title: Gender-specific gene expression in post-mortem human brain

city: Irvine

first: Marquis

last: Vawter

address: Gillespie Neuroscience, Room 2119

department: Psychiatry and Human Behavior

institute: University of California, Irvine

summary:
Gender differences in brain development and in the prevalence of neuropsychiatric disorders such as depression have been reported. Gender differences in human brain might be related to patterns of gene expression. Microarray technology is one useful method for investigation of gene expression in brain. We investigated gene expression, cell types, and regional expression patterns of differentially expressed sex chromosome genes in brain. We profiled gene expression in male and female dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum using the Affymetrix oligonucleotide microarray platform. Differentially expressed genes between males and females on the Y chromosome (DBY, SMCY, UTY, RPS4Y, and USP9Y) and X chromosome (XIST) were confirmed using real-time PCR measurements. In situ hybridization confirmed the differential expression of gender-specific genes and neuronal expression of XIST, RPS4Y, SMCY, and UTY in three brain regions examined. The XIST gene, which silences gene expression on regions of the X chromosome, is expressed in a subset of neurons. Since a subset of neurons express gender-specific genes, neural subpopulations may exhibit a subtle sexual dimorphism at the level of differences in gene regulation and function. The distinctive pattern of neuronal expression of XIST, RPS4Y, SMCY, and UTY and other sex chromosome genes in neuronal subpopulations may possibly contribute to gender differences in prevalence noted for some neuropsychiatric disorders. Studies of the protein expression of these sex-chromosome-linked genes in brain tissue are required to address the functional consequences of the observed gene expression differences.

Experimental design:  Two groups of male control subjects and female control subjects were selected that had no history of psychiatric disorder.  Each subject was analyzed by microarray in 3 brain regions: AnCg (anterior cingulate cortex), DLPFC (dorsalateral prefrontal cortex), and CB (cerebellum).   Total RNA aliquots for some subjects were analyzed at either 1 site, 2 sites, or 3 sites (UM , University of Michigan); UCD (University of California, Davis); or UCI (University of California, Irvine).  The data was analyzed by looking at each Male vs Female comparison separately at each site by a t-test for gender differences.  Thus for one brain region,  a Male vs Female comparison was run at 3 sites, and the overlapping significant genes from the three comparisons were reported.

We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications.
Keywords: other

first: M

first: S

last: Evans

first: P

last: Choudary

first: H

last: Tomita

first: J

last: Meador-Woodruff

last: Molnar

last: Li

middle: F

last: Lopez

last: Myers

first: D

last: Cox

last: Watson

last: Akil

first: E

middle: G

last: Jones

first: W

last: Bunney


title: Human endothelial progenitor cells (EPC) vs. human umbilical vein endothelial cells (HUVEC) vs. CD14+ monocytes

status: Public on Dec 09 2004

city: Frankfurt

first: Carmen

last: Urbich

country: Germany

institute: Molecular Cardiology

summary:
Comparison of mRNA expression in human EPC vs. HUVEC vs. human monocytes. Cell-type specific gene expression under basal cell culture conditions (no stimulation). The hybridization was performed with three samples of EPC vs. three samples of HUVEC vs. 3 samples of CD14+ monocytes.

•	The origin of the biological sample:
Human endothelial progenitor cells (EPC): EPC were ex vivo cultivated from human peripheral blood-derived mononuclear cells (PBMC). PBMC were isolated by density gradient centrifugation from healthy human volunteers as previously described (Dimmeler et al., 2001).
Pooled human umbilical vein endothelial cells (HUVEC) were purchased from Cambrex (Verviers, Belgium).
CD14+ monocytes were purified from PBMC by positive selection with anti-CD14-microbeads (Miltenyi Biotec, Bergisch-Gladbach, Germany). Purity assessed by FACS analysis was greater than 95%.

•	Manipulation of biological samples and protocols used: for example, growth conditions, treatments, separation techniques:
EPC:
8000000 PBMC/ml were plated on human fibronectin (Sigma, Taufkirchen, Germany) and maintained in endothelial basal medium (Cambrex) with EGM SingleQuots and 20% fetal calf serum (FCS). After 3 days, nonadherent cells were removed and adherent cells were incubated in fresh medium for 24 h before starting experiments.
HUVEC:
HUVEC were cultured in endothelial basal medium (Cambrex) supplemented with hydrocortisone, bovine brain extract, gentamicin, amphotericin B, epidermal growth factor, and 10% FCS until the third passage according to the manufacturer’s recommendations.
CD14+ monocytes: No culture.

•	Protocol for preparing the hybridization extract: for example, the RNA or DNA extraction and purification protocol.
Total RNA was extracted from EPC, HUVEC, and CD14+ monocytes using the RNeasy cleanup system (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Quantity and quality of total RNA was analyzed by the 2100 Bioanalyzer system (Agilent Technologies, Waldbronn, Germany) and agarose gel electrophoresis.

•	Labeling protocol(s):
The detailed protocol for the sample preparation and microarray processing is available from Affymetrix (Santa Clara, CA). Briefly, 10 µg of purified total RNA was reverse transcribed by Superscript II reverse transcriptase (Life Technologies, Grand Island, NY) using T7-(dT)24 primer containing a T7 RNA polymerase promoter. After synthesis of the second complementary DNA (cDNA) strand, this product was used in an in vitro transcription reaction to generate biotinylated complementary RNA (cRNA).

•	The protocol and conditions used during hybridization, blocking and washing:
Fifteen micrograms of fragmented, biotinylated cRNA were hybridized to a HG-U95Av2 microarray (Affymetrix Inc.) for 16 hours at 45° C with constant rotation at 60 rpm. This high-density oligonucleotide array targets 9,670 human genes as selected from the National Center for Biotechnology Information (NCBI) Gene Bank database with a total of 12,000 oligonucleotide sets. Each microarray was used to assay a single sample. After hybridization, the microarray was washed and stained on an Affymetrix fluidics station and scanned with an argon-ion confocal laser, with a 488 nm emission and detection at 570 nm.

•	GeneChip image analysis was performed using the Microarray Analysis Suite 5.0 (Affymetrix, Inc.). Expression data were analyzed utilizing the GeneSpring™ software version 4.2 (Silicon Genetics Inc., San Carlos, CA).
Keywords: parallel sample

first: Christopher

last: Heeschen

first: Alexandra

last: Aicher

first: Ken-ichiro

last: Sasaki

first: Thomas

last: Bruhl

first: Mohammad

middle: R

last: Farhadi

first: Peter

last: Vajkoczy

first: Wolf

middle: K

last: Hofmann

first: Christoph

last: Peters

first: Len

middle: A

last: Pennacchio

first: Nasreddin

middle: D

last: Abolmaali

first: Emmanouil

last: Chavakis

last: Reinheckel

first: Andreas

middle: M

last: Zeiher

first: Stefanie

last: Dimmeler


title: Combining gene expression data from different generations of oligonucleotide arrays

status: Public on Dec 08 2004

city: Cambridge

first: Sek Won

last: Kong

state: MA

address: 7 Divinity Avenue

country: USA

institute: Harvard University

summary:
Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different generations of microarrays can be combined more effectively. The dataset of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays for this purpose. Signal values from GCOS 1.2 with Detection call and p-value are provided here, and CEL files are also available for download.
Keywords: parallel sample

first: Kyu-Baek

last: Hwang

first: Steve

last: Greenberg

middle: J

last: Park


title: PBMCs from CCI-779 Treated RCC subjects

status: Public on Dec 01 2004

city: Collegeville

first: Michael

middle: E.

last: Burczynski

state: PA

address: 500 Arcola Road

department: Pharmacogenomic Biomarkers

institute: Wyeth

summary:
Clinical Pharmacogenomics study. Renal Cell Carcinoma subjects were treated with CCI-779 and peripheral blood mononuclear cells were profiled over time of treatment.

Population pharmacokinetics of
CCI-779: Correlations to safety and pharmacogenomics responses in
patients with advanced renal cancer. Clin Pharm Therapeutics Dec 2004
Keywords: other

first: J

middle: P

last: Boni

first: C

last: Leister

first: G

last: Bender

first: V

last: Fitzpatrick

first: N

last: Twine

last: Stover

first: A

last: Dorner

first: F

last: Immermann

first: M

middle: E


title: T98G growth arrest

status: Public on Nov 05 2004

city: New York

first: Brian

last: Dynlacht

state: NY

address: 550 First Avenue

department: Pathology

institute: NYU Cancer Institute

summary:
Triplicate experiments from T98G cells under asynchronously growing, and growth arrest by serum deprivation and contact inhibition.
Keywords: other

first: Hugh

last: Cam

first: Egle

last: Balciunaite

first: Alexandre

last: Blais

first: Alexander

last: Spektor

first: Richard

last: Scarpulla

last: Young

first: Yuval

last: Kluger


title: Portrait of transcriptional responses to ultraviolet and ionizing radiation in human cells

status: Public on Nov 16 2004

city: Stanford

first: Wan-Jen

last: Hong

state: CA

address: 269 Campus Dr., CCSR Room 1140

department: Medicine/Biochemistry

institute: Stanford University School of Medicine

summary:
Peripheral blood lymphocytes from a total of 15 healthy individuals without history of cancer (NoCa) were immortalized with Epstein-Barr virus.

Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR).  For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later.  For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later.  For example, NoCa1-Mock refers to cells from healthy patient 1 exposed to mock treatment.  The published manuscript (NAR 32:4786, 2004) can be found at http://nar.oupjournals.org/cgi/content/abstract/32/16/4786

Data were analyzed with Affymetrix MAS version 4.0.

Normalization – A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization.
Keywords: repeat sample

first: Kerri

last: Rieger

first: Gilbert

last: Chu

first: Virginia

last: Tusher

first: Jean

last: Tang

first: Robert

last: Tibshirani


title: IFN-gamma priming

first: Xiaoyu

last: Hu

address: 535 East 70th Street

department: Research

institute: Hospital for Special Surgery

summary:
IFN-gamma transcriptional responses in control and IFN-gamma primed primary human macrophages
Keywords: repeat sample


title: Carboplatin Sensitivity in Ovarian Carcinoma

city: Pittsburgh

first: David

middle: Gerard

last: Peters

department: Medicine

institute: University of Pittsburgh

summary:
Use Of Expression Arrays To Identify Genes From Ovarian Cancer Cells That Are Associated With Carboplatin Sensitivity And Resistance as defined by ChemoFX Assay
Keywords: parallel sample

first: John

last: Freund

middle: L

last: Ochs


title: TGFbeta targets in M091 cell line

status: Public on Oct 28 2004

first: Agnes

last: Viale

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary:
Treatment of Leukemia derived M091 cell line with TGF beta
Keywords: other

first: Joseph

last: Scandura

first: Joan

last: Massague

first: Piernicola

last: Boccuni

first: Stephen

last: Nimer


title: TGFbeta lung fibroblasts

status: Public on Nov 02 2004

city: London

first: Elisabetta

middle: Augusta

last: Renzoni

address: EKB, 1B Manresa Rd

department: Dept of Occupational and Environmental Medicine

country: United Kingdom

institute: Royal Brompton Hospital/Imperial College of Science, Technology and Medicine

summary:
The response to a 4 hour treatment with TGFbeta (4 ng/ml) was evaluated in lung fibroblasts derived from three controls (normal periphery of resected tumor), open lung biopsies from three patients with idiopathic pulmonary fibrosis (usual interstitial pneumonia pattern on biopsy) and from three patients with fibrosing alveolitis associated with systemic sclerosis (fibrotic non specific interstitial pneumonia pattern on biopsy). Lung fibroblasts were grown to confluence in DMEM with 10% fetal calf serum. At confluence, lung fibroblasts were serum-deprived overnight, and exposed to either 4 ng/ml of activated TGF-ß1 (R&D Systems) or serum-free culture medium with 0.1% BSA for four hours.
Keywords: other

last: Abraham

first: Sarah

last: Howat

first: Xu

last: Shi-Wen

first: Piersante

last: Sestini

first: George

last: Bou-Gharios

first: Athol

middle: U

last: Wells

first: Srihari

last: Veeraraghavan

first: Andrew

last: Nicholson

first: Christopher

last: Denton

first: Carol

last: Black

first: Kenneth

middle: I

last: Welsh

first: Roland

last: du Bois


title: Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage

status: Public on Sep 06 2004

first: Wan-Jen

last: Hong

summary:
Peripheral blood lymphocytes from a total of 57 patients were immortalized with Epstein-Barr virus.  Fourteen radiation-therapy patients suffered unusual levels of radiation toxicity (RadS).  Thirteen radiation-therapy patients with limited toxicity (RadC) were enrolled as controls.  Fifteen patients diagnosed with skin cancer before age 40 (SkCa) were used as a second group of controls.  Fifteen healthy subjects without any history of cancer (NoCa) were matched to the skin cancer patients and used as a third group of controls.

Cells were exposed to mock treatment (Mock), ultra-violet radiation (UV), or ionizing radiation (IR).  For UV radiation treatment, cells were exposed to 10 J/m^2 and harvested for RNA 24 hours later.  For IR treatment, cells were exposed to 5 Gy of IR and harvested for RNA 4 hours later.  For example, RadS1-Mock refers to cells from radiation sensitive patient 1 exposed to mock treatment.  The published manuscript (PNAS 101:6634, 2004) can be found at http://www.pnas.org/cgi/doi/10.1073/pnas.0307761101

Data were analyzed with Affymetrix MAS version 4.0.

Normalization – A reference data set was generated by averaging the expression of each gene over all data sets. The data for each hybridization were compared with the reference data set in a cube root scatter plot. A linear least-squares fit to the cube root scatter plot was then used to normalize each hybridization.
Keywords = Gene expression in lymphoid cells of cancer patients
Keywords: repeat sample

first: Kerri

last: Rieger

first: Virginia

last: Tusher

first: Jean

last: Tang

first: Robert

last: Tibshirani

first: Gilbert

last: Chu


title: Effect of Vitamin D on gene expression by CaCO2 cells

status: Public on Oct 26 2004

city: Natick

first: Larry

middle: Allen

last: Sonna

address: 42 Kansas Street

department: Thermal and Mountain Medicine Division

institute: USARIEM

summary:
The raw data are presented.  The computations in the manuscript were based on the fold-changes reported by the MAS 4.0 software, not on ratios taken from raw data
Keywords: parallel sample

first: Richard

last: Wood


title: Role of LANA in KSHV latent infection

status: Public on Oct 27 2004

city: Cleveland

first: Feng-Qi

last: An

state: OH

address: 10900 Euclid Avenue

institute: Case Western Reserve University

summary:
Gene expression profiling of three PEL cell lines compare to three Burkitt's lymphoma lines to figure out the changed genes under KSHV latent infection.

Gene expression profiling of two time points on TIVE cells after infection by KSHV compare to TIVE cell without infection by KSHV to figure out the changed genes on TIVE cell under latent infection of KSHV.

Gene expression profiling of four time points after inducing recombinant LANA protein expression when compare to no inducing BJAB/Tet-On/LANA cells to figure out the changed genes under the latency-associate nuclear antigen (LANA) of KSHV expression.

Gene expression profiling of three time points after inducing recombinant LANA protein expression when compare to no inducing Jurkat/Tet-On/LANA cell line to figure out the changed genes under the latency-associate nuclear antigen (LANA) of KSHV expression.

Gene expression profiling of two time points after inducing recombinant LANA protein expression when compare to no inducing 293/Tet-On/LANA cell line to figure out the changed genes under the latency-associate nuclear antigen (LANA) of KSHV expression.
Keywords = TIVE
Keywords = KSHV
Keywords = LANA
Keywords = PEL
Keywords = BJAB
Keywords = 293
Keywords = Jurkat
Keywords: other

first: Edward

last: Horwitz

first: Erik

middle: S

last: Knudsen

first: Hope

last: Folarin

first: Justin

last: Roth

first: Keith

last: McCrae

first: Michael

last: Sramkoski

first: Nicole

last: Compitello

first: Rolf

last: Renne

first: Stanton

last: Gerson


title: Microarray analysis of activated mixed glial (microglia) and monocyte-derived macrophage gene expression.

city: Philadelphia

first: Andrew

middle: V.

last: Albright

address: 255 CRB  415 Curie Blvd

department: Neurology

institute: University of Pennsylvania

summary:
Since macrophage activation can now be studied at a global level using modern microarray and proteomic analyses, discovery of novel macrophage activation genes is inevitable and important for understanding HIV-associated dementia (HAD). We isolated two different types of primary human macrophages, microglia and monocyte-derived macrophages (MDM) from brain tissue and whole blood respectively. The microarray analysis of differentially regulated macrophage activation genes reported here supports our previous assertions that the mixed glia (MIX) cultured in starvation conditions (DMEM alone) are a non-activated, or “quiescent”, tissue culture model for studying macrophage activation in the brain. Transcript levels from these quiescent cultures provided a background level of gene expression, and allowed for the identification of upregulated macrophage activation genes in the MIX brain cultures upon treatment with an array of soluble activation factors: serum components, cytokines, and growth factors. We found that 914 genes in the MIX cultures and 734 genes in the MDM cultures had a greater than 2-fold increase in expression. We discovered 180 genes that were increased greater than 2 fold in both culture types. Microarray-specific statistical analyses were performed to complement fold change analysis: Significance Analysis of Microarrays (SAM), and Partek Pro. In the MIX cultures, we detected over a hundred fold increase in IL-1? and TIMP1 transcription; Caspase 9, S100A8 and 9, MMP-12, IL-8, MCP-1, MRC-1, and IL-6 were also upregulated. Activation of starved MDM cultures resulted in fewer upregulated genes compared to MIX cultures. Genes upregulated in both MIX and MDM included CCL2 (MCP1), CCL7, CXCL5, TNFSF14, kinases, and phosphatases. These microarray data may provide leads for identifying previously unknown neurotoxins, disease biomarkers, and pathways responsible for the neuronal apoptosis observed in HAD, and for the eventual identification of therapeutic targets and treatments.

For each gene, we performed a per-gene normalization, whereby an expression ratio was calculated by dividing the raw data from the activated media samples by the raw signal for the same gene from the non-activated media samples (Fig. 1). The same microarray data were also analyzed again using the very common per-chip normalization method recommended by the manufacturer where raw signals for each chip were multiplied by a scaling factor such that the trimmed mean for each chip became an arbitrary number (150) (Affymetrix, 2001).
The per-chip normalization method reduces person-to-person biological variability and potentially hides important changes in gene expression (Hill et al., 2001),(Bolstad et al., 2003). Therefore, we report our data using a per-gene normalization method, which yielded higher signal and low noise (uninteresting non-biological variability caused by chips, and/or experimental sample preparation), and given our experimental design, reduced person-to-person variability that these experiments cannot address directly. For later statistical analyses, the data were log transformed in order to obtain a normal distribution of the expression values of the >12,625 genes (Bolstad et al., 2003)
Keywords = Microarray
Keywords = macrophage
Keywords = microglia
Keywords = activation
Keywords = brain
Keywords: dose response

middle: V

first: Francisco

last: Gonzalez-Scarano


title: Determination of mRNA transcripts in HeLa cells that are regulated by RENT1

status: Public on Aug 25 2004

city: Baltimore

first: Joshua

middle: T

last: Mendell

state: MD

address: 733 N. Broadway, BRB 471

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

summary:
HeLa cells were treated with siRNA directed against Luciferase or RENT1 in duplicate (as described in Mendell et al., Science, 2002; PubMed ID:12228722).  Transcripts that are differentially expressed between the two experimental conditions are putatively regulated by RENT1.
Keywords: repeat sample


title: Tassiulas IFN Array v1.0

status: Public on Sep 09 2004

first: Ioannis

last: Tassiulas

institute: The Hospital for Special Surgery

summary:
Type I IFN-inducible gene expression in human blood monocytes primed with Type II IFN.
Keywords: repeat sample


title: Juvenile Rheumatoid Arthritis Profiles In PBMC and SFMC

status: Public on Aug 11 2004

city: Cincinnati

last: Barnes

address: 3333 Burnet Ave

department: Rheumatology

institute: Cincinnati Childrens Hospital Medical Center

summary:
Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA).  57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course.
Keywords = juvenile rheumatoid arthritis (JRA)
Keywords = peripheral blood mononuclear cells (PBMC)
Keywords = synovial fluid mononuclear cells (SFMC)
Keywords: other

first: M

middle: G

first: B

last: Aronow

first: L

middle: K

last: Luyrink

middle: B

last: Moroldo

first: P

last: Pavlidis

middle: H

last: Passo

first: A

middle: A

last: Grom

first: R

last: Hirsch

first: E

last: Giannini

last: Colbert

first: D

middle: N

last: Glass

first: S

last: Thompson


title: Caco-2 differentiation

status: Public on Jul 29 2004

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

summary:
This is an analysis of Caco-2 BBe cell spontaneous differentiation.  JF2dR1-JF2dR4 = proliferating cells; JF8dR1-JF8dR4 = 4 d post-confluent; JF15dR1-JF15dR4 = 11 d pc, differentiated
Keywords: time-course


title: Time and Exercise effects on Human Skeletal Muscle

status: Public on Oct 14 2004

city: Claremont

first: Alexander

last: Zambon

address: 517 Watson Drive

department: Biopharmaceutical Sciences

institute: Keck Graduate Institute

summary:
Four healthy human volunteers underwent an acute bout of resistance exercise with the right leg at 2 pm. Biopsies were removed from the Vastus Lateralis muscle 6 h (8 pm) and 18 h (8 am) after exericise
Keywords = Human skeletal muscle
Keywords = resistance exerise
Keywords = diurnal
Keywords = circadian
Keywords: time-course

first: Erin

last: McDearmon

first: Nathan

last: Salomonis

first: Karen

middle: M

last: Vranizan

first: Kirsten

last: Johansen

first: Deborah

last: Adey

first: Joseph

last: Takahashi

first: Morris

last: Schambelan

first: Bruce

middle: R

last: Conklin


title: Kidney Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes

status: Public on Jul 14 2004

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary:
We used DNA microarrays (HG-U95Av2 GeneChips) to determine gene expression profiles for kidney biopsies and peripheral blood lymphocytes (PBLs) in transplant patients. Sample classes include kidney biopsies and PBLs from patients with 1) healthy normal donor kidneys, 2) well-functioning transplants with no clinical evidence of rejection, 3) kidneys undergoing acute rejection, and 4) transplants with renal dysfunction without rejection. Nomenclature for samples is as follows: 1) all sample names include either BX or PBL to indicate that they were derived from biopsies or PBLs respectively, 2) C indicates samples from healthy normal donors, 3) TX indicates samples from patients with well-functioning transplants with no clinical evidence of rejection, 3) AR indicates samples from transplant patients with kidneys undergoing acute rejection, 4) NR indicates samples from transplant patients with renal dysfunction without rejection.
Abbreviations used to describe patient samples include the following: BX - Biopsy; PBL- Peripheral Blood Lymphocytes; CsA -Cyclosporine; MMF - Mycophenolate Mofetil; P - Prednisone; FK - Tacrolimus;  SRL - Sirolimus; CAD -Cadaveric;  LD - Live Donor; Scr - Serum Creatinine; ATN - Acute Tubular Necrosis CNI - Calcineurin Inhibitor; FSGS - Focal Segmental Glomerulosclerosis
several array data sets did not pass quality control and were not analyzed. These include AR1PBL, NR4BX, and NR6PBL
Keywords = DNA microarrays, gene expression, kidney, rejection, transplant
Keywords: other

first: Stuart

last: Flechner

first: Sunil

last: Kurian

first: Starlette

last: Sharp

first: Thomas

last: Whisenant

first: Jie

last: Zhang

first: Jeffrey

middle: D

last: Chismar

first: Steve

last: Horvath

first: Tony

last: Mondala

first: Timothy

last: Gilmartin

first: Daniel

middle: J

last: Cook

last: Kay

first: John

last: Walker

last: Salomon


title: Epithelial stem cells co-cultured with the dermal papilla

status: Public on Jun 10 2004

city: Boston

first: Stephen

middle: R.

last: Lyle

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

summary:
Clonogenic keratinocyte stem cells isolated from the bulge area of human telogen follicles were co-cultured with dermal papilla cells in a transwell system. RNA was isolated from stem cells for different periods of time (day 0, 1, 2, and 5) after co-culture with DP and analyzed for changes in gene expression using Genechip microarrays.
Keywords = epithelial stem cells
Keywords = DP
Keywords = co-culture
Keywords: other

first: Cecilia

last: Roh

first: Qingfeng

last: Tao


title: Gene regulation and DNA damage in the aging human brain

status: Public on Jul 21 2004

first: Tao

last: Lu

address: 300 Longwood Ave

institute: The Children's Hospital

summary:
Transcriptional profiling of the human frontal cortex from individuals ranging from 26 to 106 years of age. The postmortem brain tissue samples used in this study were neuropathologically normal for age, and were derived from non-demented individuals.
Keywords: other

first: Ying

last: Pan

first: Shyan-Yuan

last: Kao

first: Cheng

last: Li

first: Isaac

last: Kohane

first: Jennifer

last: Chan

last: Yankner


title: CCF_Almasan_CaPK

status: Public on Jun 01 2004

middle: Gilmary

last: Hissong

address: 9500 Euclid Ave.

department: Cancer Biology

institute: Lerner Research Institute Cleveland Clinic Foundation

summary:
The experiment was a time course experiment on LNCaP C4-2 human prostate adenocarcinoma cells following irradiation to a dose of 10 Sv from a Cesium-137 gamma source. Total RNA was extracted from cells at 1, 2, 4, 6, 8, 12, 16, 20 and 24 hours after irradiation. The untreated control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr. After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual. Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray
Keywords: time-course

last: Buchsbaum

first: Bendi

last: Gong

first: Subrata

last: Ray

first: Eric

last: Klein

first: Warren

middle: E

last: Heston

first: Alexandru

last: Almasan


title: CCF_Almasan_CaPGSE56

summary:
The experiment was a response to radiation experiment using LNCaP C4-2 human prostate adenocarcinoma cells with dominant negative p53 function.  Cells were irradiated to a dose of 10 Sv from a Cesium-137 gamma source.  Total RNA was extracted from cells at 6 and 24 hours after irradiation.  The control sample, labeled 0, was collected concurrently with the cells extracted at 24 hr.  It was not irradiated and was transfected with the base pLXSN retrovirus, lacking the inserted GSE56 coding region.  After extraction, the samples were processed and hybridized to the Affymetrix (Santa Clara, CA, www.affymetrix.com) HG-U95Av2 chip, and then washed, stained and scanned according to Affymetrix's protocols contained in the GeneChip(R) Expression Analysis Manual.  Transcript abundance data from the scans was processed initially with Affymetrix' Microarray Suite 5(R), then by Silicon Genetics' (Redwood City, CA, www.silicongenetics.com) GeneSpring(R).
Keywords = Human
Keywords = Prostate
Keywords = Cancer
Keywords = Adenocarcinoma
Keywords = Ionizing Radiation
Keywords = Microarray
Keywords = p53
Keywords = GSE56
Keywords: time-course

first: Jeffrey


title: Human prostate cancer tissues analyses

status: Public on May 26 2004

city: Wuhan

first: Xiao-Qin

last: Xia

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

department: Center for Molelcular and Cellular Biology of Aquatic Organisms

country: China

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

summary:
Human prostate cancer tissues analyses
Keywords: other


title: HIV-based vector infected cells

status: Public on May 19 2004

first: Richard

middle: Steven

last: Mitchell

address: 10010 North Torrey Pines Rd

department: Infectious Disease Laboratory

institute: The Salk Institute

summary:
SupT1, PBMC, or IMR90 cells were infected with an HIV-based vector (see Schroder et al., Cell 110:521-9) and the RNA isolated 48 hours after infection.

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

middle: S

first: Brett

middle: F

last: Beitzel

first: Astrid

last: Schroder

first: Paul

last: Shinn

first: Huaming

last: Chen

first: Charles

last: Berry

first: Joseph

last: Ecker

first: Frederic

last: Bushman


title: Breast Cancer Cell Line Experiment

status: Public on Apr 13 2004

first: Brig

last: Mecham

address: 20 Shattuck St

institute: Harvard Medical School

summary:
This series represents a set of experiments preformed using RNA isolated from human mammary epithelial cells, human MDA-MB-436 cells and HCC1954 cells.
Keywords: parallel sample

first: Zoltan

last: Szallasi

first: Brigham

first: Thomas

last: Mariani

first: Isaac

last: Kohane

first: Gregory

last: Klus

first: Daniel

middle: Z

last: Wetmore

last: Strovel

first: Meena

last: Augustus

first: David

last: Byrne

first: Peter

last: Bozso


title: primary trophoblast study

summary:
Primary cultures of human trophoblasts were established from normal, term placenta. Cells were treated five hours after plating. This sample was treated with 1 uM GW7845. RNA was extracted after 48 hours of treatment using Tri-reagent. Each sample was pooled from three individual placentas prior to target generation. Targets were produced using standard Affymetrix procedures from 30ug of total RNA.
Keywords: parallel sample

first: Yoel

last: Sodovksy

last: Sodovsky


title: Myb specificity determinants

status: Public on Apr 16 2004

city: Albuquerque

first: Scott

middle: A.

last: Ness

state: NM

department: Internal Medicine

institute: U. of New Mexico HSC

summary:
Recombinant adenovirus vectors were used to express wild type or domain swap mutants of A-Myb and c-Myb transcription factors in MCF-7 cells or pimary lung epithelial cells or fibroblasts. The results show that Myb proteins have extreme context specificity and identify sub-domains responsible for the activation of specific sets of target genes.
Keywords = Myb proteins
Keywords = oncogenes
Keywords = transcription
Keywords = gene activation
Keywords: ordered

first: Wanli

last: Lei

first: John

last: Rushton

first: Lisa

last: Davis

first: Fan

last: Liu


title: Pre-analytical changes of mRNA Gene Expression as the result from prolonged storage

status: Public on Apr 28 2004

city: Heidelberg

first: Matthias

last: Nees

address: Im Neuenheimer Feld 156

department: Pediatric Oncology & Hematology

institute: Heidelberg University, Children's Hospital

summary:
Impact of pre-analytical handling on Bone Marrow (BM) mRNA Gene Expression: We have investigated the impact of RNA extraction protocols and time delays (24 and 48h) between sample aspiration and RNA extraction on RNA quality and gene expression profiles. Intact RNA can be extracted from BM samples stored at room temperature for up to 48h after aspiration. However, storage of BM has dramatic effects on mRNA expression of individual transcripts.
Keywords: time-course

first: Stephen

last: Breit


title: Diabetic nephropathy

status: Public on Apr 01 2004

city: Leiden

first: Hans

last: Baelde

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: LUMC

summary:
Gene expression profiling in glomeruli from human kidneys with diabetic nephropathy
Keywords = Diabetes
Keywords = kidney
Keywords = glomeruli
Keywords: other

first: Michael

last: Eikmans

last: Lappin

last: Doran

first: Emile

last: de Heer

first: Jan Anthonie

last: Bruijn


title: HGPC, in monolayer, 0.5% serum

city: Jacksonville

first: Robert

middle: C.

last: Olney

state: FL

address: 807 Children's Way

department: Pediatrics

institute: Nemours Children's Clinic

summary:
Human growth plate chondrocytes were isolated from the distal femoral growth plate from 3 different adolescents undergoing epiphysiodesis.  Cell were isolated and grown in monolayers, long term, in 20% serum.  Cells were replated and cultured 48 h in 0.5% serum.
Keywords: repeat sample

first: Jianwei

last: Wang

first: James

last: Sylvester

first: Edward

middle: B

last: Mougey


title: HGPC, in monolayer, 0.5 vs. 20% serum

summary:
Human growth plate chondrocytes were isolated from the distal femoral growth plate from a single adolescent undergoing epiphysiodesis.  Cell were isolated and grown in monolayers, long term.  Cells were replated and cultured in 0.5% or 20% serum.
Keywords: parallel sample


title: aging of cultured human myotubes

status: Public on May 31 2004

city: St. Louis

first: Matthew

middle: Alan

last: Roberts

state: MO

address: 1 Checkerboard Square

department: Global Strategic Business Unit and R&D

institute: Nestle Research Center

summary:
Aging of skeletal muscle tissue is characterized by loss of metabolic and contractile competence. It is thought that this phenomenon is driven via extrinsic and intrinsic factors. In order to identify age-dependent changes intrinsic to the muscle cell, microarray transcriptional profiles and measurements of glucose metabolism were performed in primary cultured human myotubes at different time points over seven weeks. Aging in culture tended to reduce myotube glucose metabolism, oxidative and storage capacities, despite elevation of glucose transport. The mitochondrial membrane potential slightly increased, whereas peroxidation of cell membrane lipids declined and membrane integrity was preserved. Transcriptional analysis revealed a fall in genes involved in glucose metabolism and oxidative phosphorylation, while stress defense genes were elevated. Expression of numerous genes coding for muscle contractile proteins and calcium-regulating proteins, was gradually decreased during aging of cultured myotubes. Transcripts of genes involved in cell growth, matrix and motility markedly rose while those involved in cell adhesion dropped. In conclusion, aging myotubes in culture exhibit a loss of glucose metabolic capacity. They are characterized by a shift from a contractile to a growth-survival, matrix-remodeling phenotype. This pattern of changes, linked to intrinsic factors, displays significant similarities with aging of muscle from primates and human subjects.
Keywords = aging
Keywords = muscle cell biopsy
Keywords = myotubes
Keywords = glucose
Keywords: time-course

middle: A

first: Andreu

last: Ferrer-Martínez

first: Eulàlia

last: Montell

first: Anna

last: Gómez-Foix

last: Mansourian

first: Katherine

last: Macé


status: Public on Jan 01 2004

city: Chicago

first: M Rosario

last: Hernandez

state: IL

address: 330 Chicago Avenue

department: Ophthalmology

institute: Northwestern University

summary:
Gene expression in human optic nerve head (ONH) astrocytes exposed to either 60 mm Hg hydrostatic pressure (HP) or control ambient pressure (CP) was compared using Affymetrix GeneChip microarrays to identify HP-responsive genes. Primary ONH astrocytes from two male Caucasian donors (passage 4) were grown to 75% confluence and were exposed for 6, 24 or 48 h to control ambient pressure (CP6, CP24, CP48) or hydrostatic pressure (HP6, HP24, HP48), or harvested at the beginning of the pressure experiment (CP0). Total RNA was extracted using Qiagen RNeasy columns and converted to biotin-labeled cRNA by standard Affymetrix protocols available at web site http://pathology.wustl.edu/~mgacore/genechip.htm#Preparing. Hybridization of the labeled cRNA to Human Genome U95Av2 chips (Affymetrix) was carried out by using Genechip Instrument System (Affymetrix) at Genechip Core Facility of Washington University. A total of 44 chips were generated and distributed as follows: seven for control pressure (CP) at time 0, four CP at 6 h, seven for hydrostatic pressure (HP) at 6 h, eight for CP at 24 h, eight for HP at 24 h, five for CP at 48 h and five for HP at 48h P. The arrays were washed and stained with streptavidin-phycoerythrin  followed by scanning on an Agilent GeneArray Scanner G2500A (Agilent Technologies, Palo Alto, CA), and then scanned by an Affymetrix GeneArray Scanner. Data was analyzed by Affymetrix Microarray Suite (version 5.0), linear regression analysis, and GeneSpring expression Analysis Software (version 6.0, Silicon Genetics). For analysis, the samples were scaled to the same target intensity (1500) to allow comparison of multiple samples, and raw data were normalized to median of each gene across all chips for fold change analysis using GeneSpring.
Keywords: time-course

first: Olga

last: Agapova

first: Ping

last: Yang

first: Amy

last: Parker

first: William

last: Shannon

first: Paula

last: Pecen

first: Jill

last: Duncan

first: Mercedes

last: Salvador-Silva

first: M


title: MRI lytic and no lytic lesions

city: Little Rock

first: John

middle: D.

last: Shaughnessy

state: AR

address: 4301 West Markham St., Slot 776

department: Division of Basic Sciences

institute: Myeloma Institute for Research and Therapy

summary:
This series represents samples of multiple myeloma patients with and without bone lytic lesion by MRI.
Keywords = multiple myeloma
Keywords = osteolytic lesions
Keywords = MRI
Keywords = osteoblast
Keywords = mesenchymal stem cell
Keywords = Wnt signaling
Keywords = DKK1
Keywords: other

first: Erming

last: Tian

first: Fenghuang

last: Zhan

first: Ronald

last: Walker

first: Erik

last: Rasmussen

first: Yupo

last: Ma

first: Bart

last: Barlogie


title: MRI-lytic-lesion

summary:
This series represents samples of multiple myeloma patients with bone lytic lesion by MRI.
Keywords = multiple myeloma
Keywords = osteolytic lesions
Keywords = MRI
Keywords = osteoblast
Keywords = mesenchymal stem cell
Keywords = Wnt signaling
Keywords = DKK1
Keywords: other


title: Molecular profiles (HG-U95A) of dystrophin-deficient and normal human muscle

status: Public on Jan 29 2004

first: Judith

last: Haslett

summary:
Molecular profiles of dystophin-deficient patients and normal human skeletal muscles on Affymetrix HG-U95A arrays
Keywords = DMD
Keywords = Duchenne muscular dystrophy
Keywords = dystrophin
Keywords = Affymetrix U95A array
Keywords = skeletal muscle
Keywords = gene expression profiles
Keywords: other

middle: N

first: Despina

last: Sanoudou

first: Alvin

middle: T

last: Kho

first: Richard

last: Bennett

first: Steven

last: Greenberg

first: Isaac

last: Kohane

first: Alan

middle: H

last: Beggs

first: Louis

middle: M

last: Kunkel


title: MRI-no-lytic-lesion

summary:
This series represents samples of multiple myeloma patients without bone lytic lesion by MRI.
Keywords = multiple myeloma
Keywords = osteolytic lesions
Keywords = MRI
Keywords = osteoblast
Keywords = mesenchymal stem cell
Keywords = Wnt signaling
Keywords = DKK1
Keywords: other

middle: D


title: Scott B cell studies

status: Public on Mar 05 2004

city: Le Kremlin-Bicetre

first: Daniele

last: Kerbiriou-Nabias

country: France

institute: INSERM U143

summary:
B lymphoblast samples from control individual, Scott syndrome patient and Scott syndrome daughter. From each samples one part was treated with A23187 ca2+ ionophore. Treated and non-treated samples were then cultured further. Each sample was then processed in duplicate for hybridization on the microarray
Keywords: ordered

first: Detlef

last: Kozian

first: Valerie

last: Proulle

first: Almut

last: Nitsche

first: Marie

last: Galitzine

first: Carmen

last: Martinez

first: Beatrice

last: Schumann

first: Dominique

last: Meyer

first: Matthias

last: Herrmann

first: Jean-Marie

last: Freyssinet

last: Kerbiriou Nabias


title: Human skeletal muscle

status: Public on Dec 10 2003

city: Athens

first: Despina

last: Sanoudou

address: Soranou Efesiou 4

department: Molecular Biology

country: Greece

institute: Foundation for Biomedical Research, Academy of Athens

summary:
Standard Affymetrix procedure, RNA from frozen tissue
Keywords: equivalent probe

first: Peter

last: Kang

first: Judith

last: Haslett

first: Mei

last: Han


title: Neural stem and neuroblastoma cells

status: Public on Oct 22 2003

city: Madison

first: Jiang

last: Li

state: WI

address: 777 Highland Ave.

department: School of Pharmacy

institute: University of Wisconsin Madison

summary:
Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from (1) human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20µM) for 24h, and (2) neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10µM) for 24h.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Jeffrey

last: Johnson


title: GeneNote-Gene Normal tissue Expression

status: Public on Nov 19 2003

city: Rehovot

first: Orit

last: Shmueli

state: Israel

address: Rehovot

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary:
Normal human tissue expression profiling
Keywords: other

first: Hila

last: Benjamin-Rodrig

first: Vered

last: Chalifa-Caspi

first: Ron

last: Ophir

first: Michael

last: Shmoish

first: Itai

last: Yanai

first: Marylin

last: Safran

first: Doron

last: Lancet

first: Shirley

last: Horn-Saban


title: RASF + IKB/Adtet + TNFa

status: Public on Oct 23 2003

city: Birmingham

first: Grier

last: Page

state: AL

institute: University of Alabama at Birmingham

summary:
Rheumatoid arthritis synovial fibroblasts (RASF) were transected with an adenovirus (Ad) expressing a dominant negative (DN) form of Ik-B stimulated 18 hours later with TNF-a. Controls were RASF transfected with Adtet then treated with TNF-a 18 hours later. RNA was extracted 3 hours after TNF-a application. The same cell line was split into 6 lots grown up  and then treated with the virus independent. Each of the Ik-B and Adtet has 3 replications. Data is Hu95Av2 processed with MAS 4.0.
Keywords: repeat sample

first: Huang-Ge

last: Zhang

first: Karren

last: Hyde

first: Hui-Chen

last: Hsu

first: David

last: Allison

middle: P

first: John

last: Mountz

first: Jacob

last: Brand

first: Juling

last: Zhou

first: Shaohua

last: Yu


title: NIH/NIAID Chronic Granulomatous Disease Neutrophils

status: Public on Dec 31 2003

city: Hamilton

first: Frank

middle: R.

last: DeLeo

state: MT

address: 903 South 4th Street

department: Laboratory of Human Bacterial Pathogenesis

summary:
Polymorphonuclear leukocytes (PMNs) were obtained from healthy individuals (Healthy1, Healthy2, Healthy3, and Healthy4) or patients with X-linked chronic granulomatous disease (XCGD1, XCGD2, XCGD3, XCGD4, XCGD5, and XCGD6). The studies were performed in accordance with a protocol approved by the Institutional Review Board for Human Subjects, National Institute of Allergy and Infectious Diseases, and the Institutional Review Board for Human Subjects at the University of Iowa. All studies were conducted according to Declaration of Helsinki principles.
PMNs (107) were combined with or without IgG and C3bi-coated latex beads (8 x 107) in wells of a 12-well tissue culture plate (pre-coated with 20% normal human serum) and centrifuged at 350 x g for 8 min at 4oC to synchronize phagocytosis. For the purpose of these studies, activated or "Stimulated" PMNs are defined as those that have been stimulated by phagocytosis of IgG- and C3bi-coated latex beads. "Control" PMNs are defined as resting cells or those left unstimulated throughout the time-course. Following centrifugation, plates were incubated at 37 deg. C in a CO2 for the indicated times. At the indicated times, tissue culture medium was aspirated from the plate and PMNs were lysed directly with RLT buffer (Qiagen, Valencia, CA). Purification of PMN RNA and subsequent preparation of labeled cRNA target (12  g) was performed as described in Methods. Labeling of samples, hybridization of cRNA with Hu95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA), and scanning were performed according to standard Affymetrix protocols. Gene expression in healthy control and XCGD individuals was always compared at the same time points after phagocytosis
Keywords = HUMAN PMN CHRONIC GRANULOMATOUS DISEASE NEUTROPHILS
Keywords: parallel sample

first: Scott

last: Kobayashi

first: Jovanka

last: Voyich

first: Kevin

middle: R

last: Braughton

first: Adeline

last: Whitney

first: William

last: Nauseef

first: Harry

middle: L

last: Malech


title: Long oligonucleotide arrays verse short oligonucleotide arrays -IMR32 cells

first: Jiang

last: Li

summary:
Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to measure differential gene expression in RNA samples generated from human neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10µM) for 24h.
For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11865, 11866, 11858, 11857, 11870, and 11871) which represent the RNA preps harvested at three different time (April 17, 2001, March 15, 2001, and Feb 21, 2001).
For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The RNA prep used for Agilent array analysis was not the same as the one used for Affymetrix array analysis. Finally, three replicates (GSM 11828, 11831 and 11835) were generated.
Keywords: parallel sample

first: Jeffrey

last: Johnson


title: Long oligonucleotide arrays verse short oligonucleotide arrays-CTX066

summary:
Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20µM) for 24h.
For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11755, 11756, 11780, 11781, 11782, and 11783) which represent the RNA preps harvested at three different time (Jan 16, 2002, Jan 24, 2002, and Feb 20, 2002).
For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The same RNA preps used for Affymetrix array analysis were also used for Agilent array analysis. Finally, three replicates (GSM 11803, 11804 and 11809) were generated.
Keywords: parallel sample


title: SCID vs Normal Thymocyte Comparisons

status: Public on Oct 10 2003

city: Toronto

first: Harjit

middle: Kaur

last: Dadi

state: Ontario

address: 555 University Avenue,

department: Infection, Immunity, Injury & Repair Research

country: Canada

institute: Hospital for Sick Children

summary:
Gene expression data from thymocytes of a 6 month old infant and thymocytes of a SCID patient
Keywords: other

middle: K

first: Amos

middle: J

last: Simon

first: Chaim

last: Roifman


title: CVB3-infected HeLa cells (multiple time points)

status: Public on Oct 09 2003

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

institute: PROOF Centre of Excellence

summary:
HeLa cells were serum starved and preincubated with DMSO (vehicle) and infected with CVB3.  Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process.  At 0, 30 minutes, 1, 3, 5, 7 and 9 hours following CVB3 infection, RNA was isolated, processed and hybridized to GeneChip®s.
Keywords: time-course

first: Bobby

last: Yanagawa

first: Honglin

last: Luo

first: Nana

last: Rezai

first: Zsuzsanna

last: Hollander

first: Raymond

last: Ng

first: Ji

last: Yuan

first: Jingchun

last: Zhang

first: Decheng

last: Yang

first: Timothy

last: Triche


title: UV radiation-induced DNA damage

status: Public on Oct 08 2003

city: Helsinki

first: Massimiliano

last: Gentile

state: Finland

address: Haartmaninkatu 8

department: Biomedicum Bioinformatics Unit

country: Finland

institute: Biomedicum Helsinki

summary:
DNA damage caused by UV radiation initiates cellular recovery mechanisms, which involve activation of DNA damage response pathways, cell cycle arrest and apoptosis. To assess cellular transcriptional responses to UVC-induced DNA damage we compared time course responses of human skin fibroblasts to low and high doses of UVC radiation known to induce a transient cellular replicative arrest or apoptosis, respectively. UVC radiation elicited >3-fold changes in 460 out of 12,000 transcripts and 89% of these represented downregulated transcripts. Only 5% of the regulated genes were common to both low and high doses of radiation. Cells inflicted with a low dose of UVC exhibited transcription profiles demonstrating transient regulation followed by recovery, whereas the responses were persistent after the high dose. A detailed clustering analysis and functional classification of the targets implied regulation of biologically divergent responses and suggested involvement of transcriptional and translational machinery, inflammatory, anti-proliferative and anti-angiogenic responses. The data support the notion that UVC radiation induces prominent, dose-dependent downregulation of transcription. However, the data strongly suggest that transcriptional repression is also target gene selective. Furthermore, the results demonstrate that dose-dependent induction of cell cycle arrest and apoptosis by UVC radiation are transcriptionally highly distinct responses.
Keywords: other

first: Leena

last: Latonen

first: Marikki

last: Laiho


title: Aortic stiffness

status: Public on Aug 28 2003

city: Boston

first: Richard

middle: E.

last: Pratt

state: MA

address: 75 Francis Street

department: Medicine

institute: Brigham and Women's Hospital

summary:
BACKGROUND: Previous genomic studies with human tissues have compared differential gene expression between 2 conditions (ie, normal versus diseased) to identify altered gene expression in a binary manner; however, a potentially more informative approach is to correlate the levels of gene expression with quantitative physiological parameters. METHODS AND RESULTS: In this study, we have used this approach to examine genes whose expression correlates with arterial stiffness in human aortic specimens. Our data identify 2 distinct groups of genes, those associated with cell signaling and those associated with the mechanical regulation of vascular structure (cytoskeletal-cell membrane-extracellular matrix). Although previous studies have concentrated on the contribution of the latter group toward arterial stiffness, our data suggest that changes in expression of signaling molecules play an equally important role. Alterations in the profiles of signaling molecules could be involved in the regulation of cell cytoskeletal organization, cell-matrix interactions, or the contractile state of the cell. CONCLUSIONS: Although the influence of smooth muscle contraction/relaxation on arterial stiffness could be controversial, our provocative data would suggest that further studies on this subject are indicated.
Keywords: other

first: Stephane

last: Laurent


title: RNA degradation and apoptosis

status: Public on Sep 17 2003

city: Columbus

first: Herbert

last: Auer

state: OH

address: 420 West 12th Ave

institute: Human Cancer Genetics

summary:
RNA degradation and apoptosis studies in PMBCs and NB 4 cells
Keywords: other

first: Sandya

last: Lyianarachchi

first: David

last: Newsom

first: Marko

middle: I

last: Klisovic

first: Guido

last: Marcucci

first: Karl

last: Kornacker


title: CVB3-infected HeLa cells (multiple time points and triplicate sample per time point)

status: Public on Oct 07 2003

first: Bruce

last: McManus

summary:
HeLa cells were serum starved and either preincubated with DMSO (vehicle), preincubated with U0126 (10µM in DMSO) and infected with CVB3 (MOI 10), or preincubated with DMSO (vehicle) and infected with CVB3.  Following infection, virus was removed and fresh media containing 10% fetal bovine serum was added for the remainder of the infectious process.  At 0, 30 minutes, 3 and 9 hours following CVB3 infection (N=3 plates per time point), RNA was isolated, processed and hybridized to GeneChip®s (N=3 per sample)
Keywords: time-course

first: Bobby

last: Yanagawa

first: Honglin

last: Luo

first: Nana

last: Rezai

first: Zsuzsanna

last: Hollander


title: WS1 response to high dose of UV-C

status: Public on Aug 09 2003

summary:
The transcriptional response to 50 J/m2 of UV-light (254 nm) was assessed with HGU95AV2 Affymetrix probe arrays at 6, 12, 18 and 24 hours after exposure. Mock-treated samples were assessed at 6 and 24 hours.
Keywords: time-course


title: HeLa CD4+ cells transfected with epitope-tagged eTat plasmids

status: Public on Aug 04 2003

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

summary:
Expression profiles of HeLa CD4+ cells transfected with epitope-tagged eTat plasmid. Cells are treated with nocodazole and hydroxyurea.

Keywords: time-course

first: Anil

last: Maddukuri

first: Fatah

last: Kashanchi


title: HeLa CD4+ transfection

summary:
Expression profiles of HeLa CD4+ cells transfected with epitope-tagged eTat plasmid, or parental plasmid pCep4. Cells are unsynchronized and untreated.
Keywords: other


title: Leprosy lesion gene expression

status: Public on Jun 08 2003

city: Los Angeles

first: Joshua

last: Bleharski

state: CA

institute: UCLA

summary:
Leprosy presents as a clinical and immunological spectrum of disease. With the use of gene expression profiling, we observed that a distinction in gene expression correlates with and accurately classifies the clinical form of the disease. Genes belonging to the leukocyte immunoglobulin-like receptor (LIR) family were significantly up-regulated in lesions of lepromatous patients suffering from the disseminated form of the infection. In functional studies, LIR-7 suppressed innate host defense mechanisms by shifting monocyte production from interleukin-12 toward interleukin-10 and by blocking antimicrobial activity triggered by Toll-like receptors. Gene expression profiles may be useful in defining clinical forms of disease and providing insights into the regulation of immune responses to pathogens.
Keywords: other


title: Resistant

status: Public on Jun 26 2003

city: Houston

first: Eric

middle: C

last: Wooten

state: TX

address: One Baylor Plaza

department: Breast Center

institute: Baylor College of Medicine

summary:
These patients proved resistant to docetaxel treatment, exhibiting residual tumor of 25% or greater remaining volume.
Keywords: repeat sample

first: J

last: Chang

first: E

first: A

last: Tsimelzon

first: S

middle: G

last: Hilsenbeck

first: M

last: Gutierrez

first: R

last: Elledge

last: Mohsin

first: C

last: Osborne

first: G

last: Chamness

first: D

last: Allred

first: P

last: O'Connell


title: Gorilla Fibroblast Set:  Hacia Laboratory

status: Public on May 08 2003

first: Shailender

last: Nagpal

institute: University of Southern California

summary:
Data from gorilla fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts"
Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human
Keywords: ordered

first: Mazen

middle: W

last: Karaman

first: Maryls

last: Houck

first: Leona

last: Chemnick

first: Daniel

last: Chawannakul

first: Dominick

last: Sudano

first: Brian

last: Pike

first: Vincent

middle: V

last: Ho

first: Oliver

middle: A

last: Ryder

first: Joseph

last: Hacia


title: TNF treated Synoviocytes

status: Public on Jul 03 2003

city: Dublin

first: Jill

last: Howlin

address: University College Dublin Belfield

department: Pharmacology

country: Ireland

institute: The Conway Institute of Biomedical and Biomolecular Research

summary:
Time series of human arthritic synoviocytes treated with TNFalpha.
Keywords: time-course

first: Joanne

last: Gallagher

first: Jillian

first: Conor

last: Mc Carthy

first: Evelyn

last: Murphy

first: Barry

last: Bresnihan

last: Fitzgearald

first: Catherine

last: Godson

first: Hugh

last: Brady

first: Finian

last: Martin


first: Winnie

last: Liang

summary:
Expression profiles of HeLa CD4+ cells transfected with parental vector pCep4. Cells are treated with nocodazole and hydroxyurea.

Keywords: time-course

first: Anil

last: Maddukuri

first: Fatah

last: Kashanchi


title: Epidermal keratinocytes and IFNg, TNFa and IL1 treatment

status: Public on Jun 24 2003

city: New York

first: Miroslav

last: Blumenberg

state: NY

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

summary:
Cultured epidermal keratinocyte controls used for IFNg, TNFa and IL1 treatment.
Keywords: other

first: M

first: T

last: Banno


title: Fibroblast Gene Expression:  Hacia Laboratory

first: Shailender

last: Nagpal

summary:
Data files from Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts"
Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human
Keywords: other

sample_organism:
Gorilla gorilla
Pan paniscus
Homo sapiens

first: Mazen

last: Karaman

first: Maryls

last: Houck

first: Leona

last: Chemnick

first: Daniel

last: Chawannakul

first: Dominck

last: Sudano

first: Brian

last: Pike

first: Vincent

last: Ho

first: Oliver


title: HDMTX_MP

status: Public on Apr 21 2003

city: Memphis

first: William

middle: E

last: Evans

state: TN

address: 332 N. Lauderdale St.

department: Pharmaceutical Sciences

institute: St.Jude Children's Research Hospital

summary:
primary ALL cells from bone marrow aspirates taken two days after in vivo treatment with high-dose methotrexate and mercaptopurine
Keywords: other

middle: H

last: Cheok

first: W

last: Yang

first: C

last: Pui

first: J

last: Downing

last: Cheng

last: Naeve

last: Relling


title: LDMTX_MP

summary:
primary ALL cells from bone marrow aspirates taken two days after in vivo treatment with low-dose methotrexate and mercaptopurine
Keywords: other


title: MP

summary:
primary ALL cells from bone marrow aspirates taken two days after in vivo treatment with mercaptopurine
Keywords: other


title: HDMTX

summary:
primary ALL cells from bone marrow aspirates taken two days after in vivo treatment with high-dose methotrexate
Keywords: other


title: Human Fibroblast Set:  Hacia Laboratory

summary:
Data from human fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts"
Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human
Keywords: ordered

first: Dominick

last: Ryder

first: Joseph

last: Hacia


title: MP-9 pair

summary:
pre- and post-treatment sample pair
Keywords: time-course

first: M


title: MP-7 pair


title: MP-8 pair


title: MP-6 pair


title: MP-4 pair


title: WS1 response to low dose of UV-C

first: Massimiliano

last: Gentile

summary:
The transcriptional response to 10 J/m2 of UV-light (254 nm) was assessed with HGU95AV2 Affymetrix probe arrays at 6, 12, 18 and 24 hours after exposure. Mock-treated samples were assessed at 6 and 24 hours.
Keywords: time-course

first: Leena

last: Latonen

first: Marikki

last: Laiho


title: MP-2 pair


title: Sensitive

first: Eric

last: Wooten

summary:
These patients were sensitive to docetaxel treatment, exhibiting less than 25% residual tumor.
Keywords: repeat sample

last: Chang

first: E

first: A

last: Tsimelzon

first: S

last: Hilsenbeck

last: Gutierrez

first: R

last: Elledge

last: Mohsin

last: Osborne

first: G

last: Chamness

first: D

last: Allred

first: P

last: O'Connell


title: LDMTX_MP-9 pair

first: William

last: Evans

last: Cheok

first: W

last: Yang

last: Pui

last: Downing

last: Cheng

last: Naeve

last: Relling


title: MP-1 pair

first: C

first: J


title: Bonobo Fibroblast Data:  Hacia Laboratory

first: Shailender

last: Nagpal

summary:
Data from bonobo fibroblast cell lines described in Genome Research paper "Comparative analysis of gene expression patterns in human and African great ape cultured fibroblasts"
Keywords = African Great Ape, Human Evolution, Fibroblast, Bonobo, Gorilla, Human
Keywords: ordered

first: Mazen

last: Karaman

first: Maryls

last: Houck

first: Leona

last: Chemnick

first: Daniel

last: Chawannakul

first: Dominick

last: Sudano

first: Brian

last: Pike

first: Vincent

last: Ho

first: Oliver

last: Ryder

first: Joseph

last: Hacia


title: LDMTX_MP-7 pair

last: Evans

first: M

last: Cheok


title: LDMTX_MP-6 pair

last: Yang

last: Pui


title: LDMTX_MP-4 pair

last: Downing

last: Cheng


title: LDMTX_MP-2 pair

last: Naeve

last: Relling


title: LDMTX_MP-3 pair


title: MP-5 pair


title: MP-3 pair


title: LDMTX_MP-14  pair


title: LDMTX_MP-10 pair


title: LDMTX_MP-1 pair


title: HDMTX-7 pair


title: HDMTX-6 pair


title: MP-12 pair


title: MP-11 pair


title: LDMTX_MP-12 pair


title: LDMTX_MP-8 pair


title: HDMTX-3 pair


title: LDMTX_MP-5 pair


title: HDMTX-5 pair


title: HDMTX-20 pair


title: MP-10 pair


title: LDMTX_MP-16 pair


title: LDMTX_MP-15 pair


title: HDMTX-16 pair


title: LDMTX_MP-11 pair


title: HDMTX-9 pair


title: LDMTX_MP-13 pair


title: HDMTX-15 pair


title: HDMTX-8 pair


title: HDMTX-14 pair


title: HDMTX-10 pair


title: HDMTX-4 pair


title: HDMTX_MP-9 pair


title: HDMTX-22 pair


title: HDMTX-21 pair


title: HDMTX_MP-6 pair


title: HDMTX_MP-8 pair


title: HDMTX_MP-5 pair


title: HDMTX-2 pair


title: HDMTX-19 pair


title: HDMTX_MP-3 pair


title: HDMTX-18 pair


title: HDMTX_MP-10 pair


title: HDMTX-17 pair


title: HDMTX_MP-2 pair


title: HDMTX_MP-4 pair


title: HDMTX-13 pair


title: HDMTX_MP-1 pair


title: cAMP-induced differentiation of endometrial stromal cells

status: Public on Apr 14 2003

city: Stanford

first: Said

last: Talbi

department: Reproductive Endocrinology

institute: Stanford University School of Medicine

summary:
Timecourse of cAMP-induced decidualization of endometrial stromal cells.
Keywords: time-course

first: E

middle: P

last: Tierney

first: S

last: Tulac

last: Huang

first: L

last: Giudice


title: HDMTX-12 pair

first: William

first: W

first: C


title: HDMTX-11 pair

first: J


title: Spotted long oligonucleotide arrays

status: Public on Mar 18 2003

city: San Francisco

first: David

last: Erle

institute: University of California San Francisco

summary:
Both spotted long oligonucleotide arrays and Affymetrix GeneChips were used to measure differential gene expression in two RNA samples (K562 erythroleukemia RNA and the Stratagene Universal Human Reference RNA).

For Affymetrix technology, the two RNAs were analyzed separately. There are two replicates for K562 RNA (GSM4843 and GSM4844) and three for the Stratagene Universal reference (GSM4845-GSM4847).

Two types of spotted long oligonucleotide arrays were used. These arrays were used to do two-color hybridizations to directly compare K562 and Universal reference RNAs.

One array (GPL273) was made with probes from the Operon Human Genome Oligo Set Version 1. These arrays were used with unamplified cDNA probes (6 replicates, GSM4848-GSM4853), with aRNA probes produced by one round of T7 RNA polymerase-based amplification (6 replicates, GSM4854-GSM4859), and with aRNA probes produced by two rounds of amplification (2 replicates, GSM4860-GSM4861).
Keywords: parallel sample

first: A

last: Barczak

last: Rodriguez

first: K

last: Hanspers

last: Koth

first: Y

last: Tai

first: B

middle: M

last: Bolstad

first: T

last: Speed

first: D


title: HDMTX_MP-7 pair

last: Evans

last: Cheok

last: Yang

last: Pui

middle: R

last: Downing


title: HDMTX-1 pair

last: Cheng

last: Naeve

last: Relling


title: Large-scale analysis of the human transcriptome

status: Public on Dec 06 2002

city: San Diego

first: John

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

summary:
High-throughput gene expression profiling has become an important tool for investigating transcriptional activity in a variety of biological samples. To date, the vast majority of these experiments have focused on specific biological processes and perturbations. Here, we have generated and analyzed gene expression from a set of samples spanning a broad range of biological conditions. Specifically, we profiled gene expression from 91 human and mouse samples across a diverse array of tissues, organs, and cell lines. Because these samples predominantly come from the normal physiological state in the human and mouse, this dataset represents a preliminary, but substantial, description of the normal mammalian transcriptome. We have used this dataset to illustrate methods of mining these data, and to reveal insights into molecular and physiological gene function, mechanisms of transcriptional regulation, disease etiology, and comparative genomics. Finally, to allow the scientific community to use this resource, we have built a free and publicly accessible website (http://expression.gnf.org) that integrates data visualization and curation of current gene annotations.
Keywords: other

last: Su

last: Cooke

last: Ching

last: Hakak

last: Wiltshire

last: Orth

first: R

last: Vega

last: Sapinoso

last: Moqrich

last: Patapoutian

first: G

last: Hampton

first: P

last: Schultz

middle: B

last: Hogenesch


title: Macrophages and dendritic cells exposed to phylogenetically distinct parasites

status: Public on Mar 26 2003

city: Dallas

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

summary:
Monocyte-derived dendritic cells (DC) and macrophages (MΦ) generated in vitro from the same individual blood donors were exposed to five different pathogens, and gene expression profiles were assessed by microarray analysis.  Responses to Mycobacterium tuberculosis and to phylogenetically distinct protozoan (Leishmania major, L. donovani, Toxoplasma gondii) and helminth (Brugia malayi) parasites were examined, each of which produces chronic infections in humans yet vary considerably in the nature of the immune responses they trigger.
Keywords: equivalent probe

middle: T

last: Semnani

first: M

last: McDowell

last: Sacks

last: Sher

last: Nutman