title: To identify genes that are modulated in keratinocytes in response to wounding.

last: Head

summary: Dendritic epidermal T cells (DETC) reside in murine skin and participate in homeostasis and wound repair.  Upon wounding, DETC become activated through the recognition of an unidentified ligand expressed by keratinocytes proximal to sites of injury.  Such DETC activation is mediated through a monoclonal T cell receptor (TCR).  Using a soluble form of this monoclonal TCR, we have shown that keratinocytes upregulate DETC TCR ligands in wounded tissue within 2 hours following wounding.  Down-modulation of the ligand is seen 3 hours following wounding, and no expression is evident in non-wounded skin.  In vitro studies on cell lines which express this unknown ligand indicate that antigen recognition by the DETC TCR is dependent upon N-linked glycosylation of the ligand.  Given the glycosylation sensitivity of the ligand and the restricted expression following wounding, we are interested in pursuing microarray analysis to identify genes that are modulated in keratinocytes in response to wounding.

overall_design:
Keratinocytes represent 90% of the cells in the epidermis (DETC and Langerhan’s cells make up the remaining 10%).  As such, we propose to isolate RNA from whole epidermis under either wounded or resting conditions.  In addition to comparing RNA from wounded and non-wounded epidermis, we would like to compare RNA from tissue that has been wounded for different times.  Initially, we would like to analyze 4 sampes (non-wounded epidermis, and epidermal cells isolated 30 minutes, 2 hours, and 4 hours following wounding).  These time points would correlate to a period prior to cell surface expression of ligand (30 minutes), during cell surface expression (2 hours), and following down regulation of cell surface expression (4 hours).  In addition to providing possible identification of the unknown DETC TCR ligand, such analysis would provide novel information about early responses by keratinocytes in response to physical wounding in vivo.
We propose to isolate RNA from whole epidermis under either wounded or resting conditions.  In addition to comparing RNA from wounded and non-wounded epidermis, we would like to compare RNA from tissues that has been wounded for different times.

first: Wendy

last: Havran

first: Alex


title: To study the relationship between 5-HT7 gene expressions and the expression of the glycan binding protein NCAM

status: Public on Sep 06 2011

city: La Jolla

first: Steven

state: CA

address: 10550 N Torrey Pines Rd

country: USA

institute: The Scripps Research Institute

summary: Adult Neurogenesis and Gene Expression Changes in 5-HT7 Receptor Knockout Mice: In the adult, the formation of new nerve cells in the CNS is restricted to the subependymal layer and to the subgranular zone of the hippocampus (Duman et al., 2001). Clinically adult neurogenesis has received most attention for its possible role in major depression. Depressed patients have reduced hippocampal neurogenesis (Kasper & McEwen, 2008) and hippocampal volume (Colla et al., 2007). It has also been shown that chronic, but not acute, treatment with currently widely used antidepressants, most notably fluoxetine, results in increased hippocampal neurogenesis (Malberg et al., 2000; Miller et al., 2007). Pharmacologically antidepressants act by elevating the amount of synaptic serotonin (5-HT) and they do that within minutes of administration, but the clinical effect is often delayed, sometimes for weeks (Miller et al., 2007). This delay is believed to involve changes in plasticity and neurogenesis. With currently available treatment options for depression 20% or more of patients do not respond to the therapy. Thus, there is a need for an increased understanding of the mechanism behind plasticity and neurogenesis, and for the development of improved therapies for depression.

overall_design:
We have in an ongoing project with the aim to functionally characterize the 5-HT7 receptor, one of the most recently discovered receptor subtypes for 5-HT (Lovenberg et al., 1993). Interestingly, we have found that this receptor might be a new target for the treatment of depression. Inactivation or pharmacological blockade of this receptor induces an antidepressant-like profile in several preclinical models of depression (Hedlund et al., 2005; Guscott et al., 2005; Wesolowska et al., 2006a, 2006b) and in sleep patterns (Thomas et al., 2003; Hedlund et al., 2005). Of special interest is also the finding that inhibition of the 5-HT7 receptor potentiates the effect of antidepressants in behavioral models of depression (Wesolowska et al., 2007; Bonaventure et al., 2007). We have recently determined that mice lacking lacking the 5-HT7 receptor show a 25% decrease in the number of proliferating cells in the subgranular zone of the hippocampus compared to wildtype mice. The mice were treated with BrdU, a thymidine analog that is incorporated into the DNA of cells undergoing mitosis. BrdU was then detected immunohistochemically. Both wildtype and knockout mice responded to fluoxetine treatment with an increase in the number of dividing cells. The reduction in the number of dividing cells in the 5-HT7 receptor knockout mice seemingly contradicts the antidepressant-like profile previously observed in these mice, but might on the other hand help to explain previously observed impairments in hippocampus-dependent learning seen in the knockout mice (Roberts et al., 2004) and after pharmacological blockade (Meneses, 2004).
The observation that 5-HT7 receptors influence neurogenesis constitutes an entirely new regulatory mechanism for this physiologically and pathophysiologically important process. In order to further understand hippocampal neurogenesis and how it is influenced by 5-HT in general and 5-HT7 receptors in particular we propose to perform a microarray study using the glycogene array designed by the Consortium for Functional Glycomics using total RNA from the hippocampus. A comparison will be made between young adult male mice lacking the 5-HT7 receptor and wildtype sibling controls. Such a study should yield new valuable insights into the pathways regulating neurogenesis. The glycogene array is of particular interest as it includes several genes that have been shown to be either directly or indirectly involved in adult neurogenesis and to be regulated by 5-HT and antidepressants. Of particular interest are cell adhesion molecules which are glycoproteins. One such molecule is NCAM, a marker for immature neurons undergoing remodeling and plasticity (Nakagawa et al., 2002), which is upregulated by fluoxetine treatment (Varea et al., 2006). In contrast, NCAM is downregulated following  5-HT depletion (Brezun & Daszuta, 1999). Chronic fluoxetine treatment has also been shown to upregulate neuropeptide Y, Galectin I, Activin A receptor and Inhibin beta-A, all included in the glycogene array (Miller et al., 2007). Another relevant gene on the glycogene chip is ST8SiaIV (Nakagawa et al., 2002).
Experimental Design:  The hippocampus will be dissected and total RNA will be extracted according to recommended protocols for array studies. RNA from a sufficient number (2-3 animals) of male 5-HT7 receptor knockout mice will be pooled for each of the three replicates. Control samples will be similarly generated from wildtype siblings. The 5-HT7 receptor mice are on a genetically homogeneous background (backcrossed for 16 generation on a C57BL6/J background) so inter-animal variability should be negligible. The RNA will be analyzed on the glycogene array. 3 KO replicates + 3 WT replicates per glycogene array = 6 arrays

first: Peter

last: Hedlund

middle: R

middle: T

last: Moffit


title: Continue study of the roles of galectins in parasitic infection

summary: Our laboratory previously reported that galectins may act as parasite recognizing molecules (Leishmania) (JBC 277:17663 and JBC 278:22223).  Now we are studying the role of galectin-3 in leishmaniasis in vivo, using G3KO mice.

overall_design: Thus, we analyzed RNA from leuckotyes of draining lymph nodes of both KO and WT mice at 3 different time points using gene microarrays.

first: Sachiko

last: Sato


title: Expression analysis of OsCc1:AP37 and OsCc1:AP59 transgenic rice plants

city: Yongin

first: Jin

middle: Seo

last: Jeong

state: Gyeonggido

address: San 38-2 Namdong, Cheoin-gu

country: South Korea

institute: Myongji University

type: Expression profiling by genome tiling array

summary: For identification of genes up-regulated in OsCc1:AP37, OsCc1:AP59 plants, total RNA (100 μg) was prepared from leaf tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions.

overall_design: Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85 °C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in OsCc1:AP37, OsCc1:AP59 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.

first: Se-Jun

last: Oh

first: Youn

middle: S

last: Kim

first: Chang-Woo

last: Kwon

first: Hye

middle: K

last: Park

first: Ju-Kon


summary: Conduct gene profiling experiment from a melanoma cell line which silenced galectin-3 gene expression to understand different phenotypic properties observed during tumor growth.

overall_design:
A melanoma cell line which silenced galectin-3 gene expression was obtained. This cell line was used in overexpression experiments, using a galectin-3 coding plasmid. Both galectin-3 negative and positive cells were obtained in syngeneic wild type and galectin-3 knockout mice.
Altogether, we had evidence that while galectin-3 derived from the tumor cells impaired tumor growth, galectin-3 derived from stromal cells apparently favored tumor growth. Angiogenic response within tumors derived from galectin-3 expressing melanoma cells was delayed as compared to control conditions. Cells recruited to these distinct microenvironments seem to control tumor growth. Gene profiling of this tissue will allow for an integrative view of the process that was somehow orchestrated by galectin-3.

first: Roger

last: Chammas


title: Bile Salts Influence Virulence Properties of E. coli O157:H7

city: Toronto

first: Debora

last: Foster

state: Ontario

address: 350 Victoria Street

department: Chemistry and Biology

country: Canada

institute: Ryerson University

summary:
Enterohemorrhagic Escherichia coli (EHEC), including serotype O157:H7, cause severe food-borne illness. On route to the human colon, they encounter and resist, numerous anti-microbial ingestion stresses. We hypothesize that these stresses cue EHEC to alter virulence properties. This study investigated the impact of bile salts on virulence properties and examined the genetic basis of the phenotypes.
Established assays were used to examine adhesion to human epithelial cells, motility, verotoxin (VT) production and antimicrobial resistance with/without bile salt stress. Bacteria treated for 90 minute in DMEM plus 0.15% (w/v) bile salt mix demonstrated significantly enhanced adhesion to epithelial cells and resistance to several antibiotics but did not increase motility or VT production. To determine the genetic basis of these phenotypes a microarray experiment was conducted. EHEC strain 86-24, in mid-log phase of growth, were grown in DMEM pH 7.4 (control), or DMEM plus bile salt mix (0.15% w/v), for 90 minutes, statically at 37˚C, 5% CO2 prior to harvesting RNA for the microarray study. Four biological replicates were produced for each treatment. Microarray and gene expression analysis (semi-quantitative RT-PCR and beta-galactosidase reporter assays) of bile salt-treated EHEC revealed significant up-regulation of genes for lipid A modification, fimbriae, an efflux pump, and a two-component regulatory system relative to the bacteria grown in DMEM alone.
This work points to several mechanisms that EHEC employs to resist the stresses of the human small intestine, notably efflux, antimicrobial resistance, and outer membrane alterations. Bile salts enhanced the virulence-related properties of increased adhesion and resistance to antimicrobials but not VT production or motility. This research contributes to our understanding of how EHEC senses and responds to host environmental signals and the mechanisms this pathogen uses to successfully colonize and infect the human host.

overall_design: Bacteria were grown in LB broth overnight with shaking, then subcultured into DMEM and grown statically at 37˚C, 5%CO2 to mid-log phase. Bacteria were then subjected to one of two 90 minute treatments: 1) Control: DMEM pH 7.4, or 2) Bile Salt Stress: DMEM pH 7.4 plus 0.15%, grown statically at 37˚C, 5%CO2.

first: Julianne

middle: V

last: Kus

first: Vica

last: Dang

first: Ahferom

last: Gebremedhin

first: Anca

last: Serbanescu

last: Barnett-Foster


title: Expression analysis of RCc3:OsNAC10 and GOS2:OsNAC10 transgenic rice plants

summary: For identification of genes up-regulated in RCc3:OsNAC10, GOS2:OsNAC10 plants, total RNA (100 μg) was prepared from root and leaf tissues of 14-d-old transgenic and non-transgenic rice seedlings (Oryza sativa cv Nipponbare) grown under normal growth conditions.

overall_design: Expression profiling was conducted using a Rice 3’-Tiling Microarray. Information on the microarray can be found at http://www.ggbio.com (GreenGene Biotech). The Rice 3’-Tiling Microarray was designed from 27,448 genes deposited at IRGSP, RAP1 database (http://rapdb.lab.nig.ac.jp). Among these, 20,507 genes were from representative RAP1 sequences with cDNA/EST supports and 6,941 genes were predicted without cDNA/EST supports. Ten 60-nt long probes were designed from each gene starting 60 bp ahead the end of stop codon with 10 bp shifts in position so that 10 probes covered 150 bp in the 3' region of the gene. In total, 270,000 probes were designed (average size, 60-nt) to have Tm values of 75 to 85C. The microarray was manufactured by NimbleGen Inc. (http://www.nimblegen.com/). Random GC probes (38,000) were used to monitor the hybridization efficiency and fiducial markers at the four corners (225) were included to assist with overlaying the grid on the image. The microarray was used to profile gene expression in RCc3:OsNAC10, GOS2:OsNAC10 and Non-transgenic plants. Cy3-labeled target cDNA fragments were synthesized using a Cy3-9mer primer. For normalization, data were processed with cubic alpine normalization using quartiles to adjust signal variation between chips and with Rubust Multi-Chip Analysis using a median polish algorithm implemented in NimbleScan (Workman et al., 2002; Irizarry et al., 2003). To assess the reproducibility of the microarray analysis, we repeated the experiment three times with independently prepared total RNAs.

first: Kwang

middle: H

last: Baek

first: Harin

last: Jung

first: Sun-Hwa

last: Ha

first: Yang

middle: D

last: Choi

first: Minkyun

first: Christophe

last: Reuzeau


title: Atorvastatin, rosuvastatin and rifampicin effect on human primary hepatocyte transcriptome [Steroltalk platform]

status: Public on Sep 05 2011

city: Ljubljana

first: Peter

last: Juvan

address: Zaloska 4

department: Institute of Biochemistry

country: Slovenia

institute: Faculty of Medicine, University of Ljubljana

summary:
With particular emphasis on interactions between cholesterol homeostasis and drug metabolism we investigate the transcriptome of human primary hepatocytes treated by two commonly prescribed cholesterol lowering drugs atorvastatin and rosuvastatin and by rifampicin that serves as an outgroup as well as a model substance for induction of nuclear receptor PXR.
Expression profiling with dedicated Steroltalk cDNA arrays shows that statins induce extensive transcriptome changes.

overall_design: 10 condition experiment: 3 treatments (atorvastatin, rifampicin, rosuvastatin), each measured at 3 time points (12, 24 and 48 hours), and untreated cells. 3-7 biological replicates for each treatment condition, 20 biological and technical replicates for untreated cells. Common reference design.

first: Mateja

last: Hafner

first: Tadeja

last: Režen

first: Damjana

last: Rozman


title: Gender specific comparisons of gene expression during Zebrafish pectoral fin regeneration

status: Public on Sep 03 2011

city: Durham

first: Michael

last: Czerwinski

state: North Carolina

address: 4034 GSRBII Research Drive

department: Cell Biology

institute: Duke University

summary:
To identify gender specific differences in gene expression during fin rgeneration, pectoral fins were amputated from both male and female adult fish.
Fins were allowed to recover for 4 days in standard tank condtions then tissue was collected for RNA isolation and microarray analysis

overall_design: Pooled samples from male and females, injured and uninjured in biological trilicate.

first: Gregory

last: Nachtrab

first: Kenneth

last: Poss


title: Gene Expression Analysis in the Thalamus and Cerebrum of Horses Experimentally Infected with West Nile Virus

status: Public on Sep 01 2011

city: Gainesville

first: Melissa

last: Bourgeois

state: FL

address: 2015 SW 16th Ave

institute: University of Florida

summary: The purpose of this experiment was to further our understanding of gene expression in the central nervous system (thalamus and cerebrum) after exposure to West Nile virus.   To that end, three different analyses were performed.  The first examined differences in gene expression between horses not vaccinated and exposed to WNV and normal control horses (exposure).  The second examined differences in gene expression between horses not vaccinated and exposed to WNV and horses vaccinated and exposed to WNV (survival).  And the third examined differences between the nonvaccinated cerebrum and nonvaccinated thalamus of horses exposed to WNV (location).

overall_design: Six conditions- Gene expression in the thalamus and cerebrum of three different groups of horses (Non-vaccinated horses exposed to West Nile virus, Vaccinated horses exposed to West Nile virus, normal horses not exposed to West Nile virus).  Biological replicates- 6 normal cerebrums, 6 normal thalamus, 6 vaccinated and exposed cerebrums, 6 vaccinated and exposed thalamus, 6 non-vaccinated and exposed cerebrum, 6 non-vaccinated and exposed thalamus.

first: Bourgeois

last: Melissa

first: Long

last: Maureen


title: Gene expression profiling in primary breast cancer distinguishes patients developing local recurrence after breast-conservation surgery, with or without postoperative radiotherapy.

city: Lund

first: Morten

last: Krogh

address: Skrivarevagen 9

country: Sweden

institute: Amber Biosciences

summary: Gene expression profiling of breast tumors for prognosis of local reccurence.

overall_design: Dual channel arrays with a tumor sample in one channel and a common reference in the other channel.

first: Emma

last: Niméus-Malmström

first: Per

last: Malmström

first: Carina

last: Strand

first: Irma

last: Fredriksson

last: Karlsson

first: Bo

last: Nordenskjöld

first: Olle

last: Stål

first: Görel

last: Östberg

first: Carsten

last: Peterson

first: Mårten

last: Fernö


title: Sporisorium reilianum Infection Changes Inflorescence and Branching Architectures of Maize

city: Giza

first: Hassan

middle: Abdelalim

last: Ghareeb

address: El Buhouth Str., Dokki

department: Department of Plant Biotechnology

country: Egypt

institute: National Research Centre

summary: S. reilianum triggered loss of organ and meristem identity, and loss of meristem determinacy in male and female inflorescences and flowers. Microarray analysis showed that these developmental changes were accompanied with transcriptional regulation of genes proposed to regulate floral organ and meristem identity, and meristem determinacy in maize.

overall_design:
Infected ears were compared with mock infected ears. Each treatment had 3 biological replicates
Disease: S. reilianum-infected ears with elongated kernel: Zm_Sr5_15_2_Leafy ears4weeks_I, Zm_Sr5_15_2_Leafy ears4weeks_II, Zm_Sr5_15_2_Leafy ears4weeks_III
Disease: Mock infected ears at: Zm_Sr5_15_2_Mock4weeks_I, Zm_Sr5_15_2_Mock4weeks_II, Zm_Sr5_15_2_Mock4weeks_III
biological replicate:  Zm_Sr5_15_2_Leafy ears4weeks_I, Zm_Sr5_15_2_Leafy ears4weeks_II, Zm_Sr5_15_2_Leafy ears4weeks_III
biological replicate: Zm_Sr5_15_2_Mock4weeks_I, Zm_Sr5_15_2_Mock4weeks_II, Zm_Sr5_15_2_Mock4weeks_III

first: Annette

last: Becker

first: Tim

last: Iven

first: Ivo

last: Feussner

first: Jan

last: Schirawski


title: DNA Methyltransferase 1 and DNA Methylation Patterning Contribute to Germinal Center B-Cell Differentiation

city: New York

first: Rita

last: Shaknovich

state: NY

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medical Center

type: Methylation profiling by genome tiling array

summary: We performed DNA methylation (HELP) and gene expression profiling in 17 samples of purified Germinal center B cells (GCBs) and Naive B cells (NBC).  We performed  supervised analysis using HELP data and defined DNA methylation signature differentiting 2 subgroups of B cvells.

overall_design: Study included purification of human B cells form reactive tonsils, DNA purification and DNA methylation analysis using HELP assay.

first: Leandro

last: Cerchietti

first: Ari

last: Melnick

first: Olivier

last: Elemento


title: The human Whole miRNOme project version 1

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

summary: This project analyzes peripheral blood profiles of controls and patients of 14 different diseases, all collected, measured, and analyzed using exactly the same SoP. Since miRNAs are known to be valuable diagnostic markers we asked whether respective patterns of patients can be detected in peripheral blood samples rather than in biopsies. The project aimed at an impoved understanding of complex profiles rather than single markers. Thus, a high-throughput technique was necessary, profiling all known miRNAs integratively and combining different diseases to achieve a high degree of specificity.

overall_design: A total of 454 samples was screened, containing patients with different cancer types (lung cancer, melanoma, prostate cancer, wilms tumors, tumor of stomach, pancreatic cancer, ovarian cancer), autoimmune diseases (multiple sclerosis), cardiovascular (acute myocardial infarction), and chronic inflammatory diseases (sarcoidosis, periodontitis, pancreatitis, chronic obstructive pulmonary diseases), as well as healthy control individuals. Please note that each miRNA has been measured in at least seven replicates and the median of the replica has been computed.

first: Petra

last: Leidinger


title: Transcriptomic response to variation in habitual n-3 polyunsaturated fatty acid intake

city: Dublin

first: Helen

middle: M

last: Roche

state: Belfield

address: UCD Conway Institute of Biomolecular and Biomedical Research

country: Ireland

institute: University College Dublin

summary: Analysis of variation in subcutaneous adipose tissue gene expression in response to dietary intake of n-3 polyunsaturated fatty acids, as assessed in a cohot of individuals with metabolic syndrome. Outcomes from this study provide insight on molecular details of dietary effects on gene expression and metabolic health.

overall_design: Subcutaneous adipose tissue samples were taken from a cohort of seventeen individuals with metabolic syndrome. Habitual intake of n-3 polyunsaturated fatty acids was assessed with 3-day weighed food journals.


title: Expression profiling of the Staphylococcus aureus GraSR regulon

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary: The GraS/GraR two-component system has been shown to control cationic antimicrobial peptide (CAMP) resistance in the major human pathogen Staphylococcus aureus. We identified a highly conserved ten base pair palindromic sequence (5’ ACAAATTTGT 3’) located upstream from GraR-regulated genes (mprF and the dltA and vraFG operons), which we show to be essential for transcriptional regulation by GraR and induction in response to colistin, a bacterial CAMP, suggesting it is the likely GraR binding site. Genome-based predictions and transcriptome analysis revealed several novel GraR target genes.

platform_organism: Staphylococcus aureus subsp. aureus NCTC 8325

overall_design: Global expression changes between the wild type strain HG001 (a rsbU+ variant of strain NCTC 8325) and a DgraSR mutant, grown to mid-exponential phase in TSB with 50 µg/ml colistin, were examined. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

first: Melanie

last: Falord

first: Tarek

last: Msadek


title: Identification of early target genes of the DELLA protein GAI in etiolated seedlings

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

summary: The hormones gibberellins (GA) control many aspects of plant growth and development thruough the whole life cycle of the plant. For instance, GA participate in the establishment of the skotomorphogenic developmental program that is triggered when seeds germinate in darkness, i.e. under the soil. Under these conditions seedlings appear etiolated and developmental features usually triggered by light are kept repressed. The GA signaling elements GAI and RGA have a major, partially redundant role in this process. These proteins belong to the DELLA family of transcriptional regulators and are destabilized by GA, acting as negative regulators of the pathway. In order to understand the molecular basis of the regulation of the skotomorphogenesis by GA, we sought to identify early target genes of the activity of GAI in etiolated seedlings. For that purpose we analyzed rapid, global changes in gene expression in response to a transient accummulation of a dominant version of GAI, gai-1, which is resistant to GA-induced destabilization.

overall_design: Experiments were performed using wild type Col-0 and the transgenic line HS:gai-1 that expresses the dominant version gai-1 under the control of the promoter of the HSP18.2 gene, which is highly and rapidly induced at 37ºC. Three biological repeats were performed, and wild type and transgenic samples were labelled with Cy3 and Cy5, respectively. For each point in the time course (0, 1, 2 and 4h after a 30 minute treatment at 37ºC), a sample from the transgenic line was compared to the corresponding wild type control.

first: Javier

last: Gallego-Bartolomé

first: Miguel

middle: A

last: Blázquez

last: Alabadí


title: Effects of the total replacement of fish meal and fish oil with plant protein and oil sources on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) sub-families exhibiting different growth potentials on an all plant-based diet

city: Brest

last: Mazurais

address: tecnopole Brest Iroise

country: France

institute: Ifremer

summary: Comparison of the hepatic transcriptomes for two half-sib-families of European sea bass fed on vegetable and fish diet. These two half-sib-families exhibit similar growth on fish diet while significantly different on vegetable diet. The aim of the study is to point out the large panel of metabolic and physiological effects induced by total substitution of both fish meal and fish oil in the diets of European sea bass and to reveal physiological characteristics associated to the two half-sib-families.

overall_design: Fish from both two half-sib-families (G and g) were fed a a fish diet (FD) or a vegetable diet (VD) diet for 9 months.  Five to eight independent experiments were performed for each experimental groups (G-FD; G-VD; g-FD; g-VD)  using different fishes for each experiment.

first: Florian

last: Geay

first: Serena

last: Ferraresso

first: Lucas

last: Bargelloni


title: Differential gene expression analysis in Enchytraeus albidus exposed to natural and chemical stressors at different exposure periods

city: Aveiro

first: Sara

last: Novais

address: Campus de Santiago, Department of Biology, University of Aveiro

department: Biology

country: Portugal

institute: CESAM & University of Aveiro

summary: The soil oligochaete Enchytraeus albidus is a standard test organism used in biological testing for Environmental Risk Assessment (ERA). Although effects are known at acute and chronic level, through survival, reproduction and avoidance behaviour endpoints, very little is known at the sub-cellular and molecular levels. In this study, the effects of soil properties (clay, organic matter and pH) and of the chemicals copper and phenmedipham were studied on gene expression in E. albidus during exposure periods of 2 days, 4 days and 3 weeks, using DNA microarrays based on a normalised cDNA library for this test species (Amorim et al., 2011) The main objectives of this study were: 1) to assess changes in gene expression of E. albidus over time, and 2) to identify molecular markers for natural and chemical exposures. Results showed a clear influence of exposure time in gene expression. Transcriptional responses to phenmedipham were seen at 2 days while the responses to copper and the different soils were more pronounced at 4 days of exposure. Some genes were differentially expressed in a stress specific manner and, in general, the responses were related with effects at energy metabolism and cell growth level.

overall_design: Fluorescently labelled cDNA, from enchytraeids exposed during 4 days and 3 weeks to control soil (LUFA 2.2) and to the different exposure conditions was synthesized for microarray analysis and hybridizations were performed. After scanning, spots were identified and ratios quantified using the QuantArray (Packard Biochip Technologies). Statistical analysis of the microarrays was performed using limmaGUI package (1.18.0) (Smyth, 2005) in the R (2.8.0) software environment (http://www.R-project.org/). After being submitted to local background subtraction, microarrays were normalized using global loess method. To statistically evaluate the differential gene expression between the different conditions, a gene-per-gene linear model (limma – linear model for microarray analysis) and empirical Bayes methods were applied. The results were then corrected for multiple testing using the Benjamini-Hochberg’s method (adjusted p<0.05 was considered significant) (Benjamini and Hochberg, 1995).

middle: C

first: Clara

last: Howcroft-Ferreira

first: Laura

last: Carreto

first: Patrícia

last: Pereira

first: Manuel

last: Santos

first: Wim

last: De Coen

first: Amadeu

last: Soares

first: Mónica

middle: J

last: Amorim


title: affy_petaldvt_lyon_rose: Flower/Petal initiation and development in roses

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
affy_petaldvt_lyon_rose. The objective is to identify genes involved in petal development in rose. We aim at identifying genes whose expression correlates with flower opening and scent emission. In this study, we used a microarray approach to compare the transcriptome of a scented rose flower (PF) versus non-scented rose flower (RF). Samples (petal tissues) were collected at the same time early in the afternoon. Total RNA was extracted using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays.

Keywords: scented vs non-scented flowers

overall_design:
4 arrays - rose.
Scented and non-scented flowers, 2 replicates each.

first: Sandrine

last: Balzergue

first: Mohammed-

last: Bendahmane

first: Sylvie

last: Baudino

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Human adenoid cystic carcinoma vs. human normal lymphocyte

city: Ube

first: Atsunori

last: Oga

state: Yamaguchi

address: Minami-Kogushi 1-1-1

department: Pathology

country: Japan

institute: Yamaguchi University

type: Genome variation profiling by genome tiling array

summary:
We analyzed ten adenoid cystic carcinomas of head and neck by array-based comparative genomic hybridization (a-CGH) using DNA chips spotted 4,030 BAC clones. After data smoothing by the adaptive weights smoothing (AWS) procedure with the gain and loss analysis of DNA (GLAD) algorithm, a total of 89 DNA copy number aberrations (DSCNAs) were detected. The frequent (≥30%) DSCNAs were loss of 6q24, 6q25, 8p23, 6q25, and 6q23 and gains of 6q23, 8p23, 9p11-13, and 22q13. High-level gain was detected on 12q12-15 including MDM2 in two cases. These two cases showed immunohistochemically positive status of MDM2 and negative status of p53 and p21. Furthermore, the total number of DSCNAs was significantly greater in ACC with loss of 6q than in other ACC, in ACC without loss of 8p23 than in other ACC, and in ACC with 8p23 gain than in ACC with 8p23 loss, respectively. Though there is a limit in the evidence, a-CGH detected several candidate chromosomal imbalances associated with DSCNA accumulation in ACC.
6q loss, 12q gain

overall_design: aCGH DNA copy number aberrations screening in human cancer adenoid cystic carcinoma (ACC).

first: A


title: affy_duplicature_lyon_rose. Double flower phenomenon: Control of petal number in roses

summary:
affy_duplicature_lyon_rose. The objective is to identify the genes involved in petal doubling in rose. In this study we are using two rosa gallica genotypes: wild-type (simple flower rose) and Cardinal de Richelieu (double flower rose), and two rosa hybrida genotypes : Souvenir de la Malmaison, which has about 110 petal, and its bud sport cultivar, Souvenir de St Anne’s. In this study, we used a microarray approach to compare the transcriptome of double flower rose (CDR) versus simple flower rose (G). The objective is to identify genes whose expression is associated with the double flower phenotype. These genes are putative candidates involved in the control of petal organ number per flower. Floral buds were dissected under a microscope and pooled in eppendorf tubes. Tissue samples were harvested at the same time during 3 weeks in April 2007. Total RNA was extracted from the pools of flowers using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays.

Keywords: genotype comparison

sample_organism:
Rosa gallica
Rosa hybrid cultivar

overall_design:
8 arrays - rose.
4 genotypes, 2 replicates each.

first: Olivier-

last: Raymond

first: Annick

last: Dubois


title: Human lung ADC and SCC comparsion study

status: Public on Aug 31 2011

city: Oxford

first: Jiangting

last: Hu

state: Oxfordshire

address: Headley Way

department: NDCLS

country: United Kingdom

institute: University of Oxford

summary: Gene expression profiling comparing biological mechanisms for lymphatic metastases in lung adenocarcinoma and squamous cell carcinoma

overall_design: Two-condition comparison: primary invasive tumors (TN+),  without lymph node metastasis (TN-),  matched tumor cells in metastatic lymph nodes (MT) in ADC and SCC separately

last: hu

first: Laticia

last: Campo

first: Graham

last: Steer

first: Zainina

last: Seman

first: Kevin

last: Gatter

first: Alfredo

last: Cesario

first: Ugo

last: Pastorino

first: Francesco

last: Pezzella


title: Systems analysis identifies an essential role for SHARPIN in macrophage TLR2 responses (Affymetrix)

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

institute: Seattle Biomedical Research Institute

summary: Our systems analysis reported here demonstrates that TLR-responses in macrophages are markedly impaired by SHARPIN deficiency, and that SHARPIN controls expression of a subset of TLR2-induced, NF-kB and AP-1 dependent genes that overlaps with those affected by the hypomorphic panr2 mutation in NEMO.

overall_design:
46 total RNA samples from murine bone marrow derived macrophages were analyzed (32 by Agilent array, 14 by Affymetrix Exon array)

On Affymetrix Exon array, the responses of macrophages to 12hr stimulation with the TLR2 ligand PAM3CSK4 (300ng/mL) were analyzed in biological duplicates for the Map3k8(sluggish) mutant and respective controls and in singlet for the Tnf(KO) mutant compared to two respective WT controls.

middle: E

first: Frank

last: Schmitz

first: Bruce

last: Beutler

first: Alan

last: Aderem


title: Chip-chip from Human Pulmonary Fibroblasts with H3K9me2 antibody

status: Public on Aug 29 2011

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 N. Wolfe Street

department: Center for Epigenetics and Department of Medicine

institute: Johns Hopkins University

type: Genome binding/occupancy profiling by genome tiling array

summary: Histone modification H3K9me2 is associated heterochromatin and gene silencing, but the relationship between DNA methylation and H9K9me2 haven’t been checked in a genome-wide scale. This dataset was generated to compare with genome-wide DNA methylation data.

overall_design: Genome-wide distribution of H3K9me2 in human fibroblasts was mapped using ChIP-chip.

first: Bo

last: Wen

first: Hao

last: Wu

middle: P


title: Comparison of Gene expression profiles between myometrium, MED12 mutation positive uterine leiomyomas and MED12 wildtype uterine leiomyomas

status: Public on Aug 26 2011

city: Helsinki

first: Miika

last: Mehine

address: P.O. Box 63 (Haartmaninkatu 8)

country: Finland

institute: University of Helsinki

summary: Gene expression profiles of 10 uterine leiomyomas and their matched normal myometrium specimens were studied using Affymetrix GeneChip   Human Genome U133 Plus 2.0 gene expression arrays. Four tumors displayed a codon 44 mutation, four carried a intron 1 mutation, and the remaining two displayed no MED12 mutation.

overall_design: Unsupervised hierarchical clustering was performed to assess similarity in gene expression profiles between myometrium, MED12 mutation positive uterine leiomyomas and MED12 wildtype uterine leiomyomas. Gene expression data from the MED12 mutation positive leiomyomas was compared to matched myometrium to identify differentially expressed genes.

first: Taru

last: Koski

first: Massimiliano

last: Gentile

first: Eevi

last: Kaasinen

first: Yilong

last: Li

first: Heli

last: Lehtonen

first: Netta

last: Mäkinen

first: Jian

last: Yan

first: Martin

last: Enge

first: Minna

last: Taipale

first: Mervi

last: Aavikko

first: Riku

last: Katainen

first: Elina

last: Virolainen

first: Tom

last: Böhling

first: Jaana

last: Tolvanen

first: Virpi

last: Launonen

first: Jari

last: Sjöberg

first: Jussi

first: Pia

last: Vahteristo

first: Lauri

last: Aaltonen


title: Salmonella wild type and mutant baeR in LB and tungstate

status: Public on Aug 30 2011

city: Norwich

first: Corinne

last: Appia-Ayme

state: Norfolk

address: UEA

department: BIO

institute: University of East Anglia

summary: Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and deleted of the response regulator encoding gene baeR grown to OD600=1 in LB alone or in LB supplemented with 20mM of Sodium Tungstate. The goal is to determine Salmonella response to tungstate and to define the BaeR regulated genes in this conditions.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

platform_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

platform_organism: Salmonella enterica subsp. enterica serovar Enteritidis str. P125109

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

overall_design: 4 differents conditions tested, the reference on each hybridisation is the chromosomique DNA of the wild type strain. 3 replicates for the wild type on LB, 3 replicates for the baeR on LB, 3 replicates for the wild type on LB+ tungstate and 5 replicates for baeR on LB+tungstate.

first: Gary

last: Rowley


title: Gene expression profiling of high (HAB) vs. low (LAB) anxiety-related behavior mice in seven brain regions.

city: München

first: Ludwig

last: Czibere

address: Kraepelinstrasse 2

institute: Max Planck Institute of Psychiatry

summary:
Investigating the molecular basis and correlates of anxiety-related and depression-like behaviors, we generated a mouse model consisting of high (HAB) and low (LAB) anxiety-related behavior mice. We utilized the elevated plus-maze for testing the genetic predisposition to anxiety-related behavior and, consequently, used this as selection criterion for the inbreeding of our animals. In depression-related tests, HAB mice display a more passive, depression-like coping strategy than LAB mice, resembling clinical comorbidity of anxiety and depression as observed in psychiatric patients.
Using a microarray approach, the hypothalamic paraventricular nucleus (PVN), the basolateral/lateral (BLA), the medial (MeA) and central amygdala (CeA), the nucleus accumbens (NAc), the cingulate cortex (Cg) and the supraoptic nucleus (SON) – centers of the central nervous anxiety and fear circuitries – were investigated and screened for differences between HAB and LAB mice.

overall_design: Analysis was performed from six animals per line (HAB and LAB, respectively) pooled per brain region in ten technical replicates, thereof five with a dye-swapped design giving a total of 70 array slides analyzed. The LAB mouse line is referred to as reference.

first: Peter

last: Weber

first: Benno

last: Pütz

first: Markus

last: Panhuysen

first: Melanie

last: Keßler

first: Claudia

last: Kühne

first: Florian

last: Holsboer

first: Jan

last: Deussing

first: Rainer

last: Landgraf


title: Expression profiling in Macaca fascicularis liver samples

status: Public on Aug 25 2011

city: Basel

first: Tobias

last: Heckel

address: Grenzacherstr. 124

country: Switzerland

institute: F.Hoffmann-La Roche AG

summary: The long-tailed macaque, also referred to as cynomolgus monkey (Macaca fascicularis), is one of the most important non-human primate animal models in basic and applied biomedical research. To improve the predictive power of primate experiments for humans, we determined the genome sequence of a Macaca fascicularis female of Mauritian origin using a whole-genome shotgun sequencing approach. We applied a template switch strategy which employs either the rhesus or the human genome to assemble sequence reads. The 6-fold sequence coverage of the draft genome sequence enabled discovery of about 2.1 million potential single-nucleotide polymorphisms based on occurrence of a dimorphic nucleotide at a given position in the genome sequence. Homology-based annotation allowed us to identify 17,387 orthologs of human protein-coding genes in the M. fascicularis draft genome and the predicted transcripts enabled the design of a M. fascicularis-specific gene expression microarray. Using liver samples from 36 individuals of different geographic origin, we identified 718 genes with highly variable expression in liver, whereas the majority of the transcriptome shows relatively stable and comparable expression. Knowledge of the M. fascicularis draft genome is an important contribution to both the use of this animal in disease models and the safety assessment of drugs and their metabolites. In particular, this information allows high-resolution genotyping and microarray-based gene expression profiling for animal stratification, thereby allowing the use of well-characterized animals for safety testing. Finally, the genome sequence presented here is a significant contribution to the global "3R" animal welfare initiative, which has the goal to reduce, refine and replace animal experiments.

overall_design:
A 36-microarray study using total RNA recovered from liver samples of untreated Cynomolgus monkeys of good laboratory practice (GLP) drug safety studies. The monkeys were from the Philippines, a Chinese colony, and Mauritius. Each microarray measures the expression level of 16,896 genes using 20,047 probe sets with six 60-mer probes (PM) per probe set. Each probe set is represented once on the array.

The Cynomolgus monkey gene expression results analyzed in this study are further described in Ebeling et al. (2011) (PMID 21862625).

first: Angela

last: See

first: Ulrich

last: Certa


title: Transcriptomic analysis reveals cold responsive genes implicated in peach low temperature tolerance

city: Legnaro

first: claudio

last: Bonghi

state: Padova

address: Viale dell'UNiversità, 16

country: Italy

institute: University of Padova

summary: A transcriptome analysis was applied on two peach (Prunus persica L.) cultivars with different sensitivity to low temperature regimes to identify cold-responsive genes that might be involved in tolerance to long low temperature storage. Peach fruit from ‘Morettini No2’ and ‘Royal Glory’, a sensitive and a tolerant, to chilling injury cultivars, respectively, were harvested at commercial maturity stage and allowed to ripen at room temperature (25°C) or subjected to 4 and 6-weeks of cold storage (0°C, 95% R.H.) followed by ripening at room temperature. Microarray experiments, employing the peach microarray platform (μ PEACH 1.0), were carried out by comparing harvested fruit against 4- and 6-week cold-stored fruit. The analysis identified 173 and 313 genes that were differentially expressed in ‘Morettini No2’ and ‘Royal Glory’ fruit after 4 weeks, respectively. However, the 6 weeks cold storage provoked a decrease in the total number of genes differentially expressed in both cultivars. RNA blot analysis validated the differential expression of certain genes showed in microarray data. Among these genes, two heat shock proteins (hsps), a putative β-D-xylosidase, an expansin, a dehydrin and a pathogenesis-related protein PR-4B precursor were induced during cold storage in both cultivars. The induction of hsps and the putative β-D-xylosidase appeared to be independent on the duration of postharvest treatment. On the other hand, transcript levels of lipoxygenase were quite constant during postharvest ripening, while a strong reduction or disappearance was observed after cold storage. A dehydration-induced RD22-like protein showed a reduction in the accumulation of transcripts during postharvest ripening independently on the temperature conditions. Overall, the current study shed some light on the molecular aspects of cold stress in peach fruit quality and identified some ripening and/or cold-induced genes which function need further elucidation.

overall_design: A direct comparison approach has been used to investigate the effect at the transcriptional level of 4 (4w) or 6 (6w) weeks of cold storage  (0°C, 95% R.H.) plus 1 day at room temperaure on ripe peaches  (Prunus persica cv Morettini N°2 and Royal Glory). RNA has been extracted from either cold stored fruit and from fruit  at harvest   plus 1 day at room temperature (control). At least four hybridization have been conducted for a total of four technical replicates (with dye-swap).

first: Claudio

first: Vanessa

last: Falara

first: George

last: Manganaris

first: Fiorenza

last: Ziliotto

first: A

first: Angelo

last: Ramina

first: Angelos

last: Kanellis


title: Characterisation of modular response of  E. coli Keio collection mutant library to acid adaptation

status: Public on Aug 24 2011

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

institute: University of Birmingham

summary:
To study the dynamics of acid adaptation in E.coli Keio collection mutant library at pH7 and pH5.5 after 15 minutes of adaptation

Keywords: Single channel hybridisation were carried out using cy5 dye.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Samples were collected from steady state system at pH7 and at pH5.5 after 15 minutes of adaptation

first: Nazish

last: Daudi

first: Francesco

last: Falciani


title: A metabolomics analysis of gallbladder lipid droplet formation due to Salmonella infection

status: Public on Aug 23 2011

city: Vancouver

first: L. Caetano

middle: M.

last: Antunes

state: BC

department: Michael Smith Laboratories

institute: The University of British Columbia

summary: To cause disease, Salmonella enterica serovar Typhimurium requires two type-III secretion systems, encoded on Salmonella Pathogenicity Islands 1 and 2 (SPI-1 and -2). These secretion systems serve to deliver virulence proteins, termed effectors, into the host cell cytosol. While the importance of these effector proteins to promote colonization and replication within the host has been established, the specific roles of individual secreted effectors in the disease process are not well understood. In this study, we used an in vivo gallbladder epithelial cell infection model to study the function of the SPI-2-encoded effector, SseL. Deletion of the sseL gene resulted in bacterial filamentation and elongation and unusual localization of Salmonella within infected epithelial cells. Infection with the ΔsseL strain also caused dramatic changes in lipid metabolism and led to massive accumulation of lipid droplets in infected cells. Some of these changes were investigated through metabolomics of gallbladder tissue. This phenotype was directly attributed to the deubiquitinase activity of SseL, as a Salmonella strain carrying a single point mutation in the catalytic cysteine resulted in the same phenotype as the deletion mutant. Excessive buildup of lipids due to the absence of a functional sseL gene was also observed in S. Typhimurium-infected livers. These results demonstrate that SseL alters host lipid metabolism in infected epithelial cells by modifying ubiquitination patterns of cellular targets.

overall_design: Female C57BL/6 mice were infected with the indicated strain of Salmonella enterica serovar Typhimurium by oral gavage. Four gallbladders were collected and pooled per sample group and metabolites extracted using a mixture of methanol and chloroform. Extracts were infused into a 12-T Apex-Qe hybrid quadrupole-FT-ICR mass spectrometer equipped with an Apollo II electrospray ionization source, a quadrupole mass filter and a hexapole collision cell. Raw mass spectrometry data were processed as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140). To identify differences in metabolite composition between different groups of samples, we filtered the list of masses for metabolites which were present on one set of samples but not the other. Additionally, we calculated the ratios between averaged intensities of metabolites from each group of mice. To assign possible metabolite identities, monoisotopic neutral masses of interest were queried against MassTrix (http://masstrix.org). Masses were searched against the Mus musculus database within a mass error of 3 ppm.

first: Ellen

last: Arena

first: Sigrid

last: Auweter

first: Wayne

last: Vogl

first: L

first: Jun

last: Han

first: Julian

last: Guttman

first: Matthew

last: Croxen

first: Alfredo

last: Menendez

first: Christoph

last: Borchers

first: B

middle: B

last: Finlay


title: affy_floral_rose-Study of floral initiation and recurrent blooming in rose

first: sandrine

last: balzergue

summary:
affy_floralangers_rose - affy_floral_rose - - Which genes are induced during floral initiation? - Are the genes involved in floral initiation identical between our 3 genotypes? - Which genes are involved in the control of recurrent blooming in rose? - Which genes are diferentially expressed between buds that will become floral and buds that will remain vegetative?-This project aims to find in rose genes involved in flowering control (floral initiation and recurrent flowering). First, the floral initiation will be observed in 3 genotypes. Then we will check if same genes are regulated within genotypes for this process. Concerning recurrent blooming, we will compare flower bud versus vegetative buds in non-recurrent conditions and finally bud from non-recurrent and recurrent genotypes.

Keywords: time course

sample_organism:
Rosa lucieae
Rosa hybrid cultivar

overall_design: 26 arrays - rose

first: Sandrine

last: Balzergue

first: Arnaud

last: Remay

first: Fabrice

last: Foucher

first: Marie-Laure

last: Martin-Magniette


title: B. japonicum USDA110 low manganese vs. high manganese

city: Buffalo

first: Mark

middle: R.

last: O'Brian

address: 140 Farber Hall

department: Biochemistry

institute: State University of New York at Buffalo

summary: Transcriptional profiling of B. japonicum manganese responsive cells and mur mutant responsive cells

overall_design: 3 independent biological materials were prepared for Wt manganese deplete, replete cultured cells and mur mutant manganese replete cultured cells

first: Thomas

last: Hohle

first: William

last: Franck

first: Gary

last: Stacey

middle: R


title: E. faecalis transcriptional responses to copper stress

status: Public on Aug 22 2011

city: Oeiras

first: Marta

middle: Coelho

last: Abrantes

address: Av. da República - EAN

institute: ITQB-UNL

summary: Transcriptional profiling of Enterococcus faecalis V583 comparing the transcriptome of cells grown in M17 + glucose 0.5% (GM17) with the transcriptome of cells grown in M17 + glucose 0.5% + 0.05 mM CuSO4

overall_design: 2 condition experiment: V583 grown in GM17 vs. V583 grown in GM17 + 0.05mM CuSO4. Three biological replicates, one of which is a dye-swap. Three replicates per array.

first: Maria

last: de Fátima Lopes

first: Jan

last: Kok


title: Breast, colon, glioblastoma, lung, melanoma, ovarian, pancreas, prostate tumors and cell lines.

city: Woodbury

first: Yi

last: Su

state: New York

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Lab

summary: DNA copy number profiling for all primary tumor samples and cell lines was performed by ROMA, a form of comparative genomic hybridization.  The aim was to identify commonly amplifiied and deleted regions.

overall_design: 538 primary tumor samples and 253 human cell lines were analyzed.

first: Scott

last: Powers

first: Ken

last: Nguyen


title: Diclofenac affects global hepatic gene expression in fish at plasma concentrations similar to human therapeutic levels

city: Göteborg

first: Erik

last: Kristiansson

address: Chalmers Tvärgata 3

department: Department of Mathematical Sciences

institute: Chalmers University of Technology

summary:
Background: Diclofenac is a non-steroidal anti-inflammatory drug frequently found in the aquatic environment. Previous studies have reported histological changes in the liver, kidney and gills of fish at concentrations similar to those measured in treated sewage effluents (~1 µg/L). Analyses or predictions of blood plasma levels in fish allow a direct comparison with human therapeutic plasma levels, and may therefore be used to indicate a risk for pharmacological effects in fish. To relate internal exposure to a pharmacological interaction we therefore investigated global hepatic gene expression together with bioconcentration to blood plasma and liver of rainbow trout (Oncorhynchus mykiss) exposed to waterborne diclofenac.

Results: At the highest exposure (81.5µg/L) the fish plasma concentration reached ~88% of the human therapeutic levels (Cmax) after two weeks. Using an oligonucleotide microarray followed by quantitative PCR we found extensive effects on hepatic gene expression at this concentration, and some genes were regulated down to the lowest concentration tested (1.6 µg/L) corresponding to ~1.5% of the human Cmax. Functional analysis of differentially expressed genes revealed effects on biological processes such as inflammation and immune response, in agreement with the expected mode of action of diclofenac. In contrast to some previously reported results, the bioconcentration factor was found to be stable (4.02±0.75 for blood plasma and 2.54±0.36 for liver) regardless of the water concentration.

Conclusions:  Hepatic gene expression is affected in fish at blood levels similar to and below the human Cmax. This adds confidence to the use of fish blood plasma levels to predict risks for pharmacological responses in fish. The microarray results indicate similarities in the mode of action of diclofenac between humans and fish. The identified set of regulated genes may contain useful exposure biomarkers to be used in complex exposure scenarios.

overall_design:
Juvenile rainbow trout was exposed to waterborne diclofenac at a series of different concentrations for 14 days. A flow-through system was used for eight aquaria (two per concentration), each containing 12 trouts. Nominal exposure concentrations: 1µg/L, 10 µg/L, 100 µg/L and control.

Total RNA for biotinylated aRNA synthesis was extracted from the liver. Samples of aRNA from two fish from the same aquarium were pooled before the assay. In total, four biochips were analyzed corresponding to 32 microarrays. As we used two aquaria per concentration, these 32 microarrays allowed the analyses of four aRNA pools (eight fish) per aquarium, which is equal to eight pools per concentration of diclofenac.


title: E. faecalis transcriptional responses to manganese stress

summary: Transcriptional profiling of Enterococcus faecalis V583 comparing the transcriptome of cells grown in M17 + glucose 0.5% (GM17) with the transcriptome of cells grown in M17 + glucose 0.5% + 4 mM MnSO4

overall_design: 2 condition experiment: V583 grown in GM17 vs. V583 grown in GM17 + 0.4mM MnSO4. Three biological replicates, one of which is a dye-swap. Three replicates per array.

last: de Fa¡tima Lopes


title: Comparison of the expression profiles of 630E strain and a sigH mutant after 10h of growth

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

summary: Transcriptionnal profiling of C. difficile 630E strain vs a sigH mutant after 10h of growth in TY

overall_design: Two-conditions experiments, 630E strain 10h vs sigH mutant 10h, 4 biological replicates for each condition

first: Laure

last: Saujet

first: Marc

last: Monot


title: Comparison of the expression profiles of 630E strain after 4h and 10h of growth

summary: Transcriptional profiling of C. difficile 630E strain after 4h vs 10h of growth

overall_design: Two-conditions experiments, 630E strain 4h vs 630E strain 10h, 4 biological replicates for each condition


title: Nucleosome mapping data from GR and cell-cycle regulated genes in human cell lines

status: Public on Aug 21 2011

city: Boston

first: Gavin

last: Schnitzler

state: MA

address: 800 Washington St. Box 80

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

summary:
Human UL3 cells (U20S derivatives containing GR and an MMTV-luc transgene) were treated with dexamethasone for 0, 1 or 4 hrs. Chromatin was harvested, digested with to ~70% mononucleosomes with MNase, and isolated mononucleosome fragments were used to probe custom Nimblegen genomic tiling microarrays.
In addition, human HL60 cells were treated with or without DMSO to induce granulocyte differentiaton, and mononucleosome positions mapped. MNase digested bare DNA fragments of ~500 bp average length from UL3 cells was used as a control.

overall_design: Mononucleosome positions at tiled genes for UL3 cells +/- dexamethasone and HL60 cells +/- DMSO.


title: Expression analysis of Shewanellla oneidensis MR-1  to Fe nanoparticle decorated anodes in microbial electrolysis cells

status: Public on Aug 20 2011

city: corvallis

first: Shoutao

last: Xu

state: OR

address: 116 gilmore hall, OSU

department: Department of biological and ecological engineering

institute: oregon State University

summary: Investigation of whole genome gene expression level changes in a Shewanella oneidensis MR-1 to Fe nanoparticle decorated anodes, compared to the carbon plate anodes in microbial electrolysis cells. Whole genome microarray analysis of the gene expression showed that the encoding biofilm formation genes were significantly up-regulated as response to nanoparticle decorated anodes which indicated thickness improvements contributed to enhance current density. The increased expression genes related to nanowire, flavins and c-type cytochromes also have partially contributed to enhance current density by Fe nanoparticle decorated anode. The majority of additional differentially expressed genes associated with electron transport, anaerobic metabolism in response to the nanostructured anodes possibly play roles in current density enhancement.

overall_design: A six chip study using total RNA recovered from three separate replicates of biofilm on Fe Nanoparticle decorated anode of Shewanella oneidensis MR-1 and three separate replicates of carbon plate control.  Each chip measures the expression level of 4,295 genes .

first: Hong

last: Liu

first: Frank

last: Chaplen


title: E. faecalis transcriptional responses to zinc stress

summary: Transcriptional profiling of Enterococcus faecalis V583 comparing the transcriptome of cells grown in M17 + glucose 0.5% (GM17) with the transcriptome of cells grown in M17 + glucose 0.5% + 4 mM ZnSO4

overall_design: 2 condition experiment: V583 grown in GM17 vs. V583 grown in GM17 + 4mM ZnSO4. Two biological replicates and a dye-swap. Three replicates per array.


title: Bacitracin upregulates mbrAB transcription via mbrCD to confer bacitracin resistance in Streptococcus mutans

status: Public on Aug 18 2011

city: Chiyoda-ku

first: Hiromasa

last: Tsuda

state: Tokyo

address: 1-8-13 Kanda-surugadai

institute: Nihon University School of Dentistry

summary: Streptococcus mutans is a bacterial cause of dental caries that is resistant to bacitracin. This study aimed to elucidate the mbrABCD-related bacitracin resistance mechanism of S. mutans. Transcriptome data demonstrated that 33 genes were induced more than 2 times in expression by bacitracin. Fourteen genes were selected from the upregulated genes and each defective mutants were constructed for measurement of their sensitivity to bacitracin. Among the mutants, only the mbrA- or mbrB-deficient mutants exhibited 100 to 121-fold greater sensitivity to bacitracin when compared with the wild-type strain. Moreover, knockout of the mbrC and mbrD genes abolished the bacitracin-induced mbrAB upregulation. These results suggest that bacitracin upregulates mbrAB transcription via mbrCD, which confers the bacitracin resistant phenotype on S. mutans.

overall_design: Single experiment data using Streptcoccus mutans wild-type strain UA159, a comparison of transcriptome between control sample and experimental (bacitracin-treated) one.

first: Yoshikazu

last: Mikami


title: Methylation study of Theobroma cacao L. clones raised under alternative temperature conditions.

status: Public on Aug 19 2011

city: Reading

first: Nicholas

last: Cryer

state: Berkshire

address: Whiteknights Campus

department: School of Biological Sciences

institute: University of Reading

summary: Methylation differences between SIC 5 cocoa seedlings germinated in a common environment before growth for 74 days under semic controlled environmental conditions set to mimic the Malaysian or Brazilian temperature environment. Genomic DNA sonicated and the methylated fraction enriched using a 5-methylcytosine antibody before whole genome amplification and hybridisation to the array.

overall_design:
Two-condition experiment, Methyl enriched gDNA Malaysian vs. Brazilian leaf samples. 7 Biological replicates independently grown and harvested.

Environmental (temperature) effect

first: Viacheslav

middle: N

last: Bolshakov


title: Whole genome expression array profiling highlights differences in mucosal defense genes in Barrett's esophagus and esophageal adenocarcinoma.

status: Public on Aug 17 2011

city: Herston

first: Derek

middle: John

last: Nancarrow

state: Queensland

address: 300 Herston Road

department: Genetics & Population Health

country: Australia

institute: Queensland Institute of Medical Research

summary: Esophageal adenocarcinoma (EAC) has become a major concern in Western countries due to rapid rises in incidence coupled with very poor survival rates. One of the key risk factors for the development of this cancer is the presence of Barrett’s esophagus (BE), which is believed to form in response to repeated gastro-esophageal reflux. In this study we performed comparative, genome-wide expression profiling (using Illumina whole-genome Beadarray) on total RNA extracted from esophageal biopsy tissues from individuals with EAC, BE (in the absence of EAC) and those with normal squamous epithelium. We combined these data with publically accessible raw data from three similar studies to investigate key gene and ontology differences between these three tissue states. The results support the deduction that BE is a tissue with enhanced glycoprotein synthesis machinery (DPP4, ATP2A3, AGR2) designed to provide strong mucosal defenses aimed at resisting gastro-esophageal reflux. EAC exhibits the enhanced extracellular matrix remodeling (collagens, IGFBP7, PLAU) effects expected in an aggressive form of cancer, as well as evidence of reduced expression of genes associated with mucosal (MUC6, CA2, TFF1) and xenobiotic (AKR1C2, AKR1B10) defenses. When our results are compared to previous whole-genome expression profiling studies keratin, mucin, annexin and trefoil factor gene families are the most frequently represented gene families. Eleven genes identified here are also represented in at least 3 other profiling studies. We used these genes to discriminate squamous, BE and EAC within the two largest cohorts using a support vector machine leave one out cross validation analysis. While this method was satisfactory for discriminating squamous and BE, it demonstrates the need for more detailed investigations into profiling changes within BE leading to the progression towards EAC.

overall_design: A comparison of three esophageal biopsy groups from separate individuals: normal squamous (n=9), Barrett's esophagus without dysplasia (n=22) & adenocarcinoma (n=23). Adenocarcinoma samples overlap with members of DNA copy number analysis GEO series GSE10506 such that, in each case genomic DNA and total RNA were extracted from the same biopsy. The matching copy number data GEO samples IDs are noted in characteristics: Matching CN Sample ID

first: Andrew

last: Clouston

first: B

last: Smithers

first: David

last: Gotley

first: Paul

last: Drew

middle: I

last: Watson

first: Sonika

last: Tyagi

middle: K

last: Hayward

last: Whiteman


title: Comparative analysis of chicken Intestinal Intraepithelial lymphocytes (IEL) following Eimeria acervulina (EA), E. maxima (EM), or E. tenella (ET) infection

status: Public on Aug 15 2011

city: Beltsville

first: Duk Kyung

last: Kim

address: Bldg. 1043, BARC-East

country: USA

institute: USDA, ARS

summary: Relative expression levels of mRNAs in chicken IEL experimentally infected with EA, EM, or ET were measured at 1 to 6 days post-infection (dpi) following primary and secondary infections.  One week-old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of EA, EM, or ET.  One week later, the infected chickens were challenged with an identical inoculum of the homologous parasite.  Intestinal samples were collected daily from 5 birds in a treatment group at from 1 to 6 dpi following primary and secondary infections.  Cecum, duodenum, and jejunum were collected from the birds challenged with E. acervulina, E. maxima, and E. tenella, respectively.  Uninfected control samples and one of the 3 infection group samples were labeled with different fluorescent dyes and hybridized simultaneously on the same slide using a reference design with a dye swap protocol.

overall_design: Thirty seven-condition experiment, Non-infected control vs. Primary or secondary EA, EM, or ET infected IEL at 1 to 6. Biological replicates: 2 replicates with dye-switching from each infection groups. Two replicates per array.

first: Duk-Kyung

first: Hyun

middle: S

last: Lillehoj


title: Homo sapiens immortalized MSCs: KP vs. 3A6

city: Taipei

first: Chih

middle: Chien

last: Tsai

address: No. 201, Sec. 2, Shih-Pai Road, Taipei 112, Taiwan

country: Taiwan

institute: Taipei Vaterans General Hospital

summary: Gene methylation profiling of immortalized human mesenchymal stem cells comparing HPV E6/E7-transfected MSCs cells with human telomerase reverse transcriptase (hTERT)- and HPV E6/E7-transfected MSCs. hTERT may increase gene methylation in MSCs. Goal was to determine the effects of different transfected genes on global gene methylation in MSCs.

overall_design: Two-condition experiment, KP MSCs vs. 3A6 MSCs.

first: Chih-Chien

first: Chun-Li

last: Chen

first: Shih-Chieh

last: Hung


title: Experimental annotation of Histoplasma capsulatum transcribed regions using high-resolution tiling arrays

status: Public on Aug 12 2011

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary:
The fungal pathogen Histoplasma capsulatum is thought to be the most common cause of fungal respiratory infections in immunocompetent humans, yet little is known about its biology.  Here we provide the first genome-wide studies to experimentally validate its genome annotation. A functional interrogation of the Histoplasma genome provides critical support for continued investigation into the biology and pathogenesis of H. capsulatum and related fungi.

We employed a three-pronged approach to provide a functional annotation for the H. capsulatum G217B strain. First, we probed high-density tiling arrays with labeled cDNAs from cells grown under diverse conditions. These data defined 6,172 transcriptionally active regions (TARs), providing validation of 6,008 gene predictions. Interestingly, 22% of these predictions showed evidence of anti-sense transcription. Additionally, we detected transcription of 264 novel genes not present in the original gene predictions. To further enrich our analysis, we incorporated expression data from whole-genome oligonucleotide microarrays. These expression data included profiling under growth conditions that were not represented in the tiling experiment, and validated an additional 2,249 gene predictions. Finally, we compared the G217B gene predictions to other available fungal genomes, and observed that an additional 254 gene predictions had an ortholog in a different fungal species, suggesting that they represent genuine coding sequences.

These analyses yielded a high confidence set of validated gene predictions for H. capsulatum. The transcript sets resulting from this study are a valuable resource for further experimental characterization of this ubiquitous fungal pathogen.  The data is available for interactive exploration at http://histo.ucsf.edu.

overall_design: The non-redundant genome sequence of Histoplasma capsulatum G217B was tiled over a set of 93 CombiMatrix arrays, which were then hybridized with labeled cDNA samples from yeast-form (red channel) or mycelial-form (green channel) Histoplasma.  Due to low yields from the mycelial samples, only the red channel intensities were analyzed (and the red foreground intensities are, therefore, reported in the VALUE column for each sample).  Rather than normalizing intensities across arrays, each probe was evaluated as detected or undetected relative to the negative control intensities on the corresponding array, and the density of detected probes as a function of genome position was used for the remaining analysis.

first: Catherine

last: Foo

first: Anita

last: Sil


title: ecdysone treated KC167 cells during Heat Shock and at Room Temperature

city: Mississauga

first: Zak

last: Razak

state: Ontario

address: 3359 Mississauga Rd

country: Canada

institute: Canadian Drosophila Microarray Centre

overall_design: 2-colour microarray desgin using 9 spotted oligonucleotide microarrays printed at the Canadian Drosophila Microarray Centre. Total RNA from Ecdysone treated KC167 cells were compared to Total RNA from an EtOH (the solvent for ecdysone) control sample pool.

first: Sarah

last: Gonsalves


title: Over-expression of a Cytochrome P450 is Associated with Resistance to Pyriproxyfen in the Greenhouse Whitefly Trialeurodes vaporariorum

status: Public on Aug 11 2011

city: Harpenden

first: Nikos

last: Karatolos

state: Herts

address: West Common

institute: Rothamsted Research

summary: Trialeurodes vaporariorum (Westwood), also known as the greenhouse whitefly, is a serious pest of protected vegetable and ornamental crops in most temperate regions of the world. The juvenile hormone mimic, pyriproxyfen, is a very effective mean of controlling this pest. Microarray analysis of a selected strain and a susceptible strain revealed a number of differentially expressed genes that were candidates for a role in resistance.

overall_design: Analysis used total RNA from a susceptible strain (s) as control samples for comparison to the experimental resistant strain (r).

first: Martin

last: Williamson

first: Ian

last: Denholm

first: Kevin

last: Gorman

first: Richard

middle: H

last: ffrench-Constant

first: Chris

last: Bass


title: Image defocus and altered retinal gene expression in chicks

city: Philadelphia

first: Alice

middle: M

last: McGlinn

state: PA

address: 602D Richards Building 3700 Hamilton Walk

department: Ophthalmology

institute: University of Pennsylvania School of Medicine

summary: Because refractive development is governed largely by the retina, we analyzed the retinal transcriptome in chicks wearing a spectacle lens, a well-established means to induce refractive errors, to identify gene expression alterations and to develop novel mechanistic hypotheses about refractive development.

overall_design: One-week-old white Leghorn chicks wore a unilateral spectacle lens of + or –15 diopters for 6 hours or 3 days (n=6 for each condition). With total RNA from the retina/retinal pigment epithelium (RPE), Affymetrix Chicken GeneChips were used to compare gene expression levels between lens-wearing and contralateral control eyes. Normalized microarray signal intensities were evaluated by an analysis of variance approach. Selected differentially expressed genes were validated by qPCR in biologically independent samples.

middle: A

last: Stone

first: Donald

last: Baldwin

first: John

middle: W

last: Tobias

first: P

last: Iuvone

first: Tejvir

last: Khurana


title: Molecular studies on sex-different control of the hepatic metabolism in relations to insulin sensitivity (set 2)

status: Public on Aug 10 2011

city: Stockholm

first: Carolina

last: Gustavsson

address: CMM L8:01

department: Molecular medicine and surgery

institute: Karolinska institutet

summary: In this study we have analyzed gene expression and metabolite levels in the livers of male and female Zucker diabetic fatty (ZDF) rats. We speculated that the sex different development of diabetes in the ZDF animals presents the opportunity to relate gender to diabetes (since only males become diabetic on normal diet). In this model one can search for parameters that distinguish  females fed normal diet compared to high fat diet (i.e. components that vary with the development of diabetes)  and evaluate if such changes can be related to components that characterize  male diabetic animals..

overall_design:
Biological replicates: 4 male ZDF rat livers from rats on a standard diet (SD) and 4 ZDF female rat livers from rats on a standard diet (SD). One replicate per array.
Hepatic gene expression, hepatic metabolites, sex-differences

middle: E

first: Tomoyoshi

last: Soga

first: Gunnar

last: Norstedt

first: Petra

last: Tollet-Egnell


title: Molecular studies on sex-different control of the hepatic metabolism in relations to insulin sensitivity (set 1)

overall_design:
Biological replicates:  4 ZDF female rat livers from rats on a standard diet (SD) and 4 ZDF female rat livers from rats on high-fat diet (HFD) (6 weeks).  One replicate per array.
Hepatic gene expression, hepatic metabolites, sex-differences


title: Characterization of miRNA expression profile during human monocytes differentiation in macrophages

city: Dijon

first: Laurent

last: Delva

address: 7 boulevard Jeanne d'Arc

institute: Inserm U866

summary: Colony-stimulating factor-1 (CSF-1) triggers the differentiation of human peripheral blood monocytes into macrophages through an integrated cytokine/transcription factors circuitry. However, the role of miRNAs in the development of macrophages is just beginning to be explored. Here, we used microarray profiling to identify miRNAs involved in this molecular circuitry.

overall_design: In this study, a sample of RNA extracted from human monocytes were compared with a sample of RNA extracted from the same monocytes after 6 days of CSF-1 treatment.


title: Transcriptional profiling of cumulus cells entoured the oocyte after in vitro or in vivo maturation in bovine (Bos taurus)

status: Public on Aug 09 2011

city: Nouzilly

first: Svetlana

last: UZBEKOVA

address: PRC INRA

institute: INRA

summary:
In vitro maturation (IVM) of the oocytes is a routine method in bovine embryo production. The competence of bovine oocytes to develop into embryo after IVM and in vitro fertilization (IVF) is lower as compared to in vivo preovulatory oocytes.
Cumulus cells (CC) that enclose an oocyte are involved in the acquisition of oocyte quality during maturation. Using transcriptomic approach we compared cumulus cells gene expression during IVM with that in vivo preovulatory period.

overall_design: Global transcriptional profiling was performed using cumulus cells collected from mature bovine oocytes (metaphase-II stage) after maturation performed either in vivo or in vitro. In vivo matured cumulus cells were collected from ovulatory follicles of Montbeliard adult cows by ovum pick-up in vivo (OPU, n=4). In vitro matured cumulus cells were recovered from the oocytes after 22h of in vitro culture of cumulus-oocyte complexes (50 COC per experiment) from 2-6 mm ovarian follicles of adult cows (MIV, n=4). Gene expression analysis was carried out between in vivo and in vitro matured cumulus representing a total of 8 slides (dye swap protocol)

first: Sophie

last: Pollet

last: Uzbekova

first: Mohamad

last: Salhab

first: Sylvain

last: Auclair

first: Christelle

last: Hennequet-Antier

first: Catherine

last: Guyader-Joly


title: Transcriptional Responses of Karenia brevis to Phosphorus Depletion and Addition

city: Charleston

first: Frances

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

summary: The role of coastal nutrient sources in the persistence of Karenia brevis red tides in coastal waters of Florida is currently a contentious issue that warrants investigation into the nutrient physiology of this dinoflagellate species.  The molecular mechanisms by which dinoflagellates respond to nutrient availability are essentially unexplored.  The current study sought to determine if the transcriptome of K. brevis is responsive to phosphorus and informative of nutrient status.  Stationary phase P-limited cultures did not exhibit up-regulation of transcripts considered to be hallmark of P depletion relative to nutrient-replete stationary phase cultures, despite rapid growth upon addition of the limiting nutrient.  To study transcriptome responses to nutrient addition, the limiting nutrient was added to depleted cells and changes in global gene expression were assessed over the first 48 hours following nutrient addition.  P-addition resulted in significant changes in approximately 4% of genes on the microarray, using a significance cutoff of 1.7-fold and p<10-4.  By far, the earliest responding genes were dominated by pentatricopeptide repeat (PPR) proteins, which increased in expression up to 3-fold by 1 h following nutrient addition.  PPR proteins are nuclear encoded proteins involved in chloroplast and mitochondria RNA processing.  Correspondingly, other functions enriched in response to both nutrients were photosystem and ribosomal genes.  Transcriptomic responses to the addition of P reflected primarily chloroplast functions.  Even the earliest responding transcripts, those encoding PPR proteins, possess a 5’ trans-spliced leader sequence, suggesting that the observed rapid response of the transcriptome may be achieved, in part, through post-transcriptional mechanisms.

overall_design: Cultures were acclimated to 0.1 µM phosphate for a minimum of two months during which time cultures were transferred weekly in log phase.  For addition experiments, nutrient replete and P-limited 1L cultures were grown to stationary phase. (Day 12)  Using sodium phosphate, 168 µM PO4 was added to stationary phase cultures.  Nutrient replete cultures and P-limited cultures were harvested at the time of nutrient addition (Time 0; n=3) and total RNA extracted.  Following phosphorus addition, triplicate cultures were harvested at 1, 4, 24, and 48 h post-addition and total RNA extracted.  One color arrays were then run on all biological replicates (n=3 at each time point).

first: Jeanine

last: Morey


title: Transcriptional Responses of Karenia brevis to Nitrogen Depletion and Addition

summary: The role of coastal nutrient sources in the persistence of Karenia brevis red tides in coastal waters of Florida is currently a contentious issue that warrants investigation into the nutrient physiology of this dinoflagellate species.  The molecular mechanisms by which dinoflagellates respond to nutrient availability are essentially unexplored.  The current study sought to determine if the transcriptome of K. brevis is responsive to nitrogen and informative of nutrient status.  Stationary phase N-limited cultures did not exhibit up-regulation of transcripts considered to be hallmark of N depletion relative to nutrient-replete stationary phase cultures, despite rapid growth upon addition of the limiting nutrient.  To study transcriptome responses to nutrient addition, the limiting nutrient was added to depleted cells and changes in global gene expression were assessed over the first 48 hours following nutrient addition.  N-addition resulted in significant changes in approximately 4% of genes on the microarray, using a significance cutoff of 1.7-fold and p<10-4.  By far, the earliest responding genes were dominated by pentatricopeptide repeat (PPR) proteins, which increased in expression up to 3-fold by 4 h following nutrient addition.  PPR proteins are nuclear encoded proteins involved in chloroplast and mitochondria RNA processing.  Correspondingly, other functions enriched in response to both nutrients were photosystem and ribosomal genes.  Transcriptomic responses to the addition of N reflected primarily chloroplast functions.  Even the earliest responding transcripts, those encoding PPR proteins, possess a 5’ trans-spliced leader sequence, suggesting that the observed rapid response of the transcriptome may be achieved, in part, through post-transcriptional mechanisms.

overall_design: Cultures were acclimated to 10 µM nitrate for a minimum of two months during which time cultures were transferred weekly in log phase.  For addition experiments, nutrient replete and N-limited 1L cultures were grown to stationary phase. (Day 9)  Using sodium nitrate, 155 µM NO3 was added to stationary phase cultures.  Nutrient replete cultures and N-limited cultures were harvested at the time of nutrient addition (Time 0; n=3) and total RNA extracted.  Following nitrogen addition, triplicate cultures were harvested at 4, 12, 24, and 48 h post-addition and total RNA extracted.  One color arrays were then run on all biological replicates (n=3 at each time point).


title: Mulcom: a multiple comparison statistical test for microarray data in Bioconductor (Illumina)

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary:
Background
Many microarray experiments search for genes with differential expression between a common “reference” group and multiple test groups, like in the case of time-course designs or of various treatments versus a control condition. In such cases, currently employed statistical approaches based on t-test or close derivatives have limited efficacy, mostly because estimation of noise is done on only two groups at time. Alternative approaches based on ANOVA correctly capture noise from all the groups, but then do not confront single test groups with the reference. We therefore conceived a statistical test for pairwise comparisons between the reference group and each test group that uses within-group variance calculated from all the groups.

Results
We implemented an R-Bioconductor package named Mulcom, with a statistical test derived from the Dunnett’s test, designed to compare multiple experimental groups against a common reference. In addition to the basic Dunnett’s t value, the package includes an optional minimal fold-change threshold, m. Thanks to automated, permutation-based estimation of False Discovery Rate (FDR), the package also permits fast optimization of the test, to obtain the maximum number of significant genes at a given FDR value. When applied on a time-course experiment profiled in parallel on two microarray platforms, and compared with currently used tests, Mulcom displayed higher concordance of significant genes in the two array platforms, and higher enrichment in functional annotation to categories related to the biology of the experiment.

Conclusions
The Mulcom package provides a fast and powerful tool for the identification of differentially expressed genes when several experimental conditions are compared with a common reference. We found that Mulcom leads to lists of differentially expressed genes that are particularly consistent across microarray platforms and enriched in significant classes of genes. In our opinion, the main reasons for these good performances are three: (i) within-group variability is estimated from all experimental groups even if only two of them are compared each time; (ii) the optional fold-change threshold m avoids false positives due to aberrantly low within-group variability; (iii) automated test optimization allows maximizing sensitivity without compromising specificity.

overall_design: Ten MDA-MB-435 samples, biological duplicates of each condition (untreated, integrin Beta4 treatment, hepatocyte growth factor treatment for 1 hr, 6 hrs, or 24 hrs).

first: Claudio

last: Isella


title: Identification of Arabidopsis Long Intergenic Noncoding RNA regulated by RNA-dependent RNA polymerase 2 (RDR2)

status: Public on Aug 06 2011

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

country: China

institute: Institute of Crop Science

summary: RNA-dependent RNA polymerase 2 (RDR2) is a crucial regulator of RNA-directed DNA methylation (RdDM). Recentily RDR2 was reported to regulate expression of long intergenic noncoding RNAs. Here we used ATH lincRNA v1 expression arrays to compare lincRNA expression in inflorescence tissues of rdr2-1 and WT. Among the 4,634 lincRNAs detected we found that more than 34% of them were differentially expressed, including 676 lincRNAs that were up-regulated and 890 down-regulated in rdr2-1.

overall_design: Inflorescences(Col-0) x Inflorescences(rdr2-1), 3 biological replicates.

last: Xu

first: Choonkyun

last: Jung

first: Lucia

last: Bernad

first: Huan

last: Wang

first: Catalina

last: Arenas

first: Nam-Hai

last: Chua


title: Identification of small non coding RNAs in S. pyognes M49  using intergenic tiling arrays

city: Rostock

first: Nadja

last: Patenge

address: Schillingallee 70

department: Institute of Medical Microbiology, Virology and Hygiene

institute: University of Rostock

type: Non-coding RNA profiling by genome tiling array

summary: Small non-coding RNAs (sRNAs) have attracted attention as a new class of gene regulators in eukaryotes and in bacteria. In this study, we identified novel sRNAs of  the human pathogen Streptococcus pyogenes M49 (GAS M49). A temporal expression profile of potential sRNAs was determined for (GAS M49). Cells were grown in chemical defined medium (CDM), Todd-Hewitt broth (Invitrogen) supplemented with 0.5% yeast extract (THY) or Brain-Heart-Infusion (BHI) complex medium using tiling arrays representing the intergenic regions of the GAS M49 genome. We identified 55 putative sRNAs in GAS M49 that were expressed during growth. Of those, 35 sRNAs were novel, whereas 20 sRNAs were known. Already described sRNAs included molecules belonging to one of the common non-coding RNA families covered by the rfam collection and streptococcal sRNAs that have been detected in previous studies. Comparison to a recently published bioinformatics screen showed a low overlap between putative sRNA genes. This is in accordance with the results from other studies, which underlines the fact that a comprehensive analysis of sRNAs expressed by a given organism requires the complementary use of different methods and the investigation of several environmental conditions. Despite a high conservation of sRNA genes within streptococci, the expression of sRNAs is rather strain specific.

overall_design: Identification of sncRNA candidates transcribed by S. pyogenes was undertaken with bacteria from cultures grown to exponential (OD600: 0.4) and stationary (OD600: 1.2) phase of growth and each for three growth media. For samples from bacteria grown in CDM medium four biological replicates were included, for samples from bacteria grown in THY and BHI medium two biological replicates were included.

first: Valesca

last: Boisguérin

first: Carsten

last: Kuenne

first: Julia

last: Retey

first: André

last: Billion

first: Kerstin

last: Ganter

first: Thomas

last: Hartsch

first: Markus

last: Beier

first: Torsten

last: Hain

first: Bernd

last: Kreikemeyer


title: Widespread, focal copy number variations (CNV) in Trypanosoma cruzi strains

city: Athens

first: Todd

last: Minning

state: GA

address: Rm 310 Coverdell

department: CTEGD

institute: University of Georgia

summary: Trypanosoma cruzi is a protozoan parasite and the etiologic agent of Chagas disease, an important public health problem in Latin America.  T. cruzi is diploid, almost exclusively asexual, and displays an extraordinarily diverse population structure both genetically and phenotypically.  Yet, to date the genotypic diversity of T. cruzi and its relationship, if any, to biological diversity have not been studied at the whole genome level.  In this study, we used whole genome oligonucleotide tiling arrays to compare gene content in biologically disparate T. cruzi strains by comparative genomic hybridization (CGH).  We observed that T. cruzi strains display widespread and focal copy number variations (CNV) and a substantially greater level of diversity than can be adequately defined by the current genetic typing methods.  As expected, CNV were particularly frequent in gene family-rich regions containing mucins and trans-sialidases but were also evident in core genes.  Gene groups that showed little variation in copy numbers among the strains tested included those encoding  protein kinases and ribosomal proteins, suggesting these loci were less permissive to CNV.   Moreover, frequent variation in chromosome copy numbers were observed, and chromosome-specific CNV signatures were shared by genetically divergent T. cruzi strains, suggesting a greater degree of chromosome exchange than previously thought.

overall_design: Genomic DNA samples from 16 T. cruzi strains were compared to genomic DNA from the CL Brener strain by competitive hybridizations on whole genome oligonucleotide tiling arrays.

first: D

last: Weatherly

first: Rick

middle: L

last: Tarelton

first: Stephane

last: Flibotte


title: Shoot tip tissue: Tall Mokka vs Typica.

status: Public on Aug 04 2011

city: Waipahu

first: Ratnesh

last: Singh

state: HI

address: 94-340 Kunia Rd

institute: Hawaii Agriculture Research Center

summary: The closely related Coffea arabica cultivars ‘Tall Mokka’ and ‘Typica’, with excellent flavor, but differing distinctively in the size of aerial organs, branching pattern and branch numbers. Differential gene expression analysis of shoot tips of arabica coffee cultivars 'Tall Mokka' and 'Typica' were done using Potato cDNA microarray as cross-species platform. Using cross-species microarray hybridization, we identified a prolyl oligopeptidase (CaPOP) gene as differentially expressed between the shoot tips of ‘Tall Mokka’ and ‘Typica’. Isolation and sequencing of POP genes from coffee identified three paralogs, CaPOP1, CaPOP2 and CaPOP3. All three genes were present in both cultivars, which suggest that differences in the expression of CaPOP are caused by factor(s) regulating the transcription of CaPOPs. CaPOP1 differs in sequence from CaPOP2 primarily in having two large deletions in the promoter region. CaPOP genes are homologous to arabidopsis At1g20380, encoding a post-proline cleaving enzyme that acts on substrates shorter than 30 amino acids. Ectopic expression of CaPOP1 under its native promoter in transgenic arabidopsis resulted in more secondary branches than in the wild type. This is the first study to successfully isolate CaPOP genes and characterize their expression in the developing tissues of coffee. This study also identified a novel role for prolyl oligopeptidase in control of branching.

overall_design:
Eight coffee trees of 'Typica' ('K') and six trees of 'Tall Mokka' ('M') cultivar were used in this study. The trees were equally divided into two groups 'A' and 'B' for each cultivar ('MA','MB', 'KA' and 'KB') and treated as biological replicates. Eight two channel microarray hybridizations were done in following pairs: MA x KA, MA x KB, MB x KA, MB x KB and dye swap replicate of each pair.

Summary: Two-sample experiment: Tall Mokka vs. Typica . 8 Hybridizations. 2 Biological replicates per sample. 1 Dye swap per array.

first: Ming-Li

last: Wang


title: LATE-REPLICATING HETEROCHROMATIN IS CHARACTERISED BY DECREASED CYTOSINE METHYLATION IN THE HUMAN GENOME (expression)

city: Bronx

first: John

last: Greally

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

summary: Heterochromatin is believed to be associated with increased levels of cytosine methylation.  With the recent availability of genome-wide, high-resolution molecular data reflecting cytosine methylation or heterochromatic organization, such relationships can be explored systematically.  As a well-defined surrogate for heterochromatin, we tested the relationship between DNA replication timing and cytosine methylation in two human cell types, unexpectedly finding that the later-replicating, more heterochromatic regions to be less methylated than early-replicating regions.  When we integrated gene expression data into the study, we found that regions of increased gene expression were earlier replicating, as previously identified, and that transcription-targeted cytosine methylation (TTCM) in gene bodies accounts for the positive correlation with early replication.  A Self-Organising Map (SOM) approach was able to identify genomic regions with early replication and increased methylation but lacking annotated transcripts, which would have been missed in simple two variable analyses and may encode unrecognized intergenic transcripts.  We conclude that the relationship of cytosine methylation with heterochromatin is not simple, and depends on whether the genomic context is tandemly-repetitive sequences often found near centromeres, which are known to be heterochromatic and methylated, or the remaining majority of the genome, where cytosine methylation is targeted preferentially to the transcriptionally-active, euchromatic compartment of the genome.

overall_design: comparison of human fibroblast and GM06690

first: Masako

last: Suzuki

first: Mayumi

last: Oda

first: María-Paz

last: Ramos

first: Marién

last: Pascual

first: Kevin

last: Lau

first: Edyta

last: Stasiek

first: Frederick

last: Agyiri

first: Reid

middle: F

last: Thompson

first: Jacob

last: Glass

first: Qiang

last: Jing

first: Richard

last: Sandstrom

first: Melissa

middle: J

last: Fazzari

first: R

last: Hansen

last: Stamatoyannopoulos

first: Andrew

last: McLellan


title: Ofd2+/-hypoxia

city: Cambridge

first: David

last: Lando

address: Tennis Court Road

department: Gurdon Institute

institute: Cambridge University

summary: Investigation of mRNA expression level changes in S. pombeOfd2 (SPAP8A3.02c) deletion strain compared to wild-type strain at both normal oxygen (normoxia) and low oxygen (hypoxia) growth conditions.

overall_design: Four samples in total consisting of two S. pombeyeast strains, wild type (WT) and a gene deleted strain for Ofd2 (SPAP8A3.02c), analysed for gene expression under two growth conditions, normal oxygen (normoxia) and low oxygen (hypoxia). Five micrograms of total RNA from two independent experiments were pooled and mRNA levels were quantified by Roche NimbleGen using the S. pombe 72K array service

first: Tony

last: Kouzarides