title: Effects of flight on gene expression and aging in the honey bee brain and flight muscle

status: Public on Oct 01 2012

city: Las Vegas

first: Joseph

last: Margotta

address: 4505 S. Maryland Parkway

department: SOLS

institute: University of Nevada, Las Vegas

summary: Honey bees move through a series of in-hive tasks (“nursing”) to outside tasks (“foraging”) that coincident with an intense increase in metabolic activity. Social context can cause worker bees to speed up, or slow down this process and foragers may revert back to their earlier in hive  tasks accompanied by reversion to earlier physiological states. To determine if the transcriptional profile of forager bees can revert, or if the effects of flight on gene expression are irreversible, we used whole-genome microarrays. Brain tissue and flight muscle exhibited independent patterns of expression during behavioral transitions, with patterns of expression in the brain reflecting both age and behavior, while flight muscle exhibited primarily age-related patterns of expression.  Our data suggest that the transition from little to no flight (nurse) to intense flight (forager), rather than the amount of flight has a major effect on gene expression.  Following behavioral reversion there was a partial reversion in gene expression but some aspects of forager expression patterns, such as those for genes involved in immune function, remained. These data suggest an epigenetic control and energy balance role in honey bee functional senescence.

overall_design: Brains and thoraces from the same individuals of all behavioral groups were compared on a total of 132 arrays. The samples were hybridized against each other using a loop design. The groups tested are outlined as follows: Typical aged nurse 'YN' (8-10 days old; <1 day flight experience), Precocious forager 'PF' (8 to 10 days old; 2 to 3 days flight experience), Overaged nurse 'ON' (19 to 22 days old; < 1 day flight experience), Forager - low flight 'TFL' (19 to 22 days old; 2 to 3 days flight experience), Forager - high flight 'TFH' ( 19 to 22 days old; 7 to 9 days flight experience), Forager - old 'OF' (25 to 26 days old; 10 to 12 days flight experience), Reverted nurse 'RN' (25 to 26 days old; 7 to 9 days flight experience).  The comparisons are outlined as follows: YN:ON (6 arrays), ON:RN (6 arrays), RN:TFH (6 arrays), TFH:TFL (6 arrays), TFL:PF (6 arrays), PF:YN (6 arrays), ON:TFL (12 arrays), YN:OF (6 arrays), OF:RN (6 arrays), RN:YN (6 arrays). Each comparison was done for individual brains and thoraces. Total: 132 arrays

first: Michelle

last: Elekonich

first: Andrew

last: Ammons

first: Stephen

middle: P

last: Roberts

first: Georgina

middle: E

last: Mancinelli

first: Azucena

last: Benito


title: The Genetic Regulation of the Terminating Phase of Liver Regeneration

status: Public on Jan 01 2013

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

summary: The liver regeneration process terminates when the normal liver-mass/body-weight ratio of 2.5 % has been re-established. We aimed to generate and analyse global expression profiles to study the genetic interactions in relation to liver regeneration, to illuminate the genetic interactions between genes regulating the cell cycle and apoptosis, and to clarify the role of TGF-ß signalling in the terminating phase of liver regeneration. Twelve pigs were randomised to either 60% liver resection (n=4), sham operation (n=4) or control animals (n=4). Liver biopsies were taken at time of resection, after three weeks and upon termination the sixth week. Global gene expression profiles in the biopsies were obtained using porcine oligonucleotide microarrays, representing approximately 20000 porcine genes. Microarray analysis revealed a clear dominance of genes regulating apoptosis towards the end of regeneration, compared to the sham and control groups. Caspase Recruitment Domain-Containing Protein 11 (CARD11) was upregulated six weeks after liver resection, suggesting the involvement of the caspase system at this time. Zinc Finger Protein (ZNF490) gene, with a potential negative effect on cell cycle progression and promotion of apoptosis, was only up regulated at three and six weeks after liver resection indicating a central role at this time. TGF-ß was not found to be significantly affected. CARD11 and ZNF490 appear to play a central role in the termination of liver regeneration in the present study. The lack of TGF-ß could indicate that signaling by TGF-ß is not required for termination of liver regeneration.

overall_design: time course, treatment comparison

first: Ingvild

last: Nygård

first: Kim

last: Mortensen

first: Lene

middle: N

last: Conley

first: Trine

last: Karlstad

first: Christian

last: Bendixen

first: Arthur

last: Revhaug


title: Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers

status: Public on Feb 01 2012

city: Cambridge

first: Ana Teresa

last: Maia

state: Cambridgeshire

address: Robinson Way

department: Department of Oncology

country: United Kingdom

institute: University of Cambridge

type:
SNP genotyping by SNP array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Crossroads of the p53, ER, NFkB stress response networks

status: Public on Jun 01 2011

city: Mattarello - Trento

first: Toma

last: Tebaldi

state: Trento

address: via delle Regole 101

country: Italy

institute: Centre for Integrative Biology

summary:
We explored the combinatorial interactions between p53, estrogen receptors and NFkB using the breast adenocarcinoma-derived MCF7 cells. Recently, we have established that p53 can modulate transcription also through non-canonical response elements (REs), consisting of half-sites and ¾ sites. In particular, we identified a half-site p53 response element in the promoter of FLT1/VEGFR-I gene that was required but not sufficient for the p53 responsiveness of the promoter. The transcriptional control required also estrogen receptor (ER) half-sites (EREs) located in close proximity to the p53 RE. Further studies led us to establish that p53-mediated transcription from the FLT1 half site RE is dependent on ER binding at the EREs and strongly influenced by the level of ER proteins, and the specific nature of the p53-inducing stress as well as ER ligand. In another study we found an enrichment of NFkB REs nearby p53 REs in p53 target genes, suggesting an additional mode of functional interactions between these two transcription factors. To identify at a genome scale the transcriptional network that selectively responds to the concomitant activation of p53, ER and/or NFkB, we measured  gene expression upon treatment with specific chemotherapeutic agents combined with 17-β estradiol (E2) and/or the inflammatory cytokine TNFα. Firstly we measured using MCF7 cells growing in estrogen-depleted media the transcriptome changes induced by doxorubicin (doxo) and 5-fluorouracil (5FU), two different drugs both able to stabilize and activate the p53 protein. We next obtained the expression profiles in the presence of E2 with or without doxo or 5FU. We also measured transcriptome changes in response to TNFα alone or in combination with doxo and/or E2. All these analyses were conducted using the same batch of MCF7 cells (wild type for p53, ERα, ERβ -weakly-, and NFkB positive) that we had previously used to characterize the cis-mediated transcriptional cooperation between p53 and ER at the FLT1 gene.

Keywords: transcription factor, transcriptional networks, p53, ER, NFkB, p53-ER-NFkB crosstalk, doxorubicin, 5-fluorouracil, 17-β estradiol, TNFα, combined genotoxic, estrogenic and inflammatory responses, composite DNA binding site signatures, MCF7.

overall_design: The cooperation at the transcriptional level among p53, ERs and NFkB was analyzed by transcriptome analysis in response to different stimuli (doxo or 5FU, E2, TNFα). To identify mRNA molecules that would be modulated by the coordinated activity of the three TFs, gene expression signals derived from the combinatorial treatment were compared by microarrays analyses to those obtained from each drug when individually administered. Total RNA was isolated from MCF7 cells grown in estrogen-depleted medium and treated so as to stimulate the activity of the three different transcription factors (p53, ERs and NFkB). Cells lysates were collected after 10 hours from the treatments. All experiments were run from triplicate to septuples.

first: Alessandra

last: Bisio

first: Yari

last: Ciribilli

first: Veronica

last: De Sanctis

first: Mattia

last: Lion

first: Alberto

last: Inga


title: Evolutionary conservation of nuclear lamina-genome interactions

status: Public on Oct 10 2012

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by genome tiling array

summary:
Regulation of gene expression is highly conserved between vertebrates, yet the genomic binding patterns of transcription factors are poorly conserved, suggesting that other mechanisms may contribute. The spatial organization of chromosomes in the nucleus is known to affect gene activity, but it is unclear to what extent this organization is conserved in evolution. Genome-wide maps of nuclear lamina (NL) interactions show that human and mouse chromosomes have highly similar folding patterns inside the nucleus. Breaks in synteny are often located at transition points between NL interacting and intra-nuclear regions. Data were compared against data from Peric-Hupkes, Meuleman et al. (Molecular Cell, 2010).

The procedure to arrive at the provided Hidden Markov Model (HMM) state calls is as follows:
We fitted a two-state HMM whereby emissions are distributed as Student's t variables. Mean and variance of DamID signals differ between states, but the degree of freedom (nu) is the same. Gaps in the probe coverage were filled by evenly spaced null probe-values. The parameters were estimated by an adaptation of the ECME algorithm to the HMM framework, showing faster convergence than regular EM when nu is unknown (Filion et al., Cell, 2010). State calls were derived through the Viterbi algorithm. This process was repeated separately for each cell type, yielding per-probe calls. Probes in the ‘bound’ (1) state are indicated as LAD-probes, probes in the ‘unbound’ (0) state as inter-LAD-probes.

All data are mapped to human reference genome assembly NCBI36 / hg18

overall_design: LaminB1-chromatin interactions were assayed in human ESCs and human HT1080 cells.  LaminA-chromatin interactions were assayed in human HT1080 cells. For the all samples there were 2 biological replicates, that were hybridized in a dye-swap design.

first: Wouter

last: Meuleman

first: Daan

last: Peric Hupkes

first: Jop

last: Kind

first: Ludo

last: Pagie

first: Marcel

last: Reinders

first: Lodewyk

last: Wessels


title: Time-course leaf expression data from Populus deltoides

status: Public on May 23 2011

city: Monticello

first: Joshua

last: Adams

state: AR

address: PO Box 3468

department: Forest Resources

country: USA

institute: University of Arkansas-Monticello

summary: We conducted micro-array analysis to quantify the global transcriptome variations in leaves through the course of the year allowing for identification of changing developmental signals. We used RNA samples from pre-formed and mature leaves in the upper crown of a sexually mature Populus deltoides tree 2 hours after sunrise.

overall_design: Three independent samples of leaf/pre-formed leaf tissues were collected from the upper crown of a single sexually mature tree. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array. Tissues represented two batches (batch 1 from 2005 and batch 2 from 2006).  Therefore, March samples were used to normalize the other month samples within the same batch.

first: Olga

last: Pechanova

first: Chuan-Yu

last: Hsu

first: Lindsay

last: Vandervelde

first: Jenny

last: Drnevich

first: Sara

last: Jawdy

first: Ardeshir

last: Adeli

first: Jeffrey

middle: C

last: Suttle

first: Amanda

middle: M

last: Lawrence

first: Timothy

middle: J

last: Tschaplinski

first: Armand

last: Séguin

first: Cetin

last: Yuceer


title: Transcriptome analysis of Arabidopsis thaliana G protein subunit mutants in response to abscisic acid (ABA)

status: Public on Dec 06 2010

city: State College

first: Sarah

middle: M.

last: Assmann

state: PA

address: 210 Mueller Laboratory, University Park

department: Biology

institute: Pennsylvania State University

summary:
Heterotrimeric G proteins mediate crucial and diverse signaling pathways in eukaryotes. To gain insights into the regulatory modes of the G protein and the co-regulatory modes of the G protein and the stress hormone abscisic acid (ABA), we generated and analyzed gene expression in G protein subunit single and double mutants of the model plant Arabidopsis thaliana.
Through a Boolean modeling approach, our analysis reveals novel modes of heterotrimeric G protein action.   Keywords: transcriptome analysis; G protein subunit mutants;  abscisic acid (ABA)

overall_design: Microarray data were generated from four genotypes (wild type, gpa1-4 mutant, agb1-2 mutant, agb1-2 gpa1-4 double mutant) with or without ABA treatment. Arabidopsis plants were grown in growth chambers with an 8 hr light/16hr dark. Three hundred Arabidopsis leaves excised from 60-70 five-week-old plants were used as the starting material for each guard cell microarray. Ten mature leaves taken from 3-4 plants grown side-by side with the plants for guard cell isolation were used for each leaf sample. Excised leaf and isolated guard cell samples were treated with ABA (50 μM) or EtOH (solvent control) for 3 hrs. For each type of sample (guard cells or leaves), three independent biological replicates were performed, resulting in a total of 48 microarray hybridizations (2 sample types ´ 4 genotypes ´ two treatments ´3 replicates).


title: Expression data from melanoma cells grown under neural crest cell culture conditions (spheroid cells) versus under classical adherent conditions (adherent cells) - 2 different specimens of melanoma tumors

status: Public on Mar 28 2011

city: Paris

first: Reem

last: Al-Daccak

address: Bat Bazin - 1 Av Claude Vellefaux

country: France

institute: INSERM

summary:
Summary: Melanoma spheroids grown under neural crest cell conditions are highly plastic migratory/invasive tumor cells endowed with immunomodulator function
Background: The aggressiveness of melanoma tumors is likely to rely on their well-recognized heterogeneity and plasticity. Melanoma comprises multi subpopulations of cancer cells some of which may possess stem cell-like properties supporting the notion of plasticity. Although useful for certain tumors, the use of the sphere-formation assay to identify stem cell-like or tumor initiating cells subpopulations in human melanoma has been recently challenged. Our study reveals that this assay predicts a functional phenotype associated with aggressive behavior of tumor cells.
Methodology/Principal Findings: We analyzed the molecular and functional phenotypes of melanoma spheroids formed in neural crest cell medium. Whether from metastatic (SLM8) or advanced primary (Mela1) tumors, spheroid cells expressed melanoma-associated markers. They displayed higher capacity to differentiate along mesenchymal lineages, and showed enhanced expression of SOX2, NANOG, KLF4, and/or OCT4 transcription factors, but not extensive self-renewal or enhanced tumorigenicity when compared to their adherent counterparts. To determine whether melanoma spheroids in our model could predict a molecular or functional phenotype, we performed gene expression profiling experiments using Affymetrix microarrays. Gene expression profiling attributed a neural crest cell signature to these spheroids and indicated that a migratory/invasive and immune-function modulating program could be associated with these cells. In vitro assays confirmed that these spheroids are endowed with enhanced migratory/invasive capacities. In immune activation assays, spheroid cells elicited a poorer allogenic response from immune cells and inhibited mitogen-dependent T cells activation and proliferation more efficiently than their adherent counterparts. Thus, our findings reveal novel immune-modulator function of melanoma spheroid cells and suggest specific roles for these spheroids in invasion and in evasion of antitumor immunity.
Conclusion/Significance: The association of a more plastic, invasive and evasive, thus a more aggressive tumor phenotype with melanoma spheroid cells reveals a previously unrecognized aspect of tumor cells expanded as spheroid cultures. While of limited efficiency for melanoma initiating cell identification, our melanoma spheroid model predicted aggressive phenotype and could therefore, be constructive to investigate melanoma aggressiveness, relevant to patients and clinical transferability.

overall_design: 12 Total samples were analyzed: SLM8 adherent (SLMA) and spheroids (SLMS) cells, and Mela1 adherent (MelaA) and spheroid (MelaS) cells, all performed in triplicates. Paired statistical analyses were performed using Student's paired t-test on the gene signal intensities (gene level) and results were considered statistically significant at p-values <=0.05 and fold-change >=1.5.


title: Lung biopsies from asthmatics pre- and post- steroid treatment and from healthy control

status: Public on Jan 18 2011

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
To better understand the therapeutic potential of targeting Th2 inflammation in asthma, we performed genome-wide expression profiling of endobronchial biopsies in asthmatics and healthy controls stratified according a previously defined three-gene Th2 signature in bronchial epithelium.
The Th2 signature is defined as relatively high expression of POSTN, CLCA1, and SERPINB2.

overall_design: Endobronchial biopsies from 27 asthmatics and 13 healthy controls were assayed on expression microarrays.  Biopsies were obtained from asthmatics before and one week after treatment with Flovent, an inhaled corticosteroid commonly used to treat asthma.

first: Alexander

middle: R

first: David

middle: F

last: Choy

first: Barmak

last: Modrek

last: Kummerfeld

first: Hilary

last: Clark

first: Lawren

last: Wu

first: Grazyna

last: Fedorowicz

first: Zora

last: Modrusan

first: John

middle: V

last: Fahy

first: Prescott

middle: G

last: Woodruff

first: Joseph

last: Arron


title: Regulation of miRNAs in macrophages in response to Candida albacans

status: Public on Dec 31 2010

city: DUNDEE

first: Claire

last: Monk

address: James Black Centre, University of Dundee, Dow Street

institute: University of Dundee

summary: In this study we have analysed the regulation of miRNA in bone marrow derived macrophages in response to the fungal pathogen heat killed Candida albicans and bacterial cell wall component, LPS. The aim of the study was to identify and validate miRNAs involved in the innate immune system in response to fungal and bacterial stimuli and investigate potential mechanisms for their transcription.

overall_design: Three mice were used as 3 biological replicates. The bone marow derived macrophages from each mouse were divided into two and either left untreated or were stimulatred for 16 h with heat killed Candida albicans.

first: Gyorgy

last: Hutvagner

first: J

middle: S

last: Arthur


title: Retinal Pigment Epithelial Cells Upregulate Expression of Complement Factors after Co-culture with Activated T Cells

status: Public on Feb 02 2011

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

institute: National Genome Center

summary: In this study we examined the effect of T cell-derived cytokines on retinal pigment epithelial (RPE) cells with respect to expression of complement components. We used an in vitro co-culture system in which CD3/CD28-activated human T cells were separated from the human RPE cell line (ARPE-19) by a membrane. Differential gene expression in the RPE cells of complement factor genes was identified using gene arrays, and selected gene transcripts were validated by q-RT-PCR. Protein expression was determined by ELISA and immunoblotting. Co-culture with activated T cells increased RPE mRNA and/or protein expression of complement components C3, factors B, H, H-like 1, CD46, CD55, CD59, and clusterin, in a dose-dependent manner. Soluble factors derived from activated T cells are capable of increasing expression of complement components in RPE cells. This is important for the further understanding of inflammatory ocular diseases such as uveitis and age-related macular degeneration.

overall_design: 10 samples investigating variations of co-cultures of RPE cells and T-cells. Variable parameters include the cell type, the co-culturing of the counter-part cell type and the orientation of the system (apical vs basolateral).

first: Helene

middle: B

last: Juel

first: Charlotte

last: Kæstel

first: Carsten

last: Faber

first: Niels

last: Heegaard

first: Mogens

middle: H

last: Nissen


title: Expression profiling in cellular miRNAs of human bone marrow stromal cells derived from multiple myeloma patients

status: Public on Jun 08 2018

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

summary:
Bone marrow stromal cells (BMSCs) and their exosomes are a promising area of cancer therapy.
Multiple myeloma (MM) is a refractory hematologic malignancy. Bone marrow stromal cells (BMSCs) interact with MM cells in the bone marrow (BM), and also create a permissive microenvironment for MM cell growth and survival. Recent evidence indicated that exosome-mediated MM cell-BMSC communication plays an important role in the MM microenvironment. In this study, we investigated the biological property of the exosomes and exosomal miRNAs derived from BMSCs, aiming to establish the emerging strategies to target MM microenvironment to prevent tumor growth and spread.

overall_design: Human BMSCs of elderly (68 and 72 years old) healthy donors were purchased from Lonza (Normal-BMSCs). BM samples were obtained from multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS) patients in accordance with the Declaration of Helsinki and using protocols approved by the research Ethics Committee of Tokyo Medical University (IRB No. 2648), and BMSCs derived from MM patients (MM-BMSCs) and MGUS patients (MGUS-BMSCs) were isolated using the classical plastic adhesion method. Total RNA from each BMSCs (2 Normal-BMSCs, 6 MM-BMSCs and 3 MGUS-BMSCs) was extracted by the miRNeasy mini kit (Qiagen). The cellular miRNA profiling was done using a TaqMan low-density array (ABI), and Student’s t-test was used to determine statistical significance for comparisons between young and old groups using R software.


title: Expression data from normal or DM1 myoblasts

status: Public on Oct 01 2010

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

summary:
We are investigating the transcriptional response of changes in RNA steady-state levels between normal and DM1.
We used microarrays to detail the global programme of gene expression differences in normal or DM1 myoblasts.

Keywords: comparison

overall_design: Two types of cells were analyzed, normal or DM1 deficient. The expression differences were compared to each other and we have deciphered a gene expression profile that is representative of DM1 deficiency.

first: Dansithong

last: Warunee

first: Jog

last: Sonali

first: Fry

last: Rebecca

first: Marjoram

last: Paul

first: Comai

last: Lucio

first: Reddy

last: Sita


title: Microarray-based gene expression profiles of silkworm brains

status: Public on Nov 16 2010

city: Chongqing

first: Ling

last: Gan

address: 160#Xue Yuan Road,RongchangCounty

department: 1The Department of Veterinary Medicine

country: China

institute: Southwest University

summary: Molecular genetic studies of Bombyx mori have led to profound advances in understanding the regulation of development. Bombyx mori brain, as a main endocrine organ, plays important regulatory roles in various biological processes. The microarray technology will allow the genome-wide analysis of gene expression patterns in silkworm brains. We reported microarray-based gene expression profiles in silkworm brains at four stages including V7, P1, P2 and P3. A total of 4,550 genes were transcribed in at least one selected stage. Of these, clustering algorithms separated the expressed genes into stable expressed genes and variable expressed genes. The results of the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analysis of stable expressed genes showed that the ribosomal and oxidative phosphorylation pathways were principal pathways. Secondly, four clusters of genes with significantly different expression patterns were observed in the 1,175 variable expressed genes. Thirdly, thirty-two neuropeptide hormones genes, nine neuropeptide-like precursor genes, and 117 cuticular protein genes were expressed in selected developmental stages. The present study deﬁned major characteristics of the transcriptional profiles in the brains of Bombyx mori at the specific development stages. Our data will provide abundant information that will be useful in future research.

overall_design: Transcription profiling experiments, 4 developmental stages (samples) were analyzed. Dual-channel experiments, with test samples labeled by Cy5 and common reference samples labeled by Cy3. Common reference sample was used for data normalization. One Biological replicate. No dye-swaps.

first: Xilong

last: Liu

first: Zhonghuai

last: Xiang

first: Ningjia

last: He


title: Transcriptome analyses based on genetic screens for Pax3 myogenic targets in the mouse embryo

status: Public on Dec 01 2010

city: paris

first: mounia

last: lagha

address: 25 rue du Dr Roux

institute: Institut Pasteur


title: Discovery and comparative profiling of microRNAs in sweet oranges

status: Public on Sep 22 2010

city: Ithaca

first: Qiang

last: Xu

state: NY

address: Tower Road, Cornell University

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNAs (sRNAs) are emerging as important regulators of biological processes in plants. To characterize the small RNA species and expression changes in ‘Anliu’ sweet orange (wild type, WT) and its red-flesh mutant (MT) with lycopene accumulation, we used high-throughput pyrosequencing to identify and quantitatively profile sRNAs. We identified 112 known miRNAs belonging to 64 families from the sweet orange. Comparative analysis revealed that 63 of the 112 known miRNAs exhibited significant expression differences between WT and MT. We also identified 12 novel miRNAs and 9 miRNA candidates from sweet orange; the 12 novel miRNAs are in line with the biogenesis characteristics including the stem-loop structure of the pre-miRNAs and existence of the miRNA*s in the sRNA libraries. Comparative profiling revealed that 10 novel miRNAs and 8 miRNA candidates are differentially expressed between WT and MT. Potential targets of these differentially expressed miRNAs included several important genes that are involved in carotenoid biosynthesis, such as geranylgeranyl pyrophosphate synthase (GGPS) and lycopene β-cyclase (LYCb). Moreover, GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. We proposed that miRNA-target genes are the hot-spots for generating sRNAs. This study provides the first large scale cloning and characterization of citrus miRNAs, which also lays a foundation for unraveling the mechanism of lycopene accumulation in the sweet orange mutant on post-transcription level.

overall_design: Size fractionated small RNAs (16-30 bp)  from total RNA extracts was ligated to 5' and 3' adapters,  and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value.  The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.

first: Xiuxin

last: Deng


title: Statin-induced Myopathy

status: Public on Jul 09 2010

city: Buffalo

first: Paul

middle: J.

last: Isackson

address: 100 High St

department: Pediatrics

institute: University at Buffalo

summary: We performed a genome-wide association study in pooled DNA samples from patients with severe statin myopathy and persistent symptoms post-therapy versus pooled DNAs from an age-adjusted statin-tolerant group.

overall_design: Affymetrix 100K SNP arrays were used according to the manufacturers instructions with two pools of 19 and 20 statin myopathy patients and two pools of 20 statin-tolerant controls.


title: Emergence of Non-Random Chromosomal Alterations (Trisomy 7 and 20) Derived from Diploid Human Colonic Epithelial Cells

status: Public on Sep 14 2010

city: Dallas

first: Kimberly

last: Batten

state: TX

address: 5323 Harry Hines Blvd

department: Cell biology

institute: UT Southwestern Medical Center

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

summary: Aneuploidy from chromosomal instability is frequently detected in the vast majority of sporadic colorectal cancer patients and is believed to be an early driving force in disease progression. Despite this observation, the cellular advantages conferred by these cytogenetic alterations are poorly understood. We have isolated and immortalized non-transformed human colonic epithelial cells (HCECs) from non-cancerous biopsy tissue from a previous CRC patient undergoing routine colonoscopy. While these cells maintain a diploid karyotype under 2% serum conditions, we have isolated derivatives in serum-free culture with an extra copy of chromosome 7 (+7), a non-random trisomy detected in over 40% of human colorectal adenomas and carcinomas. We report here that +7 HCECs were not detectable in the initial cell population and appeared from an originally diploid population under serum-free culture conditions. The emergence of +7 cells correlates with a slight growth advantage that may be attributed to aberrant regulation of the epidermal growth factor receptor. We also provide evidence that +7 HCECs have defects in cell migration. A subpopulation with trisomy 20, another non-random chromosomal alteration in CRC, emerged following stable knockdown of TP53 and expression of oncogenic K-RASV12 in +7 HCECs. We describe isogenic HCECs that represent non-random cytogenetic changes occurring in sporadic colorectal cancer progression. These unique cellular reagents may serve as useful in vitro models for studying chromosomal instability-mediated tumorigenesis and the discovery of novel chemopreventive strategies.

overall_design: Copy number analysis of Affymetrix Genome-Wide Human SNP 5.0 Array was performed for immortalized human colonic epithelial cells that are either diploid or trisomy 7 for detection of large chromosomal amplifications or deletions.

first: Peter

last: Ly

first: Andres

middle: I

last: Roig

first: Suzie

middle: K

last: Hight

first: Ugur

last: Eskiocak

first: Sang

last: Kim

first: Ying

last: Zou

first: Woodring

last: Wright

first: Jerry

middle: W

last: Shay


title: Staphylococcus epidermidis: wild type vs lytSR mutant

status: Public on Mar 08 2010

city: Shanghai

first: Tao

last: Zhu

address: 138, Dongan Road

institute: Fudan university

summary: The custom-made S. epidermidis GeneChips(Shanghai Biochip Co., Ltd) included qualifiers representing open reading frame (ORF) sequences identified in the genomes of the S. epidermidis strain RP62A, as well as unique ORFs in S. epidermidis strain 12228. The GeneChips were composed of cDNA array containing PCR products of 2316 genes and oligonucleotide array containing 252 genes.Two-component regulatory systems (TCSs) play a pivotal role in bacterial adaptation, survival, and virulence by sensing changes in the external environment and modulating gene expression in response to a variety of stimuli.To investigate the regulatory role of LytSR, one of the TCSs identified in the genomes of S. epidermidis, we used the GeneChips to perform a transcriptional profile analysis of the wild strain and lytSR mutant.

overall_design: Wild type untreated in triplicate is compared to lytSR mutant in triplicate for cDNA array and four replicates on the oligo array.

first: Di

last: Qu


title: NCI60 Expression Profiling using the Agilent Whole Human Genome Oligo Microarray

status: Public on Aug 01 2010

city: Bethesda

first: Hongfang

last: Liu

state: MD

address: 9000 Rockville Pike

institute: National Cancer Institute

summary: We present here a new expression profiling study of the 60 cell lines of the National Cancer Institute (NCI) Developmental Therapeutics program (DTP) drug screen (NCI-60) using the 41,000-probe Agilent Whole Human Genome Oligo Microarray. The expression levels of ∼21,000 genes  were measured.

overall_design: The profiling study includes quadruplicate technical replicates for six cell lines and duplicates for the remaining cell lines. The resulting data sets are freely available and searchable online in the CellMiner database (http://discover.nci.nih.gov).

first: William

last: Reinhold

first: J

last: Weinstein

first: Y

last: Pommier

first: P

last: D'Andrade

first: S

last: Fulmer-Smentek


title: Transcriptional Profiling of Host Gene Expression in Chicken Embryo Lung Cells Infected with Laryngotracheitis Virus

status: Public on Mar 11 2010

city: Fayetteville

first: Byung-whi

last: Kong

address: 1260 W. Maple, POSC, L-426

department: Poultry Science

institute: University of Arkansas

summary: Transcriptional profiling of chicken embryo lung cells infected infectious laryngotracheitis virus (ILTV) comparing control uninfected lung cells. Goal was to determine the changes of host gene expression by ILTV infection and host-virus interaction.

overall_design: Two-condition experiment, uninfected chicken embryo lung cells vs. infected chicken embryo lung cells. Biological replicates: 1 control uninfected sample, 1 infected experimental sample at each 1dpi, 3dpi, 5dpi, and 7 dpi.

first: Jeong

middle: Y

last: Lee

first: Byung-Whi


title: BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject

status: Public on Jan 06 2010

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.

Characterization of chromatin modification by ChIP-Seq in human subject.

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

overall_design:
BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.1561

first: Bradley

middle: E

last: Bernstein

first: Alex

last: Meissner


title: Primary human leukocyte RNA expression of unrelated Dutch and UK individuals

status: Public on Feb 28 2010

city: Groningen

first: Lude

last: Franke

state: Groningen

department: Genetics

institute: University Medical Centre Groningen

summary:
Multiple common variants for celiac disease influencing immune gene expression
The goal of this study was to study the effect of genetic variation on gene expression of untouched primary leucocytes.
We obtained peripheral blood RNA from unrelated Dutch and UK individuals using PAXgene tubes.
We performed a second-generation genome wide association study of 4,533 celiac disease cases and 10,750 controls. We genotyped 113 selected SNPs with PGWAS<10-4, and 18 SNPs from 14 known loci, in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome wide significance (Pcombined<5x10-8), most contain immune function genes (BACH2, CCR4, CD80, CIITA/SOCS1/CLEC16A, ICOSLG, ZMIZ1) with ETS1, RUNX3, THEMIS and TNFRSF14 playing key roles in thymic T cell selection. A further 13 regions had suggestive association evidence. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P<0.0028, FDR 5%) with cis gene expression.

*** Due to privacy concerns, the SNP data is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access directly from the submitter (contact info below). ***

overall_design: Gene expression data was determined of untouched primary leucocytes (n=229) from unrelated Dutch and UK individuals.

first: Rudolf

last: Fehrmann

first: Cisca

last: Wijmenga

first: David

last: van Heel

first: Leonard

last: van den Berg

first: Roel

last: Ophoff

first: Jan

last: Veldink


title: Human airway epithelial cell comparisons

status: Public on Apr 15 2010

city: Iowa City

first: Bartley

middle: Joseph

last: Brown

state: IA

institute: The University of Iowa

summary:
Expression data from airway brush biopsy samples, differentiated primary cultures of human airway epithelia, CaLu3 cultures at the air liquid interface, and primary cultures of human airway epithelia submerged in nutrient media

Organotypic cultures of primary human airway epithelial cells have been used to investigate the morphology, ion and fluid transport, innate immunity, transcytosis, infection, inflammation, signaling, cilia and repair functions of this complex tissue.  However, we do not know how close these cultures resemble the epithelia in vivo. In this study, we examine the genome-wide expression profile of human airway epithelial cells in vivo obtained from brush biopsies of the trachea and bronchus of healthy volunteers and compare it to the expression profile of primary cultures of human airway epithelia grown at the air-liquid interface.  For comparison we also investigate the expression profile of Calu3 cells grown at the air-liquid interface and primary cultures of human airway epithelia submerged in nutrient media.

overall_design: We compare the transcriptional profile of human in vivo airway epithelia from trachea and bronchus to differentiated primary human airway epithelia cultures, also from trachea and bronchus, and grown at the air-liquid interface.  We also included the profile of Calu3 cultures grown at the air-liquid interface and primary cultures submerged in nutrient media.

first: Alejandro

middle: A

last: Pezzulo

first: Todd

last: Scheetz

first: Paul

last: McCray

first: Joseph

last: Zabner


title: Mouse lung CD103+ and CD11b-high dendritic cell (DC) subsets

status: Public on Mar 15 2010

city: Charlottesville

first: Sun-sang

last: Sung

state: VA

address: Box 800133, U. of Virginia Health Sciences Center

department: Medicine

institute: University of Virginia

summary:
Mouse lung CD11c+ dendritic cells are composed of 2 major DC subsets, the CD103+CD11b-low/intermediate DC (CD103+ DC) and the CD11b-highCD103- DC (CD11b-high DC).  These 2 subsets are functionally distinct.  Comparison of their functions showed CD103+ DC
Microarray analysis was performed to compare the gene expression profiles of the 2 lung DC subsets in naïve mice.

overall_design: Perfused lungs from 6-8-week naïve BALB/cByJ mice were pooled and digested with collagenase D.  CD11c+ cells were selected by anti-CD11c magnetic microbeads (Miltenyi) and stained by fluorochrome-conjugated mAb against I-A, CD103, CD11b, and CD11c plus 7-

middle: J


title: Expresson from human THP-1 stimulated with IFN-g and/or infected with TB

city: Newark

first: Richard

last: Pine

state: NJ

address: 225 Warren St

department: PHRI/Medicine

institute: UMDNJ-NJMS

summary: Investigation of interacting effects of TB and IFN-g on gene expression regulation within human macrophage-like THP-1 cells

overall_design: To investigate the effect TB infection has on THP-1 macrophage’s response to IFN-g post-infection, in multiple experiments, THP-1 cells were exposed to each of the following four conditions: not treated, IFN-γ treated, M. tuberculosis infected and M. tuberculosis infected then IFN-γ treated.  Total cellular RNA was then extracted.  Recovered RNAs were pre-qualified for reproducibility by comparing qRT-PCR results of IFIT-2 and IP10 between replicate experiments.  Four most reproducible replicate experiments were then selected for genome-wide mRNA abundance assays using Affymetrix microarray-based technology.


title: Gene atlasing of digestive and reproductive tissues in Schistosoma mansoni

status: Public on Sep 03 2010

city: Brisbane

first: Geoffrey

last: Gobert

address: 300 Herston Rd

country: Australia

institute: QIMR

summary: This study provides a detailed transcriptomic analysis of the reproductive tissues (ovary, vitelline and testes) and gastrodermis S. mansoni. The results obtained will help direct future research on the functional aspects of these specific tissues, and will allow the characterisation of currently unannotated genes in S. mansoni

overall_design: Quantification of gene expression within specific, biologically important tissues of S. mansoni was achieved by a combination of laser microdissection microscopy (LMM) and oligonucleotide microarray analysis. We compared the gene expression profile of the adult female gastrodermis and male and female reproductive tissues with whole worm controls. This is complemented by a set of data from macrodissected samples from different regions of the worm.

first: Sujeevi

last: Nawaratna

middle: N


title: Gene expression data from forelimb buds of E10.5 mouse embryos

first: mounia

last: lagha

summary: We used microarrays to identify Pax3 targets during myogenesis in the mouse embryo

overall_design: Mouse embryos were genotyped Pax3GFP/+ or Pax3PAX3-FKHR/GFP and dissected at E10.5 under a fluorescent binocular. The forelimb buds were dissected and dissociated and GFP positive cells were then sorted by flow cytometry before RNA extraction and hybridization on Affymetrix microarrays. We also sorted GFP negative cells.

first: Mounia

last: Lagha

first: Béatrice

last: Regnault

first: Frédéric

last: Relaix

first: Margaret

last: Buckingham


status: Public on Aug 05 2009

first: BROAD

last: INSTITUTE

summary:
The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease.

Characterization of the reference epigenome in humans by use of ChIP-Seq in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

overall_design:
BI Human Reference Epigenome Mapping Project - samples and experiments will continue to be added to this study over the course of the project.

EDACC Genboree Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSTUDY%2FEDACC.949

first: Bradley

last: Bernstein

first: Alex

last: Meissner


title: Primary human leucocyte RNA expression of unrelated Dutch individuals.

first: Lude

last: Franke

summary:
Multiple common variants for celiac disease influencing immune gene expression
The goal of this study was to study the effect of genetic variation on gene expression of untouched primary leucocytes.
We obtained peripheral blood RNA from unrelated Dutch individuals using PAXgene tubes.
We performed a second-generation genome wide association study of 4,533 celiac disease cases and 10,750 controls. We genotyped 113 selected SNPs with PGWAS<10-4, and 18 SNPs from 14 known loci, in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome wide significance (Pcombined<5x10-8), most contain immune function genes (BACH2, CCR4, CD80, CIITA/SOCS1/CLEC16A, ICOSLG, ZMIZ1) with ETS1, RUNX3, THEMIS and TNFRSF14 playing key roles in thymic T cell selection. A further 13 regions had suggestive association evidence. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P<0.0028, FDR 5%) with cis gene expression.

*** Due to privacy concerns, the SNP data is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access directly from the submitter (contact info below). ***

overall_design: Gene expression data was determined of untouched primary leucocytes (n=1,240) from unrelated Dutch individuals.

first: Rudolf

last: Fehrmann

first: Cisca

last: Wijmenga

first: David

last: van Heel

first: Leonard

last: van den Berg

first: Roel

last: Ophoff

first: Harry

last: Groen

first: Rinse

last: Weersma

first: Jan

last: Veldink


title: Transcriptome profiling of embryonic development rate in rainbow trout advance backcross introgression lines

status: Public on Nov 12 2009

city: West Lafayette

first: Peng

last: Xu

state: IN

address: 915 W State St

institute: Purdue University

summary: Embryonic development rate is a key trait significantly associated and genetically linked with both growth rate and sexual maturity in rainbow trout. To identify candidate genes underlying embryonic development rate, whole genome expression microarray analyses were conducted using embryos from a fourth generation backcross family; each backcross generation involved the introgression of the fast-developing alleles for the major development rate QTL (from the Clearwater clonal line [CW]) into a slow-developing clonal line (Oregon State University [OSU]). Embryos were collected at 15, 19, and 28 days post-fertilization. Microsatellite markers (One112ADFG, OMM1009 and OmyFGT12TUF) linked to the major embryonic development rate QTL region were used to determine the QTL genotype. The sex marker OMY-Y1 was used to determine the genotypic sex of each embryo. cDNA from 48 individual embryos were used for microarray expression analysis. An ANOVA modeling approach was used to detect differential gene expression between embryos possessing fast-developing genotypes and slow-developing genotypes. A total of 182 features have been identified with significant differences between embryonic development rate genotypes. Quantitative PCR was conducted on ten representative genes using the rainbow trout homologous  sequences and microarray results were validated.

platform_organism:
Osmerus mordax
Oncorhynchus mykiss
Salmo salar
Coregonus clupeaformis
Oncorhynchus tshawytscha

overall_design: Microarrays were co-hybridized with one sample labeled with Cy3 and another with Cy5 (dual channels). Hybridizations on each slide involved direct co-hybridization within time points (15, 19 and 28 dpf) between individuals of the same sex, but with different QTL genotypes (CW vs. OSU). A total of 24 microarray slides were hybridized by cDNA from 48 individual embryos, 8 slides for each development time point. Dye swap design was involved throughout the whole experiment.

first: Lauren

last: McIntyre

first: Paul

last: Wheeler

first: Gary

last: Thorgaard

first: Krista

last: Nichols


title: Pseudomonas aeruginosa PA14 MvfR-dependent QS regulatory pathway

status: Public on Jul 17 2009

city: Boston

first: Laurence

last: Rahme

address: 50 Blosson St, Thier 340

department: Surgery

institute: Massachusetts General Hospital

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

overall_design: Refer to individual Series


title: Pseudomonas aeruginosa PA14, mvfR and anthranilic acid analogs

summary: The Pseudomonas aeruginosa MvfR-dependent QS regulatory pathway controls the expression of key virulence genes; and is activated via the extracellular signals 4-hydroxy-2-heptylquinoline (HHQ) and 3,4-dihydroxy-2-heptylquinoline (PQS), whose syntheses depend on anthranilic acid (AA), the primary precursor of 4-hydroxy-2-alkylquinolines (HAQs). We identified halogenated AA analogs that specifically inhibited HAQ biosynthesis and disrupted MvfR-dependent gene expression. These compounds restricted P. aeruginosa systemic dissemination and mortality in mice, without perturbing bacterial viability, and inhibited osmoprotection, a widespread bacterial function.

overall_design:
mvfR mutants of PA14 and control PA14 cells were grown to OD 2.5, a point where QS is turned on, and their expression profiles were compared.

AA analogs 4CABA and 6CABA were added directly to the culture media of PA14 cells.

first: Eric

last: Deziel

first: Biliana

last: Lesic

first: Francois

last: Lepine

first: Gaoping

last: Xiao

first: Jianxin

last: He


title: Predicting drug activity in non-small cell lung cancer based on genetic lesions

status: Public on Jul 29 2009

city: Cologne

first: martin

last: sos

address: Gleuelerstr. 50

country: Germany

institute: Max-Planck Institute for neurological research

summary:
84 NSCLC cell lines were collected from various sources (Supplemental Table 1) and formed the basis for all subsequent experiments. Cell lines were derived from tumors representing all major subtypes of NSCLC tumors, including adenocarcinoma, squamous-cell carcinoma and large-cell carcinoma.

The genomic landscape of these cell lines was characterized by analyzing gene copy number alterations using high-resolution single-nucleotide polymorphism (SNP) arrays (250K Sty1). We used the statistical algorithm Genomic Identification of Significant Targets in Cancer (GISTIC) to distinguish biologically relevant lesions from background noise. The application of GISTIC revealed 16 regions of recurrent, high-level copy number gain (inferred copy number > 2.14) and 20 regions of recurrent copy number loss (inferred copy number < 1.86)

overall_design: copy number changes data was generated for all cell lines

first: Roman

last: Thomas

first: Matthew

last: Meyerson


title: Children's Oncology Group Study 9906 for High-Risk Pediatric ALL

status: Public on Jun 25 2009

city: Albuquerque

first: Maurice

last: Murphy

state: NM

address: 9501 Camino de Salud

department: UNM Cancer Center

institute: UNM Health Sciences Center

summary:
PAPER 1:"Identification of novel subgroups of high-risk pediatric precursor B acute lymphoblastic leukemia (B-ALL) by unsupervised microarray analysis: clinical correlates and therapeutic implications. A Children's Oncology Group (COG) study."

ABSTRACT

We examined gene expression profiles of pre-treatment specimens from 207 patients from the COG P9906 study to identify signatures of children with high risk B-precursor acute lymphoblastic leukemia (ALL) and to determine whether the resulting clusters are associated with either specific clinical features or treatment response characteristics.

Four unsupervised clustering methods were utilized to classify patients into similar groups.  The different clustering algorithms showed significant overlap in cluster membership.  Two clusters contained all cases with either t(1;19)(q23;p13) translocations or MLL rearrangements. The other six clusters were novel and had no recurring chromosomal abnormalities or distinctive clinical features.  Members of two of these novel clusters had significant survival differences when compared to the overall 4-year relapse-free survival (RFS) of 61%.  These included clusters of patients with either significantly better (94.7%) or worse (21.0%) RFS at 4 years.  Children of Hispanic/Latino ethnicity were disproportionately present in the poor outcome cluster.  The poor outcome cluster represents a novel biologically distinctive subset of B-precursor ALL that may occur at least as frequently as BCR/ABL. Further molecular characterization of this cluster may lead to the discovery of genomic abnormalities that can be targeted to improve the currently dismal outcome for children with this gene signature.

The Sample data have also been used in another study:

PAPER 2: "Gene expression classifiers for minimal residual disease and relapse free survival improve outcome prediction and risk classification in children with high risk acute lymphoblastic leukemia. A Children's Oncology Group study".

ABSTRACT

Background. Nearly 25% of children with B-precursor ALL present with   "high-risk" disease (HR-ALL) that is resistant to current therapies. Gene expression profiling may yield molecular classifiers for outcome prediction that can be used to improve risk classification and therapeutic targeting.

Methods.  Expression profiles were obtained in pre-treatment leukemic samples from 207 uniformly treated children with HR-ALL.  Relapse free survival (RFS) was 61% at 4 years and flow cytometric measures of minimal residual disease (MRD) at the end of induction (day 29) were predictive of outcome (P<0.001).  Molecular classifiers predictive of RFS and MRD were developed using extensive cross-validation procedures.

Results.  A 38 gene molecular risk classifier predictive of RFS (MRC-RFS) distinguished two groups in HR-ALL with different relapse risks: low (4 yr RFS: 81%, n=109) vs. high (4 yr RFS: 50%, n=98) (P<0.0001).  In multivariate analysis, the best predictor combined MRC-RFS and day 29 flow MRD data, classifying children into low (87% RFS), intermediate (62% RFS), or high risk (29% RFS) groups (P<0.0001). A 21 gene molecular classifier predictive of MRD could effectively substitute for day 29 flow MRD, yielding a combined classifier that similarly distinguished three risk groups at pre-treatment (low: 82% RFS; intermediate: 63% RFS; and high risk: 45% RFS) (P<0.0001).  This combined molecular classifier was further validated on an independent cohort of 84 children with HR-ALL (P = 0.006).

Conclusions.   Molecular classifiers predictive of RFS and MRD can be used to distinguish distinct prognostic groups within HR-ALL, significantly improving risk classification schemes and the ability to prospectively identify children at diagnosis who will respond to or fail current treatment regimens.

NOTE: Due to Children's Oncology Group (COG) restrictions, outcome and MRD data cannot be provided as part of the covariate data for this dataset at the present time. If you would like to arrange individual access to this data, please contact COG or the PI of this study, Dr. Cheryl Willman, at the University of New Mexico Cancer Center (cwillman@unm.edu) to arrange a collaboration.

overall_design:
Unsupervised clustering and supervised risk classification analyses of 207 diagnostic samples and associated clinical covariate data.
See the Summary for greater details.

The data were analyzed using Microarray Suite version 5.0 (MAS 5.0) in the Affymetrix Gene Chip Operating Software Version 1.4. Probe masking was used (see 9906_TT207_Affymetrix_probe_mask.msk, linked below as a supplementary file). Otherwise all Affymetrix default parameter settings were used. Global scaling as the normalization method, with the default target intensity of 500, was used.

first: Cheryl

middle: L

last: Willman

first: Kerem

last: Ar

first: Susan

middle: R

last: Atlas

first: Edward

last: Bedrick

first: Deepa

last: Bhojwani

first: Michael

last: Borowitz

first: W

middle: P

last: Bowman

first: Bruce

last: Camitta

first: Andrew

last: Carroll

first: William

first: I-Ming

last: Chen

first: George

last: Davidson

first: Meenakshi

last: Devidas

first: Richard

middle: C

last: Harvey

first: Stephen

last: Hunger

first: Huining

last: Kang

first: Jeanette

last: Pullen

first: Gregory

last: Reaman

first: Xuefei

last: Wang

first: Carla

last: Wilson


title: Expression data from androgen treated LNCaP cells

status: Public on Dec 30 2009

city: Ann Arbor

first: Adaikkalam

last: Vellaichamy

state: MI

address: 1400 E. Med. Center Dr.

institute: University of Michigan

summary:
Androgens are required for the development of normal prostate, and they are also linked to the development of prostate cancer.
We used microarrays to understand the role of androgen in an androgen dependent, androgen receptor (AR) positive human metastatic cell line, LNCaP.

overall_design: LNCaP cells were grown in RPMI medium and they were subjected to stay in phenol-red free, RPMI with charcoal stripped serum for 48h. Synthetic androgen R1881 was added and the cells were allowed to grow for 48h. Control cells were given with corresponding amount of ethanol as vehicle which is used for the solubilization of R1881. Cells were harvested and RNA was isolated for microarray analysis.

first: Arun

last: Sreekumar

first: Gilbert

last: Omenn

first: Arul

middle: M

last: Chinnaiyan


title: Using high-density exon arrays to profile gene expression in closely related species

status: Public on May 05 2009

first: Yi

last: Xing

address: 3294 CBRB, 285 Newton Rd

department: Internal Medicine, Biomedical Engineering

institute: University of Iowa

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens


title: Using high-density exon arrays to profile gene expression in closely related species (HJAY)

summary:
Global comparisons of gene expression profiles between species provide significant insight into gene regulation, evolutionary processes, and disease mechanisms. In this work, we describe a flexible and intuitive approach for global expression profiling of closely related species, using high-density exon arrays designed for a single reference genome. The high-density probe coverage of exon arrays allows us to select the identical set of perfect-match probes for measuring expression levels of orthologous genes. This eliminates a serious confounding factor in probe affinity effects of species-specific microarray probes, and enables direct comparisons of estimated expression indexes across species.

Keywords: analysis of gene expression in tissues

overall_design: We conducted Affymetrix Human Exon Junction array (HJAY array) profiling of RNAs from human, chimpanzee and rhesus macaque cerebellums, with three replicates per species.


title: Using high-density exon arrays to profile gene expression in closely related species (Exon 1.0 ST)

overall_design: We conducted Human Exon 1.0 array profiling of RNAs from three chimpanzee cerebellums and three chimpanzee livers


title: Pseudomonas aeruginosa PA14, pqsE and PQS

first: Laurence

middle: G

last: Rahme

summary: The Pseudomonas aeruginosa MvfR-dependent QS regulatory pathway controls the expression of key virulence genes; and is activated via the extracellular signals 4-hydroxy-2-heptylquinoline (HHQ) and 3,4-dihydroxy-2-heptylquinoline (PQS). Our findings reveal a multi-layered homeostatic regulation of PQS and HHQ and the MvfR regulon component PqsE which is a key mediator in orchestrating this homeostatic regulation.

overall_design: We assessed the expression profile of pqsE mutant in contrast to constitutive expression of PqsE from PA14 and its mvfR mutant. In addition we tested the effect of addition of 20ug/ml PQS on mvfR mutant expressing PqsE

first: Ronen

last: Hazan

first: Jianxin

last: He

first: Gaoping

last: Xiao


title: NPAS2 ChIP-on-chip in MCF7 cells

status: Public on Mar 07 2009

city: New Haven

first: Aaron

middle: Ezra

last: Hoffman

state: CT

address: 60 College St.

department: LEPH

institute: Yale School of Medicine

type: Genome binding/occupancy profiling by array

summary: The aim of the current study is to create a transcriptional profile of genes regulated by the circadian gene NPAS2, using a human binding ChIP-on-chip analysis of NPAS2 in MCF-7 cells.

overall_design:
The ChIP assay was performed using the ChIP Assay Kit ((Millipore, Billerica, MA) according to the manufacturer’s protocol. Briefly, cells were grown in 100 mm cell culture plates to 80% confluence. Cross-linking of protein and DNA was performed using cell culture medium containing 1% formaldehyde at room temperature for 10 minutes. Sonication was performed using an Omni Ruptor 250 Ultrasonic Homogenizer (omni International, Marietta, GA) to generate input material. This input sample was then incubated with primary antibody (anti-NPAS2) and negative control (Rabbit IgG) for immunoprecipitation (IP). Agarose beads were added to the reactions to bind protein-conjugated antibody. The antibody-protein-DNA complex was then eluted from the agarose beads with freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3) and the cross-linking was reversed by adding 5M NaCl for 4 hours at 65ºC followed by proteinase K digestion at 45ºC for one hour.  The final DNA, representing NPAS2 target sequences, was purified using the GENECLEAN Turbo kit (Qbiogene, Carlsbad, CA) according to the manufacturer’s instructions. Ligation-mediated PCR (LM-PCR) (Agilent Technologies, Foster City, CA) was used to amplify DNA according to the manufacturer’s protocol. Two ChIP assays were performed independently and both amplified DNA samples were used in the subsequent human binding microarray analysis.

Binding microarray analysis
We worked with MOgene Inc (St Louis, MO) to perform the Human Binding Array (Agilent) using the amplified DNA obtained from the ChIP experiment. Labeling, hybridization, and image analyses were all performed at MOgene, an Agilent certified service provider for ChIP-on-chip analysis. The binding array includes a total of 488k probes that target ~17,000 of the best defined human transcripts covering 5.5 kb upstream to 2.5 kb downstream from the transcriptional start sites. A whole-chip error model was used for array data analysis and to call a bound gene (target gene). The neighborhood error model takes into account neighboring probes and calls a region as bound, not just a single probe. Genes associated with significant regions are therefore considered target genes. The binding array analysis was performed for both duplicate samples from the ChIP assay, and since the array requires two slides per sample, there are four total samples included in this submission

first: Chun-Hui

last: Yi

first: Tongzhang

last: Zheng

first: Derek

last: Leaderer

first: Yong

last: Zhu


title: MUC1-induced transcriptional alterations in rat 3Y1 embryonic fibroblasts

status: Public on Apr 10 2009

city: Chicago

first: Sean

middle: Pravin

last: Pitroda

state: IL

address: 5841 South Maryland Avenue, MC 1105

department: Radiation and Cellular Oncology

institute: The University of Chicago

summary:
The MUC1 oncoprotein is aberrantly overexpressed in diverse human malignancies including breast and lung cancer. Although MUC1 modulates the activity of several transcription factors, there is no information regarding the effects of MUC1 on global gene expression patterns and the potential role of MUC1-induced genes in predicting outcome for cancer patients. We have developed an experimental model of MUC1-induced transformation that has identified the activation of gene families involved in oncogenesis, angiogenesis and extracellular matrix remodeling. A set of experimentally-derived MUC1-induced genes associated with tumorigenesis was applied to the analysis of breast and lung adenocarcinoma cancer databases. A 35-gene MUC1-induced tumorigenesis signature (MTS) predicts significant decreases in both disease-free and overall survival in patients with breast (n = 295) and lung (n = 442) cancers. The data demonstrate that the MUC1 oncoprotein contributes to the regulation of genes that are highly predictive of clinical outcome in breast and lung cancer patients.

Keywords: Expression profiling by microarray

overall_design: To investigate the genes associated with MUC1-CD-induced transformation and tumorigenesis, we performed expression profiling of 3Y1/Vector (empty vector-transfected 3Y1) and 3Y1/MUC1-CD (MUC1-CD-transfected 3Y1) cells growing in vitro, and of 3Y1/MUC1-CD cells growing as tumor xenografts in athymic mice. Cells grown in vitro or as tumor xenografts were lysed to collect total RNA for hybridization with GeneChip® Rat Genome 230 2.0 Arrays.

first: Nikolai

last: Khodarev

first: Michael

last: Beckett

first: Dhara

last: MacDermed

first: Lei

last: Huang

first: Donald

last: Kufe

first: Ralph

last: Weichselbaum


title: CoCl2 Response in Cryptococcus neoformans

status: Public on May 01 2009

first: Yun

last: Chang

address: 10 Center Dr.

institute: NIH

summary:
We investigated the effects of the hypoxia-mimetic CoCl2 on the gene expression of pathogenic fungus Cryptococcus neoformans.
Keywords: compound treatment design

overall_design: Three biological repeats were performed using three independent RNA sets isolated from cells cultured on different days and the dye-reverse hybridizations were performed for all three sets. One set of RNA was also subjected to technical repeats.


title: CRY2 knockout in MCF7 cells

status: Public on Jan 29 2009

summary: CRY2 expression was silenced in MCF7 cells using siRNA oligos, in order to examine the impact of CRY2 knockdown on carcinogenic processes.  CRY2 was ~3-fold down-regulated in both replicates, relative to negative control.

overall_design: MCF7 cells were transfected with either a negative control siRNA, or an siRNA oligo targeting CRY2.  Each treatment was performed on two independent cell populations (biological replicates).  Knockdown was confirmed by qRT-PCR.


title: P. syringae pv. phaseolicola NPS3121 responses to bean leaf extract

status: Public on Mar 03 2009

city: Irapuato

first: Jose Luis

last: Hernandez-Flores

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León

department: Ingeniería Genética

country: Mexico

institute: Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional

summary: Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. Bean leaf extract was obtained from healthy bean leaves.  In this work we investigated the effect of bean leaf extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without extract from healthy bean leaves.

overall_design: Two RNA samples were compared, one prepared from cells grown in minimal medium and the other from cells grown in minimal medium supplemented with bean leaf extract. To control de biological variation that might interfere with data interpretation, a minimum of three biological replicates were prepared and two technical replicates with the same RNA (swap).

first: Alejandro

last: Hernández-Morales

first: Enrique

last: Ibarra-Laclette

first: Ariel

last: Álvarez-Morales


title: Expression data from garlic-fed mouse

status: Public on Dec 31 2008

city: Urla

first: Bunyamin

last: Akgul

state: izmir

address: Gulbahcekoyu

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary:
Garlic is a popular flavor enhancer in modern cuisines. Although anti-atherosclerotic, anti-proliferative, hypolipidemic and chemopreventative effects of garlic are known for a long time, the mechanisms of garlic as a dietary supplement ramain largely unknown.
We used microarrays to analyze the global programme of gene expression in control (cellulose) and garlic-fed mice and identified erythropoietic and heme biosynthetic genes that could, in part, be responsible for the pleiotropic effects of garlic on health
Keywords: diet, garlic

overall_design: 8-week old male C57BL/6J mice were divided into two diet groups and maintained at an SPF facility. Mice were fed (ad libitum) a special diet (Yeh and Yeh, 1994) with 4% cellulose (Control group, 3 mice) or 4% lyophilized raw garlic powder (Treatment group, 3 mice). At the end of the 15-week treatment, spleen organs were used for RNA isolation and arraying.

first: Bünyamin

last: Akgül

first: Kai-Wei

last: Lin

first: Chen-Pei

middle: D

last: Tu


title: Regions of acquired UPD at diagnosis of FL are associated with both overall survival and risk of transformation

status: Public on Jan 30 2009

city: London

first: derville

last: o'shea

address: Charterhouse Square

institute: Medical Oncology

summary:
SNP array analysis was performed using the Affymetrix 10K 2.0 Gene-chip array on DNA from 181 diagnostic Follicular Lymphoma (FL) patients to assess the prognostic relevance of aUPD. Genetic abnormalities were detected in 118/181 (65%) patients. Number of abnormalities was predictive of outcome; > 3 abnormalities was associated with inferior overall survival (OS) (p<0.03). Sites of recurrent aUPD were detected on 6p (n=25), 16p (n=22), 12q (n=17), 1p36 (n=14), 10q (n=8) and 6q (n=8). On multivariate analysis aUPD 1p36 correlated with shorter OS (p=0.05). aUPD 16p was predictive of transformation (p=0.03) and correlated with poorer progression free survival (p=0.02).

Keywords: Genomic analysis of FL samples

overall_design: Genomic DNA from 181 diagnostic FL samples were analysed using Affymetrix 10K 2.0 SNP arrays.  Genomic DNA from the blood of ten unrelated Hapmap controls was used as reference for all FL samples. Prevalence and regions of homozygosity were identified.

first: Derville

middle: O

last: Shea

first: Ciaran

last: Riain

first: Manu

last: Gupta

first: Rachel

last: Waters

first: Youwen

last: Yang

first: David

last: Wrench

first: John

last: Gribben

first: Andreas

last: Rosenwald

first: German

last: Ott

first: Lisa

last: Rimsza

first: Harald

last: Holte

first: Jean-Baptiste

last: Cazier

first: Nathalie

last: Johnson

first: Elias

last: Campo

first: Wing

last: Chan

first: Randy

last: Gascoyne

first: Bryan

last: Young

first: Louis

last: Staudt

first: Andrew

last: Lister

first: Jude

last: Fitzgibbon


title: IL17 and IL22 stimulation of T84 colonic epithelial cell line

status: Public on May 07 2008

city: Davis

first: Michael

last: George

state: CA

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary:
The effects of stimulating intestinal epithelial cells with Th17 cytokines, IL17 and IL22, was investigated
Keywords: dose response

overall_design: The human colonic epithelial cell line, T84 was grown to confluency in standard transwell plates and either mock treated, or treated with cytokines IL17 and IL22

first: Manuela

last: Raffatellu

last: Baumler


title: P. syringae pv. phaseolicola NPS3121 responses to bean pod extract

first: Jose Luis

last: Hernandez-Flores

summary: P. syringae pv. phaseolicola is the causal agent of the halo blight disease of beans (Phaseolus vulgaris L). The disease attacks both foliage and pods of plant host. Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. In this work we investigated the effect of bean pod extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without bean pod extract.

overall_design: Two RNA samples were compared, one prepared from cells grown in minimal medium M9 and the other from cells grown in minimal medium supplemented with bean pod extract.To control de biological variation that might interfere with data interpretation, a minimum of three biological replicates and two technical replicates (swap) were prepared.

first: Alejandro

last: Hernández-Morales

first: Enrique

last: Ibarra-Laclette

first: Ariel

last: Álvarez-Morales


title: Molecular characterization of murine IFN producing killer dendritic cells

status: Public on Jun 28 2008

city: Baltimore

first: Franck

last: Housseau

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University

summary:
IKDCs have been newly characterized in mouse and shared functional and phenotypic properties of NK cells and dendritic cells. To formaly distinguish them from NK cells, we have performed a gene expression profile analysis of splenic and LN cell sorted IKDC and compared them with CDC and NK.We are looking for gene or group of genes specifically expressed by IKDCs and which would allow us to specifically isolate and characterize them.

Keywords: Freshly isolated cells

overall_design: IKDC, NK and CDC were cell-sorted from spleen and lymph node (LN) of naïve BALB/c mice (6-8 weeks).

first: Drew

last: Pardoll


title: Exon Level Expression Profiling: a Novel Unbiased Transcriptome Analysis for Body Fluids

status: Public on May 20 2008

city: Los Angeles

first: David

last: Wong

email: dtww@ucla.edu, mikehu@ucla.edu

address: 10833 Le Conte Ave, CHS 73-017

department: Dental Research Institute

institute: University of California, Los Angeles

summary:
Transcriptome analysis of partially degraded and fragmented RNA samples from body fluids

Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals.

overall_design: We analyzed saliva from 18 healthy subjects (7 males, 11 females) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.

first: Zhanzhi

last: Hu

first: Hui

last: Zhou

first: Bernhard

last: Zimmermann

first: Bradley

middle: S

last: Henson

first: Weixia

last: Yu

last: Elashoff

first: Guido

last: Krupp

middle: T


title: The genomic-level expression patterns of human mononuclear cells subjected heat shock or lipopolysaccharide stress

status: Public on Dec 18 2007

city: Cincinnati

first: Hector

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

summary:
Direct comparison of the genome-level expression patterns of THP-1 cells exposed to either LPS or heat shock
Peripheral blood mononuclear cells (PBMC) serve a sentinel role allowing the host to efficiently sense and adapt to the presence of danger signals. Herein we have directly compared the genome-level expression patterns (microarray) of human PBMC (THP-1 cells) subjected to one of two canonical danger signals, heat shock and lipopolysaccharide (LPS). Based on sequential expression and statistical filters, and in comparison to control cells, we found that 3,988 genes were differentially regulated in THP-1 cells subjected to LPS stress, and 2,921 genes were differentially regulated in THP-1 cells subjected to heat shock stress. Venn analyses demonstrated that the majority of differentially regulated genes (greather than or equal to 70%) were uniquely expressed in response to one of the two danger signals. Functional analyses demonstrated that the two danger signals induced expression or repression of genes corresponding to unique pathways, molecular functions, biological processes, and gene networks. In contrast, there were 184 genes that were commonly upregulated by both stress signals, and 430 genes that were commonly downregulated by both stress signals. Interestingly, the 184 commonly upregulated genes corresponded to a gene network broadly related to inflammation, and more specifically to chemokine signaling. These data demonstrate that the mononuclear cell responses to the canonical stress signals, heat shock and LPS, are highly divergent. However, there is a heretofore unrecognized common pattern of gene network expression corresponding to chemokine-related biology. The data also serve as a reference database for investigators in the field of stress signaling.
Keywords: treated vs non treated

overall_design: In vitro exposure of THP-1 cells to control conditions, LPS (1 micogram/ml for 4 hrs), or heat shock (43 deg C for 1 hour, followed by a 4 hour recovery at 37 deg C)

first: Kelli

last: Odoms

first: Bhuvaneswari

last: Sakthivel


title: A predictive and prognostic 38-gene expression signature for metastatic relapse in breast cancer

status: Public on Nov 28 2008

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

institute: ICO (Integrated Center of Oncology Nantes)

summary:
Background
Currently, no gene-expression signature (GES) established from node-positive cohorts, able to predict breast cancer evolution after systemic adjuvant chemotherapy, exists.
Methods
Gene-expression profiles of 252 node-positive patients (median follow-up: 7.7 years), mostly included in a randomized clinical trial (PACS01), receiving systemic adjuvant regimen, were determined by means of cDNA custom array representing 5,776 distinct genes.
Findings
In the training cohort, we established a 38-GES for the purpose of predicting time to distant metastasis. The 38-GES yielded unadjusted hazard ratio of 4.86 (95% CI=2.76-8.56). Even when adjusted with the two best clinicopathological prognostic scoring: NPI and Adjuvant!, 38-GES HR were 3.30 (1.81-5.99) and 3.40 (1.85-6.24), respectively. Furthermore, 38-GES improved mostly NPI and Adjuvant! intermediate-risk classified patients. NPI intermediate-risk patients (7-year MFS=87.2%) were divided into 2/3 (7-year MFS=95.5%) close to NPI low-risk group and 1/3 (7-year MFS=69.3%) close to NPI high-risk group (HR=6.97 [2.51-19.36]). Adjuvant! intermediate-risk patients (7-year MFS=88.0%) were divided into 2/3 (7-year MFS=94.8%) close to Adjuvant! low-risk group and 1/3 (7-year MFS=71.7%) close to Adjuvant! high-risk group (HR=5.31 [5.38-11.87]). The 38-GES was validated on gene-expression datasets from three external node-positive breast cancer subcohorts (n=224) generated from different microarray platforms. The 38-GES yielded unadjusted HR=2.95 (1.74-5.01). Furthermore, 38-GES showed performance in supplementary cohorts with different lymph-node status and endpoint (1,031 new patients).
Interpretation
The 38-GES represents a robust tool able to type systemic adjuvant treated node-positive patients at high risk of metastatic relapse, and especially powerful to separate NPI or Adjuvant! intermediate-risk node-positive patients.
Keywords: disease-state analysis

overall_design:
252 breast cancer patients at diagnosis examined with spotted cDNA nylon membrane.

Patient details:
PACS01x are 2 parts of a clinical trial :
PACS01A : patients had received 6 cycles of FEC100
PACS01B : patients had received 3 cycles of FEC100 then 3 cycles of Docetaxel
CCRG are patients from our local cancer center (Cancer Center René Gauducheau) included with the same criteria as PACS01A (6 cycles of FEC100).

first: Pascal

last: Jézéquel

first: Mario

last: Campone

first: Henry

last: Roché

first: Catherine

last: Charbonnel

first: Gabriel

last: Ricolleau

first: Florence

last: Magrangeas

first: Stéphane

last: Minvielle

first: Jean

last: Genève

first: Anne-Laure

last: Martin

first: Régis

last: Bataille

first: Loïc

last: Campion


title: HybridPoplar_H11-11_Leaves_MalacosomaDisstria_Herbivory

status: Public on Apr 22 2008

city: Vancouver

first: Joerg

last: Bohlmann

state: BC

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

summary:
From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139 007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385 000 publicly available Populus ESTs. Clustering and assembly of 107 519 3'-end ESTs resulted in 14 451 contigs and 20 560 singletons, altogether representing 35 011 putative unique transcripts, or potentially more than three-quarters of the predicted c. 45 000 genes in the poplar genome. Using this EST resource, we developed a cDNA microarray containing 15 496 unique genes, which was utilized to monitor gene expression in poplar leaves in response to herbivory by forest tent caterpillars (Malacosoma disstria). After 24 h of feeding, 1191 genes were classified as up-regulated, compared to only 537 down-regulated. Functional classification of this induced gene set revealed genes with roles in plant defence (e.g. endochitinases, Kunitz protease inhibitors), octadecanoid and ethylene signalling (e.g. lipoxygenase, allene oxide synthase, 1-aminocyclopropane-1-carboxylate oxidase), transport (e.g. ABC proteins, calreticulin), secondary metabolism [e.g. polyphenol oxidase, isoflavone reductase, (–)-germacrene D synthase] and transcriptional regulation [e.g. leucine-rich repeat transmembrane kinase, several transcription factor classes (zinc finger C3H type, AP2/EREBP, WRKY, bHLH)]. This study provides the first genome-scale approach to characterize insect-induced defences in a woody perennial providing a solid platform for functional investigation of plant–insect interactions in poplar.
Keywords: stress response

overall_design: Ten hybridizations were performed comparing FTC-treated poplar leaves after 24 h of continuous feeding and untreated control leaves harvested at the same time. RNA isolated from each of the five individual FTC-treated trees was compared directly against the five individual untreated control trees using two hybridizations with a dye flip for each tree pair.

first: Steven

last: Ralph


title: P. syringae pv. phaseolicola NPS3121 responses to apoplastic fluid of bean leaf

first: Jose Luis

last: Hernandez-Flores

summary: Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. Plant apoplast is the primary site of infection for P. syringae, which obtain nutrients directly from apoplastic fluid of host plants. In this work we investigated the effect of apoplastic fluid on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without apoplastic fluid extracted from healthy bean leaves.

overall_design: Two RNA samples were compared, one prepared from cells grown in minimal medium  and the other from cells grown in minimal medium supplemented with apoplastic fluid from bean leaves. To control de biological variation that might interfere with data interpretation, a minimum of three biological replicates were prepared and two technical replicates with the same RNA (swap).

first: Alejandro

last: Hernández-Morales

first: Enrique

last: Ibarra-Laclette

first: Ariel

last: Alvarez-Morales


title: Microarray analysis of perichondral and reserve growth plate zones

status: Public on Mar 28 2008

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary:
In the growth plate, the reserve and perichondral zones have been hypothesized to have similar functions, but their exact functions are poorly understood.  Our hypothesis was that significant differential gene expression exists between perichondral and reserve chondrocytes that may differentiate the respective functions of these two zones. Normal Sprague-Dawley rat growth plate chondrocytes from the perichondral zone (PC), reserve zone (RZ), proliferative zone (PZ), and hypertrophic zone (HZ) were isolated by laser microdissection and then subjected to microarray analysis.  In order to most comprehensively capture the unique features of the two zones, we analyzed both the most highly expressed genes and those that were most significantly different from the proliferative zone (PZ) as a single comparator.
Keywords: cell specific expression profiles

overall_design: 2 microarray replicates were obtained for each zone, using pooled quantities of RNA from 3 rats each at 42 and 46 days of age.

first: Mingliang

last: Zhang

first: Meredith

last: Pritchard

first: Jason

last: Horton

first: Timothy

last: Damron


title: Cicardian regulation in rat liver

status: Public on Sep 11 2007

city: Binghamton

first: Eric

last: Hoffman

address: PO Box 6000

department: Pharmaceutical Sciences

institute: Binghamton University - SUNY

summary:
In intact animals, time of drug administration may be an important factor influencing drug response. Our general goal seeks to incorporate circadian time into the study of corticosteroid regulated gene expression. Since levels of endogenous steroid exhibit circadian fluctuations, it is our hypothesis that the expression of genes controlled by corticosteroids either directly or indirectly, will also exhibit a circadian pattern in normal animals.
Keywords: time series design

overall_design: This study is designed to examine fluctuations in gene expression in liver within the 24 hour circadian cycle in normal animals.  Fifty-four male normal Wistar rats (250-350 g body weight) were housed in a strictly controlled stress free environment with light:dark cycles of 12 hr:12hr.  Three animals were sacrificed at each of 18 selected time points within the 24 hour cycle.  RNA was prepared from livers for gene arrays.  Time point designations reflect time after lights on in hours.

first: Richard

last: Almon


title: Transcriptional analysis of  BCR-triggered immature and mature mouse B cells

status: Public on Dec 15 2008

city: Evry

first: Olivier

last: ALIBERT

address: 2 rue Gaston Crémieux

department: IRCM

institute: CEA

summary:
The B cell antigen receptor (BCR) is a signaling complex that mediates differentiation stage-specific cell fate decisions in B lymphocytes. While several studies have evidenced differences in signal transduction components as being key to contrasting phenotypic outcomes, little is known about the differential BCR-triggered gene transcription. Here we defined transcriptional changes underlying BCR-induced apoptosis and proliferation of immature and mature B cells, respectively. These findings provide the first insights into the early transcriptional events leading to deletion or clonal expansion of B cells upon antigen recognition.
Keywords: cell type comparison, development or differentiation design, time course, compound treatment design, microarray experiment record

overall_design:
Total RNA was extracted from immature (IM) and mature (M) B cells both freshly isolated (0h) and stimulated with (BCR) or without (ctrl) anti-μ F(ab’)2 for 2, 8 or 24h. Following RNA extraction, one round of mRNA amplification was applied using the MessageAmpTM Kit (Ambion). All samples, including the amplified Universal Mouse Reference RNA (Stratagene) which served as a reference at each hybridization, were reverse-transcribed and indirectly labeled with Cy3 and Cy5 (Amersham). Quality was controlled by performing 6 or 8 hybridizations of each sample to the cDNA arrays using a dye-swap strategy.
94 arrays were used for hybridization in total.

first: Jernej

last: Murn

first: Xavier

last: Gidrol


title: Preclinical CNS changes following peripheral murine RML prion challenge

status: Public on Jul 01 2008

city: Zurich

first: Gino

last: Miele

address: Schmelzbergstrasse 12

department: Institute for Neuropathology

country: Switzerland

institute: University Hospital Zurich

summary:
Mice were challenged with either RML prions or mock brain homogenate intraperitoneally.  Whole brains were harvested and processed at 145 days post-inoculation, with mice reaching terminal stages of disease in this model at approximately 200 days post-inoculation.
Keywords: Transcriptional profiling

overall_design: Brains were pooled into three groups of three biological replicates.

first: Adriano

last: Aguzzi


title: Genome-Wide Profiling of Airway Epithelial Cells in Asthmatics, Smokers and Healthy Controls

status: Public on Oct 12 2007

city: San Francisco

first: Prescott

middle: Gurney

last: Woodruff

address: 505 Parnassus Ave

department: Medicine

institute: UCSF

summary:
We collected airway epithelial brushings for microarray analysis from 42 asthmatics and two control groups – 28 healthy subjects and 16 smokers.  A subgroup of 32 asthmatics completed a randomized placebo-controlled trial of fluticasone propionate in which collection of brushings was repeated after 1 week of treatment.
Keywords: disease state analysis, clinical trial

overall_design:
1) Comparison of gene expression in asthmatics to healthy controls
2) Comparison of smokers to healthy controls
3) Comparison of change in gene expression in the fluticasone treated group to the change in the placebo treated group

first: Homer

last: Boushey

first: Gregory

last: Dolganov

first: Chris

last: Barker

first: Yee

middle: H

last: Yang

first: Samantha

last: Donnelly

first: Trang

last: Dao-Pick

first: David

last: Erle

first: John

middle: V

last: Fahy


title: Gene expression-based global role of CovR in GBS A909

status: Public on Oct 18 2007

city: Seattle

first: Lakshmi

last: Rajagopal

state: WA

address: 1900 9th Ave

department: Pediatric Infectious Disease

institute: Seattle Children's Hospital Research Institute

summary:
Global regulatory roles of the TCS response regulator CovR  in GBS serotype 1a A909
Keywords: Strain comparison; global regulation

overall_design: Deletion mutant was examined for alterations in gene expression

first: Wan-Jung

last: Lin

first: Kelsea

last: Jewell


title: Induction of DAN/TIR yeast cell wall mannoprotein genes in response to high hydrostatic pressure and low temperature

status: Public on Oct 05 2007

city: Yokosuka

first: Fumiyoshi

last: Abe

state: Kanagawa

address: 2-15 Natsushima-cho

department: Extremobiosphre Research Center

institute: Japan Agency for Marine-Earth Science and Technology

summary:
Global transcriptional profiles of Saccharomyces cerevisiae were studied following changes in growth conditions to high hydrostatic pressure and low temperature. These profiles were quantitatively very similar, encompassing 561 co-upregulated genes and 161 co-downregulated genes. In particular, expression of the DAN/TIR cell wall mannoprotein genes, which are generally expressed under hypoxia, were markedly upregulated by high pressure and low temperature, suggesting the overlapping regulatory networks of transcription. In support of the role of the mannoproteins in cell wall integrity, cells acquired resistance against treatment with SDS, Zymolyase and  lethal level of high pressure when preincubated under high pressure and low temperature.
Keywords: stress response

overall_design: Cells of strain BY4742 were grown until cell density of 1-2 × 10^7 cells/ml at 0.1 MPa and 24 °C had been reached with a volume of 50 ml in a 100-ml conical flask. Total RNA was prepared from the cells for the control sample using the hot phenol method. Cells were also incubated at 25 MPa and 24 °C or 0.1 MPa and 15 °C for 5 h, followed by total RNA preparation. To average accidental errors in total RNA preparation, equal amounts of total RNA purified from three independent cultures under each condition were mixed and the mixture was used for the experiments. Subsequent procedures including the isolation of poly A+-RNA, sample labeling and hybridization for DNA microarrays were performed by NimbleGen Systems Inc. (Madison, WI, USA) and GeneFrontier Inc. (Tokyo, Japan). Fifteen perfectly matching 60-mer probes for individual genes were used for hybridization. Because this analysis yields results with a high confidence level, a 1.5-fold difference between multiple samples generally corresponds to the level of significance (P < 0.05) obtained from hybridization signals from 15 perfectly matching probes for each gene.


title: HCMV virus produced in different cell types induces different transcriptional responses

status: Public on Nov 10 2007

city: Princeton

first: Eain

middle: Anthony

last: Murphy

address: Lewis Thomas Laboratories

department: Molecular Biology

institute: Princeton University

summary:
Human cytomegalovirus infects multiple cell types, including fi-
broblasts and epithelial cells. It penetrates fibroblasts by fusion at
the cell surface but is endocytosed into epithelial cells. In this
report, we demonstrate by electron microscopy that the virus uses
two different routes to enter retinal pigmented epithelial cells,
depending on the cell type in which the infecting virus was
produced. Virus produced in epithelial cells preferentially fuses
with the plasma membrane, whereas fibroblast-derived virus
mostly enters by receptor-mediated endocytosis. Treatment of
epithelial cells with agents that block endosome acidification
inhibited infection by virus produced in fibroblasts but had only a
modest effect on infection by virus from epithelial cells. Epithelial
cell-generated virions had higher intrinsic ‘‘fusion-from-without’’
activity than fibroblast-generated particles, and the two virus
preparations triggered different cellular signaling responses, as
evidenced by markedly different transcriptional profiles. We propose
that the cell type in which a human cytomegalovirus particle
is produced likely influences its subsequent spread and its contribution
to pathogenesis.
Keywords: cell type comparison, viral infection, cell tropism, viral entry

overall_design: A single strain of Human Cytomegalovirus (HCMV), termed BADrUL131, was used to prepare viral stocks from either fibroblast cells or from endothelial cells.  These viral preparations (fibroBADrUL131 and epiBADrUL131) were used to infect ARP-19 cells (Human retinal pigmented epithelial cells) for either 6 hours or 10 hours.  Total RNA was collected, labeled and used to hybridize to Agilent whole genome oligo microarrays and were normalized to a control reference RNA pool.

first: Dai

last: Wang

first: Qian-Chun

last: Yu

first: Jorg

last: Schroer

first: Thomas

last: Shenk


title: Identification of novel markers of beef sensory quality and muscle growth potential

status: Public on Aug 18 2007

city: Saint-Genès-Champanelle

first: Isabelle

last: CASSAR-MALEK

address: Theix

department: Centre de Clermont-Fd/Theix

institute: INRA

summary:
The transcriptome of bovine Longissimus thoracis muscles from 15- and 19-month-old Charolais young bulls were analyzed in order to identify genes whose expression level was associated to beef quality scores, in particular to tenderness, juiciness and flavor, and to muscle growth potential. The expression of over 5000 genes was compared between high and low meat quality samples according to the three sensory traits, taken individually, and between animals with either a high or a low muscle growth potential.
Keywords: meat sensory quality, growth potential

platform_organism:
Homo sapiens
Mus musculus

overall_design: Twenty-five samples were analyzed. Each sample was hybridized on 4 independent microarrays and compared to a reference pool.

first: Carine

last: Bernard

last: Cassar-Malek

first: Hervé

last: Dubroeucq

first: Gilles

last: Renand

first: Martine

last: LeCunff

first: Jean

last: Léger

first: Jean-François

last: Hocquette


title: Expression profiling of MMTV-PyMT tumors retrovirally over-expressing GATA-3

status: Public on Jul 06 2007

city: Indianapolis

first: Hosein

last: Kouros-Mehr

address: 533 Merrill St.

institute: Eli Lilly

summary:
The primary cause of mortality in breast cancer is metastasis, a process which is still poorly understood. To study the process of breast cancer metastasis, we isolated focal hyperplasias from the MMTV-PyMT transgenic breast cancer model and transplanted to syngeneic hosts. The transplants underwent stereotyped progression to adenoma, early carcinoma, and late carcinoma at 5, 8 and 18 weeks post-transplant, respectively. We compared the gene expression profiles of adenomas and late carcinomas by microarray. Analysis of the data revealed that the most differentially expressed gene family between adenomas and late carcinomas were luminal differentiation genes, among them GATA-3.
Adenomas were uniformly immunopositive for GATA-3, whereas early carcinomas displayed partial loss of GATA-3.  Disseminated tumour cells and 18-week late carcinomas were invariably GATA-3 negative.  We found that re-introduction of GATA-3 in late carcinomas induced markers of luminal differentiation and inhibited tumour dissemination to distant sites.
Keywords: spotted oligonucleotide

overall_design: Full length GATA-3 was cloned into the PMIG retroviral vector, which contains an IRES-GFP cassette.  Primary cultures of non-fluorescent MMTV-PyMT carcinomas were infected with the GATA-3 and control retroviruses and transplanted back into the cleared mammary fat pads of wild-type mice.  After six weeks of growths, tumors were isolated and total RNA harvested by the Trizol method.  Total RNA from GATA-3 infected tumor outgrowths were compared to empty vector infected tumor outgrowths.

first: Zena

last: Werb