title: Transcriptomics of environmental adaptation and survival in wild adult Pacific Sockeye Salmon (Oncorhynchus nerka) during spawning migration

status: Public on Jun 12 2011

city: Nanaimo

first: Tyler

middle: G

last: Evans

state: British Columbia

address: 3190 Hammond Bay Road

department: Pacific Biological Station

institute: Fisheries and Oceans Canada

summary: a salmonid microarray was used to characterize environmentally-regulated shifts in gene expression between ocean and river habitats in gill and liver tissues of wild migrating adult Pacific sockeye salmon (Oncorhynchus nerka). To correlate gene expression with survival, non-lethal biopsy sampling of gill tissue and microarray-based profiling was combined with biotelemetry and genetic stock identification so that transcriptomic profiles could be compared between fish reaching spawning grounds and presumed mortalities.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: Fish were captured fish at two marine sampling sites, one within Johnstone Strait (JS), BC. Canada and one within Juan De Fuca Strait (JDFS), BC Canada. Ocean sites were contrasted to fish sampled within the Fraser River at Whonnock (W), BC, Canada. Gill and liver tissues were dissected at each of these sites. Non-lethal biopsy sampling was performed on migrating sockeye salmon intercepted within the Fraser River at Mission, BC, Canada and genetically-based stock ID was used to determine the stock-specific spawning grounds for each fish, giving an intended end-point of migration for each of the stocks investigated in this study.Gene expression levels were determined by comparing the amount of mRNA transcript in the experimental samples relative to a reference sample. A total of 123 microarrays were used to generate the dataset, corresponding to individual hybridizations of both gill and liver samples collected from JS (gill n=14; liver n=15), JDFS (gill n=15; liver n=13), W (gill n=11; liver n=10), and biopsy sampled gill tissue collected at Mission (n=45).Total RNA was amplified (1 round) with MessageAmpTMII-96 kit (Ambion, TX, USA), and reverse transcribed to cDNA before labelling with ALEXA dyes using the Invitrogen Indirect Labelling Kit. The reference contained the combined aRNA of all individuals used in the experiment, excluding bioposy sampled fish. Individual samples were labelled with Alexa 555 and the reference control with Alexa 647, and no dye swaps were perfromed.


title: Genome-Wide Microarray Analysis of Gene Expression During Starvation in Tetrahymena thermophila

status: Public on Jun 13 2011

city: Ann Arbor

first: Yifan

last: Liu

state: MI

address: 500 S. State St

country: USA

institute: University of Michigan

summary: Four genome wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila used to study gene expression in starved cells (Starvation 0 hour and Starvation 9 hour, each two replicates). Combined these four microarrays with 50 microarrays described in Miao et al (2009, PMID: 19204800; GSE11300) and other 13 microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient, the Spearman correlation coefficient and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast, and the CLR network was found to be the best network, with a Z-score threshold 3.49. Then the TGN was partitioned, and 55 modules were found. In addition, analysis for the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and found evidence indicating that some of these were involved in the same process in Tetrahymena as in human.

overall_design: For starvation, CU427 cells were starved at 2x10^5 cells/ml in 10 mM Tris (pH 7.5) for 0 and 9 hours (referred to as S-0 and S-9, respectively).


city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

country: China

institute: Institute of hydrobiology, CAS

summary: Two genome-wide microarrays containing the predicted coding sequences (putative genes) for the ciliated protozoan Tetrahymena thermophila were used to study gene expression in starved cells (starvation 0 hour and starvation 24 hour). Combining these two microarrays with 50 microarrays described in Miao et al. (2009) and 15 other microarrays, we constructed the Tetrahymena gene network (TGN) using three methods: the Pearson correlation coefficient, the Spearman correlation coefficient and the context likelihood of relatedness (CLR) algorithm. The accuracy and coverage of the three networks were evaluated using four conserved protein complexes in yeast, and the CLR network was found to be the best network, with a Z-score threshold 3.49. Then the TGN was partitioned, and 55 modules were found. In addition, analysis for the arbitrarily determined 1200 hubs showed that these hubs could be sorted into six groups according to expression profiles. We also investigated human disease orthologs in Tetrahymena that are missing in yeast and found evidence indicating that some of these were involved in the same process in Tetrahymena as in human.

overall_design: For starvation, CU428 cells were starved at 2x10^5 cells/ml in 10 mM Tris (pH 7.5) for 0 and 24 hours (referred to as S-0 and S-24, respectively).


title: Chromosome segregation in Streptococcus pneumoniae

status: Public on Jun 11 2011

city: Groningen

first: Jan-Willem

last: Veening

address: Nijenborgh 7

country: Netherlands

institute: University of Groningen

type: Genome binding/occupancy profiling by array

summary: Segregation of replicated chromosomes during cell division is an essential process in all organisms. Chromosome segregation is promoted by the action of the DNA-binding ParB protein in the rod-shaped model bacterium Bacillus subtilis. How oval shaped bacteria, such as the human pathogen Streptococcus pneumoniae, efficiently segregate their chromosomes is poorly understood. Here, we show that the pneumococcal homolog of ParB is enriched at four centromere-like DNA sequences (parS sites) that are present near the origin of replication.

overall_design: Amplified ChIP DNA was fluorescently labelled using the BioPrime Total Genomic Labeling kit from Invitrogen. Eluate DNA was labelled with AlexA Fluor 3 and input DNA with Alexa Fluor 5. Labelled DNA was hybridized to a DNA-microarray containing amplicons of all open reading frames of S. pneumoniae (Kloosterman et al., 2006).

first: A

last: Minnen

first: S

last: Gruber

first: J

middle: W


title: Transcriptional profiles of anaerobically grown Typhimurium 14028 with and without hydrogen in CRHyd

city: Irvine

first: Michael

last: McClelland

state: CA

address: 132 Med Surge I

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

summary: Transcripts of 14028 grown to OD0.4 in anaerobic CRHyd medium subsequently supplemented with hydrogen to 20% for 15min, compared to those grown without hydrogen supplementation

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: Three biological replicates, dye swapped (i.e. 6 arrays)

first: Steffen

last: Porwollik

first: Reena

last: Lamichhane-Khadka

first: Jonathan

last: Frye

first: Robert

middle: J

last: Maier


title: Gene expression profiling of a pressure-tolerant Listeria monocytogenes Scott A ctsR deletion mutant

status: Public on Jun 10 2011

city: Wyndmoor

first: yanhong

state: PA

address: 600 E. Mermaid Lane

institute: ERRS-ARS-USDA

summary: Transcriptional profling of a Listeria monocytogenes under pressure comparing ctsR mutant and wild type

overall_design: one condition (pressure 450 Moa, 3min) experiment,  mutant vs. wild type, 2 biological replicates, two technical replicates

first: Yanhong


title: Transcriptional profiling of watermelon during its incompatible interaction with Fusarium oxysporum f. sp. Niveum

status: Public on Jun 09 2011

city: Beijing

first: Yong

last: Xu

address: ShuGuang Garden Middle Road 9,Haidian district

institute: National Engineering Research Center for Vegetables

summary: Watermelon (Citrullus lanatus) is one of the most important vegetable crops in the world and accounts for 20% of the world’s total area devoted to vegetable production. Fusarium wilt of watermelon is one of the most destructive diseases in watermelon worldwide. Transcriptome profiling of watermelon during its incompatible interactions with Fusarium oxysporum f.sp. niveum (FON) was generated using an Agilent custom microarray which contains 15,000 probes representing approximately 8,200 watermelon genes. A total of 24, 275, 596, 598, and 592 genes that are differentially expressed genes between FON- and mock-inoculated watermelon roots at 0.5, 1, 3, 5 and 8 days post inoculation (dpi), respectively, were identified.  Bioinformatics analysis of these differentially expressed genes revealed that during the incompatible interaction between watermelon and FON, the expression of a number of pathogenesis-related (PR) genes, transcription factors, signaling/regulatory genes, and cell wall modification genes, was significantly induced. A number of genes for transporter proteins such as aquaporins were down-regulated, indicating that transporter proteins might contribute to the development of wilt symptoms after FON infection. In the incompatible interaction, most genes involved in biosynthesis of jasmonic acid (JA) showed expressed stronger and more sustained than those in compatible interaction in FON-infected tissues. Similarly, genes associated with shikimate-phenylpropanoid-lignin biosynthesis were also induced in incompatible interaction, but expression of these genes were not changed or repressed in the compatible interaction.

overall_design: Fusarium oxysporum f.sp. niveum induced gene expression in watermelon root was measured at 0.5,1d, 3d, 5d and 8d after inoculation. Sample inoculated with water were used as the mock controls. Three independent experiments were performed.

first: Guiyun

last: Lü

first: Shaogui

last: Guo

first: Zhangjun

last: Fei

first: Haiying

last: Zhang


title: GENE EXPRESSION PROFILING AND MOLECULAR CHARACTERIZATION OF ANTIMONY RESISTANCE IN Leishmania amazonensis

city: Quebec City

first: Frederic

last: Raymond

state: Quebec

address: 2440 Bd Hochelaga Suite 1710

department: École de nutrition

country: Canada

institute: Université Laval

summary: Background: Drug resistance is a major problem in leishmaniasis chemotherapy. RNA expression profiling using DNA microarrays is a suitable approach to study simultaneous events leading to a drug-resistance phenotype. Genomic analysis has been performed primarily with Old World Leishmania species and here we investigate molecular alterations in antimony resistance in the New World species L. amazonensis.  Methods/Principal Findings: We selected populations of L. amazonensis for resistance to antimony by step-wise drug pressure. Gene expression of highly resistant mutants was studied using DNA microarrays. RNA expression profiling of antimony-resistant L. amazonensis revealed the overexpression of genes involved in drug resistance including the ABC transporter MRPA and several genes related to thiol metabolism. The MRPA overexpression was validated by quantitative real-time PCR and further analysis revealed that this increased expression was correlated to gene amplification as part of extrachromosomal linear amplicons in some mutants and as part of supernumerary chromosomes in other mutants. The expression of several other genes encoding hypothetical proteins but also nucleobase and glucose transporter encoding genes were found to be modulated.   Conclusions/Significance: Mechanisms classically found in Old World antimony resistant Leishmania were also highlighted in New World antimony-resistant L. amazonensis. These studies were useful to the identification of resistance molecular markers.

overall_design: Three condition experiment. Wild-type (WT) Leishmania amazonensis compared to antimony resistant mutants Sb 2700.2 and Sb 2700.3. Four biological replicates of Wt and three biological replicates of each mutant.

first: Rubens

middle: L

last: do Monte Neto

first: Adriano

middle: C

last: Coelho

first: Frédéric

first: Danielle

last: Légaré

first: Jacques

last: Corbeil

first: Maria

middle: N

last: Melo

last: Frézard

first: Marc

last: Ouellette


title: Full genome qRT PCR of Staphylococcus aureus strains USA300 and TB15 during infection of 5 organs

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

summary: We used high-throughput qRT-PCR analysis to obtain full genome qRT- PCR data for the Staphylococcus aureus strains USA300 (wild type) and TB15 (mutant). Both strains were collected  during infection from 4 mouse organs ( skin, kidney, lung,liver) as well as from human neutrophil infection.

overall_design: One sample per strain per organ was used in the analysis. Each sample was tested in duplicates for each primer pair on the same PCR plate. We intended to compare gene expressions of  USA300 (wild type) and TB15 (mutant) strains in each organ separately

first: Marcus

last: Jones

first: Tatiana

last: Dracheva

first: Taeok

last: Bae

first: Qiang

last: Sun


title: microRNA expression levels in human primary fibroblasts

city: NEW-YORK

first: christelle

last: borel

state: NY

address: 14250 madison avenue

department: genetics and genomic sciences

institute: mount sinai school of medicine

summary: MicroRNAs (miRNAs) are regulatory non-coding RNAs that affect the production of a significant fraction of human mRNAs via post-transcriptional regulation. Inter-individual variation of miRNA expression levels is likely to influence the expression of miRNA target genes, and may therefore contribute to phenotypic differences in humans, including susceptibility to common disorders. The extent to which miRNA levels are genetically controlled is largely unknown. In this report, we assayed the expression levels of miRNAs in primary fibroblasts from 180 European newborns of the GenCord project, and performed association analysis to identify eQTLs (expression quantitative traits loci). We detected robust expression for 121 miRNAs out of 365 interrogated. We have identified significant cis- (10%) and trans- (11%) eQTLs. Furthermore, we detected one genomic locus (rs1522653) that influences the expression levels of five miRNAs, thus unraveling a novel mechanism for co-regulation of miRNA expression.

overall_design: Primary fibroblasts were derived from the umbilical cord of 180 newborns of Western European origin recruited for the GenCord project. Mature miRNA expression phenotypes were generated using the micro-fluidics-based TaqMan® Human MiRNA Array v1.0 (Applied Biosystems). For each sample, expression levels for 365 known human mature miRNAs were assayed .

first: Christelle

last: Borel

first: Stylianos

middle: E

last: Antonarakis


title: Functional and Transcriptomic Recovery of Infarcted Mouse Myocardium Treated with Bone Marrow Mononuclear Cells

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary:
Although bone marrow-derived mononuclear cells (BMNC) have been extensively used in cell therapy for cardiac diseases, little mechanistic information is available to support reports of their efficacy. To address this shortcoming, we compared structural and functional recovery and associated global gene expression profiles in post-ischaemic myocardium treated with BMNC transplantation. BMNC suspensions were injected into cardiac scar tissue 10 days after experimental myocardial infarction. Six weeks later, mice undergoing BMNC therapy were found to have normalized antibody repertoire and improved cardiac performance measured by ECG, treadmill exercise time and echocardiography. After functional testing, gene expression
profiles in cardiac tissue were evaluated using high-density
oligonucleotide arrays. Expression of more than 18% of the 11981 quantified unigenes was significantly altered in the infarcted hearts. BMNC therapy restored expression of 2099 (96.2%) of the genes that were altered by infarction but led to altered expression of 286 other genes, considered to be a side effect of the treatment. Transcriptional therapeutic efficacy, a metric calculated using a formula that incorporates both recovery and side effect of treatment, was 73%. In conclusion, our results confirm a beneficial role for bone marrow-derived cell therapy and provide new information on molecular mechanisms operating after BMNC transplantation on post ischemic heart failure in mice.

overall_design: We compared RNA samples extracted from whole hearts of infarcted mouse myocardium treated with bone marrow mononuclear cells control with untreated infarcted and control mice samples by analyzing hybridization to AECOM 32k mouse microarrays (http://microarray1k.aecom.yu.edu/) spotted with Operon version 3.0 70-mer oligonucleotides. The hybridization protocol and the slide type were uniform throughout the entire experiment to minimize the technical noise. Treated, control (sham) and infarcted red-labeled heart samples were hybridized against an in-house prepared green-labeled universal mouse reference.

first: Stephan

last: Lachtermacher

first: Bruno

last: Esporcatte

first: Fábio

middle: S

last: Fortes

first: Nazareth

last: Rocha

first: Fabrício

last: Montalvão

first: Patricia

last: Costa

first: Luciano

last: Belem

first: Arnaldo

last: Rabischoffisky

first: Hugo

last: Neto

first: Rita

last: Vasconcellos

middle: A

first: Sanda

first: David

last: Spray

first: Neil

middle: M

last: Thomas

first: Regina

last: Goldenberg

first: Antonio

last: Carvalho


title: qRT-PCR on Francisella tularensis LVS and ShuS4 strain during macrophage infection

status: Public on Jun 08 2011

first: John

last: Braisted

summary: Francisella tularensis is one of three bacterial species designated as a Category A select agent by the Centre for Disease Control (CDC), a category indicating agents most likely to be employed as a biological weapon. F. tularensis can be divided into four different subspecies, and it is well known that the type, severity and duration of the disease can differ substantially depending on what subspecies is responsible for the infection. Of the four subspecies, subsp. tularensis (Type A) and subsp. holartica (Type B) are of primary clinical significance, and account for nearly all recorded incidences of the disease in humans. Though Type A is considered to be more virulent than Type B, recent reports have shown that Type A can be further sub-divided into two genetically distinct populations, termed A.I and A.II, which differ with respect to geographical location, disease outcome and source of recovered isolates. Of these two subpopulations, clinical data suggests that Type A.I strains are significantly more virulent than Type A.II, and Type A.II strains appear to have a disease outcome similar to infections with Type B. During natural infections, host mononuclear phagocytes appear to be the primary target of all F. tularensis subsp. Despite the differences in disease outcome between different subspecies, the mechanisms involved in phagosomal escape, the modulation of phagosomal biogenesis, phagosomal disruption and bacterial egress appears to be indistinguishable between subspecies, at least at a physiological level. In collaboration with Dr. Patrick McGann at Walter Reed Army Institute of Research (WRAIR) we have been studying the differential gene expression of F. tularensis during macrophage infection. Dr. McGann provided the PFGRC with RNA samples from F. tularensis strains LVS and Shuh4 isolated from infected macrophages. Samples were interrogated using high throughput qRT-PCR using 1,067 primer pairs.

overall_design: The study was a timecourse with 2 strains :LVS and Schu S4 and 4 time points: 0hours, 2hours, 4hours and 8hours. Samples were interrogated using high throughput qRT-PCR using 1,067 primer pairs designed from both strains. 0hours timepoints were done in duplicates, other time points in quadruplicates. Replicates were averages and then quantile normalized for each strain.

first: Patrick

last: Mc Gann

first: Marcus

last: Jones

first: Tatiana

last: Dracheva


title: Alteration of microRNA expression during mouse brain growing

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

country: Japan

institute: National Institute of Neuroscience, NCNP

summary: We investigated expression profiles of miRNAs in the process of normal mouse brain growing from embryonic day 16.5 to one year old by means of DNA microarray. The results indicated that a major change in the expression of miRNAs occurred in the brain within the first week to the fourth week postnatally. The data also exhibited miRNAs which gradually increased and not decreased in their levels over the course of brain growing.

overall_design: Thirty-eight samples prepared from various aged mice were analyzed. Experiments were duplicated.

first: Akiko

last: Eda

first: Tatsunobu

last: Fukushima


title: Protein Interactome Reveals Converging Molecular Pathways Among Autism Disorders

city: Houston

first: Chad

middle: A.

last: Shaw

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

summary: We performed aCGH analysis using a custom Agilent oligonucleotide array to analyze 288 probands with idiopathic autism spectrum disorder (ASD) from the Simons Simplex Collection (SSC) of autism samples. The array is customized to high resolution coverage of exons for genes identified as encoding proteins included in a detailed protein interaction network for autism.

overall_design: aCGH analysis of 288 idiopathic autism samples. Controls are sex-matched commercial control DNAs from Promega (Madison, WI).

first: Yasunari

last: Sakai

first: Brian

last: Dawson

first: Diana

middle: V

last: Dugas

first: Zaina

last: Al-Mohtaseb

last: Hill

first: Huda

middle: Y

last: Zoghbi


title: Queen conch (Strombus gigas) digestive gland gene expression in the Florida Keys: offshore versus nearshore

status: Public on Jun 07 2011

city: Providence

first: Daniel

middle: James

last: Spade

state: RI

address: Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

summary: Reproduction of queen conchs at nearshore sites in the Florida Keys is known to be impaired (Delgado et al. 2004). A recent microarray study of male queen conchs collected from the Florida Keys during the early part of the reproductive season (February, 2007) indicated that NS conchs show differences in expression of spermatogenesis-related and small GTPase signaling transcripts (Spade et al. 2010). The current study investigates gene expression in the digestive gland, which is closely associated with ovary, of female queen conchs from the same sampling effort in February, 2007.

overall_design: One-color (Cy3) oligonucleotide array experiment. Each array sample is an individual biological replicate. The study includes four biological replicates offshore and three biological and one technical replicate nearshore. Offshore conchs exhibit normal reproduction, and so were considered the reference group in the analysis.

first: Robert

last: Glazer

first: Nancy

middle: D

last: Denslow


title: Bovine spongiform encephalopathy infection alters endogenous retrovirus expression in distinct brain regions of cynomolgus macaques (Macaca fascicularis)

city: Neuherberg

first: Michelle

last: Vincendeau

address: Ingolstädter Landstr. 1

country: Germany

institute: Helmholtz Zentrum München

summary:
Background: Prion diseases such as bovine spongiform encephalopathies (BSE) are
transmissible neurodegenerative diseases which are presumably caused by an infectious conformational isoform of the cellular prion protein. Previous work has provided evidence that in murine prion disease the endogenous retrovirus (ERV) expression is altered in the brain. To determine if prion-induced changes in ERV expression are a general phenomenon we used a non-human primate model for prion disease.
Results: Cynomolgus macaques (Macaca fasicularis) were infected intracerebrally with BSE-positive brain stem material from cattle and allowed to develop prion disease. Brain tissue from the basis pontis and vermis cerebelli of the six animals and the same regions from four healthy controls were subjected to ERV expression profiling using a retrovirus-specific microarray and quantitative real-time PCR. We could show that Class I gammaretroviruses HERV-E4-1, ERV-9, and MacERV-4 increase expression in BSE-infected macaques. In a second approach, we analysed ERV-K-(HML-2) RNA and protein expression in extracts from the same cynomolgus macaques. Here we found a significant downregulation of both, the macaque ERV-K-(HML-2) Gag protein and RNA in the frontal/parietal cortex of BSE-infected macaques.
Conclusions: We provide evidence that dysregulation of ERVs in response to BSE-infection can be detected on both, the RNA and the protein level. To our knowledge, this is the first report on the differential expression of ERV-derived structural proteins in prion disorders. Our findings suggest that endogenous retroviruses may induce or exacerbate the pathological consequences of prion-associated neurodegeneration.

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Cynomolgus macaques (Macaca fasicularis) were infected intracerebrally with BSE-positive brain stem material from cattle and allowed to develop prion disease. Brain tissue from the basis pontis and vermis cerebelli of the six animals and the same regions from four healthy controls were subjected to ERV expression profiling using a retrovirus-specific microarray and quantitative real-time PCR. In a second approach, ERV-K-(HML-2) RNA and protein expression was analysed in extracts from the same cynomolgus macaques.

first: Alex

last: Greenwood

first: Ann-Christin

last: Schmädicke

first: Judith

last: Montag

first: Wolfgang

last: Seifarth

first: Dirk

last: Motzkus


title: MicorRNA expression in klotho-deficient and wild-type mouse brain subregions

first: Hirohiko

last: Hohjoh

summary: The expression profiles of miRNAs in klotho-deficient and wild-type mouse brain subregions were examined. The data indicated that little or no marked difference in the miRNA expression was detected between them.

overall_design: Twelve samples prevared from 4- or 5-week-old klotho-deficient and wild-type mouse brain tissues (cerebrum, cerebellum and hippocampus) were examined.

first: Akiko

last: Eda

last: Fukushima


title: Sex-specific expression during asexual development of Neurospora crassa under constant light condition

status: Public on Jun 06 2011

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: It is widely assumed that sex-determination loci have little impact upon dominant stage in the life history of filamentous fungi, asexual development. However, this hypothesis has not been thoroughly investigated. To investigate differences between mating types during asexual development, total RNA was sampled from otherwise largely isogenic Mat-A and Mat-a N. crassa strains at early, middle, and late clonal stages of development under a condition of constant light. Mating-type loci, pheromone precursor and receptor genes were assayed with real-time PCR. Mating loci were increasingly expressed during asexual development, and expression of pheromone precursors ccg-4 and mfa-1 and receptors pre-1 and pre-2 were detected in both mating types in all development stages. A circuit of microarray hybridizations of cDNA samples from all developmental stages was also performed. Gene expression for both mating types throughout vegetative development were characterized for developmental markers such as transcription factors, for genes related to conidiation, internal clock, cell division cycle, heat shock, and for light responsive genes. We observed significant differences in overall gene expression between the mating types across clonal development, especially at late development stages. The Mat-A genotype showed a higher expression level than Mat-a for many genes, and demonstrated greater transcriptional regulatory activity. Significant up-regulation of expression was observed for many late light responsive genes at late asexual development stages in both mating types. Further investigation of the impact of light and the roles of light response genes in asexual development in this fungus are warranted.

overall_design: Neurospora crassa mat A FGSC#2489 and mat-a FGSC 4200: Three developmental stages, 36hr, 60hr, 96 hr were sampled and compared

first: Jeffrey

middle: P

last: Townsend


title: Queen conch (Strombus gigas) ovarian gene expression in the Florida Keys: offshore versus nearshore

summary: Reproduction of queen conchs at nearshore sites in the Florida Keys is known to be impaired (Delgado et al. 2004). A recent microarray study of male queen conchs collected from the Florida Keys during the early part of the reproductive season (February, 2007) indicated that NS conchs show differences in expression of spermatogenesis-related and small GTPase signaling transcripts (Spade et al. 2010). The current study investigates gene expression in the ovary of female queen conchs from the same sampling effort in February, 2007.

overall_design: One-color (Cy3) oligonucleotide array experiment. Each array sample is an individual biological replicate. The study includes four biological replicates offshore and three biological replicate nearshore. Offshore conchs exhibit normal reproduction, and so were considered the reference group in the analysis.


title: FGF-dependent regulation of VEGF signaling via transcriptional control of VEGF receptor 2 expression

city: New Haven

first: Masahiro

last: Murakami

address: 300 George St. Rm 759

department: Internal Medicine

institute: Yale University School of Medicine

summary: Numerous studies have suggested a link between fibroblast growth factor (FGF) and vascular endothelial growth factor (VEGF) signaling pathways; however the nature of this link has not been established. To evaluate this relationship we investigated VEGF signaling in endothelial cells with disrupted FGF signaling in vitro and in vivo. We find that endothelial cells lacking FGF signaling become unresponsive to VEGF due to down regulation of VEGFR2 expression caused by reduced Vegfr2 enhancer activation, which is in turn caused by reduced activation of Ets family transcription factors. In vivo this manifests in the loss of vascular integrity and morphogenesis. Thus, basal FGF stimulation of the endothelium is required for maintenance of VEGFR2 expression and the ability to respond to VEGF stimulation and accounts for the hierarchic control of vascular formation by FGFs and VEGF.

overall_design: Primary mouse lung endothelial cells were transduced with either Adeno-Null (empty) or Adeno- dominant negative FGF receptor 1 and harvested 24 hours after transduction. Total RNA was extracted and subjected to the analysis using SuperArray GEArray Q Series Mouse Angiogenesis Gene Array.  Comparisons were made between treatments.

first: Loc

middle: T

last: Nguyen

first: Kunihiko

last: Hatanaka

first: William

last: Schachterle

first: Pei-Yu

last: Chen

first: Zhen

last: Zhuang

first: Brian

last: Black

first: Michael

last: Simons


title: MicroRNA sequence and expression analysis in breast tumors by deep sequencing [mRNA expression array data]

city: New York

first: Thalia

last: Farazi

address: 1230 York Ave, BOX 186

department: Lab of RNA Molecular Biology

institute: Rockefeller University

summary: MicroRNAs (miRNAs) regulate many genes critical for tumorigenesis. We profiled miRNAs from 11 normal breast tissues, 17 non-invasive, 151 invasive breast carcinomas, and 6 cell lines by in-house-developed barcoded Solexa sequencing. miRNAs were organized in genomic clusters representing promoter-controlled miRNA expression and sequence families representing seed-sequence-dependent miRNA-target regulation. Unsupervised clustering of samples by miRNA sequence families best reflected the clustering based on mRNA expression available for this sample set. Clustering and comparative analysis of miRNA read frequencies showed that normal breast samples were separated from most non-invasive ductal carcinoma in situ and invasive carcinomas by increased miR-21 (the most abundant miRNA in carcinomas) and multiple decreased miRNA families (including mir-98/let-7), with most miRNA changes apparent already in the non-invasive carcinomas. In addition, patients that went on to develop metastasis demonstrated increased expression of mir-423, and triple negative breast carcinomas were most distinct from other tumor subtypes due to up-regulation of the mir-17~92 cluster. However, absolute miRNA levels between normal breast and carcinomas did not reveal any significant differences. We also discovered two polymorphic nucleotide variations among the more abundant miRNAs miR-181a (T19G) and miR-185 (T16G), but we did not identify nucleotide variations expected for classical tumor suppressor function associated with miRNAs. The differentiation of tumor subtypes and prediction of metastasis based on miRNA levels is statistically possible, but is not driven by deregulation of abundant miRNAs, implicating far fewer miRNAs in tumorigenic processes than previously suggested.

overall_design: mRNA profiles for 161 normal breast and invasive breast carcinomas using NKI Operon V3 arrays; These samples have matched entries for miRNA profiles also included in this GEO submission.

first: Hugo

last: Horlings

first: Jelle

last: ten Hoeve

first: Aleksandra

last: Mihailovic

first: Hans

last: Halfwerk

first: Pavel

last: Morozov

first: Miguel

last: Brown

first: Markus

last: Hafner

first: Fabien

last: Reyal

first: Marieke

last: van Kouwenhove

first: Bas

last: Kreike

first: Daoud

last: Sie

first: Volker

last: Hovestadt

first: Lodewyk

last: Wessels

first: Marc

last: van de Vijver

first: Thomas

last: Tuschl


title: Quantitative time-course profiling of Plasmodium falciparum transcripts and proteins throughout the 48-hour intraerythrocytic developmental cycle

city: Singapore

first: Bernardo

last: Foth

email: bfoth@gmx.net, ZBozdech@ntu.edu.sg

address: 60 Nanyang Drive

department: SBS

country: Singapore

institute: Nanyang Technological University

summary:
Quantitative studies of the P. falciparum transcriptome have shown that the tightly controlled progression of the parasite through the intraerythrocytic developmental cycle (IDC) is accompanied by a continuous gene expression cascade where most expressed genes exhibit a single transcriptional peak. Since proteins represent the decisive business end of gene expression, understanding the correlation between mRNA and protein levels is crucial for inferring biological activity from transcriptional gene expression data. While pertinent studies on other organisms show that as little as 20-40% of protein abundance variation may be attributable to corresponding mRNA levels, the situation in Plasmodium is further complicated by the dynamic nature of the cyclic gene expression cascade where the mRNA levels of most genes change constantly during the IDC.
In this study, we simultaneously determined mRNA and protein abundance profiles for P. falciparum parasites during the IDC at 2-hour resolution based on spotted oligonucleotide microarrays and 2D-protein gels in combination with DIGE fluorescent dyes. Intriguingly, most proteins are represented by more than one isoform, presumably due to post-translational modifications. Analysis of 366 protein abundance profiles and the corresponding mRNA levels shows that in 67.2% of cases the protein abundance peaks at least 8 hours after the mRNA level peak. While it may be tempting to interpret this as evidence for widespread post-transcriptional gene regulation additional analyses including computer modeling demonstrate that in >60% of these cases the observed protein profiles including the peak lag times could arise as a consequence of the corresponding mRNA levels when simple translation and degradation dynamics are assumed. We further characterize and illustrate these dynamics and show that even human host proteins within the parasite may be subject to similar dynamics as their parasite counterparts.

overall_design: 24 timepoint samples were harvested from a tightly synchronous 6.5 liter biofermenter culture of P. falciparum (Dd2) at 2-hour intervals during one entire intraerythrocytic developmental cycle and compared against a 3D7 RNA reference pool.

first: Neng

last: Zhang

first: Balbir

last: Chaal

first: Siu

middle: K

last: Sze

first: Peter

middle: R

last: Preiser

first: Zbynek

last: Bozdech


title: Mytilus galloprovincialis: development of female gonads

city: Alessandria

first: Francesco

last: Dondero

address: Via Michel 11

department: Department of Environmental and Life Sciences

country: Italy

institute: University of Piemonte Orientale "Amedeo Avogadro"

summary:
Transcriptional profiling of the mantle tissue across the four stages of female gonads development (winter peak) in a natural population of the marine mussel Mytilus galloprovincialis sampled in the Bizerta Lagoon, Tunisia, across November 2007 -March 2008.

Background: Seasonal environmental changes may affect the physiology of Mytilus galloprovincialis (Lam.), an intertidal filter-feeder bivalve occurring commonly in Mediterranean and Atlantic coastal areas. We investigated seasonal variations in relative transcript abundance of the digestive gland and the mantle (gonads) of males and females. To identify gene expression trends, we used a medium-density cDNA microarray (1.7 K probes) in dual-color competitive hybridization analyses.
Results: Hierarchical clustering of digestive gland microarray data showed two main branches, distinguishing profiles associated with the “hot” months (May–August) from the other months. Genes involved in chitin metabolism, associated with mussel nutrition and digestion, showed higher expression during summer. Moreover, we found different gene expression patterns in the digestive glands of males and females during the four stages of mussel gonadal development. Microarray data from gonadal transcripts also displayed clear patterns during the different developmental phases with peak relative mRNA abundance at the ripe phase (stage III) for both sexes.
Conclusion: These data showed a clear temporal pattern in gene expression profiles of mussels sampled over an annual cycle. Physiological response to thermal variation, food availability, and reproductive status across months may contribute to variation in gene expression.

overall_design: Mantle tissue from individual animals in different gonad maturation stages were analyzed in a complete loop design. Dual color competitive hybridizations (stage 4 vs stage 1, 2 vs 1, 3 vs 2, 4 vs 3) including label swap. Single individuals. Four biological replicates. One replicate per array.

first: Mohamed

last: Banni

first: Aldo

last: Viarengo


title: Mussel (Mytilus galloprovincialis) digestive gland tissue: gene expression profiles across an annual cycle

summary:
Transcriptional profiling of natural population of mussels (Mytilus galloprovincialis) -digestive gland tissue- comparing female individuals sampled in the Bizerta Lagoon, Tunisia, across May 2007 - April 2008.

Background: Seasonal environmental changes may affect the physiology of Mytilus galloprovincialis (Lam.), an intertidal filter-feeder bivalve occurring commonly in Mediterranean and Atlantic coastal areas. We investigated seasonal variations in relative transcript abundance of the digestive gland and the mantle (gonads) of males and females. To identify gene expression trends, we used a medium-density cDNA microarray (1.7 K probes) in dual-color competitive hybridization analyses.
Results: Hierarchical clustering of digestive gland microarray data showed two main branches, distinguishing profiles associated with the “hot” months (May–August) from the other months. Genes involved in chitin metabolism, associated with mussel nutrition and digestion, showed higher expression during summer. Moreover, we found different gene expression patterns in the digestive glands of males and females during the four stages of mussel gonadal development. Microarray data from gonadal transcripts also displayed clear patterns during the different developmental phases with peak relative mRNA abundance at the ripe phase (stage III) for both sexes.
Conclusion: These data showed a clear temporal pattern in gene expression profiles of mussels sampled over an annual cycle. Physiological response to thermal variation, food availability, and reproductive status across months may contribute to variation in gene expression.

overall_design: Loop design: Female individuals from 12 different months across one year (May 2007 to April 2008). Dual color competitive hybridizations (month n vs month n+1) including dye swap. Single individuals. Three (May 2007 to December 2007) or four biological replicates (January 2008 to April 2008 ). One replicate per array.


title: Mytilus galloprovincialis: development of male gonads

summary:
Transcriptional profiling of the mantle tissue across the four stages of male gonads development (winter peak) in a natural population of the marine mussel Mytilus galloprovincialis sampled in the Bizerta Lagoon, Tunisia, across November 2007 -March 2008.

Background: Seasonal environmental changes may affect the physiology of Mytilus galloprovincialis (Lam.), an intertidal filter-feeder bivalve occurring commonly in Mediterranean and Atlantic coastal areas. We investigated seasonal variations in relative transcript abundance of the digestive gland and the mantle (gonads) of males and females. To identify gene expression trends, we used a medium-density cDNA microarray (1.7 K probes) in dual-color competitive hybridization analyses.
Results: Hierarchical clustering of digestive gland microarray data showed two main branches, distinguishing profiles associated with the “hot” months (May–August) from the other months. Genes involved in chitin metabolism, associated with mussel nutrition and digestion, showed higher expression during summer. Moreover, we found different gene expression patterns in the digestive glands of males and females during the four stages of mussel gonadal development. Microarray data from gonadal transcripts also displayed clear patterns during the different developmental phases with peak relative mRNA abundance at the ripe phase (stage III) for both sexes.
Conclusion: These data showed a clear temporal pattern in gene expression profiles of mussels sampled over an annual cycle. Physiological response to thermal variation, food availability, and reproductive status across months may contribute to variation in gene expression.


title: Similar effects of an NO challenge and an lpdA knockout on transcription of Salmonella enterica sv Typhimurium 14028

status: Public on Jun 04 2011

first: Michael

last: McClelland

summary: Transcriptional profiling of Salmonella enterica sv Typhimurium under NO stress and comparison of profiles between wild type and lpdA mutant cultures. We investigated the bacteriostatic nature of NO·. S. Typhmurium 14028s is prototrophic for all amino acids but cannot synthesize Methionine or Lysine during nitrosative stress. This MK auxotrophy results from reduced availability of succinyl-CoA, a consequence of NO· targeting lipoamide-dependent LpdA activity. LpdA is an essential component of the pyruvate and α-ketoglutarate dehydrogenase complexes. Additional effects of NO· on gene regulation prevent compensatory pathways of succinyl-CoA production. By microarray analysis, more than 50% of the transcriptional response of S. Typhimurium to nitrosative stress is attributable to LpdA inhibition.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Two separate two-condition experiment: NO treated versus untreated, wild type versus lpdA mutant. Three biological replicates. Dye swaps performed on two of these.

first: Steffen

last: Porwollik

first: Stephen

middle: J

last: Libby

first: Vinai

last: Thomas

first: Ferric

last: Fang


title: Mytilus galloprovincialis: differences between male and female gene expression patterns in the digestive gland tissue

summary:
Direct comparison of the transcriptional patterns between male and female in the digestive gland of a natural population of the marine mussel Mytilus galloprovincialis sampled in the Bizerta Lagoon, Tunisia, across November 2007 -February March 2008 (four stages, winter peak).
Background: Seasonal environmental changes may affect the physiology of Mytilus galloprovincialis (Lam.), an intertidal filter-feeder bivalve occurring commonly in Mediterranean and Atlantic coastal areas. We investigated seasonal variations in relative transcript abundance of the digestive gland and the Digestive gland (gonads) of males and females. To identify gene expression trends, we used a medium-density cDNA microarray (1.7 K probes) in dual-color competitive hybridization analyses.
Results: Hierarchical clustering of digestive gland microarray data showed two main branches, distinguishing profiles associated with the “hot” months (May–August) from the other months. Genes involved in chitin metabolism, associated with mussel nutrition and digestion, showed higher expression during summer. Moreover, we found different gene expression patterns in the digestive glands of males and females during the four stages of mussel gonadal development. Microarray data from gonadal transcripts also displayed clear patterns during the different developmental phases with peak relative mRNA abundance at the ripe phase (stage III) for both sexes.
Conclusion: These data showed a clear temporal pattern in gene expression profiles of mussels sampled over an annual cycle. Physiological response to thermal variation, food availability, and reproductive status across months may contribute to variation in gene expression.

overall_design: Test/reference design (female/male). Direct comparison of RNA extracts obtained from the Digestive gland tissue of female and male animals. Two (male, female) x four conditions (gonad developmental stage 1, stage 2, stage 3, stage 4). Dual color competitive hybridizations with label swap.  Single individuals. Four biological replicates. One replicate per array.


title: Expression analysis of rat testis at early development stage

status: Public on Jun 02 2011

city: Hohhot

first: taodi

last: liu

address: xinhua street

institute: Inner Mongolia Medical College

summary: Investigation of whole genome gene expression level changes in rat testes on the postnatal day 6, 8 and 10 to compare the differentially expressed genes between them.

overall_design: A three chip study using total RNA recovered from the testes of rat postnatal day 6, 8 and 10. There are 135,000 probes in a chip,each chip measures the expression level of 26419 genes of rat from Nimblegen. Fold-change screening between the two groups obtained from the experiment. The threshold used to screen up or down regulated genes is Fold change＞＝2.0

first: Taodi

last: Liu

first: Yingji

last: Wu


title: Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon [gene expression data]

status: Public on Jun 03 2011

city: Durham

first: Amy

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

summary:
Because iron toxicity and deficiency are equally life threatening, maintaining intracellular iron levels within a narrow optimal range is critical for nearly all known organisms. However, regulatory mechanisms that establish homeostasis are not well understood in organisms that dwell in environments at the extremes of pH, temperature, and salinity. Under conditions of limited iron, the extremophile Halobacterium salinarum, a salt-loving archaeon, mounts a specific response to scavenge iron for growth.  We have identified and characterized the role of two transcription factors (TFs), Idr1 and Idr2, in regulating this important response. An integrated systems analysis of TF knockout gene expression profiles and genome-wide binding locations in the presence and absence of iron has revealed that these TFs operate collaboratively to maintain iron homeostasis.  In the presence of iron, Idr1 and Idr2 bind near each other at 24 loci in the genome, where they are both required to repress some genes. In contrast, Idr1 and Idr2 are both necessary to activate other genes in a putative a feed forward loop. Even at loci bound independently, the two TFs target different genes with similar functions in iron homeostasis.  We discuss conserved and unique features of the Idr1-Idr2 system in the context of similar systems in organisms from other domains of life.
Data in this GEO archive are linked to the publication: Schmid AK, Pan M, Sharma K, Baliga NS.2011. Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon.Nucleic Acids Res.39(7):2519-33.

overall_design:
The Δura3 parent, Δidr2 and Δidr1, and Δ idr1Δidr2 mutant strains were grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CDM with all trace metals except iron. Cultures were split in half and FeSO4 was added to one half, while the other was continued under iron limitation. 8-mL samples were collected from each culture every 20 minutes for 60 minutes (see also experimental design, Supplementary Figure 1, Schmid et al., 2011). RNA from two biological replicate time courses were prepared, averages of these replicates are reported in the published study, whereas data from each replicate are reported here. The zero time point was harvested immediately before the addition of iron.
Each Sample is based on two arrrays (one with dye-swap).

first: Min

last: Pan

first: Kriti

last: Sharma

first: Nitin

last: Baliga


title: Postia placenta MAD-698 gene expression in ball-milled aspen or ball-milled pine medium

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

summary: Transcript profiles of Postia placenta grown on media containing ball-milled aspen or ball-milled pine as the sole carbon source were analyzed. Array design was based on the DoE's Joint Genome Institute's gene models for P. placenta version 1. The research goal is to identtify genes essential for cellulose depolymerization.

overall_design: From a data set of 12,438 unique alleles, each NimbleGen (Madison, WI) array featured 10 unique 60mers per gene, all in triplicate. The dataset was manually annotated to include only the ‘best allelic model’ among CAZY-encoding genes.  Total RNA was purified from medium containing ball-milled aspen or ball-milled pine as the sole carbon source. Three biological replicates per medium were used (6 separate arrays). RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the Postia placenta MAD-698 whole genome expression array by Roche NimbleGen (Iceland).  In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 200 units of SuperScript II (Invitrogen) for 60 min at 42°C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07 units per ul DNA ligase (Invitrogen), 0.27 units per ul DNA polymerase I (Invitrogen), 0.013 units per ul RNase H (Invitrogen), at 16°C for 2 hours.  Immediately following, 10 units T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16°C.  Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies)  for 10 minutes at 37°C.  Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.  One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37°C.  Array hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42°C.


title: Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon [ChIP-chip data]

type: Genome binding/occupancy profiling by genome tiling array

overall_design:
Cultures containing either the gene encoding the Idr1 or Idr2 transcription factors with c-terminal fusions to the myc epitope were grown to mid-logarithmic phase in the presence or absence of 100 uM FeSO4. Cultures were subjected to ChIP-chip as described in Facciotti, MT, Reiss, DJ, Pan, M, Kaur, A, Vuthoori, M, Bonneau, R, Shannon, P, Srivastava, A, Donohoe, SM, Hood, LE and Baliga, NS. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 2007;104: 4630-4635.
Each Sample is based on two arrrays (one with dye-swap).


title: Gene expression analysis of primary human trabecular meshwork cells cultured in fibroblast medium following selective laser trabeculoplasty treatment

city: Genoa

first: Alberto

last: Izzotti

address: A. Pastore, 1

department: Dept. of Health Sciences

institute: University of Genoa

summary: Primary human trabecular meshwork cells cultured in fibroblast medium underwent selective laser trabeculoplasty treatment. RNA was extracted from a pool of cells 30 min after treatment while the remaining cells were further cultured and RNA was extracted respectively 2 and 6 hour after treatment. Control cells stored in incubator in absence of SLT treatment were used as reference samples. Gene expression was evaluated by hybridization on miRNA-microarray and laser scanner analysis.

overall_design: Time course experiment; HTM cells, ScienCell, San Diego, California:  cat. n. 6590: isolated from juxtacanalicular and corneoscleral region of the human eye. TMC are cryopreserved on primary culture and delivered frozen.

first: A

first: M

last: Longobardi

first: C

last: Cartiglia

first: F

last: Rathschuler

first: S

middle: C

last: Saccà


title: Exosomes isolated from M.tb infected cells modulate macrophage response to IFN-gamma

status: Public on Jun 05 2011

city: Notre Dame

first: Erliang

last: Zeng

state: IN

address: 384 Fitzpatrick Hall

institute: University of Notre Dame

summary:
we studied the role of exosomes isolated from M.tb infected macrophages in modulating the macrophage response to IFN-γ. Nimblegen microarray gene expression studies were used to compare the suppression of IFN-γ inducible genes by exosomes relative to the virulent strain of M.tuberculosis.
Overall our study suggest that exosomes, as carriers of M.tb pathogen associated molecular patterns (PAMPs), may provide a mechanistic link by which M.tb may exert its suppression of host immune response beyond the infected cell, and implies a physiological role for exosomes in immune surveillance of TB.

overall_design: Macrophages were treated with exosomes, infected with M.tb H37Rv or left untreated for 18 hours followed by +/- IFN-γ for an additional 18 hours.  Cells were harvested and RNA was isolated and converted to double stranded cDNA  and subsequently labeled and hybridized onto Mus musculus 4×72 Nimblegen microarray using Nimblegen Hybridization system 4 according to manufacturer’s instructions (Roche)

first: Prachi

last: Singh

first: Christopher

last: LeMaire

first: John

last: Tan

first: Jeffery

last: Schorey


title: Custom Illumina array DNA methylation analysis of 384 CpGs across five cancer types

status: Public on Jun 01 2011

city: College Park

first: Hector

last: Corrada Bravo

state: MD - Maryland

address: 3114F Biomolecular Sciences Building

department: Center for Bioinformatics and Computational Biology

institute: University of Maryland

type: Methylation profiling by genome tiling array

summary: Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other. We therefore hypothesized that these colon cDMRs might also be cDMRs for other cancer types. For colon, lung, breast, thyroid, and Wilms tumors, we show stochastic variation in methylation within each tumor type, but involving the same loci across tumor types, with intermediate values of variation for premalignant adenomas.

overall_design: Seeking to increase the precision of DNA methylation measurements over our previous tiling array-based approach, termed CHARM (Comprehensive High-throughput Array for Relative Methylation), we designed a custom nucleotide-specific bead array on the Illumina GoldenGate platform to analyze 151 colon cDMRs from Irizarry et al. (PMID 19151715). The resulting 384 probes covered 139 regions, with 1-7 probes per region. We studied 290 samples, including cancers from colon (10), lung (24), breast (27), thyroid (36), and kidney (Wilms) (25), with matched normal tissues to 111 of these 122 cancers, along with 30 colon premalignant adenomas, 18 normal colon, and 9 normal breast samples.

first: W

last: Timp

first: H

first: R

last: Irizarry

last: Feinberg


title: mRNA expression in mutL deletion mutant of Thermus thermophilus HB8

city: Sayo-gun

first: Kenji

last: Fukui

state: Hyogo

address: 1-1-1, Kouto, Sayo-cho

department: SPring-8 Center

institute: RIKEN

summary:
We analyzed the expression profile of mutL deletion mutant strain of Thermus thermophils HB8 during the exponential growth phase.

Keywords: cell type comparison

overall_design: Wild-type and the mutant strains were precultured in 3 mL of rich medium for two times at 70°C and then subcultured to 1000 mL of rich medium. These cells were cultured at70°C for 300 min , and then cells were harvested from 50 ml of the culture. Total RNA were extracted from wild-type and mutS-lacking strain and used for the cDNA synthesis by SuperScript II (Invitrogen, Carlsbad, CA).  The cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer’s instructions. The 3’-terminal-labeled cDNA was hybridized with a TTHB8401a520105F GeneChip (Affymetrix) which contained probe sets of 25-mer oligonucleotides for 2238 ORFs and 1096 intergenic regions.  After washing and staining with streptavidin-phycoerythrin (Invitrogen) by GeneChip Fluidics Station 450XP (Affymetrix), the array was scanned by a GeneChip Scanner 3000 (Affymetrix).  The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.2 (Affymetrix).  The data analysis was performed on the Subio platform version 1.6 (Subio Inc., Tokyo, Japan).  The genes which had detection call of “presence” more than 4 times from 8 samples were used for following analysis. The normalized intensities for the mutant strains were calculated by using the intensities for wild-type strains of each data set, and then, the average of these intensities were used. The genes which produced P value < 0.05 in the Student’s t-test were extracted. Among them, the genes whose expression level was different more than 2 fold between two strains were considered as significant.  For the biological replication, above experiments were performed three times independently.

first: K

first: Y

last: Agari

last: Shinkai

last: Kuramitsu


title: Lignocellulose-induced regulation of Phanaerochaete chrysosporium genes

first: Dan

last: Cullen

summary: Transcript profiles of Phanerochaete chrysosporium grown on ball-milled aspen or ball-milled pine were analyzed. Array design based on the DoE's Joint Genome Institute's v2.1 annotation. Goal is to define genes involved in lignocellulose degradation.

overall_design: From a data set of 10,004 unique alleles, each Roche NimbleGen (Madison, WI) array featured 12 unique 60mer probes per gene, all in triplicate. (Seven gene models composed mostly of repetitive DNA were represented by only 2 to 11 60mers.) Total RNA was purified from medium containing ball-milled aspen or ball-milled pine as the sole carbon source. In short, cultures were harvested by filtering through Miracloth (Calbiochem, EMD Biosciences, Gibbstown, NJ), squeeze dried and snap frozen in liquid nitrogen. Pellets were stored at -80 C until use. Extraction buffer was prepared by combining 10 ml 690 mM para-aminosalicylic acid (sodium salt) (Sigma-Aldrich, St. Louis, MO) with 10 ml 56 mM triisopropylnapthalene sulfonic acid (sodium salt) (Sigma-Aldrich), and placed on ice. To this was added 5 ml 5X RNB (1.0 M Tris, 1.25 M NaCl, 0.25 M EGTA). The pH of the 5X RNB was adjusted to 8.5 with NaOH. The mixture was kept on ice and shaken just before use.  Frozen fungal pellets were ground to a fine powder with liquid nitrogen in an acid washed, pre-chilled mortar and pestle. The ground mycelia were transferred to Falcon 2059 tubes (VWR International, West Chester, PA), and extraction buffer was added to make a thick slurry. The samples were vortexed vigorously and placed on ice until all samples were processed.  One half volume TE-saturated phenol (Sigma-Aldrich) and ¼ volume chloroform (Sigma-Aldrich) were added to each sample and vortexed vigorously.  Samples were spun at 2940 x g in a fixed-angle rotor for 5 minutes.  The aqueous layer was removed to a new tube, and phenol:chloroform extractions were repeated until the interface between the aqueous and organic layers was clear. The final aqueous extractions were placed in clean 2059 tubes, to which was added 0.1 volume 3M sodium acetate, pH 5.2, (DEPC-treated) and 2 volumes absolute ethanol. The tubes were shaken vigorously and stored overnight at -20˚C. The tubes were spun 1 hour at 2940 x g, the supernatants were decanted, and the pellets were resuspended in 4 ml RNase-free H2O. Total RNA was purified using the RNeasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol for RNA cleanup. RNAs were eluted from the RNeasy spin columns using two spins, for a final volume of 2 ml. The eluted RNAs were ethanol precipitated and stored overnight at -20˚C. The RNAs were spun 1 hour at 2940 x g, washed 1x with 70% ethanol, and resuspended in 50-100ul RNase-free H2O. Three biological replicates per medium were used (6 separate arrays). RNA was converted to double-strand cDNA and labeled with the Cy3 fluorophore sample for hybridization to the array by Roche NimbleGen (Iceland). In brief, 10ug of total RNA was incubated with 1X first strand buffer, 10 mM DTT, 0.5mM dNTPs, 100 pM oligo T7 d(T)24  primer, and 400U of SuperScript II (Invitrogen) for 60 min at 42˚C. Second strand cDNA was synthesized by incubation with 1X second strand buffer, 0.2mM dNTPs, 0.07U/ul DNA ligase (Invitrogen), 0.27U/ul DNA polymerase I (Invitrogen), 0.013U/ul RNase H (Invitrogen), at 16˚C for 2 hours.  Immediately following, 10U T4 DNA polymerase (Invitrogen) was added for additional 5 minute incubation at 16˚C. Double-stranded cDNA was treated with 27ng/ul of RNase A (EpiCenter Technologies) for 10 minutes at 37˚C. Treated cDNA was purified using an equal volume of phenol:chloroform:isoamyl alcohol (Ambion), ethanol precipitated, washed with 80% ethanol, and resuspended in 20ul water.  One ug of each cDNA sample was amplified and labeled with 1 unit per ul of Klenow Fragment (New England BioLabs) and 1 O.D. unit of Cy3 fluorophore (TriLink Biotechnologies, Inc.) for 2 hours at 37˚C. Array hybridization was carried out with 6ug of labeled cDNA suspended in NimbleGen hybridization solution for 17 hours at 42˚C. Arrays were scanned on the Axon4000B Scanner (Molecular Dynamics) and data was extracted from the scanned image using NimbleScan v2.4. DNASTAR ArrayStar v2.1 (Madison,WI) software was used to quantify and visualize data. Analyses were based on three biological replicates per culture medium. Quantile normalization and robust multi-array averaging (RMA) were applied to the entire dataset.


title: mRNA expression in mutS deletion mutant of Thermus thermophilus HB8

summary:
We analyzed the expression profile of mutS deletion mutant strain of Thermus thermophils HB8 during the exponential growth phase.

Keywords: cell type comparison

overall_design: The mutant strains were precultured in 3 mL of rich medium for two times at 70°C and then subcultured to 1000 mL of rich medium. These cells were cultured at 70°C for 300 min , and then cells were harvested from 50 ml of the culture. Total RNA were extracted from wild-type and mutS-lacking strain and used for the cDNA synthesis by SuperScript II (Invitrogen, Carlsbad, CA).  The cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer’s instructions. The 3’-terminal-labeled cDNA was hybridized with a TTHB8401a520105F GeneChip (Affymetrix) which contained probe sets of 25-mer oligonucleotides for 2238 ORFs and 1096 intergenic regions.  After washing and staining with streptavidin-phycoerythrin (Invitrogen) by GeneChip Fluidics Station 450XP (Affymetrix), the array was scanned by a GeneChip Scanner 3000 (Affymetrix).  The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.2 (Affymetrix).  The data analysis was performed on the Subio platform version 1.6 (Subio Inc., Tokyo, Japan).  The genes which had detection call of “presence” more than 4 times from 8 samples were used for following analysis. The normalized intensities for the mutant strains were calculated by using the intensities for wild-type strains of each data set, and then, the average of these intensities were used. The genes which produced P value < 0.05 in the Student’s t-test were extracted. Among them, the genes whose expression level was different more than 2 fold between two strains were considered as significant.  For the biological replication, above experiments were performed three times independently.


title: Genome-wide MicroRNA Downregulation as a Negative Feedback Mechanism in the Early Phases of Liver Regeneration

city: Nanjing

first: Yan

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

summary: Liver is one of the few organs that have the capacity to regenerate in response to injury. We carried out genome-wide miRNA microarray studies during liver regeneration in rats after 70% partial hepatectomy (PH) at early and mid-time points to more thoroughly understand their role. At 3, 12 and 18 hrs post-PH ~ 40% of the miRNAs tested were up-regulated. Conversely, at 24 hrs post-PH, ~ 70% of miRNAs were down-regulated. Further, we established that the genome-wide down-regulation of miRNA expression at 24 hrs was also correlated with decreased expression of genes such as Rnasen, Dgcr8, Dicer, Tarbp2 and Prkra that are associated with miRNA biogenesis. To determine if a potential negative feedback loop between miRNAs and their regulatory genes existed, 11 candidate miRNAs which were predicted to target the above genes were examined and found to be up-regulated at 3 hrs post-PH. Using reporter and functional assays, we determined that expression of these miRNA-processing genes could be regulated by a subset of miRNAs and some miRNAs could target multiple miRNA biogenesis genes simultaneously. We also demonstrated that over-expression of these miRNAs inhibited cell proliferation and modulated the cell cycle in both Huh-7 human hepatoma cells and primary rat hepatocytes. From these observations, we postulated that selective up-regulation of miRNAs in the early-phase after PH was involved in the priming and commitment to liver regeneration, while the subsequent genome-wide down-regulation of miRNAs was required for efficient recovery of liver cell mass. Conclusion: Our data suggest that miRNA changes are regulated by negative feedback loops between miRNAs and their regulatory genes that may play an important role in the steady-state regulation of liver regeneration.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Sham and Partial Hepatectomized livers at various time points.

first: Jingmin

last: Shu

first: Betsy

last: Kren

first: Phillip

last: Wong

first: Clifford

last: Steer


title: SMAD3 ChIP-on-chip on A549 cell line

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

summary: The aim of this study is to identify SMAD3 binding targets affected by the TGFb1/SMAD3 signal transduction on a genome-wide scale

overall_design: Formaldehyde cross-linked, sonicated chromatin was prepared from non-stimulated A549 cell line and stimulated with TGFb1. Chromatin immunoprecipated with anti-SMAD3 antibody is labeled with Cy5 and mock IP (with anti-FLAG antibody) is labeled with Cy3 and co-hybridized on Agilent Human Promoter Set arrays. Two biological replicates were performed.

first: Yingze

last: Zhang

first: Daniel

last: Handley

first: Naftali

last: Kaminski


title: Removing System Noise from Comparative Genomic Hybridization Data by Self-Self Analysis

city: Cold Spring Harbor

first: Yoon-Ha

last: Lee

address: One Bungtown Road

institute: Cold Spring Harbor Lab

type: Genome variation profiling by genome tiling array

summary: To minimize the distortion of genetic signal by system noise, we have explored the latter in an archive of hybridizations in which no genetic signal is expected. This archive is obtained by comparative genomic hybridization (CGH) of a reference sample in one channel to the same sample in the other channel, which we have termed ‘self-self’ data. We show that these self-self hybridizations trap a variety of system noise inherent in sample-reference (test) data. Through singular value decomposition (SVD) of self-self data, we are able to determine the principal components of system noise. Assuming simple linear models of noise generation, we present evidence that the linear correction of test data with self-self data—which we call system normalization—reduces local and long-range correlations as well as improves signal-to-noise metrics, yet does not introduce detectable spurious signal.

overall_design: 132 self-self hybridizations which should not have any genomic signal, and 3720 test hybridizations done against reference genome CSHL0001.

first: Michael

last: Wigler

first: Yoon-ha


title: Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

city: Haifa

first: Itai

last: Yanai

address: Technion City

country: Israel

institute: Technion - Israel Institute of Technology

summary: Variation in gene expression is known to be important for morphological evolution, however little is known about its general propensity. Here we examine a pair of frogs – Xenopus laevis and Xenopus tropicalis – with highly similar embryology, and ask how their transcriptomes compare. Despite separation for over ~30-90 million years we found a strong conservation in gene expression in the vast majority of the expressed orthologs. There were a significant number of changes in the level of expression of genes. Changes in timing of expression, heterochrony, were much less common, and were often found in genes and pathways that reflect responses to selective features of the environment. Differences in gene expression levels were concentrated in the earliest embryonic stages. We propose that different evolutionary rates across developmental stages may be explained by the stabilization of cell fate determination pathways in later stages.

sample_organism:
Xenopus laevis
Xenopus tropicalis

platform_organism:
Xenopus laevis
Xenopus tropicalis

overall_design: 96 microarrays, across developmental stages in Xenopus laevis and Xenopus tropicalis in wildtype embryos. For each of the two timecourse indepenent triplicates (clutches) were generated.

first: Leonid

last: Peshkin

first: Paul

last: Jorgensen

first: Marc

middle: W

last: Kirschner


title: High-throughput mapping of he promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoters

city: San Francisco

first: Eleanor

middle: Josephine

last: Clowney

department: Anatomy

institute: UCSF

summary:
We map the transcription start sites of 1085 murine olfactory receptor genes and analyze putative promoters
The bar files contain MAT analysis of RLM-RACE products hybridized to a custom olfactory genome tiling array.

overall_design: RNA from the olfactory epithelia of adult mice was prepared by RLM-RACE. Olfactroy receptor transcripts were amplified by degenerate priming and hybridized to tiling arrays to map 5' transcript structure.

first: Stavros

last: Lomvardas


title: Deregulated miRNAs in adrenocortical tumors

city: Stockholm

first: Stefano

last: Caramuta

address: CMM L8:01, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

summary: We performed miRNA expression profiling in  a series of adrenocortical carcinomas, adrenocortical adenomas and normal adreno cortex using a microarray approach. Significant differentially expressed miRNAs among groups were identified using SAM analysis.

overall_design: Agilent microarray platform containing 903 miRNAs was used to determine miRNA expression profiles in 4 normal cortices, 26 adenomas and 22 adrenocortical carcinomas. SAM analysis was adopted to identify significant differentially expressed miRNAs between groups. SAM survival analysis was used to determine the association between miRNA expression and survival among carcinoma cases. The expression levels of candidate prognostic miRNAs were evaluated using qRT-PCR in the same cohort of adrenocortical carcinomas and association with survival was evaluated  using Kaplan Meier curves and log rank tests.

first: Deniz

last: Özata

first: David

last: Velazquez-Fernandez

first: Pinar

last: Akçakaya

first: Xie

last: Hong

first: Martin

last: Bäckdahl

first: Jan

last: Zedenius

first: Catharina

last: Larsson

first: Weng-Onn

last: Lui


title: CpG islands Methylation Profiling by DMH in Epithelial Ovarian Cancer: Screening Set

city: London

first: Wei

last: Dai

address: Du Cane Road

department: Sugery and Cancer

country: United Kingdom

institute: Imperial College London

summary: We have systematically profiled DNA methylation at promoter CpG islands (CGIs) in ovarian cancer. Epithelial ovarian tumours, excluding mucinous and clear cell cancers, prospectively collected through a cohort study, were analyzed by differential methylation hybridization (DMH) (Nouzova M et al, 2004) in duplicates. The loci targeted by the custom-designed microarray are the promoter CpG islands (Gardiner-Garden and Frommer, 1987) of the genes involved in the Wnt, p53, AKT/mTOR, BRCA1/2 and Redox pathways, DNA repair (HR, NHEJ and MMR), FA family and IgLON family.

overall_design: 111 ovarian tumor samples were assayed by DMH in duplicates. McrBC digested (Cy5) and undigested (Cy3) samples were competitively hybridized on the Agilent custom-designed microarrays 8x15k.

first: Jens

last: Teodoridis

first: Constanze

last: Zeller

first: Janet

middle: S

last: Graham

first: Jenny

last: Hersey

first: James

last: Flanagan

first: Euan

last: Stronach

last: Millan

first: Nadeem

last: Siddiqui

last: Paul

first: Robert

last: Brown


title: Expression analysis, A. actinomycetemcomitans wild type (JP2) vs CRP deletion mutant both grown anaerobically.

city: SA

last: Kolodrubetz

address: 7703 Floyd Curl Dr

department: Microbiology and Immunology

institute: UTHSCSA

summary:
The goal of this analysis is to define the anaerobic regulon for the global transcription factor CRP (catabolite repressor protein) in the periodontal pathogen Aggregatibacter actinomycetemcomitans.
The objectives were met by comparing the mRNA profile of a wild type strain, JP2, to that of an isogenic mutant deleted of the CRP gene.  Both strains were grown anaerobically.

overall_design: A three biological replicates study using total RNA recovered from three separate cultures of wild-type Aggregatibacter actinomycetemcomitans strain JP2 and three separate cultures of strain AAM167, an isogenic deletion mutant  in which the gene for cAMP-Receptor-Protein (CRP) has been replaced by a spectinomycin resistance gene cassette.  The cells were grown anaerobically in pairs (wild type paired with mutant). Each chip measures the expression level of 2,116 genes from A. actinomycetemcomitans strain HK1651.   There were 11 different 60-mer probes /gene for 94% of the genes, and the entire probe set (22,537 probes) was replicated (technical replicates) three times on each array.  Each probe set is contained on a quarter of a chip and there were also 4,426 random probes per array.  Wild type and mutant RNAs from cultures #1 and #2 were hybridized to the same chip and the RNAs from cultures  #3 were hybridized in different quadrants of a second chip.

first: Leigh

middle: A

last: Feuerbacher

first: Alex

last: Burgum


title: Endoderm- vs ectoderm-specific expression of symbiosis genes in the snakelocks sea anemone

city: NICE

first: Cecile

last: Sabourault

address: Faculte des Sciences, Parc Valrose, BP 71

country: France

institute: University of Nice

summary: Transcriptional comparison between endodermal and ectodermal compartment in symbiotic sea anemones Anemonia viridis were analysed in several specimens. We generated an oligonucleotide microarray (2000 selected features), which is to date the only available oligonucleotide array for symbiotic cnidarians. We were able to identify a subset of genes clearly involved in symbiosis.

overall_design: RNA was extracted from ectodermal or endodermal samples were prepared from 4 symbiotic specimens. Hybridizations were performed against a single reference (VBl) in a dye-swap experiment.

first: Philippe

last: Ganot

first: Aurelie

last: Moya

first: Virginie

last: Magnone

first: Pascal

last: Barbry


title: Transcriptomic adaptations to symbiotic life in cnidarians: symbiotic vs bleached Anemonia viridis sea anemones

summary: Transcriptional comparison between symbiotic and non-symbiotic (bleached) sea anemones Anemonia viridis were analysed in several specimens. We generated an oligonucleotide microarray (2000 selected features), which is to date the only available oligonucleotide array for symbiotic cnidarians. We were able to identify a subset of genes clearly involved in symbiosis.

overall_design: Whole tentacle samples were prepared from 5 symbiotic and 5 bleached specimens. Hybridizations were performed against a single reference (VBl) in a dye-swap experiment.


title: mRNA expression in mutS2 deletion mutant of Thermus thermophilus HB8

first: Kenji

last: Fukui

summary:
We analyzed the expression profile of mutS2 deletion mutant strain of Thermus thermophils HB8 during the exponential growth phase.

Keywords: cell type comparison

overall_design: The mutant strains were precultured in 3 mL of rich medium for two times at 70°C and then subcultured to 1000 mL of rich medium. These cells were cultured at70°C for 300 min , and then cells were harvested from 50 ml of the culture. Total RNA were extracted from wild-type and mutS-lacking strain and used for the cDNA synthesis by SuperScript II (Invitrogen, Carlsbad, CA).  The cDNA fragments were labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer’s instructions. The 3’-terminal-labeled cDNA was hybridized with a TTHB8401a520105F GeneChip (Affymetrix) which contained probe sets of 25-mer oligonucleotides for 2238 ORFs and 1096 intergenic regions.  After washing and staining with streptavidin-phycoerythrin (Invitrogen) by GeneChip Fluidics Station 450XP (Affymetrix), the array was scanned by a GeneChip Scanner 3000 (Affymetrix).  The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.2 (Affymetrix).  The data analysis was performed on the Subio platform version 1.6 (Subio Inc., Tokyo, Japan).  The genes which had detection call of “presence” more than 4 times from 8 samples were used for following analysis. The normalized intensities for the mutant strains were calculated by using the intensities for wild-type strains of each data set, and then, the average of these intensities were used. The genes which produced P value < 0.05 in the Student’s t-test were extracted. Among them, the genes whose expression level was different more than 2 fold between two strains were considered as significant.  For the biological replication, above experiments were performed three times independently.

first: K

first: Y

last: Agari

first: S

last: Kuramitsu


title: Gene expression profiles of CARM1 overexpression in MCF7

first: Wei

last: Xu

address: 1400 University Ave

institute: UW-Madison

summary:
The goal of this study is to identify ERalpha-target genes affected by overexpression of the histone arginine methyltransferase CARM1 in breast cancer cells. The roles of CARM1 in ERalpha+ breast cancer was not well characterized. Therefore, we created a Dox inducible CARM1 overexpressing MCF7 cell line where CARM1 is overexpressed by 2 fold to determine the
created a Dox-inducible CARM1 overexpressing MCF7 cells for evaluation of the global effects of CARM1 on Eralpha-target gene expression.

overall_design: MCF7-tet-on-CARM1 clone 13 were treated under 4 conditions: DMSO; Dox; E2 (10nM); Dox+E2. In Dox+E2 condition, cells were pre-treated with Dox for 5 days before treating with E2 for 4 hours. 3 biological replicates were included and total of 12 samples were analyzed.

first: Ken

last: Higashimoto

first: Yunhong

last: Zan

first: Yuerong

last: Zhu


title: Transcriptome reorganization during wood maturation in Pinus radiata

city: Canberra

first: Xinguo

last: Li

state: ACT

address: Building 602, Black Mountain Laboratories

department: Plant Industry

country: Australia

institute: CSIRO

summary: Wood maturation produces two distinct wood tissues: juvenile wood (JW) and mature wood (LW), which are the major cause of wood qaulity variation within a tree. We investigate transcriptome reorganization during wood maturation process in radiata pine using a newly developed 18k cDNA microarrays.

overall_design: Developing xylem tissues from nine sampled trees at 5- and 13-year-old each were randomly divided into three groups with three trees each. Total RNA samples extracted from three trees within a group were pooled at equal amount before using for microarray experiments. Using this pooling strategy three biological replicates were formed for each microarray experiment. Dye swap was applied in each biological replicate. Comparisons between JW and MW in spring (EW) and autumn (LW) were arranged in two separate microarray experiments: juvenile earlywood (JE) vs. mature earlywood (ME), juvenile latewood (JL) vs. mature latewood (ML)

first: Harry

middle: X

last: Wu

first: Simon

middle: G

last: Southerton


title: affy_tj_maize-Understanding the Diversity of Maize Cell Wall

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
affy_en-tj_maize - affy_tj_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of 2 maize lines : Cm484: good digestibility F98902: bad digestibility at the following development stage : 21 days after sowing -7 leaves-

Keywords: genotype comparaison

overall_design: 4 arrays - maize

first: Sandrine

last: Balzergue

first: Magalie

last: Pichon

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Expression profiling of F2 progenies from C57BL/6J x DBA/2J

city: Seattle

first: Wan-Lin

last: Su

state: WA

address: 401 Terry Ave N

institute: Rosetta Inpharmatics (a wholly owned subsidiary of Merck & Co., Inc.)

summary: Expression profiling of a cohort of mice was derived from a standard F2 intercross using two standard inbred strains, C57BL/6J and DBA/2J.  In this study, we selected 127 male animals that had been raised on a standard rodent chow diet (Purina Chow from Ralston-Purina Co., St. Louis, MO) for eight weeks and then switched to a high fat diet for sixteen additional weeks.  At 20 weeks of age, the mice were euthanized and liver tissues were collected and flash frozen in liquid nitrogen and stored at -80 degrees C prior to RNA isolation.  All procedures of housing and treatment of animals were performed in accordance with IACUC regulations.

overall_design: RNA preparation and array hybridizations were performed at Rosetta Inpharmatics. The custom ink-jet microarrays were manufactured by Agilent Technologies (Palo Alto, CA). A custom array was designed for this study and consisted of 39,280 non-control oligonuceotides extracted from the mouse Unigene clusters and combined with RefSeq sequences and RIKEN full-length cDNA clones. Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to a previously described error model to determine significance (type I error).

first: Robert

last: Kleinhanz

first: Eric

middle: E

last: Schadt


title: affy_en_maize-Understanding the Diversity of Maize Cell Wall

summary:
affy_en-tj_maize - affy_en_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of 2 maize lines : Cm484: good digestibility F98902: bad digestibility) , at the following developmental stade 2: male flowering

Keywords: genotype comparaison


title: The Sen1 Helicase Prevents Spurious Transcription by Controlling Genome-Wide Transcription Termination by RNAPII

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

institute: Institut de recherches cliniques de Montréal (IRCM)

summary: RNA Polymerase II (RNAPII) termination for transcripts containing a polyadenylation signal (PAS) is thought to differ mechanistically from termination for PAS-independent RNAPII transcripts such as sn(o)RNAs. In a screen for factors required for PAS-dependent termination, we identified Sen1, a putative helicase known primarily for its role in PAS-independent termination. We show that Sen1 is required for termination on hundreds of protein-coding genes and suppresses cryptic transcription from nucleosome-free regions on a genomic scale. These effects often overlap with but are also often distinct from those caused by Nrd1 depletion, which also impacts termination of protein-coding and cryptic transcripts, including many genic antisense transcripts. Sen1 controls termination through its helicase activity and stimulates recruitment of factors previously implicated in both PAS-dependent (Rna14, Rat1) and PAS-independent (Nrd1) termination. Thus, RNAPII termination for both protein-coding genes and cryptic transcripts is dependent on multiple pathways.

overall_design: The 2 RNAPII datasets were produced in duplicates and the Sen1 and Nrd1 datasets in triplicates (all IP/Input).

first: Eduard

last: Nedea

first: Harm

last: van Bakel

first: Pierre-Étienne

last: Jacques

first: Daniel

last: Xia

first: Carl

last: de Boer

first: Kyle

last: Tsui

first: Bernhard

last: Suter

first: Corey

last: Nislow

first: Timothy

last: Hughes

first: Jack

middle: F

last: Greenblatt


title: Functional genomics of Aspergillus fumigatus conidiospores interacting with human bronchial epithelial cells

city: Vancouver

first: Scott

last: Tebbutt

state: BC

address: St. Paul's Hospital - Rm 166 - 1081 Burrard St.

institute: UBC - iCAPTURE Centre

summary: The cells of the airway epithelium play critical roles in host defense to inhaled irritants, and in asthma pathogenesis. These cells are constantly exposed to conidiospores of the ubiquitous mould Aspergillus fumigatus, which are small enough to reach the alveoli. This exposure is asymptomatic in most individuals but can be associated with a spectrum of diseases ranging from asthma and allergic bronchopulmonary aspergillosis to aspergilloma and invasive aspergillosis. Airway epithelial cells have been shown to internalize A. fumigatus conidiospores in vitro, but the implications of this process for pathogenesis remain unclear. We have developed a cell culture model for this interaction using the 16HBE cell line and a transgenic A. fumigatus strain expressing green fluorescent protein. The transcriptional profiles of A. fumigatus conidiospores incubated in the presence or absence of human cells were compared, revealing significant changes in fungal gene expression in response to conidial interaction with cells.

overall_design: Gene expression levels were investigated in A. fumigatus conidiospores incubated in the presence or absence of 16HBE cells for 6 hours. Four independent samples were analysed for each of these conditions, using JCVI PFGRC Aspergillus fumigatus Version 3 microarrays, with a dye-swap experimental design.

first: Pol

last: Gomez

first: Tillie

last: Hackett

first: Margo

middle: M

last: Moore

first: Darryl

last: Knight


title: Host responses in chicken embryonic fibroblasts infected with different strains of Toxoplasma gondii [F1 progeny]

status: Public on May 27 2011

city: Stanford

first: Yi-Ching

last: Ong

state: CA

address: 299 W. Campus Dr.

department: Microbiology & Immunology

institute: Stanford University

summary:
Toxoplasma gondii is a ubiquitous protozoan pathogen able to infect both mammalian and avian hosts.  Surprisingly, just three strains appear to account for the majority of isolates from Europe and N. America.
To test the hypothesis that strain divergence might be driven by differences between mammalian and avian response to infection, we examine in vitro strain-dependent host responses in a representative avian host, the chicken.

overall_design: Chicken embryonic fibroblasts were cultivated in vitro and infected with different strains of Toxoplasma gondii; host transcriptional responses were then analyzed at 24 hours post-infection.


title: Strain-dependent host responses in chicken embryonic fibroblasts infected with Toxoplasma gondii [ME49, CEP, and Mock]

overall_design: Chicken embryonic fibroblasts were cultivated in vitro and infected with different strains of Toxoplasma gondii (Type II = ME49, Type III = CEP); host transcriptional responses were then analyzed at 24 hours post-infection.


title: Evidence-based annotation of genes and transcripts in Desulfovibrio vulgaris Hildenborough (tiling array)

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

type: Expression profiling by genome tiling array

summary: High-resolution tiling analysis of the DvH transcriptome in lactate/sulfate media, both rich (LS) and defined (LS4D)

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Two replicates of rich media, one replicate of minimal media, and one “genomic control” array (genomic_control.ftr) hybridized to genomic DNA

first: Adam

last: Deutschbauer

first: Jennifer

middle: V

last: Kuehl

middle: P

last: Arkin


title: Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation

city: Oak Ridge

first: Babu

last: Raman

state: TN

address: One Bethel Valley Road

institute: Oak Ridge National Laboratory

summary:
Background: The ability of Clostridium thermocellum ATCC 27405 wild-type strain to hydrolyze cellulose and ferment the degradation products directly to ethanol and other metabolic byproducts makes it an attractive candidate for consolidated bioprocessing of cellulosic biomass to biofuels. In this study, whole-genome microarrays were used to investigate the expression of C. thermocellum mRNA during growth on crystalline cellulose in controlled replicate batch fermentations.
Results: A time-series analysis of gene expression revealed changes in transcript levels of ~40% of genes (~1300 out of 3198 ORFs encoded in the genome) during transition from early-exponential to late-stationary phase. K-means clustering of genes with statistically significant changes in transcript levels identified six distinct clusters of temporal expression. Broadly, genes involved in energy production, translation, glycolysis and amino acid, nucleotide and coenzyme metabolism displayed a decreasing trend in gene expression as cells entered stationary phase. In comparison, genes involved in cell structure and motility, chemotaxis, signal transduction and transcription showed an increasing trend in gene expression. Hierarchical clustering of cellulosome-related genes highlighted temporal changes in composition of this multi-enzyme complex during batch growth on crystalline cellulose, with increased expression of several genes encoding hydrolytic enzymes involved in degradation of non-cellulosic substrates in stationary phase.
Conclusions: Overall, the results suggest that under low substrate availability, growth slows due to decreased metabolic potential and C. thermocellum alters its gene expression to (i) modulate the composition of cellulosomes that are released into the environment with an increased proportion of enzymes than can efficiently degrade plant polysaccharides other than cellulose, (ii) enhance signal transduction and chemotaxis mechanisms perhaps to sense the oligo-saccharide hydrolysis products, and nutrient gradients generated through the action of cell-free cellulosomes and, (iii) increase cellular motility for potentially orienting the cells’ movement towards positive environmental signals leading to nutrient sources. Such a coordinated cellular strategy would increase its chances of survival in natural ecosystems where feast and famine conditions are frequently encountered.

overall_design: Total RNA was extracted from the cell pellets and the reverse transcribed cDNA was hybridized to oligo-arrays containing duplicated probes representing ~90% of the annotated ORFs in C. thermocellum ATCC27405 genome.Dual-channel dye swap experimental design was used to analyze the time-course of gene expression during cellulose fermentation using two biological replicate fermentation. The 6hr sample as the reference, to which all other time-point samples (8, 10, 12, 14, 16hr) were compared.

first: Jonathan

middle: R

last: Mielenz


title: Transcriptome analysis of rice (Oryza sativa) infected with blast fungus (Magnaporthe oryzae)

status: Public on May 31 2011

city: Sapporo

first: Kouji

last: Satoh

state: Hokkaido

address: Hitsujigaoka 1

institute: NARO/HARC

summary:
Rice blast is one of the most serious diseases and is caused by Magnaporthe grisea. SHZ-2, an indica cultivar with broad spectrum resistance to multiple races of the blast pathogen, was crossed to TXZ-13, a blast susceptible but high-quality variety, to produce one BC3 line, BC10 line, which showed strong to moderate blast resistance over eight cropping seasons in the field. In this study, we compared the transcription between blast-resistant and -susceptive lines by custom microarray.

Keywords: time course, blast infection, disease response

overall_design: Comparison between blast- and mock-infected rice. Biological replicates: 3 control (mock) and 3 blast-infected at each time point, independently grown and harvested at 24 and 48 hours after inoculation. Each sample was prepared with whole plant 5 cm above ground and was pooled from 5 plants grown under the same conditions.

first: Yan

last: Liu

first: Hiroaki

last: Kondoh

first: Setsuko

last: Kimura

first: Il-Ryong

last: Choi

first: Hei

last: Leung

first: Shoshi

last: Kikuchi