: Amanda

middle: P

last: Smith

first: Keith

last: Hoek


title: Global exploration of interaction between HBsAg expression and Hepatocytes

status: Public on Mar 28 2006

city: Shanghai

first: Xiaochen

last: Tian

address: No.138 Yixueyuan Road

department: Shanghai Medical college

country: China

institute: Fudan University

summary:
In patient serum, HBsAg particles can outnumber HBV particles by 1000:1 or higher. To explore the interactions between HBsAg and hepatocytes, concentrating on the possible effects of persistently secreting HBsAg on the functions of host cells, we have used the S gene of a full-length HBV isolate derived from an HBsAg chronic carrier (code No. C8, GenBank accession No. AF461363), cloned into pCMV vector to transfect HepG2 cells. G418 resistant clones secreting HBsAg were selected to establish permanent cell lines, and control clones transfected only with the vector were passaged as well to serve as controls. Cells were separately collected on the fourth and the eighth day after seeding, and gene expression profiles of both cell clones were studied and compared by microarray. Totally, 340 genes were suppressed and 673 genes were induced by the expression of HBsAg on the fourth day, whereas 219 genes were down-regulated and 683 genes were up-regulated on the eighth day. Arbitrarily, changes of genes detected on both 4th and 8th day cultures were selected for further study. Many cellular functions such as immune response, xenobiotic metabolism, ubiquitin pathway, transcription regulation were affected by HBsAg expression, indicating a close association between HBsAg and host cells.
Keywords: interaction, HBsAg expression, hepatocyte function

overall_design:
HBsAg particles are composed of viral envelope proteins and outnumber HBV virions by 1000:1 or even higher. This unique characteristic of HBV remains to be one of the challenges in basic and clinical aspects of viral hepatitis B.
In this study, we want to explore the interactions between HBsAg and hepatocytes, concentrating on the effects of persistently secreting HBsAg on host cell functions.

first: Jun

last: Ren

first: Chao

last: Zhao

first: Zhang-Mei

last: Ma

first: Yu-Mei

last: Wen*


title: Profiling of ER+ BrC cells with and without estradiol in both cell cultures and xenografts

status: Public on Mar 03 2006

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

summary:
We generated DNA microarray based gene expression profiles from three estrogen receptor a (ERa) positive breast cancer cell lines stimulated by 17ß-estradiol (E2) in vitro over a time course, as well as from MCF-7 cells grown as xenografts in ovariectomized athymic nude mice with E2 supplementation and after its withdrawal.
Keywords: Cell line and xenograft comparisons

overall_design: 8 MCF-7 xenograft profiles (4 with E2,4 without E2), 14 T47D profiles (with E2 treatment in culture from 0 to 24 hr), 10 BT-474 profiles (with E2 treatment from 0 to 24 hr), 12 MCf-7 profiles (with E2 treatment from 0 to 24 hr)

first: Jimmy

last: Rae

first: Marc

last: Lippman


title: Host transcriptome changes associated with episome loss and selection of keratinocytes containing integrated HPV16

status: Public on Feb 24 2006

city: Cambridge

first: Mark

middle: Robert

last: Pett

state: Cambridgeshire

address: Hills Road

department: Cancer Cell Unit

country: United Kingdom

institute: Medical Research Council

summary:
Integration of high-risk human papillomavirus (HRHPV) into the host genome is a key event in cervical neoplastic progression. Integration is associated with deregulated expression of the viral oncogenes E6 and E7 and acquisition of a selective growth advantage for cells containing integrants. Overexpression of the viral transcriptional regulator E2 from heterologous promoters has an inhibitory effect on transcription from integrated HRHPV. We therefore hypothesised that loss of E2-expressing episomes from cells in which integration had previously occurred would be required for such cells to gain a growth advantage. Using the unique W12 model of cervical squamous carcinogenesis, we show that cells containing integrated HPV16 reproducibly emerged during long-term culture when there had been a rapid fall in episome numbers. During the period of emergence it is possible to isolate single-cell clones containing an intracellular mixture of the integrant being selected and episomes at reduced load. Microarray analysis showed that episome loss was closely associated with endogenous activation of antiviral response genes that are also inducible by the type I interferon (IFN) pathway. Taken together, our results indicate that episome loss, associated with induction of antiviral response genes, is a key event in the spontaneous selection of cervical keratinocytes containing integrated HPV16. We conclude that cervical carcinogenesis requires not only HRHPV integration, but also loss of inhibitory episomes.
Keywords: Time course, human papillomavirus, episome loss

overall_design:
The overall aim was to determine host gene expression changes associated with episome loss in W12 cells undergoing selection for integrated HPV16. We therefore compared gene expression in W12 populations representing different stages in the process of integrant selection. We compared W12p10EPI (episome-only) with clones W12.MRP20 (undergoing selection for the integrant and episome loss) and W12.MRP29 (containing only the selected integrant), which are henceforth referred to as W12.MRP20MIX and W12.MRP29INT. These three conditions were treated as a time-course.

Preparation and hybridisation of probes for microarray analysis: Total RNA from W12 samples was used to generate biotin-labelled cRNA for microarray analysis. Two technical replicates were performed for each sample to control for variation in labelling and hybridisation efficiency. Double-stranded cDNA was synthesised using SuperScript (Invitrogen), employing the (dT)24-T7 promoter primer. Biotin-labelled cRNA was then generated by Bioarray in vitro transcription (Enzo), and fragmented by metal-induced hydrolysis. Probe from each replicate was hybridised, washed, stained and scanned by the Medical Research Council Geneservice (Cambridge, UK) using standard Affymetrix procedures. We used GeneChip HG-U133 Plus 2.0 Arrays (Affymetrix). MAS 5.0 transformation of raw data was performed and further statistical analysis carried out using GeneSpring (Agilent Technologies). Real-time RT-PCR of cDNA was performed to validate changes in expression of selected host genes.

middle: R

first: Michael

middle: T

last: Herdman

first: Roger

last: Palmer

first: Giles

middle: S

last: Yeo

first: Mahmud

middle: K

last: Shivji

first: Margaret

last: Stanley

first: Nicholas

last: Coleman


title: Hypoxia responsive genes in human Burkitt’s lymphoma cell line, P493-6.

city: Baltimore

first: Chi

middle: V.

last: Dang

address: 720 Rutland Ave, Ross 1032

department: Medicine

institute: Johns Hopkins University, School of Medicine

summary:
Activation of glycolytic genes by HIF-1 is considered critical for metabolic adaptation to hypoxia.  We found that HIF-1 also actively suppresses glucose metabolism through the tricarboxylic acid cycle (TCA) by directly trans-activating the gene encoding pyruvate dehydrogenase kinase 1 (PDK1).  PDK1 inactivates the TCA cycle enzyme, pyruvate dehydrogenase (PDH), which converts pyruvate to acetyl-CoA.  Forced PDK1 expression in hypoxic HIF-1α-null cells increases ATP levels, attenuates hypoxic ROS generation and rescues these cells from hypoxia-induced apoptosis. These studies reveal a novel hypoxia-induced metabolic switch that shunts glucose metabolites from the mitochondria to glycolysis to maintain ATP production and to prevent toxic ROS production.
Keywords: Hypoxia responsive, case control

overall_design: We sought to determine by microarray analysis of gene expression the genes responsive to hypoxia using the human B lymphocyte cell line, P493-6. Hypoxia-responsive genes were globally assessed in cells incubated in 0.1% O2 for 29 hours at which the highest HIF-1 levels were obtained

first: Jung-whan

last: Kim

first: Irina

last: Tchernyshyov

first: Gregg

last: Semenza

middle: V


title: Determination of expression level of gingiva expressed genes

status: Public on Feb 17 2006

first: Kong

last: Xiangyin

address: South Chongqin Rd.225

institute: Institute of Health Sciences,SIBS,CAS/SJTU

summary:
All experiment was done according to the Affymetrix manufacturer’s protocol.  The resulting HGF gingiva expression profile(Hereditary gingival fibromatosis patient Gingiva replicate1 and replicate 2)was compared to normal gingiva control(Normal Gingiva replicate1 and replicate2). The data were collected and analyzed by GCOS 1.2 and GeneSpring 7.2 1-way T test.
Keywords: tissue specific expression profile

overall_design: Hereditary gingival fibromatosis patient Gingiva (experimental) and Normal Gingiva (control) were used. N1 and P1 are gingiva tissue from female individuals while N2 and P2 are from male ones.

first: Yufei

last: Zhu

first: Yi

last: Zhang

first: Yu

last: Xia

first: Xiangyin

last: Kong

first: Landian

last: Hu


title: HeLa response to hypoxia

first: Sarah

last: Mense

summary:
Oxygen is vital for the development and survival of mammals.  In response to hypoxia, the brain initiates numerous adaptive responses at the organ level as well as at the molecular and cellular level, including the alteration of gene expression.  Astrocytes play critical roles in the proper functioning of the brain, thus the manner in which astrocytes respond to hypoxia is likely important in determining the outcome of brain hypoxia.  We used microarray gene expression profiling and data analysis algorithms to identify and analyze hypoxia-responsive genes in primary human astrocytes.  We also compared the gene expression patterns in astrocytes with those in human HeLa cells and pulmonary artery endothelial cells (ECs).  Remarkably, in astrocytes, 5 times as many genes were up-regulated as down-regulated, whereas in HeLa and pulmonary ECs, as many or more genes were down-regulated as up-regulated.  More genes encoding hypoxia-inducible functions, such as glycolytic enzymes and angiogenic growth factors, were strongly induced in astrocytes compared to HeLa cells.  The extent of induction was also greater than in HeLa cells.  Further, gene ontology and computational algorithms revealed that many target genes of the EGF and insulin signaling pathways and the transcriptional regulators Myc, Jun and p53 were selectively altered by hypoxia in astrocytes and HeLa cells to a varying degree.  These results provide a global view of the signaling and regulatory network mediating oxygen regulation in astrocytes, in comparison with that in HeLa cells.
Keywords: response to hypoxia

overall_design: Gene expression profiles of three independent batches of HeLa cells grown under normoxia were compared to gene expression profiles of three independent batches of HeLa cells grown under 1% oxygen for 24 hours.  Affymetrix U133 plus 2.0 microarrays were used.

first: Mei

last: Zhou

first: Amit

last: Sengupta

first: Changgui

last: Lan

first: Galina

last: Bentsman

first: David

last: Volsky

first: Li


title: Astrocytic response to hypoxia

overall_design: Gene expression profiles of three independent batches of astrocytes grown under normoxia were compared to gene expression profiles of three independent batches of astrocytes grown under 1% oxygen for 24 hours.  Affymetrix U133 plus 2.0 microarrays were used.


title: perro-affy-human-186940

status: Public on Jan 13 2006

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Our laboratory has developed the first mouse model overexpressing a RNA-binding protein, the ELAV-like protein HuD, in the CNS under the control of the CaMKinII alpha promoter. Initial behavioral characterization of the mice revealed that they had significant learning deficits together with abnormalities in prepulse inhibition (PPI). At the molecular level, we found that the expression of the growth-associated protein GAP-43, one of the targets of HuD, was increased in the hippocampus of HuD transgenic mice. To characterize these mice further and to evaluate the utility of these animals in understanding human diseases, we propose to use DNA microarray methods.
To test our hypothesis we propose 3 specific aims:
1) To characterize the pattern of gene expression in the hippocampus of HuD overexpressor mice
2) To compare the pattern of gene expression in our mouse model with that in the hippocampus of rats prenatally exposed to alcohol (FAS model) and
3) To compare the pattern of gene expression in our mouse model with that shown in post-mortem tissues of patients with schizophrenia.
In our previous protocols we examined the pattern of gene expression in our HuD transgenic mice and in rats prenaltally exposed to alcohol. A report by another group (Hakak et al, 2001) showed that three of the HuD targets were upregulated in the prefrontal cortex of patients with schizophrenia. To evaluate whether other target of HuD may be affected in this illness, in the current protocol, we want to compare the pattern of expression in our transgenic mice with in tissue from patients with schizophrenia
Based on the behavioral and molecular properties of our HuD transgenic mice we hypothesize that these animals may be good models for the studying the basis of learning disabilities and of diseases that show deficits in PPI such as fetal alcohol syndrome and schizophrenia.
All 28 samples are derived from cerebellar tissues for patients with schizophrenia and matched controls.  The specimens were obtained from the Maryland Brain Collection according to NIH guidelines for confidentially and privacy. The protocol used in these studies was reviewed by our HRRC which found that our studies do not fall within the category of protocols monitored by the IRB (see attached letter form the HRRC). Specimens from 14 patients with a diagnosis of schizophrenia performed according to DSM-IV criteria and 14 sex-, age- and PMI-matched controls was included in this study. No differences were found between patients and control subjects in the average age (45±12 versus 43±10 years, p=0.86) or PMI (12±5 versus 16±6 hours, p=0.11). We will provide 28 samples containing 5 ug of RNA each in DEPC water (see validation of the quality of the RNA below). In addition, we include in our study animals treated with haloperidol as control for medication. These samples will be submitted in a separate protocol.
Keywords: other

first: Nora

middle: I

last: Perrone-Bizzozero


title: Scheck-3U24NS043571-01S1

summary:
Meningiomas are typically considered a benign tumor that can be cured by complete surgical resection; however, a percentage of patients have recurrent disease, even after apparently complete resections.  These patients require additional surgeries, radiation therapy, chemotherapy, or a combination of all three.  The ability to recognize these patients prior to recurrence would promote earlier use of adjuvant therapy, thus improving overall patient outcome.  Unfortunately, identification of meningiomas with this more aggressive phenotype is difficult, and standard histopathological techniques rarely suffice.  The identification of genetic and molecular parameters that can help to define these more aggressive tumors would improve prognostication and treatment planning for patients with meningiomas.
1. Establish gene profiles for benign (grade 1) and aggressive (grades 2 and 3) meningiomas. 2. Determine if there are particular expression profiles that can help differentiate between benign and aggressive meningiomas. 3. Determine if there is/are specific gene(s) whose expression is/are altered in benign vs aggressive tumors. 4. Determine if there is a correlation between specific genetic abnormalities in these tumors (as analyzed by fluorescent in situ hybridization; FISH) and gene expression profiles.
Our overall hypothesis is that there are molecular and biochemical changes that can be used to identify meningiomas that will have a more aggressive clinical course.
Specific Aims 1 and 2: RNA from flash frozen or RNA-later preserved tissue (from all three grades of meningiomas) has been used for RNA isolation using standard protocols.  RNA quantity has been determined using a RiboGreen RNA quantitation Kit (Molecular Probes), and RNA quality has been demonstrated using standard formaldehyde gels.  These samples will be sent to the NINDS/NIMH microarray consortium for Affymetrix microarray analyses.  Data analysis will be done using GeneSpring software (Silicon Genetics, Inc.) with assistance from consortium personnel. Specific Aim 3: Differentially expressed genes identified through microarray analyses will be analyzed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR).  Real time qRT-PCR is a standard technique used in our laboratory for gene expression analysis. Specific Aim 4: FISH analyses of paraffin-embedded tissue has been completed for 77 tumors.  We have frozen tissue from a number of these patients.  RNA from these samples will be used for microarray analyses (Specific Aims 1-3).  The results of Speicifc Aims 1 and 2 will affect how we perform our correlation analyses.  This will be done with the assistance of contracted statistical personnel.
Keywords: other

first: Adrienne

middle: C

last: Scheck


title: bunge-affy-arabi-162779

summary:
Schwann cells, expanded in number by exposure to growth factors in vitro, could be useful in nervous system repair. Our previous results suggest that long term exposure to heregulin and forskolin changes the functional properties of the human Schwann cells, including the ability to myelinate axons after transplantation. Here, we propose to determine the molecular changes in the Schwann cells that occur as a result of extended growth with mitogenic factors. We believe that the information obtained in these studies will provide clues about mechanisms underlying the already observed changes in function. This information will aid in the prediction of the safety and efficacy of neural repair approaches that use cultured, expanded Schwann cells. Finally this data may provide clues into the mechanisms underlying normal human Schwann cell function.
To use gene array analysis to compare gene expression profiles in early and late passage human Schwann cells exposed to the growth factors heregulin and forskolin.
Observed changes in the function of human Schwann cells, including their capacity for growth and differentiation, after prolonged exposure to heregulin and forskolin, are caused by changes in the gene expression profiles in these cells.
Nerves from four different donors were obtained within 12-15 h postmortem, with full consent for research from the families of the donors (faxed). IRB approval not required because subjects were officially dead at nerve harvest (IRB confirmation faxed). The nerve tissue obtained consisted of the lower 15 cm of nerve extending from mid calf to ankle. Endoneurial fascicles were dissected from short (1-2 cm) nerve fragments and cultured with heregulin and forskolin for 1 week.  The nerve fascicles were then treated overnight with collagenase and dispase and dissociated by gentle trituration.  Cells were plated at low density on laminin coated dishes and maintained in culture with mitogens for 3 passages.  Schwann cell purities during this period were > 95%.   RNA was extracted from the cells  at passage 1 ( i.e. after 2 population doublings) and passage 3 (i.e. after 8 population doublings)  from the following donors: SN HSC 330, age 51; SN HSC 317, age 29; SN HSC 329, age 20 and SN HSC 351, age 42.  Thus eight samples (2 groups, 4 independent samples per group) are to be analyzed. Because both groups in this comparison have been exposed to mitogens, differences in gene expression profiles will be interpreted as indicative of changes caused by prolonged versus short term exposure to mitogens. More RNA was prepared from each group of cells than was needed for gene array analysis to allow confirmation of differentially-expressed gene transcripts by real-time RT-PCR. Since the main purpose of this project is to detect any major changes in the molecular properties of the Schwann cells, we propose that these samples be analyzed using Affymetrix U133 + 2 arrays containing the complete human genome and request Option 1: Start to Finish Profiling of all samples.  We have contacted Dr Stanley Nelson at UCLA and discussed the project with him. We request that the samples be analyzed in the UCLA facility.
Keywords: time-course

first: Mary

last: Bunge


title: Human breast tumor expression

status: Public on Feb 09 2006

city: Boston

first: Andrea

last: Richardson

state: MA

address: 75 Francis Street

department: Pathology

institute: Brigham and Women's Hospital

summary:
Gene expression for 47 human breast tumor cases;
(* normalized by GCRMA for global expression analysis)
Keywords: Type

overall_design: Gene expression of human breast tumor by Affymetrix Human Genome U133 Plus 2.0 Array


title: Effect of ionizing radiation on procoagulant activity

status: Public on Jan 29 2006

city: Berlin

first: Henning

last: Witt

address: Ihnestrasse 65

department: Hans Lehrach

institute: Max Planck Institute for Molecular Genetics

summary:
Ionizing radiation (IR) is associated with thrombotic vascular occlusion. Thrombosis in malignancy predicts a poor clinical outcome. Tissue factor (TF) is the initiator of the extrinsic co-agulation system and induces thrombus formation. Our study examined whether IR induced TF expression and procoagulability in the myelomonocytic leukemia THP-1 cell model. We further investigated coordinated gene alterations associated with TF upregulation and IR-induced thrombogenicity. Gene expression profiling revealed IR to increase the expression of inflammatory and apoptosis-related pathways, contributing to TF upregulation and increased TF procoagulability on day 7 post IR. The upregulation of these pathways together with TF upregulation contributed to the increased thrombogenic potential of tissues post application of IR.
Keywords: irridiation response

overall_design: THP-1 cells were harvested on day 3 (1 sample) and day 7 (3 samples) post irradiation. For each time point untreated control samples were run.

first: Petra

last: Goldin-Lang

first: Frank

last: Wittchen


title: Hussaini-2R01NS035122-06A1

status: Public on Feb 14 2006

summary:
Pituitary adenomas are common benign neoplasms giving rise to disorders of growth, reproductive function and cortisol production. Although recently determined to be monoclonal, very little is known about the mechanisms regulating the development of pituitary hyperplasia and neoplasia in humans. Surgical resection is the treatment of choice for most symptomatic pituitary adenomas. The goal of surgery is the complete removal of the tumor and the success of surgery is strongly affected by the presence of local invasion. However, complete tumor removal is unlikely when there is extensive local invasion. Identifying genes that control the invasiveness and recurrence of this class of tumors will provide therapeutic targets for this class of tumors.
We will determine the expression pattern of genes in recurrent and invasive and  pituitary adenomas and compare those to non-invasive and non-recurrent  tumors.
We hypothesize that the differential expression and activation of a number of genes affect pituitary adenoma recurrence  and invasiveness.
Rationale:  Preliminary result showed a differential expression of novel PKC isozymes in non-invasive and invasive pituitary adenomas. PMA, an activator of both novel and classical PKC isozymes increased the expression of gelatinase A (MMP-2) mRNA in human pituitary adenoma cell line. This result raises a fundamental question as to the functional role of novel PKC isozymes and proteases in the invasive phenotype of pituitary adenomas. The primary component of this Specific Aim is to determine whether specific genes are differentially expressed in recurrent or invasive adenomas when compared with control non-invasive tumors.  Tissue specimens from non-invasive and invasive (dural invasion based microscopic examination) and recurrent vs non-recurrent tumors will be used for microarray analysis.  Frozen pituitaryspecimens will be collected and total RNA extracted with TriZol reagent. We will  provide  total RNA (10 ug) from non-invasive, invasive, reoccurred and non-occurrent pituitary adenomas.
Keywords: other

first: Isa

middle: M

last: Hussaini


title: The role of micro-RNA genes in papillary thyroid carcinoma

status: Public on Dec 19 2005

city: Columbus

first: Sandya

last: Liyanarachchi

state: OH

address: Rm 830, 460, W 12th Avenue

department: Human Genetics

institute: OSU

summary:
We show that numerous miRNAs are transcriptionally up-regulated in papillary thyroid carcinoma (PTC) tumors compared with unaffected thyroid tissue.  Among the predicted target genes of the three most upregulated miRNAs (miRs 221, 222 and 146b), only less than 15% showed significant downexpression in transcript level between tumor and unaffected tissue.  The KIT gene which is known to be downregulated by miRNAs 221 and 222 displayed dramatic loss of transcript and protein in those tumors that had abundant mir-221, mir-222, and mir-146b transcript.
Keywords: Disease state analysis

overall_design: Total RNA was extracted from paired tumor and normal thyroid tissues from 9 PTC patients.  The same set samples were applied to Custom miRNA microarray chips (OSU_CCC version 2.0) and Affymetrix HG-U133 plus 2 chips.


title: Hypoxic regulation of gene expression is dominated by the HIF system and can be mimicked by DMOG

status: Public on Dec 01 2005

city: Oxford

first: Ioannis

last: Ragoussis

address: Roosevelt Drive

department: The Wellcome Trust Centre for Human Genetics

institute: University of Oxford

summary:
The response of cells to hypoxia is characterised by co-ordinated regulation of many genes. Studies of the regulation of the expression of many of these genes by oxygen has implicated a role for the heterodimeric transcription factor hypoxia inducible factor (HIF). The mechanism of oxygen sensing which controls this heterodimeric factor is via oxygen dependent prolyl and asparaginyl hydroxylation by specific 2-oxoglutarate dependent dioxygenases (PHD1, PHD2, PHD3 and FIH-1). Whilst HIF appears to have a major role in hypoxic regulation of gene expression, it is unclear to what extent other transcriptional mechanisms are also involved in the response to hypoxia. The extent to which 2-oxoglutarate dependent dioxygenases are responsible for the oxygen sensing mechanism in HIF-independent hypoxic gene regulation is also unclear. Both the prolyl and asparaginyl hydroxylases can be inhibited by dimethyloxalylglycine (DMOG). Such inhibition can produce activation of the HIF system with enhanced transcription of target genes and might have a role in the therapy of ischaemic disease. We have examined the extent to which the HIF system contributes to the regulation of gene expression by hypoxia, to what extent 2-oxoglutarate dependent dioxygenase inhibitor can mimic the hypoxic response and the nature of the global transcriptional response to hypoxia. We have utilised microarray assays of mRNA abundance to examine the gene expression changes in response to hypoxia and to DMOG. We demonstrate a large number of hypoxically regulated genes, both known and novel, and find a surprisingly high level of mimicry of the hypoxic response by use of the 2-oxoglutarate dependent dioxygenase inhibitor, dimethyloxalylglycine. We have also used microarray analysis of cells treated with small interfering RNA (siRNA) targeting HIF-1alpha and HIF-2alpha to demonstrate the differing contributions of each transcription factor to the transcriptional response to hypoxia. Candidate transcripts were confirmed using an independent microarray platform and real-time PCR. The results emphasise the critical role of the HIF system in the hypoxic response, whilst indicating the dominance of HIF-1alpha and defining genes that only respond to HIF-2alpha.
Keywords: Hypoxia response, gene knockdown, chemical treatment

overall_design:
MCF7 breast cancer cell lines were grown under conditions of either normoxia (21% oxygen) or hypoxia (1% oxygen) for 16 hours in an Invivo2 Hypoxia Workstation (Ruskin Technologies, UK). All culture media comprised DMEM, 2mM L-Glutamine and 10% Fetal Bovine Serum.  Total RNA was extracted from each sample using the Absolutely RNA RT-PCR Miniprep kit (Stratagene).  In total, 7 different types of sample were analysed by microarray technology.  These were: ‘normoxia’ - cells grown in normoxic (21% oxygen) conditions; ‘hypoxia’ - cells grown in hypoxic conditions  (1% oxygen) for 16 hours; ‘DMOG’ - cells grown in normoxic conditions and exposed to the 2-oxoglutarate dependent dioxygenase inhibitor dimethyloxalylglycine, DMOG (2 mM) for 16 hours; ‘OF’ - cells grown in hypoxic conditions as above and exposed to oligofectamine transfection reagent (Invitrogen) alone; ‘HIF1’ - cells grown in hypoxic conditions as above and exposed to HIF-1alpha siRNA; ‘HIF2’ - cells grown in the same hypoxic conditions with HIF-2alpha siRNA and ‘HIF12’ - cells grown in the same hypoxic conditions with both HIF-1alpha and HIF-2alpha siRNA.   Three independent samples were analysed for each experimental condition.  All of the analyses for the hypoxia and DMOG samples were compared to the normoxia samples whilst the siRNA transfected samples were compared against the OF samples.
The normoxia, hypoxia and DMOG samples (replicates 1-3) were arrayed to HG-U133A Genechips and sample types OF, HIF1, HIF2 and HIF12 (replicates 1-3) were arrayed to HG-U133 plus 2 Genechips (Affymetrix).
The normoxia, hypoxia and DMOG samples (replicates 2-3) along with the samples OF, HIF1, HIF2 and HIF12 (replicates 4-6) were arrayed to the ‘whole genome’ Sentrix Human-6 Expression BeadChips (Illumina).
All labelling, hybridisation and scanning steps were performed according to the manufacturers’ instructions.

first: Gareth

last: Elvidge

first: Louisa

last: Glenny

first: Peter

middle: J

last: Ratcliffe

first: Jonathan

last: Gleadle


title: LJMJDW: Cellular responses to 4-hydroxy-2-nonenal

city: Nashville

first: James

middle: Daryl

last: West

state: TN

address: 23rd Ave at Pierce

department: Biochemistry

institute: Vanderbilt University

summary:
Cellular responses to 4-hydroxy-2-nonenal (HNE)--dose response and time course--three replicate experiments for each treatment
Keywords: other

first: Lawrence

last: Marnett


title: siRNA mediated WTAP knockdown in HUVEC

status: Public on Nov 30 2005

city: Kawasaki

first: Horiuchi

last: Keiko

state: Kanagawa

address: 1-396 Kosugi-cho, Nakahara-ku,

department: Protein-Protein Interaction

country: Japan

institute: Institute for Advanced Medical Sciences, Nippon Medical School

summary:
The experiment studied the effect of knockdown WTAP in HUVEC. two control samples and two WTAP knockdown samples.
Keywords: other

first: Keiko

last: Horiuchi


title: Dillution series comparison of Affymetrix and Illumina Expression Platforms

status: Public on Nov 08 2005

city: Cincinnati

first: Michael

last: Barnes

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

summary:
The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and Illumina BeadArrays. The study design is based on a dilution series of two human tissues (blood and placenta), tested in duplicate on each platform. By a variety of measures the two platforms yielded data of similar quality and properties. The results of a comparison between the platforms indicate very high agreement, particularly for genes which are predicted to be differentially expressed between the two tissues. Agreement was strongly correlated with the level of expression of a gene. Concordance was also improved when probes on the two platforms could be identified as being likely to target the same set of transcripts of a given gene. These results shed light on the causes or failures of agreement across microarray platforms. The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms.
Keywords: Dilution series, platform comparison, Affymetrix, Illumina

overall_design: This experiment compares Affymetrix HG-U133 Plus 2.0 microarrays with the Illumina HumanRef-8 BeadArrays. We used a dilution design, where two different RNA samples are mixed at known proportions, and the same RNA is analyzed in duplicate on each platform.  The advantage of this design is that it is very simple to prepare and the number of differentially expressed genes is large, allowing testing of many of the probes on each array. However, in contrast to spike-in studies, the identities of the genes expected to show differential expression are not known ahead of time.

first: Johannes

last: Freudenberg

first: Susan

last: Thompson

first: Bruce

last: Aronow

first: Paul

last: Pavlidis


title: Prednisolone treated childhood ALL samples

status: Public on Nov 14 2005

city: Bolzano

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary:
Glucocorticoids (GC) are in most chemotherapy protocols for lymphoid malignancies, particularly childhood acute lymphoblastic leukaemia (ALL) for their ability to induce apoptosis in malignant blast. The underlying mechanism, however, has so far only been investigated in model systems. This study comprises Affymetrix hgu133 plus 2.0 analyses of
Peripheral blood lymphoblasts purified at three time points (0h, 6-8h, 24h after treatment initiation) from 13 children under therapy for ALL . Treated samples were compared to untreated (0h). This series consists of this set of microarrays. For comparison, expression profiles were generated from an adult ALL patient, peripheral blood lymphocytes from GC-exposed healthy donors, GC-sensitive and -resistant ALL cell lines and mouse thymocytes treated with GC in vivo and in vitro.
Findings. An essentially complete list of GC-regulated candidate genes in clinical settings experimental and was generated, enabling immediate analysis of any gene with respect to its potential significance for GC-induced apoptosis in these systems. Gene regulations previously thought responsible for cell death in experimental systems were reconfirmed in few children only. In contrast, a small number of genes, most not implicated in GC-induced apoptosis previously, were co-ordinately regulated in the majority of children.
Keywords = ALL
Keywords = apoptosis
Keywords = glucocorticoid
Keywords = leukemia
Keywords = pediatric oncology
Keywords: other

first: Stefan

last: Schmidt

last: Riml

first: Christian

last: Ploner

first: Simone

last: Jesacher

first: Clemens

last: Achmüller

first: Elisabeth

last: Presul

first: Sergej

last: Skvortsov

first: Roman

last: Crazzolara

last: Fiegl

first: Taneli

last: Raivio

first: Olli

middle: A

last: Jänne

first: Stephan

last: Geley

first: Bernhard

last: Meister

first: Reinhard

last: Kofler


title: Identification of LEDGF-regulated genes.

status: Public on Nov 07 2005

city: philadelphia

first: Chris

last: Hoffmann

address: 3610 hamilton walk

institute: University of Pennsylvania

summary:
The LEDGF transcript from the PSIP1 gene was knocked down using RNAi technology. The resulting 293T derived cell line (293TsiLL) was compared to a control cell line (293TsiScram) using microarray analysis. Genes identified as being modulated by LEDGF were preferential targets of HIV integration.
Keywords: gene knockdown effects

overall_design: 2 cell lines were used, 293TsiLL (experimental) and 293TsiScram (control). 4 independent cultures of each cell line were used for independent RNA extractions, labeling reactions and array hybridizations.

first: Angela

last: Ciuffi

first: Manuel

last: Llano

first: Eric

last: Poeshla

first: Jeremy

last: Leipzig

last: Shinn

first: Joseph

last: Ecker

first: Frederic

last: Bushman


title: Additional systems to Prednisolone treated childhood ALL samples

first: Johannes

last: Rainer

summary:
Glucocorticoids (GC) are in most chemotherapy protocols for lymphoid malignancies, particularly childhood acute lymphoblastic leukaemia (ALL) for their ability to induce apoptosis in malignant blast. The underlying mechanism, however, has so far only been investigated in model systems. This study comprises Affymetrix hgu133 plus 2.0 analyses of
Peripheral blood lymphoblasts purified at three time points (0h, 6-8h, 24h after treatment initiation) from 13 children under therapy for ALL . Treated samples were compared to untreated (0h). For comparison, expression profiles were generated from an adult ALL patient, peripheral blood lymphocytes from GC-exposed healthy donors, GC-sensitive and -resistant ALL cell lines and mouse thymocytes treated with GC in vivo and in vitro. This second series comprises the additional samples mentioned above.
Findings. An essentially complete list of GC-regulated candidate genes in clinical settings experimental and was generated, enabling immediate analysis of any gene with respect to its potential significance for GC-induced apoptosis in these systems. Gene regulations previously thought responsible for cell death in experimental systems were reconfirmed in few children only. In contrast, a small number of genes, most not implicated in GC-induced apoptosis previously, were co-ordinately regulated in the majority of children.
Keywords: treatment response

overall_design:
replicates: prednisolone treated GSM60594, GSM60595. untreated: GSM60597, GSM60599. Bone marrow samples sorted / unsorted: GSM60601, GSM60603.
Samples are assigned to various subgroups: sensitive systems, resistant systems, Prednisolone treated, ethanol (control) treated, cyclohexamide treated, untreated, 6 hours treatment and 24 hours treated.
Glucocorticoid treated samples of patients or cell lines or healthy donors were compared to their untreated or ethanol treated counterparts.

first: Stefan

last: Schmidt

last: Riml

first: Christian

last: Ploner

first: Simone

last: Jesacher

last: Achmüller

last: Presul

first: Michael


title: Oncogene Signature Dataset

city: Durham

middle: R.

last: Nevins

state: NC

address: 2133 CIEMAS, 101 Science Dr.

department: IGSP

institute: Duke University

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

overall_design: RNA was extracted from human mammary epithelial cells expressing oncogenes (or GFP control) for gene array analysis.  Experiment was performed in replicate.


title: Breast Cancer Cell Lines

summary:
Gene expression analysis on growing breast cancer cell lines.
Keywords: cancer cell line profiles

overall_design: see Bild, A. et.al.

first: Andrea

last: Bild


title: Dosage Compensation of the Active X in mammals

status: Public on Oct 06 2005

city: Seattle

first: Di

middle: Kim

last: Nguyen

address: 1959 NE Pacific St.

institute: University of Washington

summary:
Here, we show that doubling of the global expression level of the X chromosome achieves dosage compensation in somatic tissues from several mammalian species. X-linked genes are highly expressed in brain tissues, consistent with a role in cognitive functions.
Keywords: Normal Tissue

overall_design: Eight arrays were acquired from Affymetrix. Total gender-specific RNA was purchased from Stratagene. Probe labeling, array hybridization and scanning were done by the University of Washington Microarray Center (TUhttp://ra.microslu.washington.edu/UT). cDNA arrays.

first: Christine

last: Disteche


title: Gene expression signature of HPV in head and neck squamous cell carcinoma

status: Public on Nov 28 2005

middle: H.

last: Chung

address: 777 PRB

department: Internal Medicine

summary:
Introduction: Human Papilloma Virus (HPV) is associated with a subset of head and neck squamous cell carcinoma (HNSCC), between 15% and 35% of HNSCC harboring HPV, almost exclusively of subtype 16. Demographic and exposure differences between HPV-positive (+) and negative (-) HNSCCs suggest that HPV(+) tumors may constitute a subclass with different biology, while clinical differences have also been observed. In this study, gene expression profiles of HPV(+) and (-) tumors were compared to further explore the biological effect of HPV in HNSCC. Methods: Thirty-six HNSCC tumors were analyzed for gene expression using Affymetrix Human 133U Plus 2.0 GeneChip and for HPV using consensus primers for HPV L1, E6 and E7 by PCR and RT-PCR. Results: Eight (22%) of 36 tumors were positive for HPV, all of the HPV 16 subtype, and the HPV positive samples also expressed viral HPV E6 mRNA determined by RT-PCR. Patients with HPV(+) HNSCCs were on average younger than those with HPV(-) tumors (mean age 50.2 vs. 58.7). Statistical analysis using Significance Analysis of Microarrays (SAM) based on HPV status as a supervising parameter resulted in a list of 91 genes that were differentially expressed with statistical significance. Results for a sub-set of these genes were verified by RT-PCR. Genes highly expressed in HPV(+) samples included cell cycle regulators (p16INK4A, p18 and CDK2) and transcription factors (TAF7L, RFC4, RPA2 and TFDP2). The microarray data were also investigated using DIGMap to map genes by chromosomal location. A large number of genes on chromosome 3q24-qter was found to be overrepresented in HPV(+) tumors. Conclusion: The gene expression profile associated with HPV reflects alterations in cell cycle and proliferation signals. Further investigation of differentially expressed genes may reveal the unique pathways in HPV(+) tumors that may explain the different natural history and biological properties of these tumors. These properties may be exploited as a target of novel therapeutic agents in HNSCC treatment.
Keywords: HPV, HNSCC, head and neck cancer, human, human papilloma virus

overall_design:
Patient selection and specimen collection. Thirty-six freshly frozen tumor samples were prospectively collected from patients undergoing surgery or biopsy for HNSCC at the University of North Carolina (UNC) at Chapel Hill (21 patients) and Vanderbilt University (15 patients). All tissues were snap-frozen in liquid nitrogen within 30 minutes of surgical resection or biopsy, and kept at -80oC until further processing. All patients consented to participation in this study under protocols approved by IRB at the two institutions.
HPV detection and DNA sequencing. Tumor DNAs were tested for the presence of HPV DNA using a previously established PCR-based method [11]. This method employs degenerate PCR primers (MY09 and MY11, WD72/76 and WD66/67/154) that are designed to represent highly conserved HPV L1 and E6 sequences present in all major types of HPV. In addition, all HPV-positive samples were also tested with a HPV16-specific PCR for E7 (primer A: 5’-GGA CCG GTC GAT GTA TGT CT-3’ and primer B: 3’-TAA AAC CAT CCA TTA CAT CCC G-5’). Optimal conditions for this combined PCR were determined using DNA from the cervical carcinoma cell line SiHa, which harbors on average 2 copies of HPV16 DNA per cell [11]. Other positive control cell lines were CaSki (HPV16) and HeLa (HPV18). For each case, 200 nanograms of tumor DNA were tested for the presence of HPV DNA. PCR samples which showed amplification products indicating the presence of HPV were purified using PCR purification columns (Qiagen, Valencia, CA) and subjected to bi-directional sequence analysis. In all of such cases, a positive identification of the HPV type could be made.
RNA isolation and DNA microarray analysis. Each tumor was examined by H&E staining to ensure presence of tumor and enriched by macrodissection to achieve a minimum of 70% tumor cells in each preparation. Total RNA was purified from frozen tumors using Qiagen RNeasy Mini Kit according to the manufacturer’s recommendations (Qiagen, Valencia, CA) using approximately 10-20 milligram of wet tissue from each sample. Fifty nanograms of the total RNA was amplified using NuGen RNA Amplification kit (NuGen, San Carlos, CA) and labeled ENZO BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations. Fifteen micrograms of biotin-labeled aRNA was fragmented and the quality of the RNA was reconfirmed using the Agilent RNA 6000 Nano LabChip Kit and Agilent 2100 bioanalyzer. The fragmented, biotin-labeled aRNA was combined with the hybridization mix and loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip. After hybridization, the GeneChip was washed, stained with Strepavidin/phycoerythrin conjugate and biotinylated antibody, and scanned according to the manufacturer's recommendations. The raw microarray data was normalized using Perfect Match software for further statistical analyses.

first: Robbert

last: Slebos

first: Yajun

last: Yi

first: Kim

last: Ely

first: Jesse

last: Carter

first: Amy

last: Evjen

first: Xueqiong

last: Zhang

first: Yu

last: Shyr

first: Barbara

last: Murphy

first: Anthony

last: Cmelak

first: Brian

middle: B

last: Burkey

first: James

middle: L

last: Netterville

first: Shawn

last: Levy

first: Wendell

middle: G

last: Yarbrough

middle: H


title: Lung Cancer Dataset

first: Joseph

last: Nevins

summary:
Signatures of Oncogenic Pathway Deregulation in Human Cancers.

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

overall_design: RNA was extracted from frozen tissue of primary lung tumors for gene array analysis.

middle: R


title: isolated alveolar macrophages

status: Public on Oct 04 2005

city: San Francisco

first: Michael

middle: E.

last: Salazar

address: 1550 Fourth Street, RM 545

institute: University of California, San Francisco

summary:
This series represents isolated alveolar macrophages from human subjects.
Keywords: parallel sample

first: Prescott

last: Woodruff


title: Fullerene treatment of HUVECs

status: Public on Sep 27 2005

city: Suita

first: Naoharu

last: Iwai

address: 5-7-1 Fujishiro-dai

department: Epidemiology

institute: National Cardiovascular Center

summary:
Control untreated versus fullerene-treated HUVECs
Keywords: nanomaterial treatment

overall_design: Total RNA was isolated from HUVECs treated with or without C60(OH)24 (100 micro g/ml, 24 h). Two independent experiments were performed.

first: Hideyuki

last: Yamawaki


title: MK886 treatment of H720 non-small cell lung cancer cell line

status: Public on Sep 10 2005

city: Bethesda

first: Anatoly

middle: L.

last: Mayburd

address: 9000 Rockville Pyke

department: Intervention section

institute: NIH/NCI

summary:
In this experiments different treatments were applied to lung cancer cell lines

1)H720 cell line suspension was treated by 1 micromole of 5-lipoxygenase activating protein inhibitor MK886 serum-free in TIS medium for 24 h.
2) A549 cell line was treated as H720 by MK886
3) A549 was treated by 100 nM of silencing cocktail (siRNA) prepared against the 4-th exon of the gene and generated by RNASEIII digestion of double stranded RNA. The cocktail was prepared by Ambion technology, see the manufacturer's protocol. The observed  silencing was >90%
4) Based on Oligoengine vectors, silencing constructs were created against HRPA2B1 transcript(HNRPA2B1 is a subunit of spliceosome). Stable transfectants were raised harboring the construct.
Keywords: drug treatment

overall_design:
1) MK886 treatement of H720: Three chips titled MK served as "treated" part, three chips titled "control" served as controls.
2) MK886 treatment of A549: two duplicates, 1+2 and 3+4, performed on different dates
3) HNRPA2B1 silencing:  pairs of controls and silenced sample
4) FLAP silencing: 1 control, 2 treatments


title: Motexafin Gadolinium and Zinc Induce Oxidative Stress Responses and Apoptosis in B-Cell Lymphoma Lines

status: Public on Jan 01 2006

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:
We report the effect of motexafin gadolinium (MGd) and exogenous zinc on intracellular levels of free zinc, oxidative stress, proliferation, cell cycle, and cell death in exponential phase human B-cell lymphoma and other hematologic cell lines.  We find that increased levels of oxidative stress and intracellular free zinc precede and correlate with cell cycle arrest and apoptotic response.  Treatment with exogenous zinc increased oxidative stress and, conversely, oxidative stress resulted in increased intracellular free zinc levels.  To better understand the molecular basis of these results, gene expression profiling analyses were conducted on Ramos cell cultures treated with MGd and/or zinc acetate.  Cultures treated with MGd or zinc acetate alone elicited transcriptional responses characterized by induction of MTF-1 and HIF-1 regulated genes.  Cultures co-treated with MGd and zinc acetate displayed further increases in the levels of MTF-1 and HIF-1 regulated transcripts as well as additional transcripts regulated by NRF-2.  Overall, these studies suggest that co-treatment of Ramos cells with MGd and zinc acetate increase intracellular zinc levels with a concomitant rise in oxidative stress levels that activate adaptive survival responses but eventually lead to cell death.
Keywords: Dose response

overall_design: Ramos cells were treated with MGd alone or along with different concentrations of zinc acetate.  Each treatment was done in triplicates.  Expression was compared to that of cells treated with mannitol.

first: Philip

last: Lecane

middle: W

first: Mint

last: Sirisawad

first: Louie

last: Naumovski

first: Richard

last: Miller

last: Hacia

first: Darren

last: Magda


title: TLR agonists on human dendritic cells

status: Public on Sep 01 2005

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via Vela 6

department: Experimental Oncology

country: Switzerland

institute: Institute of Southern Switzerland

summary:
Toll like receptors (TLRs) sense microbial products and initiate adaptive immune responses by activating dendritic cells (DCs). Since pathogens may contain several agonists we asked whether different TLRs may synergize in DC activation. We report that in human and mouse DC TLR3 or TLR4 potently synergize with TLR7, TLR8 or TLR9 in the induction of selected cytokine genes. Upon synergistic stimulation, IL-12, IL-23 and Delta-4 are induced at levels 50-100 fold higher than those induced by optimal concentrations of single agonists, leading to enhanced and sustained TH1 polarizing capacity. Using microarray analysis we show that only 1.5% of the transcripts induced by single TLR agonists are synergistically regulated by combinations of TLR4 and TLR8 agonists.. These results identify a combinatorial code by which DCs discriminate pathogens and provide (suggest) a rationale to design adjuvants for TH1 responses.
Series_overall_design: 3 untreated, 3 treated with LPS at 2h, 3 treated with LPS at 8h,  3 treated with R848 at 2h, 3 treated with R848 at 8h,  3 treated with LPS + R848 at 2h, 3 treated with LPS + R848 at 8h
Keywords: other

first: Giorgio

last: Napolitani

first: Andrea

last: Rinaldi

first: Federica

last: Sallusto

first: Antonio

last: Lanzavecchia


title: Anaplasma phagocytophilum infected NB4 cells

status: Public on Jul 29 2005

city: New Haven

first: Joao

middle: Helbert

last: Pedra

state: CT

address: 300 Cedar Street - TAC S-410

department: Internal Medicine/ Rheumatology

institute: Yale University School of Medicine

summary:
THREE INDEPENDENT REPLICATES AND ARE THE CONTROL NON-INFECTED CELLS:
GSM49939, GSM49940, GSM49941

THREE INFECTED INDEPEDENDENT REPLICATES:
GSM49942, GSM49943, GSM49944
Keywords: ordered


title: Integrative Genomic and Proteomic Analysis of Prostate Cancer Reveals Signatures of Metastatic Progression

status: Public on Sep 20 2005

city: Ann Arbor

first: Jianjun

last: Yu

state: MI

address: 1150 W. Medical Center Dr.

institute: University of Michigan

summary:
An integrative analysis of this compendium of proteomic alterations and transcriptomic data was performed revealing only 48-64% concordance between protein and transcript levels. Importantly, differential proteomic alterations between metastatic and clinically localized prostate cancer that mapped concordantly to gene transcripts served as predictors of clinical outcome in prostate cancer as  well as other solid tumors.
Keywords: prostate cancer progression

overall_design: 13 individual benign prostate, primary and metastatic prostate cancer samples and 6 pooled samples from benign,primary or metastatic prostate cancer tissues.

first: Sooryanarayana

last: Varambally

first: Bharathi

last: Laxman

first: Rohit

last: Mehra

first: Scott

last: Tomlins

first: Arul

last: Chinnaiyan


title: Wavelet modelling of microarray data provides chromosomal pattern of expression which predicts survival in gliomas

status: Public on Dec 15 2005

city: London

first: Federico

last: Turkheimer

address: DuCane Road

department: Sensorimotor

institute: Imperial College London

summary:
Genetic and epigenetic processes result in gene expression changes through alteration of the chromatin structure.  The relative position of genes on chromosomes has therefore important functional implications and can be exploited to model microarray datasets.  Gliomas are the most frequent primary brain tumours in adults and their prognosis is related to histology and grade.  In  oligodendrogliomas, allelic loss of 1p/19q and hypermethylation of MGMT promoter is associated with longer survival and chemosensitivity.  In this work we used oligonucleotide microarray to study a group of 30 gliomas with various oligodendroglial and astrocytic components.  We used an original approach combining a wavelet model of inter-probe genomic distance (CHROMOWAVE) and unsupervised method of analysis (Singular Value Decomposition) in order to discover new prognostic chromosomal patterns of gene expression.  We identified a major pattern of variation that strongly correlated with survival (p= 0.007) and could be visualized as a genome-wide chromosomal pattern including widespread gene expression changes on 1p, 19q, 4, 18, 13 and 9q and multiple smaller clusters scattered along chromosomes.  Gene expression changes on chromosomes 1p, 19q and 9q were significantly correlated with the allelic loss of these regions as measured by FISH.  Differential expression of genes implicated in drug resistance was also a feature of this chromosomal pattern and in particular low expression of MGMT was correlated with favourable prognosis (p<0.0001).  Remarkably, unsupervised analysis of the expression of individual genes and not of their chromosomal ensemble produced a pattern that could not be associated with prognosis, emphasizing the determinant role of the wavelet mathematical modelling.
Keywords: wavelet, glioma, unsupervised

overall_design: Unsupervised analysis using wavelet models of 30 diffuse gliomas

first: Manuel

last: Deprez

first: Benoit

last: Hennuy

first: Christian

last: Herens

last: Roncaroli

first: Minh

last: Nguyen

first: Didier

last: Martin

first: Vincent

last: Bours

first: Jaques

last: Boniver


title: tourt-affy-human-131547

status: Public on Jul 06 2005

city: Phoenix

first: Winnie

last: Liang

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Nerve growth factor (NGF) is a neurotrophin that plays an important role in regulating the survival, growth, and differentiation of sympathetic neurons.  Many in vitro studies indicate that Egr transcription factors are coupled to NGF signaling and are essential signaling mediators of NGF-dependent differentiation of sympathetic neurons, such as neuroblastoma cells and pheochromocytoma cells.  Mice that are deficient for both Egr1 and Egr3 have profound sympathetic nerve system defects, including abnormal neuron degeneration and impaired differentiation (unpublished observations).  To further understand the role of Egr genes in sympathetic neuron development, it is necessary to examine the signal transduction pathways involved in NGF-mediated Egr-dependent gene regulation.  The results will be helpful in understanding the pathobiology of those diseases related to aberrant sympathetic neuron differentiation, such as neuroblastoma and dysautonomias, and may provide new insights into therapies for these refractory diseases.
To identify NGF-mediated Egr-dependent target genes in human SH-SY5Y/TrkA neuroblastoma cells:  Many potential Egr target genes have been described over the years.  However, very few have been characterized to be involved in NGF-mediated sympathetic neuron differentiation.  In order to further understand the role of Egr genes in sympathetic neuron development, it is necessary to examine the signal transduction pathways involved in NGF-mediated Egr-dependent gene regulation.  Egr1 and Egr3 are rapidly induced after NGF treatment and Egr1 is involved in activation of the differentiation marker gene NPY in SH-SY5Y/TrkA cells.  Therefore, SH-SY5Y/TtrkA cells appear to be an excellent model system to study the role of Egr transcription factors in sympathetic neuron differentiation in vitro.  A dominant negative Egr molecule that specifically blocks transcriptional activity mediated by Egr transcription factors will be used in this study to identify Egr-dependent target genes.
Egr1 and Egr3 are rapidly induced after NGF treatment in human SH-SY5Y/TrkA neuroblastoma cells, which in turn differentiate into sympathetic-like neurons.  We hypothesize that Egr transcription factors are involved in activating downstream signaling pathways during NGF mediated differentiation of SH-SY5Y/TrkA cells.  Moreover, we hypothesize that by using a dominant negative Egr (dnEgr) molecule that blocks all Egr mediated gene transcription and Affymetrix microarray analysis, it will be possible to identify NGF-mediated Egr transcription dependent gene regulatory networks that may be involved in growth and differentiation of neuroblastoma.  An unbiased approach to understanding these gene regulatory networks may lead to new insights relating to NGF signaling involved in neuronal growth and differentiation.
Human neuroblastoma SH-SY5Y/TrkA cells will be infected with either dnEgr-expressing adenovirus (SH-SY5Y/TrkA-dnEgr) or with EGFP-expressing control adenovirus (SH-SY5Y/TrkA-EGFP).  Equivalent infection efficiency and lack of viral toxicity will be verified by EGFP fluorescence microscopy 24 hours after infection and the cells will be treated with NGF (100 ng/ml).  Total RNA will be extracted from SH-SY5Y/TrkA (uninfected), SH-SY5Y/TrkA-dnEgr, and SH-SY5Y/TrkA-EGFP cells treated with NGF for 0, 1 hour and 3 hours.  Total RNA will be prepared from all of the samples and a portion subjected to real-time PCR analysis to ensure that NGF mediated Egr gene induction was not altered by the context of viral infection.  Pilot experiments demonstrate that Egr genes are still induced in the context of viral infection greater than 100-fold.  Egr1 mRNA peak expression is known to occur at 1 hour and decrease by 3 hours after NGF treatment in all of the samples.  The peak expression of Egr target genes is expected to occur later than Egr1 peak expression since Egr1 proteins need to be expressed first to initiate the transcription of target promoters.  Therefore, the RNA samples from SH-SY5Y/TrkA-dnEgr and SH-SY5Y/TrkA-EGFP treated with NGF for 3 hours will be used to probe Affymetrix high-density human genome U133 Plus 2.0 Arrays to identify differentially expressed genes.  RNA amplification for probe synthesis should not be necessary since we will provide 10 ug of intact total RNA for each sample.  We will provide three sets of samples to perform the comparative microarray analysis twice from different starting materials and a nine-way comparative analysis of the data will be performed.  We expect that cells containing high levels of dnEgr will inhibit NGF mediated Egr-dependent target gene expression and that these gene networks should be identifiable when compared to EGFP infected cells that have normal Egr gene transcriptional activity.
Keywords: time-course

overall_design: as above

first: W

last: Tourtellotte


title: A high-resolution map of active promoters in the human genome

status: Public on Jun 29 2005

city: San Diego

first: Chunxu

last: Qu

department: Gene Regulation

institute: Ludwig Institute for Cancer Research

type: Genome binding/occupancy profiling by genome tiling array

summary:
Our ability to understand the control logic embedded in the human genome is limited by a lack of accurate information of the promoter sequences for most genes.  Promoters are a unique class of control sequences, serving as the binding sites for both sequence-specific factors and the general transcription machinery during transcription initiation.  In order to obtain a comprehensive map of promoters in the human genome, we have determined the location of the RNA polymerase II preinitiation complex throughout the non-repeat sequences of the human genome in primary fibroblast cells.  The resulting map defines 10,571 active promoters corresponding to 6,763 known genes and at least 1,199 un-annotated transcriptional units.  The map indicates extensive usage of multiple promoters by the human genes and widespread clustering of active promoters in the genome.  Further examination of the genome-wide expression profile reveals four general classes of promoters that define the transcriptome of the cell.  Our results provide a global view of the functional relationship among the transcriptional machinery, chromatin structure, and gene expression in human cells.
Keywords = GALA
Keywords = gene expression
Keywords = nimblegen
Keywords = promoter profile
Keywords = LICR renlab
Keywords: other

first: Tae Hoon

last: Kim

first: Leah

middle: O

last: Barrera

first: Ming

last: Zheng

first: Michael

last: Singer

first: Todd

last: Richmond

first: Yingnian

last: Wu

first: Roland

middle: D

last: Green

first: Bing

last: Ren


title: Comparison of human and non-human primate gene expression profiles

status: Public on Jun 27 2005

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

summary:
Gene expression profiling is an important tool in the development of medical countermeasures against chemical warfare agents (CWAs).  Non-human primates (NHPs), specifically the rhesus macaque (Macaca mulatta), the cynomologus macaque (Macaca fascicularis) and the African green monkey (Chlorocebus aethiops), are vital models in the development of CWA prophylactics, therapeutics, and diagnostics.  However, gene expression profiling of these NHPs is complicated by the fact their genomes are not completely sequenced, and that no commercially available oligonucleotide microarrays (genechips) exist.  We, therefore, sought to determine whether gene expression profiling of NHPs could be performed using human genechips.    Whole blood RNA was isolated from each species and used to generate genechip probes.  Hybridization of the NHP samples to human genechips (Affymetrix Human U133 Plus 2.0) resulted in comparable numbers of transcripts detected compared with human samples.  Statistical analysis revealed intraspecies reproducibility of genechip quality control metrics; interspecies comparison between NHPs and humans showed little significant difference in the quality and reproducibility of data generated using human genechips.  Expression profiles of each species were compared using principal component analysis (PCA) and hierarchical clustering to determine the similarity of the expression profiles within and across the species.  The cynomologus group showed the least intraspecies variability, while the human group showed the greatest intraspecies variability.  Intraspecies comparison of the expression profiles identified probesets that were reproducibly detected within each species.  Each NHP species was found to be dissimilar to humans; the cynomologus group was the most dissimilar.    Interspecies comparison of the expression profiles revealed probesets that were reproducibly detected in all species examined.  These results show that human genechips can be used for expression profiling of NHP samples and provide a foundation for the development of tools for comparing human and NHP gene expression profiles.
Keywords = human
Keywords = homo sapien
Keywords = blood
Keywords = rhesus macaque
Keywords = cynomologus macaque
Keywords = African green monkey
Keywords: parallel sample

sample_organism:
Chlorocebus aethiops
Macaca fascicularis
Macaca mulatta
Homo sapiens

first: Christopher

middle: S

last: Phillips


title: A molecular classification of papillary renal cell carcinoma

status: Public on Jul 01 2005

city: Grand Rapids

first: Min-Han

last: Tan

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

summary:
BACKGROUND: Despite the moderate incidence of papillary renal cell carcinoma
(PRCC), there is a disproportionately limited understanding of its underlying genetic
programs. There is no effective therapy for metastatic PRCC, and patients are often
excluded from kidney cancer trials. A morphological classification of PRCC into Type 1 and Type 2 tumors has been recently proposed, but its biological relevance remains uncertain.

PATIENTS AND METHODS. We studied the gene expression profiles of 34 cases of
PRCC using Affymetrix HGU133 Plus 2.0 arrays (54,675 probe sets) using both
unsupervised and supervised analysis. Comparative genomic microarray analysis
(CGMA) was used to infer cytogenetic aberrations, and pathways were ranked with a curated database. Expression of selected genes was validated by immunohistochemistry in 34 samples, with 15 independent tumors.

RESULTS. We identified 2 highly distinct molecular PRCC subclasses with morphologic correlation. The first class, with excellent survival, corresponded to 3 histological subtypes: Type 1, low-grade Type 2 and mixed Type 1/low-grade Type 2 tumors. The second class, with poor survival, corresponded to high-grade Type 2 tumors
(n=11). Dysregulation of G1/S and G2/M checkpoint genes were found in Class 1 and
Class 2 tumors respectively, alongside characteristic chromosomal aberrations. We
identified a 7-transcript predictor that classified samples on cross-validation with 97% accuracy. Immunohistochemistry confirmed high expression of cytokeratin 7 in Class 1 tumors, and of topoisomerase IIα in Class 2 tumors.

CONCLUSIONS. We report 2 molecular subclasses of PRCC, which are biologically
and clinically distinct, which may be readily distinguished in a clinical setting.
Keywords: survival, prognostic classification, disease state analysis

overall_design: 34 individual samples analyzed, no technical replicates.

first: Bin Tean

last: Teh


title: Transcripts affected by RNAi to POLRMT

status: Public on Apr 05 2005

city: Cleveland

first: Peter

middle: M

last: Chumakov

address: 9500 Euclid Ave

department: Molecular Genetics

institute: Lerner Research Institute, The Cleveland Clinic Foundation

summary:
Rho0 HeLa cells (devoid of mitochondrial DNA and functional mitochondria) were infected with recombinant lentiviral vector pLSLG expressing short hairpin RNAi complementary to Exons 3 and 17 of POLRMT gene.  48 hours after infection total RNA was isolated and analyzed for inhibition of POLRMT transcripts by RT-PCR.  Total RNA from Rho0 HeLa infected with empty pLSLG vector was used as control.  The two samples of RNA were used for microarray hybridization with Affymetrix human genome U133 2.0 plus microarray in order to monitor changes in gene expression patterns after inhibition of POLRMT gene.
Keywords: parallel sample

first: Julia

middle: E

last: Kravchenko

first: Igor

last: Rogozin

first: E

middle: V

last: Koonin


title: Autophagy promotes MHC class II presentation of peptides from intracellular source proteins

status: Public on Apr 01 2005

city: Tuebingen

first: Oliver

last: Schoor

address: Auf der Morgenstelle 15

department: Institute for Cell Biology - Dept. of Immunology

institute: University of Tuebingen

summary:
Assessment of mRNA expression changes in the B-lymphoblastoid cell line Awells after 6 h and 24 h of starvation-induced autophagy
Keywords: ordered

first: Joern

last: Dengjel

first: Rainer

last: Fischer

last: Reich

first: Marianne

last: Kraus

first: Margret

last: Mueller

first: Katharina

last: Kreymborg

first: Florian

last: Altenberend

first: Jens

last: Brandenburg

first: Hubert

last: Kalbacher

last: Brock

first: Christoph

last: Driessen

first: Hans-Georg

last: Rammensee

first: Stefan

last: Stevanovic


title: cMyb and vMyb in human monocytes

status: Public on Jun 14 2005

city: Albuquerque

first: Scott

middle: A.

last: Ness

state: NM

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 primary human monocytes using recombinant adenovirus vectors. All the samples were compared to cells infected with a control adenovirus expressing only GFP.  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

middle: P

last: O'Rourke

middle: A


title: Predictors of the response to chemoradiotherapy in SCC of larynx

status: Public on May 09 2005

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

summary:
Laryngeal and hypopharyngeal squamous cell carcinoma was histopathologically confirmed on 35 samples obtained by incisional biopsy. Total RNAs from frozen specimens were isolated using Trizol reagent (Invitrogen Corporation, Carlsbad, CA) according to the manufacturer protocol. RNA quality was verified by electrophoresis through agarose gel upon visualization with ethidium bromide and only RNA samples with a ratio >1 for 28S/18S ribosomal RNA were further processed.  A two-round RNA amplification procedure was carried out. Normal larynx and hypopharynx samples was used as reference for hybridizations, these samples were processed in the same manner as tumor samples. Amplified RNA were then used in a transcriptase reverse reaction into cDNA in the presence of Cy3- or Cy5-labeled dCTP
Keywords: other

first: Bianca

last: Barreto


title: Molecular classifiers for follicular adenomas

summary:
Patients were recruited at the Hospital do Cancer AC Camargo (São Paulo/Brazil),  Instituto de Enfermedades Neoplasicas - INEN (Lima, Peru), Hospital Araujo Jorge (Goiania, Brazil) and Hospital Heliopolis (São Paulo, Brazil).All patients signed a pre-informed consent and the study was approved by the internal ethics committee. Tissue samples were snap frozen in liquid nitrogen . Before RNA extraction histopathological diagnosis was re-confirmed, all samples were micro-dissected and only tissues with at least 70% of tumor cells and no visible infiltrating inflammatory cells were used as tumor. Morphologically disease-free tissue obtained from surgical margins was considered as normal. A total of 38 samples were analyzed: 8 normal tissues, 10 goiters, 10 adenomas and 10 papillary carcinomas.
Keywords: other

first: Beatriz

last: Stolf


title: HCaRG-9 vs NEO-1

status: Public on Oct 19 2005

city: Montreal

first: Johanne

last: Tremblay

state: QUE

country: Canada

institute: CHUM Research Center, Hotel-Dieu

summary:
HEK293 cells were transfected with control plasmid (pcDNAI/Neo;Invitrogen) or with the plasmid encoding HCaRG. Stable transfectants were synchronized and grown in the presence of 10% FBS for 48 h. Total RNAs were purified with the mini RNeasy kit (Qiagen).

Chips HG-U133A:
- Labeling protocol: Enzo BioArray HighYield RNA Transcript Labeling Kit.
- Hybridization: According to the manufacturer's protocol (Affymetrix).
- Scanner: GeneArray 2500.
- Normalization: Employing GCOS software, chips were normalized using all probe sets scaling option and target signal at 500.

Chips HG-U133 Plus 2.0:
- Labeling protocol: GeneChip IVT  Labeling Kit.
- Hybridization: According to the manufacturer's protocol (Affymetrix).
- Scanner: GeneChip Scanner 3000.
- Normalization: Employing GCOS software, chips were normalized using all probe sets scaling option and target signal at 500.
Keywords: parallel sample

first: Carlos

last: El Hader

first: Sandra

first: Nicolas

last: Solban

first: Denis

last: Gingras

first: Richard

last: Béliveau

first: Sergei N.

last: Orlov

first: Pavel

last: Hamet


title: Application of genome-wide expression analysis to human health & disease

status: Public on Feb 24 2005

city: Boston

first: Wenzhong Xiao

address: 55 Fruit Street, GRV 1302

department: Department of Surgery

institute: Massachusetts General Hospital

summary:
expression files supporting: Application of genome-wide expression analysis to human health and disease. PNAS
Supplementary Information:  http://www.gluegrant.org/pubsupport/PNAS_1/
Keywords = clinical studies
Keywords = gene expression
Keywords = inflammation
Keywords = microarray
Keywords = trauma
Keywords: other

first: J

last: Cobb

first: Michael

middle: N

last: Mindrinos

first: Carol

last: Miller-Graziano

first: Steve

last: Calvano

first: Henry

last: Baker

first: Wenzhong

last: Xiao

first: Krzysztof

last: Laudanski

first: Bernard

middle: H

last: Brownstein

first: Constance

last: Elson

first: Douglas

middle: L

last: Hayden

first: David

last: Herndon

first: Steven

last: Lowry

first: Ronald

last: Maier

last: Schoenfeld

first: Lyle

last: Moldawer

last: Davis

middle: G

last: Tompkins


title: Affymetrix striptease

status: Public on Aug 20 2005

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary:
new and stripped chips
Keywords: reuse of Affymetrix GeneChips U133 Plus 2.0

overall_design:
Affy1H1 = rehyb Affy1H2;
Affy2H1 = rehyb Affy2H2

first: Karin

last: Hahnke

first: Marc

last: Jacobsen

first: Andreas

last: Grützkau

first: Joachim

middle: R

last: Grün

first: Markus

last: Koch

first: Masashi

last: Emoto

first: Thomas

last: Meyer

first: Anna

last: Walduck

first: Stefan H

last: Kaufmann

first: Hans-Joachim

last: Mollenkopf


title: Biology of adenocarcinomas of the esphagus and stomach

first: Renato

last: Puga

summary:
Patients were recruited at the Departments of Abdominal Surgery and Endoscopy of the Hospital do Cancer AC Camargo (São Paulo/Brazil) during a 4-year period (2001 to 2004). All patients signed a pre-informed consent and the study was approved by the internal ethics committee. Tissue samples were either snap frozen in liquid nitrogen (when obtained by surgery) or collected in RNAlaterTM (Ambion®, Austin, Texas USA, when obtained by biopsy).  For all samples, diagnosis was confirmed by H&E staining at the time of RNA extraction. Biopsy samples of the esophageal and gastric mucosa obtained by endoscopy had information of the correct anatomical location using a standard diagram.
Frozen samples were dissected and only those having at least 70% of tumor cells were processed. A total of 71 samples were analyzed: 39 esophagus and esophagogastric junction samples (9 normal mucosa, 6 esophagitis mucosa, 10 Barrett's mucosa - 4 for the long type and 6 for the short type, and 14 tumor samples of adenocarcinoma) and 32 stomach samples (6 normal body and antrum mucosa, 5 normal cardiac mucosa, 9 intestinal metaplasia mucosa, 7 samples of intestinal type adenocarcinoma and 5 samples of diffuse type carcinoma). For Barrett's samples, diagnosis required evidence of intestinal metaplasia together with tongues or segments of red columnar-appearing epithelium extending upwards from the esophagogastric junction. A long Barrett's esophagus was defined as longer ?3cm and a short Barrett's esophagus by ?3cm of columnar epithelium (Spechler, 2004). The tumor samples of esophagus and esophagogastric junction were not differentiated. For the gastric adenocarcinoma samples were used the Laurén's classification (Laurén, 1965) and the others gastric sample were previously described (Meireles et al, 2003).
Keywords: other

first: Luciana

middle: I

last: Gomes


title: Normal Variance of Gene Expression in the Human Lung

status: Public on Nov 15 2004

city: Aurora

first: Christopher

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

summary:
Peripheral sections of upper and lower lung from 18 human multi-organ donors without evidence of lung disease.
Keywords = Lung Pulmonary
Keywords: repeat sample

first: Michael

last: Gruber

first: Malcolm

last: Woolum

first: Gregory

last: Cosgrove

first: Chan

last: Zeng

last: Baron

first: Mark

last: Moore

first: Carlyne

last: Cool

first: G

last: Worthen

first: Kevin

middle: K

last: Brown

middle: W

last: Geraci


title: hGSTA4-4 transfection in HLE B-3 experiment

status: Public on Jul 20 2005

city: Galveston

first: Brad

middle: Allen

last: Patrick

address: 14th and Strand streets

department: Human Biological Chem & Genetics

institute: University of Texas, Medical Branch

summary:
HLE B-3 cells were transfected with either empty vector or hGSTA4-4 expressing vector to lower intracellular 4-hydroxynonenal levels.  hGSTA4-transfected sample has lower HNE levels than pTarget-transfected sample.
Keywords = HNE hGSTA4
Keywords = 4-hydroxynonenal
Keywords: dose response

first: Jie

last: Li

first: Yogesh

middle: C

last: Awasthi


status: Public on Mar 24 2004

city: Cambridge

first: Martina

last: Schinke

address: 7 Divinity Ave

department: Bauer Center for Genomic Research

institute: Harvard University

summary:
To establish changes in cardiac transcription profiles brought about by heart failure we collected myocardial samples from patients undergoing cardiac transplantation whose failure arises from different etiologies (e.g. idiopathic dilated cardiomyopathy, ischemic cardiomyopathy, alcoholic cardiomyopathy, valvular cardiomyopathy, and hypertrophic cardiomyopathy) and from "normal" organ donors whose hearts cannot be used for transplants. The transcriptional profile of the mRNA in these samples will be measured with gene array technology. Changes in transcriptional profiles can be correlated with the physiologic profile of heart-failure hearts acquired at the time of transplantation.
Keywords: other

first: Allen

last: Paul

first: Jeffrey

first: Lauren

last: Riggi

first: Seigo

last: Izumo

first: Jozef

last: Bartunek

first: Paul

last: Allen

first: Masako

last: Tsubakihara


title: Dysregulation of the circulating and tissue-based renin-angiotensin system in preeclampsia

status: Public on Jan 01 2007

first: Florian

last: Herse

address: Wiltbergstr. 50

institute: Charite

summary:
Preeclampsia complicates more than 3% of all pregnancies in the United States and Europe. High-risk populations include women with diabetes, dyslipidemia, thrombotic disorders, hyperhomocysteinemia, hypertension, renal diseases, previous preeclampsia, twin pregnancies, and low socioeconomic status. In the latter case, the incidence may increase to 20% to 25%. Preeclampsia is a major cause of maternal and fetal morbidity and mortality. Preeclampsia is defined by systolic blood pressure of more than 140 mm Hg and diastolic blood pressure of more than 90 mm Hg after 20 weeks gestation in a previously normotensive patient, and new-onset proteinuria. Abnormal placentation associated with shallow trophoblast invasion (fetal cells from outer cell layer of the blastocyst) into endometrium (decidua) and improper spiral artery remodeling in the decidua are initial pathological steps.
In this study we analyzed the renin-angiotensin system in adipose tissue, decidua and placenta from women with uneventful pregnancy and women with preeclampsia. We also analyzed the tissue by Affymetrix chips in a comparison study (control vs. preeclampsia)
Keywords: disease comparison, disease state

overall_design:
6 affymetrix human expression chips (GPL570) were analyzed.
They represent 3 tissues (pooled from 10 individuals each) from patients with preeclampsia and from patients with uneventful pregnancy (collected by cesaraen section). Tissues from patients with uneventful pregnancy are the controls in comparison to tissues of patients with preeclampsia.


title: Expression Project for Oncology (expO)

status: Public on Jan 15 2005

first: Erin

last: Curley

address: 445 N. 5th Street

institute: IGC

summary:
The mission of expO is to build on the technologies and outcomes of the Human Genome Project to accelerate improved clinical management of cancer patients.

IGC's Expression Project for Oncology (expO) seeks to integrate longitudinal clinical annotation with gene expression data for a unique and powerful portrait of human malignancies, providing critical perspective on diagnostic markers, prognostic indicators, and therapeutic targets.

The goal of expO and its consortium supporters is to procure tissue samples under standard conditions and perform gene expression analyses on a clinically annotated set of deidentified tumor samples. The tumor data is updated with clinical outcomes and is released into the public domain without intellectual property restriction.

Series-matrices are available at ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2109/.

For more information, see http://www.intgen.org/
Keywords: cancer portraits