title: Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

city: Chapel Hill

first: Jason

last: Lieb

state: NC

address: CB# 3280, 202 Fordham Hall

department: Department of Biology

institute: University of North Carolina at Chapel Hill

summary:
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first objective analysis of tiling array platforms, amplification procedures, and signal detection algorithms in a simulated ChIP-chip experiment. Mixtures of human genomic DNA and "spike-ins" comprised of nearly 100 human sequences at various concentrations were hybridized to four tiling array platforms by eight independent groups. Blind to the number of spike-ins, their locations, and the range of concentrations, each group made predictions of the spike-in locations. We found that microarray platform choice is not the primary determinant of overall performance. In fact, variation in performance between labs, protocols and algorithms within the same array platform was greater than the variation in performance between array platforms. However, each array platform had unique performance characteristics that varied with tiling resolution and the number of replicates, which have implications for cost versus detection power. Long oligonucleotide arrays were slightly more sensitive at detecting very low enrichment. On all platforms, simple sequence repeats and genome redundancy tended to result in false positives. LM-PCR and WGA, the most popular sample amplification techniques, reproduced relative enrichment levels with high fidelity. Performance among signal detection algorithms was heavily dependent on array platform. The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022  and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE9732
SuperSeries of: GSE9842
SuperSeries of: GSE9848
SuperSeries of: GSE9849
SuperSeries of: GSE10004
SuperSeries of: GSE10076
SuperSeries of: GSE10090
SuperSeries of: GSE10112


title: Appressorium induction by cyclic AMP in Magnaporthe grisea

status: Public on Jan 15 2008

city: Raleigh

first: Yeon Yee

last: Oh

address: NCSU Campus Box 7251

department: Plant Pathology

country: USA

institute: NCSU

summary:
This series examines differential gene expression during appressorium formation induced by exogeous cyclic AMP in the rice blast fungus Magnaporthe grisea. RNA was extracted from spores germinated on hydrophilic (non-inductive) side of GelBond as well as from spores elaborating appressia on hydrophilic surfaces in the presence of cAMP after 9 hrs incubation. RNA from two biological replications of each treatment was pooled in equal amounts and labeled with both cy3 and cy5 dyes using the Agilent Technologies Low Input Linear Amplification Kit. Hybridizations were performed on Agilent Technologies whole genome oligo rice blast arrays (product G4137B) using manufacturer prescribed protocols and reagents in an reference design in which each treatment was paired with every other. This series contains a total of 4 hybridizations; each treatment was used in 4 hybridizations (2 with Cy3 and 2 Cy5). Spot fluorescence was normalized using Lowess within and between microarray slides in Bioconductor.
Keywords: Cell development

overall_design: Two-condition experiment, cyclic AMP treated vs. non treated spores. 4 biological replicates with dye-swaps

first: Yeonyee

first: Sean

last: Coughlan

first: Huaqin

last: Pan

first: Ralph

middle: A

last: Dean


title: Role of CSN5 in breast cancer

status: Public on Jan 18 2008

city: South San Francisco

first: Adam

middle: S

last: Adler

state: CA

address: 1 DNA Way

institute: Genentech

type:
Expression profiling by array
Genome variation profiling by array

summary:
CSN5 has been implicated as a candidate oncogene in human breast cancers by genetic linkage with activation of the poor-prognosis, wound response gene expression signature. CSN5 is a subunit of the eight-protein COP9 signalosome, a signaling complex with multiple biochemical activities; the mechanism of CSN5 action in cancer development remains poorly understood. Here we show that CSN5 isopeptidase activity is essential for breast epithelial transformation and progression. Amplification of CSN5 is required for transformation of primary human breast epithelial cells by defined oncogenes. The transforming effects of CSN5 require CSN subunits for assembly of the full COP9 signalosome and the isopeptidase activity of CSN5, which potentiates the transcriptional activity of MYC. Transgenic inhibition of CSN5 isopeptidase activity blocks breast cancer progression evoked by MYC and RAS in vivo. These results highlight CSN5 isopeptidase activity in breast cancer progression, suggesting it as a therapeutic target in aggressive human breast cancers.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Campylobacter jejuni response to acid stress

status: Public on Jan 21 2008

city: Ottawa

first: Alain

last: Stintzi

state: Ontario

address: 451 Smyth road

department: Biochemistry, Microbiology and Immunology

country: Canada

institute: University of Ottawa

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


title: Antitumor Activity of Rapamycin in a Phase I Trial for Patients with Recurrent PTEN-Deficient Glioblastoma

status: Public on Jan 29 2008

city: Phoenix

first: Kevin

last: Brown

state: AZ

address: 445 N. Fifth Street

institute: TGen

type: Genome variation profiling by genome tiling array

summary:
Background

There is much discussion in the cancer drug development community about how to incorporate molecular tools into early-stage clinical trials to assess target modulation, measure anti-tumor activity, and enrich the clinical trial population for patients who are more likely to benefit. Small, molecularly focused clinical studies offer the promise of the early definition of optimal biologic dose and patient population.

Methods and Findings

Based on preclinical evidence that phosphatase and tensin homolog deleted on Chromosome 10 (PTEN) loss sensitizes tumors to the inhibition of mammalian target of rapamycin (mTOR), we conducted a proof-of-concept Phase I neoadjuvant trial of rapamycin in patients with recurrent glioblastoma, whose tumors lacked expression of the tumor suppressor PTEN. We aimed to assess the safety profile of daily rapamycin in patients with glioma, define the dose of rapamycin required for mTOR inhibition in tumor tissue, and evaluate the antiproliferative activity of rapamycin in PTEN-deficient glioblastoma. Although intratumoral rapamycin concentrations that were sufficient to inhibit mTOR in vitro were achieved in all patients, the magnitude of mTOR inhibition in tumor cells (measured by reduced ribosomal S6 protein phosphorylation) varied substantially. Tumor cell proliferation (measured by Ki-67 staining) was dramatically reduced in seven of 14 patients after 1 wk of rapamycin treatment and was associated with the magnitude of mTOR inhibition (p = 0.0047, Fisher exact test) but not the intratumoral rapamycin concentration. Tumor cells harvested from the Ki-67 nonresponders retained sensitivity to rapamycin ex vivo, indicating that clinical resistance to biochemical mTOR inhibition was not cell-intrinsic. Rapamycin treatment led to Akt activation in seven patients, presumably due to loss of negative feedback, and this activation was associated with shorter time-to-progression during post-surgical maintenance rapamycin therapy (p < 0.05, Logrank test).

Conclusions

Rapamycin has anticancer activity in PTEN-deficient glioblastoma and warrants further clinical study alone or in combination with PI3K pathway inhibitors. The short-term treatment endpoints used in this neoadjuvant trial design identified the importance of monitoring target inhibition and negative feedback to guide future clinical development.
Keywords: Comparative Genomic Hybridization

overall_design: Microdissected biopsies from 12 patients were subjected to oligo-CGH analysis.  Eight patients had only post-sirolimus biopsies analyzed, while four had both pre- and post-sirolimus biopsies assayed.  Each sample was labeled in Cy5 and hybridized against the same reference sample labeled in Cy3 ("normal female genomic DNA"; Promega).

first: Timothy

middle: F

last: Cloughesy

first: Koji

last: Yoshimoto

first: Phioanh

last: Nghiemphu

first: Dang

last: Julie

first: Shaojun

last: Zhu

first: Teli

last: Hsueh

first: Yinan

last: Chen

first: Wei

last: Wang

first: Youngkin

last: David

first: Linda

last: Liau

first: Neil

last: Martin

first: Don

last: Becker

first: Marvin

last: Bergsneider

first: Albert

last: Lai

first: Richard

last: Green

first: Tom

last: Oglesby

first: Michael

last: Koleto

first: Jeff

last: Trent

first: Steve

last: Horvath

first: Paul

last: Mischel

first: Ingo

middle: K

last: Mellinghoff

first: Charles

middle: L

last: Sawyers


title: Transcriptional Analysis of Medicago truncatula and Glycine max Using Tiling Microarrays

city: New Haven

first: Hang

last: He

state: CT

address: 165 Prospect St

department: MCDB

institute: Yale University

type: Expression profiling by genome tiling array

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

sample_organism:
Glycine max
Medicago truncatula

platform_organism:
Glycine max
Medicago truncatula

overall_design:
Both the barrel medic and soybean tiling arrays were produced on the Maskless Array Synthesizer platform. Briefly, tiling-paths consisting of 36-mer oligonucleotides offset by five nucleotides were designed to represent both DNA strands of the selected barrel medic and soybean genome sequence. Probes were synthesized at a feature-density of 390,000 probes per array in a “chess board” design. Microarray production and storage were carried out.
Total RNA and mRNA were sequentially isolated using the RNeasy Plant Mini kit (Qiagen, Valencia, CA) and the Oligotex mRNA kit (Qiagen) according to the manufacturer’s recommendations, respectively. mRNA from different organ types was reverse transcribed using a mixture of oligo(dT)18 and random nonamer primers, during which amino-allyl-modified dUTP (aa-dUTP) was incoporated. The aa-dUTP decorated cDNA was fluorescent labeled by conjugating the monofunctional Cy3 dye (GE Healthcare, Piscataway, NJ) to the amino-allyl functional groups in the cDNA. Two μg dye-labeled targets were used for hybridization.


title: Gene expression profile upon forced Notch1 activation in LS174T cells

status: Public on Jan 11 2008

city: Tokyo

first: Ryuichi

last: Okamoto

state: Please Select

address: Tokyo Medical and Dental University

country: Japan

institute: Tokyo Medical and Dental University

summary:
The cell line was modified to express  activated form of Notch1 (NICD1 of mouse origin) upon Doxycycline addition to the culture medium. Generation was performed by using the T-rex system (invitrogen), following manufacturer's instruction.
Keywords: Genetic modification

overall_design: Pulse-chase experiment, examining expression profile at 0h, 12h, 24h from Doxycycline addition. For details, please refer to our publication (American Journal of Physiology GI and Liver disease, e-pub at Nov 20th, 2008)

first: Tetsuya

last: Nakamura

first: Hisanobu

last: Kawamura


title: Expression signature of cardiac muscle as a potential diagnostic or prognostic tool for dilated cardiomyopathy

status: Public on Jan 09 2008

city: Toyoake

first: Masatsugu

last: Ohtsuki

state: Aichi

address: 1-98 Dengakugakubo, kutsukakecho

department: School of Medicine

institute: Fujita Health University

summary:
There is an emerging hypothesis that dilated cardiomyopathy (DCM) is a manifestation of end-stage heart failure (ESHF) resulting from “final common pathway” despite heterogeneous primary etiologies. We performed genome-wide expression profiling by means of high-density oligonucleotide microarrays using cardiac muscles from patients with DCM or specific cardiomyopathy as well as non-disease control hearts. Differentially expressed genes between ESHF and non-disease samples should include both genes reactive to heart failure (HF) and those responsible for ESHF. With the aid of samples with acute HF without DCM and those with DCM without HF (corrected with left ventricular assist device), we successfully distinguished ESHF genes from HF genes. Our findings implicate that transcriptional signature of cardiac muscle can be potentially applied as a diagnostic or prognostic tool for severe HF.
Keywords: disease state analysis

overall_design:
The expression profiles of approximately 20,227 genes were analyzed using a microarray, Human 1A ver.2 (Agilent Technologies). A total of 30 cardiac RNA samples (21 clinical samples and 9 purchased samples) were used in the hybridizations. 200ng of total RNA was used for T7 RNA polymerase-based cRNA labeling. The microarray experiments were then carried out using competitive hybridization experiments with Cy5-labeled heart RNAs as a test RNA and with Cy3-labeled pooled heart RNA (Sample N) as a template control for normalization. The glass slides were scanned using an Agilent G2565BA microarray scanner. Scanned images were then analyzed using Feature Extraction software. The average signal intensities were corrected for median background intensity and transferred with GenBank descriptors to a Microsoft Excel data spreadsheet (Microsoft, Redmond, WA).
Data analysis was performed using Genespring software version 6.1 (Silicon Genetics, Redwood City, CA). To avoid ‘false positive’ signals, we excluded certain genes from the analysis for which the average reference signal level constraints were under 70. After intensity dependent normalization (Lowess), the expression levels relative to the control were calculated as a ratio, and the expression profiles were then compared between each disease or normal sample. Statistical analysis was done using non-parametric tests. To order the samples according to the correlation coefficient, we applied “Find Similar Samples” algorithm using Spearman Correlation.

first: Hiroki

last: Kurahashi


title: IL-22 plays an indispensable role in early host defense against attaching and effacing (A/E) bacterial pathogens

status: Public on Feb 11 2008

first: Alex

last: Abbas

department: Bioinformatics

institute: Genentech, Inc.

summary:
Infection by attaching and effacing (A/E) pathogens poses a serious threat to public health, as was highlighted by the recent outbreak of E. coli O157:H7 infection in the United States. Here, by using a murine A/E pathogen, Citrobacter rodentium, we demonstrate that C. rodentium infection is lethal to IL-22-/- mice within two weeks. IL-22, in the early phase of infection, is indispensable for preventing the invasion of bacteria through the intestinal epithelium, and thereby preventing systemic spread and mortality.  We also show that IL-23 is required for the early induction of IL-22 during C. rodentium infection. Finally, our data suggest that IL-22 exerts its function by boosting the innate immune responses of colonic epithelial cells, especially though the induction of anti-microbial proteins, RegIIIβ and RegIIIγ.
Keywords: treatment comparison

overall_design: Control or IL-22-treated mouse colon in triplicate.

first: Yan

last: Zheng

first: Patricia

last: Valdez

first: Dimitry

middle: M

last: Danilenko

first: Helen

middle: Y

last: Hu

first: Qian

last: Gong

first: Alexander

middle: R

first: Zora

last: Modrusan

first: Wenjun

last: Ouyang


title: A testicular gene expression profile for NOA patients, and ART3 as a genetic susceptibility gene for NOA

status: Public on Dec 31 2007

city: Isehara

first: Tajima

last: Atsushi

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University School of Medicine

summary:
Infertility affects about one in six couples attempting pregnancy, with the man responsible in approximately half of the cases. Because the pathophysiology underlying azoospermia is not elucidated, most male infertility is diagnosed as idiopathic.  Genome-wide gene expression analyses with microarray on testis specimens from 47 non-obstructive azoospermia (NOA) and 11 obstructive azoospermia (OA) patients were performed, and 2,611 transcripts that preferentially included genes relevant to gametogenesis and reproduction according to Gene Ontology classification were found to be differentially expressed. Using a set of 945 of the 2,611 transcripts without missing data, NOA was further categorized into three classes using the non-negative matrix factorization method.  These three subclasses showed differences in Johnsen’s score, FSH level, and LH level.  In addition, the 52 genes showing high statistical difference between NOA subclasses (P < 0.01 with Tukey's post hoc test) were subjected to allelic association analyses to identify genetic susceptibilities in 442 NOA patients and 475 fertile men.  After two rounds of screening, SNPs of the ADP-ribosyltransferase 3 (ART3) gene were associated with NOA with highest significance with ART3-SNP25 (rs6836703; P = 0.0025).  Haplotypes with 5 SNPs were constructed, and the most common haplotype was found to be under-represented in patients (NOA 26.6 % versus control 35.3 %, P = 0.000073).  Subjects having the most common haplotype showed an elevated level of testosterone, suggesting a protective effect of the haplotype on spermatogenesis. Thus, genome-wide gene expression analyses were used to identify genes involved in the pathogenesis of NOA, and ART3 was subsequently identified as a susceptibility gene for NOA.  These findings clarify the molecular pathophysiology of NOA and suggest a novel therapeutic target in the treatment of NOA.
Keywords: Disease state analysis

overall_design: Comparative analysis of two disease phenotypes, using testicular biopsy specimens from 47 NOA and 11 OA patients. No experimental replicates.

first: Hiroyuki

last: Okada

first: Atsushi

last: Tajima

first: Kazuyoshi

last: Shichiri

last: Tanaka

first: Kenichi

first: Ituro

last: Inoue


title: CGH profiling of 87 indolent non-hodgkin’s lymphoma (NHL)

status: Public on Jan 01 2008

city: Madrid

first: Juan

middle: C

last: Cigudosa

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

country: Spain

institute: Centro Nacional de Investigaciones Oncologicas - CNIO

summary:
BACKGROUND AND OBJECTIVES: Low-grade B-cell lymphomas include several subtypes of tumors with different degrees of histological, biological or clinical features. Differential diagnosis is frequently compromised by the lack of specific cytogenetic or molecular features. As a consequence, therapies remain in many lymphoma types largely based in common protocols with largely variable success. Our objectives were to describe and to compare the genomic profile of a series of samples from the most prevalent low-grade lymphoma subtypes; all of them systematically analyzed with the same approach.

DESIGN-AND-METHODS: We carried out a high-resolution genomic DNA analysis (44K probes) in 87 low grade B cell lymphoma tumor samples that unambiguously presented the clinical picture, analytical features, and peripheral blood morphology and phenotype described for each entity.

RESULTS: The genomic integrity of the samples was heavily compromised (80% of the tumors presented at least one aberration). This phenomenon also involved lymphoplasmocytic and marginal zone lymphomas that have not been previously studied by this genomic approach. New aberrations have been described for almost every subtype. We have also generated reports of the extension of the genomic instability, detecting distinct patterns of genomic instability within subtypes.

INTERPRETATION-AND-CONCLUSIONS: The genomic profile of each subgroup showed substantive differences. The bioinformatic analysis of the data detected a set of new aberrations which were present in the majority of the subgroups and that pointed out to specific pathways, such as NF-kB (gains that involved REL, BCL11A and COMMD1) or DNA repair checkpoint pathways (deletion of 16q24 involving CDT1).
Keywords: Comparative Genomic Hybridization - array; Genomic Instability

overall_design: Comparative experiment: pheripheral blood pool of ten healthy female donors: CONTROL vs. 87 Low grade Lymphoma tumour samples

first: Bibiana

middle: I

last: Ferreira


title: Bovine testis gene expression profile at 2, 4 and 8 week of age

status: Public on Jan 08 2008

city: Pullman

first: Derek

middle: J

last: McLean

state: WA

department: School of Molecular Biosciences

institute: Washington State University

summary:
Bene expression profile of Angus bovine testis tissue at 2, 4 and 8 weeks of age using Affymetrix Bovine GeneChip
Keywords: developmental time course

overall_design: Samples obtained from Angus bull calves at 2, 4 and 8 weeks of age.  Two replicates at each age, 6 total samples.

first: Jonathan

last: Schmidt


title: Impact of CSN1S1 polymorphism on caprine mammary transcriptome

status: Public on Jan 03 2008

city: St Genes-Champanelle

first: Christine

last: Leroux

address: Centre INRA de Theix

department: PHASE

country: France

institute: INRA

summary:
Goat's alphaS1-casein (CSN1S1) polymorphism has a significant effect on milk protein and lipid composition, which affects the nutritional quality and technological properties of milk. Moreover, this polymorphism has a large impact on the morphology of mammary epithelial cells. To explore the metabolic pathways modulated in relation to this polymorphism, we compared the mammary gene expression profiles of two groups of lactating goats carrying either two reference or two defective alleles, using a bovine oligonucleotide microarray representing 8379 genes. We identified 41 differentially expressed genes between the two genotype groups. In particular, we showed a downregulation of two key lipogenic genes encoding fatty acid synthase and glycerol-3-phosphate acyltransferase in agreement with the low fat concentration associated with CSN1S1 deficiency. In addition, this study highlights changes in the expression level of several genes known to influence membrane fluidity, cell-cell interaction or chromatin organization. Our results open up new fields of investigation on structural modifications associated with CSN1S1 deficiency that could affect mammary gland function.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

first: Séverine

last: Ollier

first: Stéphanie

last: Chauvet

first: Patrice

last: Martin

first: Yves

last: Chilliard


title: Gene profiling of Thalassiosira pseudonana under various growth conditions

status: Public on Jan 05 2008

city: Seattle

first: E.

middle: Virginia

last: Armbrust

address: Ben Hall IRB, 616 NE Northlake Pl, Room 306

department: Oceanography

institute: University of Washington


title: The acute effects of methoxyacetic acid exposure on testis gene expression

status: Public on Jan 10 2008

first: Mike

middle: G

last: Wade

address: 50 Columbine Driveway

department: Environmental Health Science & Research Bureau

institute: Health Canada

summary:
We evaluated the possible mechanisms by which 2-methoxyacetic acid (MAA) disrupts spermatogenesis using high density microarrays.  Levels of mRNA transcripts were determined in total RNA isolated from testes of MAA-treated (650 mg/kg i.p.) or concurrent control rats sacrificed 4, 8, 12 or 24 hrs post exposure (PE).

Keywords: Toxicology, Time Course,

overall_design: Sexually mature Sprague Dawley male rats were treated i.p. with 650 mg/kg of 2-methoxyacetic acid (CAS# 625-45-6).  Treated animals were sacrificed, along with concurrent control animals 4, 8 12 or 24 hr post exposure (n=6 per treatment or control per time point, 48 total animals).  Agilent 20K oligonucleotide microarrays were used to examine the levels of transcripts in whole testis total RNA.  Universal rat RNA was used as reference.

first: Michael

first: Carole

last: Yauk

first: Andrew

last: Williams

first: Alice

last: Kawata


title: Identification of downstream genes regulated by RFL

city: Bangalore

first: Nagashree

middle: N

last: Rao

state: Karnataka

address: C.V. Raman Avenue

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary:
To gain mechanistic insights on RFL functions in rice architecture, we have employed global expression profilling to identify the genes regulated by RFL. Transgenic rice panicle RNAs down-regulated for RFL were compared with the wild type panicle RNA of similar developmental stage. Genes downregulated in transgenic lines will be those which expression requires functional RFL whereas upregulated genes will need RFL for their repression.
Keywords: Whole genome analysis for genes whose expression is regulated by RFL

overall_design: Two independent biological RNA pools of dsRNAiRFL and RFL antisense transgenic panicles were compared with two independent wild type RNA pool in two different hybridizations. Two hybridizations were performed with reciprocally dye-labeled wild type RNA and respective mutant RNA.

first: Kalika

last: Prasad

first: Puja

last: Ravikumar

first: Usha

last: Vijayraghavan


title: Gene expression changes in cecum mucosa upon dietary treatment

city: Wageningen

first: Wendy

last: Rodenburg

address: Bornsesteeg 45

department: Food Bioactives Group

country: Netherlands

institute: RIKILT-Institute of food safety

summary:
To increase our knowledge of the effects of Fructo oligosaccharides (FOS) on the intestinal barrier function in rats, a controlled rat infection study was performed. Two groups of rats (n=12 per group) were adapted to a diet with or without FOS. mRNA was collected from the mucosa of the cecum and changes in gene expression were assessed using an agilent rat whole genome microarray (G4131A Agilent Technologies). Results indicate that dietary FOS influences immune response and wound healing mechanisms, which will most likely affect the intestinal barrier.
Keywords: Dietary treatment, cecum mucosa, Rat

overall_design: In the present study, large-scale gene expression analysis was performed to reveal mechanistic details of FOS induced gene expression in vivo in the cecum mucosa. Wistar rats were adapted to diets with (n=12) or without FOS (n=12) for 14 days. RNA was isolated from cecum mucosal scrapings, two RNA samples from the control group were ecluded based on poor quality of RNA. Agilent rat whole genome microarray containing 44290 60-mer spots, were used to study FOS induced gene expression changes in order to better understand the FOS induced effects on the intestinal barrier of rats.

first: Evelien

last: Kramer

first: Ingeborg

last: Bovee-Oudenhoven

first: Jaap

last: Keijer


title: Osteosarcoma microaberrations

city: Toronto

first: Shamini

last: Selvarajah

address: 555 University Ave

department: Cancer Institute

institute: Hospital for Sick Children

summary:
Background:  Osteosarcoma (OS) is a very aggressive bone tumor characterized by highly abnormal complex karyotypes.  With the improved resolution offered by array comparative genomic hybridization (array CGH) platforms, it is possible to readily detect cryptic microaberrations in genomic DNA.  The identification of these microaberrations in genetic syndromes is currently the focus of many array CGH studies, but there have been no analyses to date documenting the occurrence of microaberrations in tumors.
Results:  In this study we utilized high-resolution oligonucleotide array CGH to identify novel microaberrations under ~750 kb in four OS-derived cell lines: U-2 OS, HOS, MG-63 and SAOS-2.  Comparative analysis of these alterations showed that SAOS-2 harbored the most microaberrations at 17, followed by MG-63 with 11, HOS with 9 and U-2 OS with 6.  SAOS-2, which has a TP53 mutation, exhibited the highest level of chromosomal instability in previous studies by our group; whereas U-2 OS, which has wild-type p53 status, exhibited the least instability.  A consensus region of gain at 5p15.33 was detected in three of the four OS-derived cell lines (HOS, MG-63 and SAOS-2) by aCGH.  Of these consensus gains, one was a microaberration of 500 kb in SAOS-2, and confirmed by fluorescence in situ hybridization analysis.  It should be noted that this microaberration is immediately telomeric to the TERT gene, which also showed gain.  TERT is correlated with increased tumor aggression, as well as decreased progression free survival in OS patients.
Keywords: comparative genomic hybridization (array CGH)

overall_design: This genome-wide analysis is the first study to utilize oligonucleotide array CGH to identify microaberrations in OS, likely to contain genes involved in OS tumor oncogenesis.  A better understanding of the underlying molecular genetic events leading to tumor initiation and progression could result in the identification of prognostic markers and therapeutic targets.


title: Global responses of a C. jejuni single domain globin mutant and wild type to nitric oxide releasing compounds

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield


title: Transcriptome analysis of GSNO treated batch and chemostat cultures of  Campylobacter jejuni


title: Effect of in ovo feeding on late-term turkey embryo in 5 tissues

status: Public on Jan 31 2008

first: Jean

middle: Eduardo

last: de Oliveira

address: 2711 Founders Dr

department: Poultry Science

institute: North Carolina State University

summary:
Turkey embryos are very sensitive to perturbations in energy metabolism because they have a wider hatching window than chicken embryos. Mortality of turkey embryos during late-term incubation is high relative to chickens, and many surviving hatchlings have compromised vitality. Intestinal maturation at hatch is also crucial to survival and post-hatch performance. The study of poultry embryo metabolism during the last stages of incubation is difficult due to many shifts and changes that occur in preparation for hatching. Microarray technology is suitable to study complex biological systems like avian late-term embryonic development. Therefore, the objectives of this study were to create a customized focused oligonucleotide microarray based on chicken genome sequences that could be used to study late-term avian metabolism and intestinal maturation, and use this array to survey turkey embryos gene expression from 20 days of incubation until hatch. The key features of this microarray are that all genes present have been annotated and gene spot replication (4) within each array chip. Microarray analysis was performed on liver, pectoral muscle, hatching muscle, and duodenum

This SuperSeries is composed of the SubSeries listed below.


title: Metabolite stress in Clostridium acetobutylicum ATCC 824

status: Public on Dec 29 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

first: Keith

middle: V

last: Alsaker

first: Carlos

last: Paredes

middle: T


title: Temporal expression profile of primary T cell culture and T cell response to Oxidative stress

summary:
Little is known about the global transcriptional program underlying T-cell activation and T-cell response to oxidative stress.  Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of human T-cell activation and T-cell response to H2O2 stress.  The goal of this study was to identify genes involved in the various facets of human T-cell activation and T-cell response to H2O2 stress.
Keywords: time course

overall_design: T cells isolated from peripheral blood were cultured with CD3, CD28, and IL-2 to induce T-cell activaiton.  Samples were splited into two parts before the cutlure started, one treated with 25 uM H2O2 for 10 minutes, the other intact. At each timepoint, cells were harvested and frozen for RNA isolation.  Three biological replicate experiments were analyzed and approximately one-half of the samples from each experiment were technically replicated.  Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference thymus total RNA labeled with Cy5.

first: Min

last: Wang


title: Spore germination in Saccharomyces cerevisiae

status: Public on Dec 23 2007

city: Rehovot

first: Naama

last: Barkai

address: P.O box 26

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute of Science


title: Gene expression in bovine mammary gland in response to increased milking frequency as determined by microarray and SAGE

city: Beltsville

first: Erin

middle: E

last: Connor

state: MD

address: 10300 Baltimore Avenue

department: Animal and Natural Resources Institute

institute: USDA-ARS, BARC

type:
Expression profiling by array
Expression profiling by SAGE

summary:
Transcript profiling was performed by Affymetrix microarray analysis and SAGE to characterize changes in gene expression in the bovine mammary gland in response to 4× versus 2× daily milking during the first week of lactation. These changes in gene expression may contribute to the increased milk production observed in response to increased milking frequency. Our results indicate that increased milking frequency alters expression of genes in the mammary gland related to increased extracellular matrix remodeling, neovascularization, metabolism, cell proliferation and apoptosis.
Keywords: Physiological response to stimulus

overall_design: Multiparous Holstein cows were milked either 2× daily (Control, n = 3) or 2× daily from day 1 to 3 of lactation, and 4× daily beginning at day 4 of lactation until day 21 post partum (IMF4, n = 4). The milking intervals were approximately 12 hours for Control cows and 9, 3, 9, and 3 hours, respectively, for IMF4 cows. Mammary biopsies were obtained at approximately day 7 of lactation for extraction of total RNA and subsequent transcript profiling my microarray (Affymetrix). Pooled Control and IMF4 RNA samples were used to synthesize two SAGE libraries using the Long SAGE kit by Invitrogen.

first: Anthony

last: Capuco

first: Stephen

last: Siferd

first: Curtis

middle: P

last: Van Tassell

first: Tad

middle: S

last: Sonstegard

first: Violet

last: Fernandes


title: Quiescent and non-quiescent deletion-mutant strains

status: Public on Dec 27 2007

city: Albuquerque

first: Sushmita

last: Roy

state: NM

institute: Biology, University of New Mexico

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


title: Gene expression profiling in glioblastoma and immunohistochemical evaluation of IGFBP-2 and CDC20

status: Public on Dec 19 2007

city: Bologna

first: Luca

last: Morandi

address: Via Altura 3

department: Oncology Dept

country: Italy

institute: University of Bologna

summary:
The different clinical behavior of low and high grade gliomas and the chance to develop novel selective agents that specifically target tumor-associated proteins in gliomas stimulate the research of molecules playing a role in glioma progression.
Gene expression profiling using microarrays allows the study at the same time of the expression patterns of thousands of genes in tumor cells.
In the present study microarrays with about 20,000 genes have been employed to discover the gene expression profile in 39 glial neoplasias (28 glioblastomas (GBM) and 11 low grade gliomas, namely 4 oligodendrogliomas, 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytomas (FA)).
Unsupervised classification through hierarchical cluster analysis identified 2 groups of tumours: one group mainly composed of low grade malignant tumours (10 low grade gliomas and 3 GBM), the other one constituted by GBM, with the exception of one low grade case.
The nearest shrunken centroid classification method was used to identify genes useful to classify and best characterize high and low grade gliomas. [Tibshirani et al. 2002]
This procedure selected 9 genes as most informative for the classification task:
Among them 7 genes were overexpressed in low grade gliomas, but underexpressed in GBM; on the contrary 2 genes were overexpressed in GBM, but underexpressed in low grade tumours
Forty five tumors were immunostained for IGFBP-2 .  81,5% GBM resulted immunopositive. On the contrary only one low grade glioma was positive.
Gene expression profiling and immunohistochemistry suggest that IGFBP-2 may play a role in glioma progression. IGFBP-2 appears to be a novel immunohistochemical marker of  malignancy in glial tumours and probably is the basis for targeted chemotherapy.
Keywords: glioblastoma, gene expression analysis, IGFBP-2, Hiearchical clustering

overall_design:
We retrieved for this study 185 randomly selected cases of gliomas. All the cases had been received unfixed. A sample of neoplastic tissue had been flash frozen over liquid nitrogen and stored at -80°C into the frozen tissue bank of the Section of Pathology of Bellaria Hospital between 1990 and 2002. The remaining (specular) tissues were formalin fixed and paraffin embedded for routine histologic diagnosis.
In the present investigation, only samples with rRNA 28S/18S ratio > 1.0 measured by Bioanalyzer 2100 (Agilent)and no evidence of ribosomal degradation were included. Some cases were excluded as the tissue samples were composed only by necrosis; other cases did not show neoplastic proliferation.  Therefore only 39 glial neoplasias were suitable for the study: i.e. 28 GBMs and 11 low grade CNS tumors, namely 4 oligodendrogliomas (OL), 5 pilocytic astrocytomas (PA), 2 fibrillary astrocytoma (FA) showed a good quality of RNA.
All the tumors were re-staged and graded according to 2000 WHO criteria at time of gene expression analysis by two pathologists (GM and VE).
39 glial neoplasias were labeled by Cy5. Common reference pool consisted of a mixture of total RNA from the low grade CNS tumor group (4 OL, 5 PA, 2 FA) labeled by Cy3. A series of the most informative genes were confirmed by RT-qPCR.

first: Gianluca

last: Marucci

first: Elisabetta

last: Magrini

first: Enrico

last: Franceschi

first: Rossella

last: Miglio

first: Daniela

last: Calo'

first: Annalisa

last: Pession

first: MariaPia

last: Foschini

first: Vincenzo

last: Eusebi

first: Anna

last: Farnedi


title: Transcriptional profiling of indica rice cultivar FR13A under salt stress condition.

status: Public on Dec 21 2007

city: Lubbock

first: Kameswara Rao

last: Kottapalli

state: TX

address: 3810 4th Street

department: Plant & Soil Science

institute: USDA-ARS Lubbock & Texas Tech University

summary:
A submergence tolerant indica rice cultivar FR13A, was also reported to withstand salt stress and proven in our experiments. The mechanism of tolerance is yet to be studied by forward genetics approach. However, it is known that salt stress tolerance is governed by several QTLs and not by a single gene. To understand the mechanism of such a complex mechanism of salt tolerance we selected, two indica rice genotypes namely, I) FR13A, a tolerant indica variety and ii) IR24, a susceptible genotype for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under constitutive and salt stress conditions at seedling stage.
Keywords: Mechanism of salt tolerance

overall_design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice plant tissues during salt stress treatment. We used two contrasting rice genotypes (FR13A tolerant and IR24 susceptible) differing in salt stress response. Plants were grown in growth chambers and treated with 150 mM salt concentration at 14th DAS. Sampling was done in both constitutive and treated plants at 3 time points. Two replications of microarray experiments were carried out by hybridizing the RNA from tolerant samples against the susceptible lines on the same slide.

first: Kameswara

first: Soshi

last: Kikuchi


title: Gene-expression patterns reveal underlying biological processes in Kawasaki disease.

status: Public on Dec 13 2007

city: Stanford

first: Stephen

last: Popper

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

overall_design: Refer to individual Series


title: Identification of Myc-regulated microRNAs: human and mouse

status: Public on Dec 05 2007

city: Baltimore

first: Tsung-Cheng

last: Chang

address: 733 N. Broadway

institute: Johns Hopkins University School of Medicine

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Caenorhabditis elegans
Homo sapiens
Mus musculus
Human betaherpesvirus 5
human gammaherpesvirus 4
Murid gammaherpesvirus 4
Human gammaherpesvirus 8


title: Temporal expression profile of primary CD8+ T cell activation

first: Eleftherios

last: Papoutsakis

summary:
Little is known about the global transcriptional program underlying CD8+ T-cell activation.  Using DNA microarrays and Q-RT-PCR, we examined the transcriptional profile of human CD8+ T-cell activation.  The goal of this study was to identify genes involved in the various facets of human CD8+ T-cell activation.
Keywords: time course

sample_organism:
Homo sapiens
Thymus

overall_design: CD8+ T cells isolated from peripheral blood were cultured with CD3, CD28, with or without IL-2 to induce T-cell activation. At each timepoint, cells were harvested and frozen for RNA isolation.  Three biological replicate experiments were analyzed and approximately one-half of the samples from each experiment were technically replicated.  Hybridizations were performed in a reference design with all samples labeled with Cy3 and a reference thymus total RNA  labeled with Cy5.

first: Min

last: Wang

first: Dirk

last: Windgassen


title: Colonic gene expression upon dietary treatment

status: Public on Dec 01 2007

first: Wendy

last: Rodenburg

summary:
To increase our knowledge of the effects of Fructo oligosaccharides (FOS) on the intestinal barrier function in rats, a controlled rat infection study was performed. Two groups of rats were adapted to a diet with or without FOS. mRNA was collected from the mucosa of the colon and changes in gene expression were assessed using an agilent rat whole genome microarray (G4131A Agilent Technologies). Results indicate that dietary FOS influences energy metabolism, which will most likely play a role in the effects of FOS on the intestinal barrier.
Keywords: Dietary treatment, colon mucosa, Rat

overall_design: In the present study, large-scale gene expression analysis was performed to reveal mechanistic details of FOS induced gene expression in vivo in the colon mucosa. Wistar rats were adapted to diets with or without FOS for 14 days. RNA was isolated from colonic mucosal scrapings. Agilent rat whole genome microarray containing 44290 60-mer spots, were used to study FOS induced gene expression changes in order to better understand the FOS induced effects on the intestinal barrier of rats.

first: W

first: E

last: Kramer

first: I

last: Bovee-Oudenhoven

first: J

last: Keijer


title: An interferon-response induced by tumor-stroma interaction in a subset of human breast cancers

status: Public on Nov 14 2007

city: Basel

first: Martin

last: Buess

state: CH

address: Petersgraben 4

department: Medizinische Onkologie

country: Switzerland

institute: University Hospital Basel


title: Transcriptional profiling of indica rice cultivar FR13A under submergence treatment.

status: Public on Nov 24 2007

summary:
An indica rice cultivar FR13A, is widely grown as submergence tolerant variety and can withstand submergence up to two weeks. The tolerance is governed by a major QTL on chromosome 9 and represented as sub1. Recently the gene for sub1 has been mapped and cloned. However, the trait is governed by several QTLs and not by a single gene. To understand the mechanism of submergence tolerance we selected, two indica rice genotypes namely, I) FR13A, a tolerant indica variety and ii) IR24, a susceptible genotype for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under constitutive and submerged conditions at seedling stage.
Keywords: Mechanism of submergence tolerance

overall_design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during submergence treatment. We used two contrasting rice genotypes (FR13A tolerant and IR24 susceptible) differing in submergence response. Plants were grown in growth chambers and treated by submerging the plants in transparent polythene bags on14th DAS. Leaf sampling was done in both constitutive and treated plants at 3 time points. Two replications of microarray experiments were carried out by hybridizing the RNA from tolerant samples against the susceptible lines.

first: Kouji

last: Satoh

first: Randeep

last: Rakwal

first: Junko

last: Shibato

first: Koji

last: Doi

first: Toshifumi

last: Nagata

first: Shoshi


title: A. fumigatus wild type and delta phoB(PHO80) strains transcriptome analysis: growth in Minimal medium (0.1mM or 11mM Pi)

status: Public on Nov 09 2007

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Café, s/n

department: Departament of Pharmaceutical Sciences

country: Brazil

institute: Faculty of Pharmaceutical Sciences of Ribeirao Preto


title: Chromosome 1 tile path analysis of astrocytomas

city: Cambridge

first: Koichi

last: Ichimura

address: Addenbrooke's Hospital Box 231

department: Pathology

institute: University of Cambridge


title: Novel mechanisms of galactose toxicity in human galactose-1-phosphate uridyltransferase (GALT)-deficient cells

status: Public on Nov 01 2007

city: Miami

first: Kent

last: Lai

state: FL

department: Pediatrics

institute: University of Miami

summary:
Comparison of gene expression profiles in GALT-deficient and GALT-reconstituted cells showed that cells lacking GALT activity responded to galactose challenge by activating a set of genes characteristic of endoplasmic reticulum (ER) stress.  This response was specific to galactose insult, as cells grown in glucose or hexose-free media did not exhibit ER stress.
Keywords: GALT infected cells

overall_design: Cells were first grown and then infected in high glucose, then transferred to DMEM, 3 experiments with dye-swap

first: Tatiana

last: Slepak

first: Vladlen

middle: Z


title: CGH profiling of 26 Ewing Sarcoma tumour samples

city: Madrid

first: Juan

last: Cigudosa

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

institute: Centro Nacional de Investigaciones Oncologicas - CNIO

summary:
Ewing’s Sarcoma (ES) is characterized by specific chromosomal translocations, the most common being t(11;22)(q24;q12). Additionally, other types of genetic abnormalities may occur and be relevant to explain the variable tumoural biology and clinical outcome. We have carried out a high-resolution array CGH and expression profiling on 25 ES tumour samples to characterize the DNA copy number aberrations (CNA) occurring in these tumours and to determine their association with gene expression profiles (GEO Series accession number: GSE8303) and their clinical outcome.  CNA were observed in 84% of the cases. We observed a median number of 3 aberrations per case. Besides numerical chromosomal changes, smaller aberrations were found and defined at chromosomes 5p, 7q and 9p. All CNA were compiled to define the smallest overlapping regions of imbalance (SORI). Thirty five SORI were delimited. Bioinformatic analyses were conducted to identify subgroups according to the pattern of genomic instability obtained. Unsupervised and supervised clustering analyses (using SORI as variables) segregated the tumours into two distinct groups: one genomically stable (≤ 3 CNA) and another genomically unstable one (> 3 CNA). The genomic unstable group showed a statistically significant shorter overall survival and was more refractory to chemotherapy. This report elucidates data about genomic instability in ES, based on CNA and expression profiling for the first time, and shows that a genomically unstable group of Ewing tumours is correlated with a significant poor prognosis.
Keywords: Comparative Genomic Hybridization - array; Genomic Instability

overall_design:
Comparative experiment: pheripheral blood pool of ten healthy female donors: CONTROL vs. 26 Ewing Sarcoma Tumour Samples.
Note that although 26 samples were profiled, only 25 were analysed (sample #11 did not pass quality control).

first: Bibiana

last: Ferreira


title: Mechanisms of constitutive NF-kappaB signaling in multiple myeloma

status: Public on Oct 29 2007

city: Bethesda

first: Christina

last: Annunziata

address: 10 Center Drive

department: Metabolism Branch

institute: Center for Cancer Research


title: Gene expression changes in human colorectal cell line HCT116 DICER Exon5 knockout cells

status: Public on Oct 26 2007

first: Wayne

last: Yu

address: 417 N. Caroline St.

department: Cancer Center

institute: Johns Hopkins University

summary:
The experiment was to study the gene expression changes in human colorectal cell HCT116 DICER Exon5 knockout cells comparing to that in parental HCT116 cellls.
Keywords: Cell type comparison

overall_design: Experiment includes using of two Agilent human 44K microarrays with dye-swap replication.

first: Angela

middle: H

last: Ting

first: Stephen

middle: B

last: Baylin

first: Hiromu

last: Suzuki


title: Time course of glucocortiocid receptor isoforms

status: Public on Dec 20 2007

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Glucocorticoids regulate diverse physiologic processes and synthetic derivatives of these natural hormones are widely used in the treatment of inflammatory diseases.  However, chronic administration often triggers insensitivity and serious side effects including osteoporosis. The underlying mechanisms regulating these side effects are not completely understood.  We report here that human osteosarcoma U-2 OS bone cells lacking the glucocorticoid receptor (GR) are resistant to glucocorticoid killing whereas the expression of wild-type GR activates an apoptotic program. Furthermore, we show that the translationally generated GR isoforms from a single GR gene have distinct abilities to induce apoptosis in these cells. Only cells expressing selective GR isoforms underwent apoptosis upon dexamethasone treatment and microarray analysis demonstrated that GR isoforms selectively stimulated the expression of pro-apoptotic enzymes such as caspase 6 and granzyme A. Chromatin immunoprecipitation assays further revealed that GR isoform-dependent induction of pro-apoptotic genes is likely due to selective coregulator recruitment and chromatin modification. Together, these findings provide evidence for a direct apoptotic effect of glucocorticoids on bone cells via selective GR isoforms and delineate multiple molecular components involved in tissue-specific glucocorticoid-induced bone cell apoptosis.
Keywords: time course, isoform comparison

overall_design:
U-2 OS cells were transfected with the BD Clontech pTET-OFF regulatory plasmid to establish the U-OFF parental cell line. MluI and EcoRV ends were generated onto the coding region of hGR-alpha, -A, -B, -C, or -D using PCR amplification of the pCMVhGR-alpha or -A plasmid. The pTRE2hyg vector was digested with MluI and EcoRV and the two DNAs were ligated to form the pTRE2hGR-alpha,-A, -B, -C, or -D plasmid. Each DNA construct was individually transfected into the U-OFF cells and clones were selected which stably expressed either hGR-alpha, -A, -B, -C, or -D using 200 microg/ml of geneticin and 500 mircorg/ml of hygromycin. Several clones were obtained for each receptor, and the receptor levels were compared using western blot analyses. In these cell lines, the expression of hGR can be repressed by the addition of tetracycline or the derivative doxycycline to the media. U-2 OS (human osteosarcoma) cells were maintained in DMEM/F-12 supplemented with 10% FCS:CS, 2 mM glutamine and pen-strep and selected clones were maintained in the same media with the addition of 200 microg/ml Geneticin and 200 mircrog/ml hygromycin. All cells were maintained in a humidified, 5% CO2 atmosphere.  Cells were either not treated (0 hours) or were treated with 100 nM dexamethasone for 6, 12, or 24 hours.
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer's protocol.  For each sample, 1.5ug of Cy3 labeled cRNAs were fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven at 65 degrees at 4 RPM.  Slides were washed with 6X SSPE + 0.005% N-lauroyl sarcosine for 1 minute then 0.06X SSPE + 0.005% N-lauroyl sracosine for 1 minute at 37 degrees.  The slides were dried by slowly removing from second wash solution and then scanned with an Agilent G2565 Scanner (10micron and with XDR) and processed with Agilent Feature Extraction v9.1.  The resulting files were imported into the Rosetta Resolver system (Version 6.0).  This system performs data pre-processing and error modeling.

first: Nick

last: Lu

first: Jennifer

last: Collins

first: Sherry

middle: F

last: Grissom

first: John

middle: A

last: Cidlowski


title: A Stem Cell-Like Chromatin Pattern May Predispose Tumor Suppressor Genes  to DNA Hypermethylation

summary:
Many cancers may originate in stem or early progenitor cells 1-4 which depend on epigenetic modulation of gene expression for normal function (ref). We have studied whether epigenetic states in cancers, and particularly abnormal gene silencing associated with promoter DNA hypermethylation in CpG rich regions (refs), may represent links between cancer and stem cell epigenetic patterns.  We studied embryonal carcinomas (EC) which are malignancies of embryonic stem (ES) cells, but retain high potential for multi-lineage differentiation 5-8.  Surprisingly, genes DNA hypermethylated and silenced in adult cancers are unmethylated in ES and EC cells. Remarkably, the promoter chromatin of the genes in EC cells is virtually identical to the same genes in adult cancers when the latter are induced to de-methylate. This chromatin, as recently reported for CpG island promoters of low expression, developmentally related, genes in ES cells (refs), is “bivalent” and contains both active and repressive histone modifications. The latter includes trimethyl lysine 27 of histone H3 (H3K27me3), which may recruit DNA methylation (refs), and the promoter regions are enriched for polycomb group (PcG) proteins which place this H3K27me3 mark. Thus, many genes which undergo abnormal DNA methylation and permanent silencing in adult cancers may be programmed to do so by a pre-existent stem cell-like chromatin pattern inherent to the cells in which they arise.
Keywords: Stem cell epigenetics expression microarray

overall_design:
Data analysis. All arrays were subject to quality checks recommended by the manufacturer.  Images were visually inspected for artifacts and distributions of signal and background intensity of both red and green channels are examined to identify anomalous arrays.   No irregularities were observed, and all arrays were retained and used.
All calculations were performed using the R statistical computing platform, (cite R) and packages from Bioconductor bioinformatics software project (cite Bioconductor).  The log ratio of red median signal  to green median signal was calculated after background-subtraction and loess normalzation as implemented in the limma package from Bioconductor. ( cite Smyth) Individual arrays were scaled to have the same inter-quartile range (75th percentile -25th percentile) Log fold changes were averaged over dye-swap replicate microarrays to produce a single set of expression values for each condition.

first: Joyce

last: Ohm

first: Kornel

last: Schuebel

first: Leslie

last: Cope

first: Steven


title: Organ-specific Profiles of Genetic Alterations in Liver, Stomach and Lung Cancers caused by AID Expression

status: Public on Oct 27 2007

city: Kyoto

first: Toshiyuki

last: Morisawa

address: 54 Kawahara-cho,Shogoin

department: Gastroenterology and Hepatology

institute: Kyoto University

summary:
To analyze the organ-specific genetic changes in the tumor-related genes commonly triggerd by the AID-mediated mutagenesis, we compared the gene expression profiles among epitherial tumors developed in AID Tg mouse.
Keywords: genetic alteration

overall_design: We analyzed the up or down regulated genes in tumor tissues compared with nontumor tissues in AID Tg mouse (see Supplementary table at the foot of the record). We compared each gene expression profile among three epitherial tumors in AID Tg mouse.

first: Hiroyuki

last: Marusawa

first: Yoshihide

last: Ueda

first: Akio

last: Iwai

first: Il-mi

last: Okazaki

first: Tasuku

last: Honjo

first: Tsutomu

last: Chiba


title: Parkin as a Tumor Suppressor Gene for Hepatocellular Carcinoma

status: Public on Nov 30 2007

first: mikio

last: fujiwra

address: 54 Kawahara-cho, Shogoin Sakyo-ku

summary:
To provide an insight into the molecular mechanism by which parkin deficiency contributes to hepatocarcinogenesis, we analyzed gene expression profiles of nontumorous and tumorous liver tissues from parkin–/– mice using cDNA microarray analyses.
Keywords: genetic alteration

overall_design: We analysed the up and down regulated genes in tumorous and non-tumorous liver tissues of parkin-/- mice compared with normal liver tissues of wild-type mice.


title: Transcriptional profiling of indica rice cultivar IET8585 (Ajaya) infected with bacterial leaf blight pathogen (Xoo)

first: Kameswara Rao

last: Kottapalli

summary:
An indica rice cultivar IET8585 (Ajaya), resists diverse races of the Xanthomonas oryzae pv oryzae (Xoo) pathogen attack, and is often cultivated as bacterial leaf blight (blb) resistant check in India. Earlier we reported a recessive blb resistance gene mapped to the long arm of chromosome 5 in IET8585. To further understand the mechanism of recessive and durable resistance response, two indica rice genotypes namely, i) IET8585 (Ajaya), a disease resistant indica veriety from India and ii) IR24, a bacterial leaf blight disease susceptible genotype were selected for this study. We used the 22K rice Oligoarray from Agilent technologies to study the transcript profile in the leaves of the two contrasting rice genotypes under inoculated and un-inoculated conditions during seedling stage.
Keywords: Bacterial leaf blight disease resistance mechanism

overall_design: We used Agilent rice gene chips (G4138A) to investigate the transcript level changes in rice leaf tissues during bacterial pathogen infection. We used two contrasting rice genotypes (IET8585 (Ajaya) blb resistant IR24 blb susceptible) differing in bacterial disease response. Plants were grown growth chambers and inoculated with bacterial pathogen on 18th DAS. Leaf sampling was done in both un-inoculated and inoculated plants at 3 time points. Two replications of microarray experiments were carried out by hybridizing the resistant samples against the susceptible samples.

first: KameswaraRao

first: Randeep

last: Rakwal

first: Kouji

last: Satoh

first: Shoshi

last: Kikuchi


title: Transcription profiling of rat colonic mucosa at different time points following Salmonella infection

status: Public on Oct 18 2007

city: Wageningen

first: Wendy

last: Rodenburg

address: Bornsesteeg 45

department: Food Bioactives Group

institute: RIKILT-Institute of food safety

summary:
Salmonella enteritidis is suggested to translocate in the small intestine. Previously we identified that prebiotics, fermented in the colon, increased Salmonella translocation in rats, suggesting involvement of the colon in translocation. Effects of Salmonella on colonic gene expression in vivo are largely unknown. The aim of this study was to characterize time dependent Salmonella induced changes of colonic mucosal gene expression in rats using whole genome microarrays. Rats were orally infected with Salmonella enteritidis to mimic a foodbore infection and colonic gene expression was determined at day 1, 3 and 6 post-infection (n=8 per timepoint). Agilent rat whole genome microarray (G4131A Agilent Technologies) were used. Results indicate that colon is clearly a target tissue for Salmonella considering the abundant changes in mucosal gene expression observed.
Keywords: Time point infection study, colon mucosa, Rat

overall_design: In the present study, large-scale gene expression analysis was performed to reveal whether Salmonella induced changes of colonic mucosal gene expression in rats. Wistar rats were infected with Salmonella enteritidis. Non-infected control rats were sham-treated. Rats were sacrificed on day 1, 3 or 6 post infection or sham-treatment (n=8 rats per treatment and per time point). RNA was isolated from colonic mucosal scrapings. mRNA samples of 8 rats per group were pooled. Each pooled group-sample was hybridised in duplicate on Agilent rat whole genome microarrays containing 44290 60-mer spots. From the 12 arrays one duplicate array (Colon mucosa non-infected day6) did not pass quality control and was left out from further analysis.

first: W

first: E

last: Kramer

first: I

last: Bovee-Oudenhoven

first: J

last: Keijer


title: Colonic gene expression upon Salmonella infection and dietary treatment

summary:
To increase our knowledge of the effects of Fructo oligosaccharides (FOS) on Salmonella infection in fats, a controlle rat infection study was performed. Two groups of 12 rats were adapted for 14 days to a cellulose diet and one group of 12 rats to a FOS diet. One cellulose-fed group and the FOS-fed group were infected with Salmonella. Two days post infection mRNA was collected from the mucosa of the colon and changes in gene expression were assessed using an Agilent rat whole genome microarray (G4131A Agilent Technologies). Results indicate that Salmonella affects colonic mucosal gene expression, which is further enhanded by dietary FOS.
Keywords: Dietary infection study, colon mucosa, Rat

overall_design: In the present study, large-scale gene expression analysis was performed to reveal whether Salmonella induced changes of colonic mucosal gene expression in rats. Furthermore, we compared the colonic gene expression changes of infected rats fed a diet supplemented with Fructo oligosaccharides (FOS) or cellulose as control. Two groups of Wistar rats (n=12) were adapted for 14 days to a cellulose diet and one group (n=12) to a FOS diet. One cellulose-fed group and the FOS-fed group were infected with Salmonella. RNA was isolated from colonic mucosal scrapings. mRNA samples of 12 rats per group were pooled. Each group-sample was hybridised in duplicate on Agilent rat whole genome microarrays containing 44290 60-mer spots.

first: S

last: Roosing


title: Comparative gene expression analysis between virus-susceptible and -resistant rice lines (NIL37 and NIL22)

status: Public on Oct 25 2007

city: Metro Manila

first: IL-RYONG

last: CHOI

address: DAPO Box 7777

country: Philippines

institute: International Rice Research Institute

summary:
Near-isogenic lines NIL37 and NIL22 were developed from the cross between Ilpum (recurrent parent susceptible to rice stripe virus (RSV)) and Shinkwang (donor parent resistant to RSV). NIL37 is susceptible to RSV, whereas NIL22 is resistant to RSV. In order to identify genes which are constitutively differentially expressed between NIL37 and NIL22, the gene expression in the two lines were compared at two different conditions (healthy, and RSV-inoculated).
Keywords: Constitutive differential expression

overall_design: Total RNA was isolated from 14-day old plants of NIL37 and NIL22 at two different conditions (healthy and RSV-inoculated). The levels of gene expression in the two lines of the same condition were compared by microarray. Each experiment was repeated twice.

first: K

first: DY

last: Kwak

first: BC

last: Lee


title: Methylation profiling of lung squamous cell carcinomas vs surrounding normal tissue

status: Public on Nov 17 2007

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

type: Methylation profiling by genome tiling array

summary:
Methylated genomic fragments from tumor and matching normal DNA were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. Samples from tumor were labeled with Cy5 while the matching normal were labeled with Cy3 so that methylation differences can be detected.
Keywords: Cancer

overall_design: Comparison of methylation patterns between tumor and matching normal; five patients with stage I lung squamous cell carcinoma

first: Tibor

last: Rauch

first: Gerd

last: Pfeifer


title: Expression data from hybrid Xenopus sex reversal experiment

status: Public on Nov 05 2007

first: John

last: Malone

department: LCDB/NIDDK

institute: NIH

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


title: Comparative gene expression analysis between virus-susceptible and -resistant rice lines (TW16-4 and -69)

summary:
Near-isogenic lines TW16-4 and TW16-69 were developed from the cross between TN1 (recurrent parent susceptible to rice tungro spherical virus (RTSV)) and Utri Merah (donor parent resistant to RTSV). TW16-4 is susceptible to RTSV, whereas TW16-69 is resistant to RTSV.
In order to identify genes which are constitutively differentially expressed between TW16-4 and TW16-69, the gene expression in the two lines were compared at three different conditions (healthy, green leafhopper (GLH)-inoculated, and RTSV-inoculated).
Keywords: Constitutive differential expression

overall_design: Total RNA was isolated from 14-day old plants of TW16-4 and TW16-69 at three different conditions (healthy, GLH-inoculated, and RTSV-inoculated). The levels of gene expression in the two lines of the same condition were compared by microarray. Each experiment was repeated twice.

first: T

last: DeLeon


title: Arsenate stress response: Saccharomyces cerevisiae

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

country: Sweden

institute: Chalmers University of Technology

overall_design:
Refer to individual Series

The individual Series represent non-comparable subsets of GSE6129.


title: Comparison of human epididymal gene expression in the caput epididymides of infertile and fertile patients

status: Public on Oct 05 2007

city: Pointe-Claire

first: Daniel

last: Cyr

state: Québec

address: 245, Boulevard Hymus

institute: INRS-Institut Armand-Frappier

summary:
Caput epididymides biopsies from 4 patients suffering from non-obstructive azoospermia and from 4 patients with active spermatogenesis were compared. 414 genes in the caput epididymides were differentially regulated in infertile men by at least a 2-fold change as compared to the fertile men.
Keywords: Comparison of infertile and fertile caput epididymides

overall_design: Comparative caput epididymal gene expression from 4 patients with either active spermatogenesis (reference samples) or non-obstructive azoospermia. On each array, infertile tissue were compared to fertile tissue. Whenever the fertile tissues were labeled with cyanine 5 (see samples entitled "Patients 1 and 2" and "Patients 7 and 8"), the fluorescence ratios were swapped. Data was normalized using a locally weighted regression Lowess method and genes were considered differentially expressed in infertile sample versus fertile sample if there was at least a 2-fold change in 3 patients out of 4.

first: Evemie

last: Dubé

first: Louis

last: Hermo

first: Peter

last: Chan


title: Comparative gene expression analysis between virus-susceptible and -resistant rice lines (TW16-1263 and -1029)

summary:
Near-isogenic lines TW16-1263 and TW16-1029 were developed from the cross between TN1 (recurrent parent susceptible to rice tungro spherical virus (RTSV)) and Utri Merah (donor parent resistant to RTSV). TW16-1263 is susceptible to RTSV, whereas TW16-1029 is resistant to RTSV. In order to identify genes which are constitutively differentially expressed between TW16-1263 and TW16-1029, the gene expression in the two lines were compared at three different conditions (healthy, green leafhopper (GLH)-inoculated, and RTSV-inoculated).
Keywords: Constitutive differential expression

overall_design: Total RNA was isolated from 14-day old plants of TW16-1263 and TW16-1029 at three different conditions (healthy, GLH-inoculated, and RTSV-inoculated). The levels of gene expression in the two lines of the same condition were compared by microarray. Each experiment was repeated twice.

last: Satoh


title: 5 min mechanical wounding

status: Public on Oct 01 2007

city: La Jolla

first: Justin

last: Walley

address: 9500 Gilman Ave

department: Biological Sciences

institute: UCSD

summary:
Plants are continuously exposed to a myriad of abiotic and biotic stresses. However, the molecular mechanisms by which these stress signals are perceived and transduced are poorly understood. To begin to identify primary stress signal transduction components we have focused on genes that respond rapidly (within 5 min) to stress signals. Because it has been hypothesized that detection of physical stress is a mechanism common to mounting a response against a broad range of environmental stresses, we have utilized mechanical wounding as the stress stimulus and performed whole genome microarray analysis of Arabidopsis thaliana leaf tissue. This led to the identification of a number of rapid wound responsive (RWR) genes. Comparison of RWR genes with published abiotic and biotic stress microarray datasets demonstrates a large overlap across a wide range of environmental stresses.  Interestingly, RWR genes also exhibit a striking level and pattern of circadian regulation, with induced and repressed genes displaying antiphasic rhythms.  Using bioinformatic analysis, we identified a novel motif overrepresented in the promoters of RWR genes, herein designated as the Rapid Stress Response Element (RSRE). We demonstrate in transgenic plants that multimerized RSREs are sufficient to confer a rapid response to both biotic and abiotic stresses in vivo, thereby establishing the functional involvement of this motif in primary transcriptional stress responses.  Collectively, our data provide evidence for a novel cis-element that is distributed across the promoters of an array of diverse stress-responsive genes, poised to respond immediately and coordinately to stress signals.  This structure suggests that plants may have a transcriptional network resembling the general stress signaling pathway in yeast and that the RSRE element may provide the key to this coordinate regulation.
Keywords: Stress response, wounding

overall_design: Three biological replicates of pooled plants were used for each treatment (Not wounded vs 5 min wounded). Each biological replicate is comprised of 2 technical replicates and a dye swap was performed for each technical replicate.

middle: W

first: Sean

last: Coughlan

first: Gopalin

last: Banu

first: Kayatoon

last: Dehesh


title: Rice plants infected by Rice blast fungus

city: Tsukuba

first: Tomoaki

last: Kato

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

summary:
To investigate plant-fungus interactions in early stage of infection, we analyzed response of rice against Magnaporthe grisea infection deficient mutants.  In M. grisea, Mgb1 and Mst12 are essential for development of infection structures.  Deletion of MGB1 results in defect in appresorium formation, and MST12, in penetration peg development.
Analysis of gene expression profiles in rice by microarray revealed the mutant-specific and R gene dependent gene expression, strongly suggesting that gene-for-gene interaction commences before the penetration into rice cell.
Keywords: disease state analysis

overall_design: Agilent rice oligo microarray was used to investigate the gene expression profiling in rice plants infected with Guy11, Mgb1 and Mst12. Total RNAs were isolated from fourth leaves at 24 and 48 hpi. Agilent rice DNA chips were used according to the manufacture’s protocol.  After hybridization, arrays were scanned using an Agilent Microarray Scanner, and Feature Extraction version 9.1 was used for image analysis and data extraction.  Signal intensities derived from inoculated leaved were compared with that of mock-inoculated leaves. In each treatment, the experiment was performed independently three times.

first: Marie

last: Nishimura

first: Yoko

last: Nishizawa

first: Eiichi

last: Minami


title: The PI3K domain of Tra1 is required for transcriptional regulation

status: Public on Oct 10 2007

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

department: Biochemistry

institute: University of Western Ontario

summary:
Tra1 is an essential component of the S. cerevisiae SAGA and NuA4 complexes. Using targeted mutagenesis, we identified residues within its C-terminal phosphatidylinositol-3 kinase (PI3K) domain that are required for function. The phenotype of tra1-P3408A, S3463A and SRR3413-3415AAA included temperature sensitivity and reduced growth in media containing 6% ethanol or aminotriazole. These alleles resulted in ≥2-fold change in expression of ~7% of yeast genes in rich media and reduced activation of PHO5 and ADH2 promoters. Tra1-SRR3413 associated with components of both the NuA4 and SAGA complexes and with the Gal4 transcriptional activation domain similar to wild-type protein. Tra1-SRR3413 resulted in a decreased ratio of acetylated histone H3 and H4 to total histone H3 at the PHO5 promoter that appeared largely due to increased unacetylated histone. Slow growth of a tra1-SRR3413 strain in aminotriazole was suppressed by deletion of Vps1 and the Vps1 interacting protein, Rad16. In addition, ethanol sensitivity was suppressed by loss of Vam3, suggesting that Tra1 is involved with protein trafficking and membrane sorting.  Furthermore, tra1-SRR3413 results in generation dependent telomere shortening. While the tra1 alleles have some phenotypic similarities with deletions of SAGA and/or NuA4 components, the pattern of gene expression, genetic interactions and telomere shortening suggest possible novel functions for the PI3K-domain of Tra1.
Keywords: yeast, Tra1, PI3-kinase domain, gene expression, genetic modification

overall_design: Two dye-swapped, biological replicate experiments were performed for yeast strains CY1507(TRA1::Tn10LUK with 1643(myc-tra1_P3408A-YCplac111)), CY1531(TRA1::Tn10LUK with 1644(myc-tra1_SRR3413-YCplac111)) and CY1514(TRA1::Tn10LUK with 1688(myc-tra1_S3463A-YCplac111)) with reference to CY1524(TRA1::Tn10LUK with 1614(myc-TRA1_SB-YCplac111)).

first: Ana

middle: I

last: Mutiu

first: Stephen

middle: M

last: Hoke

first: Julie

last: Genereaux

first: Katherine

last: MacKenzie

first: Carol

last: Hannam

first: Dana

last: Abrassart

first: Olivier

last: Jobin-Robitaille

last: Guzzo

first: Brenda

last: Andrews

first: Jacques

last: Cote

first: David

last: Haniford

middle: J


title: Gene Expression Analysis of the Rat Retina during Maturation

city: Jerusalem

first: Dror

last: Sharon

department: Ophthalmology

institute: Hadassah- Hebrew University Medical Center

summary:
Recently we reported that the rat inner retina undergoes significant functional changes during maturation. Aiming to gain knowledge on additional aspects of retinal development and maturation, we used the microarray system to monitor gene expression patterns in the rat retina at ages 5, 11, and 20 weeks. The analysis revealed the expression of many well-documented retinal genes as well as a high number of non–annotated genes. Quantitative realtime PCR analysis verified the microarray results in the majority of studied genes. A statistical analysis of the 4 microarray slides revealed 603 differentially expressed genes which were grouped into 6 expression clusters. A bioinformatic analysis of these clusters revealed sets of genes encoding proteins with functions that are likely to be relevant to inner retinal function (e.g. potassium, sodium, calcium, and chloride channels, synaptic vesicle transport, and axonogenesis). In addition, we performed a histological analysis of the maturing retina and studied different aspects of retinal structure. The analysis revealed a significant reduction of outer nuclear layer thickness between 11 and 19 weeks of age and a significant reduction of retinal ganglion cell number at 11 and 19 weeks comparing to 5 weeks.
	We identified in this study genes with differential expression pattern during retinal maturation. Some of the genes encode proteins that may be involved in the functional maturation of inner retinal cells. These data, taken together with our histological and electrophysiological data, contribute to our understanding of the developmental processes occurring in the retina of this widely-used animal model.
Keywords: Dye-swap, Ganglion cells, Gene, Gene expression, Histology, Inner retina, Maturation, Microarray, Rat, Retina, Vision.

overall_design: Rat retinal samples at ages 5, 11, and 20 weeks were studied using 4 microarray slides in a dye-swap design: 5-11, 11-5, 5-20, and 20-5.

first: Gil

last: Ben-Shlomo

first: Ron

last: Ofri

first: Dikla

last: Bandah

first: Mordechai

last: Rosner


title: CGH analysis of inbred mouses strains

status: Public on Nov 06 2007

city: South San Francisco

first: Gene

last: Cutler

address: 1120 Veterans Blvd

department: Lead Discovery

institute: Amgen Inc

summary:
The contribution to genetic diversity of genomic segmental copy number variations (CNVs) is less well understood than that of single-nucleotide polymorphisms (SNPs).  While less frequent than SNPs, CNVs have greater potential to affect phenotype.  In this study, we have performed the most comprehensive survey to date of CNVs in mice, analyzing the genomes of 42 Mouse Phenome Consortium priority strains.  This microarray comparative genomic hybridization (CGH)-based analysis has identified 2094 putative CNVs, with an average of 10 Mb of DNA in 51 CNVs when individual mouse strains were compared to the reference strain C57BL/6J.  This amount of variation results in gene content that can differ by hundreds of genes between strains.  These genes include members of large families such as the major histocompatibility and pheromone receptor genes, but there are also many singleton genes including genes with expected phenotypic consequences from their deletion or amplification.  Using a whole-genome association analysis, we demonstrate that complex multigenic phenotypes, such as food intake, can be associated with specific copy number changes.
Keywords: comparative genomic hybridization

overall_design: DNA from two individual mice per strain, for each of 42 strains was hybridized onto Agilent CGH arrays along with DNA from a reference C57BL/6J sample.  One replicate per strain was labeled with Cy5 and one with Cy3, so each biological replicate is also a dye-flip replicate.

first: Lisa

last: Marshall

first: Ni

last: Chin

first: Helene

last: Baribault

first: Paul

middle: D

last: Kassner


title: Five distinct biological processes and 14 differentially expressed genes characterize TEL/AML1-positive leukemia

status: Public on Sep 27 2007

city: RENNES

first: virginie

last: gandemer

address: 2 av du Pr Léon Bernard

department: génétique et developpement

institute: CNRS UMR6061/Université Rennes1

summary:
Background
The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AML1-positive patients are thus an interesting subgroup to study, and such studies should elucidate the biological processes underlying TEL/AML1 pathogenesis. We report an analysis of gene expression in 60 children with B-lineage ALL using Agilent whole genome oligo-chips (44K-G4112A) and/or real time RT-PCR.
Results
We compared the leukemia cell gene expression profiles of 16 TEL/AML1-positive ALL patients to those of 44 TEL/AML1-negative patients, whose blast cells did not contain any additional recurrent translocation. Microarray analyses of 26 samples allowed the identification of genes differentially expressed between the TEL/AML1-positive and negative ALL groups. Gene enrichment analysis defined five enriched GO categories: cell differentiation, cell proliferation, apoptosis, cell motility and response to wounding, associated with 14 genes –RUNX1, TCFL5, TNFRSF7, CBFA2T3, CD9, SCARB1, TP53INP1, ACVR1C, PIK3C3, EGFL7, SEMA6A, CTGF, LSP1, TFPI— highlighting the biology of the TEL/AML1 sub-group. These results were first confirmed by the analysis of an additional microarray data-set (7 patient samples) and second by real-time RT-PCR quantification and clustering using an independent set (27 patient samples). Over-expression of RUNX1 (AML1) was further investigated and in one third of the patients correlated with cytogenetic findings.
Conclusions
Gene expression analyses of leukemia cells from 60 children with TEL/AML1-positive and -negative B-lineage ALL led to the identification of five biological processes, associated with 14 validated genes characterizing and highlighting the biology of the TEL/AML1-positive ALL sub-group.
Keywords: Acute lymphoblastic leukemia, gene expression profiles, TEL/AML1 fusion transcript, functional annotation

overall_design: We carried out a prospective multicentric study on childhood B-ALL leukemia to elucidate the molecular processes involved in TEL/AML1-positive leukemia. All the patients included in this study received treatment according to the French FRALLE 2000 trial. We used Agilent whole-genome oligo-chips (44K-G4112A) to compare the gene expression signatures of TEL/AML1-positive patients to those of TEL/AML1-negative patients with no recurrent chimeric products irrespective of their clinical risk category. Previous microarray gene expression studies  had revealed the effect of chromosomal alteration on transcription profiles, so we excluded from our cohort those patients with other recurrent chromosomal translocations or fusion transcripts (BCR/ABL, E2A/PBX1, MLL rearrangements). We then searched for the biological pathways associated with genes differentially expressed in TEL/AML1-positive leukemia (ETV6/RUNX1).

last: Gandemer

first: AnneGaelle

last: Rio

first: Marie

last: de Tayrac

first: Vonnick

last: Sibut

first: Stéphanie

last: Mottier

first: Béatrice

last: Ly Sunnaram

first: Catherine

last: Henry

first: Annabelle

last: Monnier

first: Christian

last: Berthou

first: André

last: LeTreut

first: Claudine

last: Schmitt

first: Jean-Yves

last: Le Gall

first: Jean

last: Mosser

first: Marie-Dominique

last: Galibert


title: Expression profiling of human adipose tissue in obese and lean subjects and in various clinical conditions

status: Public on Sep 26 2007

city: Paris

first: Corneliu

last: Henegar

state: Ile de France

address: 15 Rue de l'Ecole de Medecine

institute: Institut national de la santé et de la recherche médicale

summary:
This SuperSeries is related to a manuscript published in Genome Biology. The abstract of this manuscript follows here:
Background
Investigations performed in mice and humans have acknowledged obesity as a low-grade inflammatory disease. Several molecular mechanisms have been convincingly involved in activating inflammatory processes and altering cell composition in white adipose tissue (WAT); however, the overall importance of these alterations, and their long-term impact on the metabolic functions of the WAT and on its morphology, remain unclear.
Results
Here, we analyzed the transcriptomic signature of the WAT in obese human subjects, in stable weight conditions and after weight loss following bariatric surgery. An original integrative functional genomic approach was applied to quantify relations between relevant structural and functional themes annotating differentially expressed genes, to construct a comprehensive map of transcriptional interactions defining the obese WAT. These analyses highlighted a significant up-regulation of genes and biological themes related to extracellular matrix (ECM) constituents, including members of integrins family, and suggested that these elements could play a major mediating role in a chain of interactions which connects local inflammatory phenomena to the alteration of WAT metabolic functions in obese subjects. Tissue and cellular investigations, driven by the analysis of transcriptional interactions, revealed an increased amount of interstitial fibrosis in obese WAT, associated with an infiltration of different types of inflammatory cells, and suggested that phenotypic alterations of human preadipocytes, induced by a proinflammatory environment, may lead to an excessive synthesis of ECM components.
Conclusions
This study opens new perspectives in understanding the biology of human WAT and its pathologic changes indicative of tissue deterioration, associated with the development of obesity.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series.

first: Joan

last: Tordjman

first: Daniele

last: Lacasa

first: Karine

last: Clement


title: Acetaminophen (APAP) Rat Blood Training Gene Expression Data Set

status: Public on Sep 19 2007

first: Pierre

middle: Robert

last: Bushel

department: Biostatistics and Computational Biology Branch

summary:
Gene expression training data set from rat blood samples exposed to either 150, 1500 or 2500 mg/kg of APAP for 6, 12 or 24 hours.
Keywords: Dose response, Time course, Microarray, Gene expression

overall_design:
Male F344/N rats, 10-12 weeks old, were exposed to 0 (vehicle only), 150, 1500 or 2500 mg/kg APAP in 0.5% ethyl cellulose by oral gavage in two doses to increase absorption. The animals were sacrificed after 6, 12 or 24 hours. Equal amounts of RNA from the blood from each of four vehicle-only treated animals at the 6 and 12 hour time point and from each of six vehicle-only treated animals at the 24 hour time point, were pooled for control gene expression.  The pooled controls were compared with individual treated animals at each dose and time period.  The samples were hybridized in duplicate for each individual rat for a total of 8 (exception due to insufficient RNA quality: 150 mg/kg APAP and 1500 mg/kg APAP at 12 hour time point only 3 animals) microarray chips per dose and time period.

Experiments were performed according to the guidelines established in the NIH Guide for the Care and Use of Laboratory Animals and an approved Animal Study Protocol was on file prior to initiation of the study.

middle: R

first: Alexandra

middle: N

last: Heinloth

first: Richard

last: Paules


title: Precise Delination of 5q-Breakpoints and Detection of Hidden Aberrations in patients with MDS using Array CGH

status: Public on Sep 11 2007

city: Duesseldorf

first: Brigitte

last: Royer-Pokora

address: Universitätsstr. 1

country: Germany

institute: Institute of Human Genetics and Anthropology, Heinrich-Heine-University Duesseldorf

summary:
Isolated deletions of the long arm of chromosome 5 (del(5q)) are observed in 10% of myelodysplastic syndromes (MDS) and are associated with a more favorable prognosis, although the clinical course varies considerably. If one or more additional chromosomal aberration/s are present this correlates with a significant shorter overall survival. To assess the frequency of hidden abnormalities in cases with an isolated cytogenetic del(5q), we have performed a genome wide high resolution 44K 60mer oligonucleotide array CGH study using DNA from bone marrow cells of 12 MDS and one AML patient. Additional chromosomal aberrations were identified in three of 13 cases (23%): in one case, a single additional hidden 5.6 Mb deletion of 13q14 and in two cases, multiple larger aberrations involving many chromosomes. Fluorescence in situ hybridization (FISH) demonstrated that aberrations present in only 10% of the bone marrow cells were detectable by aCGH. Furthermore with oligonucleotide aCGH the deletion end points in 5q were mapped precisely, revealing a cluster of proximal break points in band q14.3 (n=8) and a distal cluster between bands q33.2 to q34 (n=11). This study shows the high resolution of oligonucleotide CGH arrays for precisely mapping genomic alterations and for refinement of deletion end points. In addition the high sensitivity of this method enables the study of whole bone marrow cells from MDS patients, a disease with a low blast count. Future studies of more patients with isolated del(5q) for hidden abnormalities will be necessary to evaluate the impact of these on the variable prognosis in these patients and to further define new genetic subgroups.
Keywords: Myelodysplastic syndromes, MDS, array CGH, del(5q), hidden aberrations

overall_design: 13 samples analyzed

first: Christina

last: Evers

first: Manfred

last: Beier

first: Kati

last: Servan

first: Barbara

last: Hildebrandt

first: Anne

last: Poelitz

first: Matthias

last: Drechsler

first: Ulrich

last: Germing

first: Hans-Dieter

last: Royer


title: SuperSeries for the study of expression analysis of the T. thermophilus sigE (TTHB211)

status: Public on Sep 04 2007

city: Hyogo

first: Akeo

last: Shinkai

address: 1-1-1, Kouto, Sayo

department: SPring-8 Center

institute: RIKEN Harima Institute

overall_design: Refer to individual Series


title: Non-additive and imprinted gene expression in hybrid maize endosperm_13DAP and 19DAP

status: Public on Sep 01 2007

city: Saint Paul

first: Nathan

last: Springer

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota


title: Evaluation of the impact of neoplastic histamine secretion on melanoma progression

status: Public on Sep 15 2007

city: Budapest

first: Zoltan

last: Pos

address: 4 Nagyvarad ter

department: Dept. of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

summary:
We previously showed that transgenic enhancement of histamine production in B16-F10 melanomas strongly supports tumor growth in C57Bl/6 mice (Cancer Res, 2005 Pos et al.). In this array experiment, gene expression profiles of transgenic mouse melanomas, secreting different amounts of histamine, were compared by whole genome microarrays.
Keywords: genetic modification

overall_design:
By modifying the levels of L-histidine decarboxylase (HDC), the sole enzyme responsible for histamine production, we introduced three novel variants of the B16-F10 mouse melanoma cell line, displaying diminished (B16-F10 HDC-A), unmodified (B16-F10 HDC-M) or enhanced (B16-F10 HDC-S) capacities to produce and secrete histamine.
In this experiment, B16-F10 HDC-A, HDC-M, and HDC-S experimental mouse melanomas were compared by analyzing 6-6 tumors in each group.
In order to reduce the amount of arrays required, equal amounts of randomly chosen RNA sample pairs were pooled in each group, thus, at the end, each group consisted of 3 pooled tumor samples. All samples were biological replicates, no technical replicates or dye swapping were done.
Gene expression patterns of the three tumor groups were compared indirectly, via a common reference samplei n a two-color array design. Arrays shown here represent gene expression patterns of individual tumor samples compared to the reference sample.

last: Wiener

first: Peter

last: Pocza

first: Melinda

last: Racz

first: Sara

last: Toth

first: Zsuzsanna

last: Darvas

first: Viktor

last: Molnar

first: Hargita

last: Hegyesi

first: Andras

last: Falus


title: Chromatin IP of POF, HP1 and H3K9ac and transcript profiling in S2 cells and salivary glands

status: Public on Oct 03 2007

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

institute: Umea University

type: Genome binding/occupancy profiling by genome tiling array

summary:
Two chromosome-targeting and gene regulatory systems are present in Drosophila melanogaster. The male X-chromosome is targeted by the male-specific lethal complex believed to mediate the two-fold up-regulation of the X-linked genes. The highly heterochromatic 4th chromosome is specifically targeted by the Painting of Fourth (POF) protein which together with heterochromatin protein 1 (HP1) modulate the expression level of genes on the 4th chromosome. Here we report high-resolution mapping of POF and HP1 on the 4th chromosome using chromatin immunoprecipitation followed by tiling microarrays (ChIP-chip) in S2 cells and salivary glands. The enrichments are compared to transcript profiles of the two cell types used. POF specifically binds to genes with a strong preference for exons. The POF binding profile correlates to the binding profile of HP1 which in addition displays a typical “peak” in the promoter regions of bound genes. POF and HP1 binds to active genes and the binding correlates with levels of transcription and changes in binding levels are paralleled by a comparable change in transcription. Our results provide a high resolution description of the chromosome 4 specific gene regulatory system provided by the combinatorial effects of POF and HP1.

This SuperSeries is composed of the SubSeries listed below.


title: CHRF-288-11 and primary human megakaryocytic cell cultures provide novel insights into lineage-specific differentiation

status: Public on Aug 30 2007

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware


title: Gene expression profiling reveals a regulatory role for RORalpha and RORgamma in Phase I and Phase II Metabolism

status: Public on Aug 24 2007

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary:
Retinoid-related orphan receptors RORalpha and RORgamma are both expressed in liver; however, their physiological functions have not yet been clearly defined. RORalpha1 and RORgamma1, but not RORalpha4, show an oscillatory pattern of expression during circadian rhythm. To obtain insight into the physiological functions of ROR receptors in liver, we analyzed the gene expression profiles of livers from WT, RORalpha-deficient staggerer mice (RORalphasg/sg), RORgamma-/-, and RORalpha sg/sgRORgamma-/- double knockout (DKO) mice by microarray analysis. DKO mice were generated to study functional redundancy between RORalpha and RORgamma. These analyses demonstrated that RORalpha and RORgamma affect the expression of a number of genes. RORalpha and RORalpha are particularly important in the regulation of genes encoding several Phase I and Phase II metabolic enzymes, including several 3beta-hydroxysteroid dehydrogenases (Hsd3b), the cytochrome P450 (Cyp) enzymes Cyp7b1, Cyp4a14, and Cyp8b1, and the sulfotransferases Sult1e1 and Sult2a1. Our data show that RORalpha and RORgamma can influence gene expression positively as well as negatively. In addition, our results indicate that RORalpha and RORgamma each affect the expression of a specific set of genes but also exhibit functional redundancy. Our study shows that RORalpha and RORgamma receptors influence the regulation of several metabolic pathways, including those involved in the metabolism of steroids, bile acids, and xenobiotics, suggesting that RORs are important in the control of metabolic homeostasis.
Keywords: knockout comparison

overall_design: We generated RORalpha and RORgamma double knockout (DKO) mice and compared the gene expression profiles of livers from wild type (WT), RORalphasg/sg, RORgamma-/-, and DKO mice by microarray analysis

first: Hong-Soon

last: Kang

first: Martin

last: Angers

first: Ju-Youn

last: Beak

first: Xiyung

last: Wu

first: Jeffrey

last: Gimble

first: Taira

last: Wada

first: Wen

last: Xie

first: Jennifer

last: Collins

first: Sherry

last: Grissom

first: Anton

last: Jetten


title: Acetaminophen (APAP) Rat Liver Test Gene Expression Data Set

first: Pierre

last: Bushel

summary:
Gene expression test data set from rat liver samples exposed to either 150, 1500 or 2000 mg/kg of APAP for 3, 6 or 24 hours.

The Supplementary file (appended below) contains the mapping for the decoding of blinded samples.
Keywords: Dose response, Time course, Microarray, Gene expression

overall_design:
Male F344/N rats, 10-12 weeks old, were exposed to 0 (vehicle only), 150, 1500 or 2000 mg/kg APAP in 0.5% ethyl cellulose by oral gavage in two doses to increase absorption. The animals were sacrificed after 3, 6, or 24 hours.  At the time of sacrifice, liver sections from the left lobe were isolated, cubed, flash frozen and pulverized.  Total hepatic RNA was isolated from individual rat livers.  Equal amounts of RNA from the liver from each of six vehicle-only treated control animals were pooled at each time point and compared to individual control and treated animals at each dose and time period. The samples were hybridized in duplicate for each individual rat for a total of 12 (test set) microarray chips per dose and time period.

Experiments were performed according to the guidelines established in the NIH Guide for the Care and Use of Laboratory Animals and an approved Animal Study Protocol was on file prior to initiation of the study.

first: Alexandra

last: Heinloth

first: Richard

last: Paules


title: B. thetaiotaomicron Study

city: Saint Louis

first: Herbert

last: Chiang

state: MO

address: 4444 Forest Park

department: Center for Genome Sciences

institute: Washington University

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

platform_organism:
Bacteroides thetaiotaomicron
Bifidobacterium longum