title: DamID from Drosophila CNS with Dam fused FruMA, FruMB, FruMC.

status: Public on Jan 16 2014

city: Oxford

first: Megan

last: Neville

address: South Park Road

department: DPAG

institute: University of Oxford

summary: In Drosophila,male courtship behaviour serves as an excellent paradigm to study how innate behaviors are controlled by the nervous system. These behaviors are in large part regulated by the gene fruitless (fru). fru encodes a set of putative transcription factors that promote male sexual behaior by controlling the development of sexually-dimorphic neuronal circuitry. Little is known about how Fru proteins function at the level of transcriptional regulation. To characterize the roles of fru sex-specific isoforms in specifying male behavior, we generated novel isoform-specific mutants, and used a genomic approach to identify direct Fru isoform targets during development. We demonstrate that all Fru isoforms directly target genes involved in the development of the nervous system, with individual isoforms exhibiting unique binding specificities. We observe that fru behavioral phenotypes are specificed by either a single, or combination, of isoforms. Finally, we illustrate the utility of these data for the identification of novel sexually dimorphic genoic enhancers, and novel downstream regulators of male-sexual behavior.

overall_design: 3 replicates per condition, one dye swap; per condition: one control, one experimental per replicate. No processed data for GSM1261882 and GSM1261883 are available.

first: Elizabeth

middle: L

last: Ashley


title: Ste18p is a positive control element in the mating process of Candida albicans

status: Public on Jan 14 2014

city: Montreal

first: Yuan

last: Sun

state: Quebec

address: 7141 Sherbrooke Street West

department: Biology Department

country: Canada

institute: Concordia University

summary: Disruption of STE18 gene which encodes a γ subunit of a heterotrimeric G protein in Candida albicans is shown to block pheromone-induced gene expression. Ectopic expression of either the Gα or the Gβ subunit of the heterotrimeric G protein is able to restore pheromone-induced gene expression.

overall_design: The transcriptional response to pheromone treatment was measured in the wild type strain, in a strain deleted for STE18, and in STE18 deleted strains ectopic expressing either the Gα or the Gβ subunit of G protein in opaque forms under RT.

first: Malcolm

last: Whiteway


title: Multistrain Probiotic Modulation of Intestinal Epithelial Cells' Immune Response to a Double-Stranded RNA Ligand, Poly (I:C)

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

institute: Lallemand Health Solutions Inc.

summary: A commercially available product containing three probiotic bacterial strains (Lactobacillus helveticus R0052, Bifidobacterium longum subsp. infantis R0033, and Bifidobacterium bifidum R0071) was previously shown in animal trials to modulate both TH1 and TH2 immune responses. Clinical studies on this combination of bacteria have also shown positive health effects against seasonal winter diseases and rotavirus infection. The goal of this study was to use a well-established in vitro intestinal epithelial (HT-29) cell model that has been shown to constitutively express double-stranded RNA (dsRNA) sensors (Toll-like receptor 3[TLR3], retinoic acid-inducible gene I, melanoma differentiation-associated gene 5, and dsRNA-activated protein kinase). By using the HT-29 cell model, we wanted to evaluate whether or not this combination of three bacteria had the capacity to immune modulate the host cell response to a dsRNA ligand, poly(I•C). Using a custom-designed, two-color expression microarray targeting genes of the human immune system, we investigated the response of HT-29 cells challenged with poly(I•C) both in the presence and in the absence of the three probiotic bacteria. We observed that the combination of the three bacteria had a major impact on attenuating the expression of genes connected to proinflammatory TH1 and antiviral innate immune responses compared to that obtained by the poly(I•C)-only challenge. Major pathways through which the multistrain combination may be eliciting its immune-modulatory effect include the TLR3-TRIF, mitogen-activated protein kinase, and NF-KB signaling pathways.Such a model may be useful for selecting potential biomarkers for the design of future clinical trials

overall_design: The overall design consisted of 3 samples of HT-29 cells treated with poly (I:C)-only, probiotic combination (PC) and poly (I:C) + PC versus unchallenged HT-29 cells. A minimum of four dye-swap hybridizations (4 biological replicates) were performed for each of the 3 samples analyzed. Unchallenged HT-29 cells were controls and challenged HT-29 cells with poly (I:C)-only, PC-only and poly (I:C) + PC were treated samples.

first: Chad

last: MacPherson

first: Julie

last: Audy

first: Olivier

last: Mathieu

middle: A


title: Candida lusitaniae ime2Δ/ime2Δ a/alpha WT meiosis

status: Public on Feb 01 2014

city: Providence

first: Christine

last: Scaduto

state: RI

address: 171 Meeting Street

department: Molecular Microbiology and Immunology

country: USA

institute: Brown University

summary: Transcriptional profiling of C. lusitaniae ime2Δ/ime2Δ a/alpha WT cells on 0.37% PDA (potato dextrose agar) for 0 hours, 12h, 18h and 24h hybridized against WT a/alpha cells in YPD (yeast peptone dextrose) for 4h

overall_design: Two condition experiment: ime2Δ/ime2Δ a/alpha WT on PDA vs. WT a/alpha  on YPD, 3 biological replicates

first: Racquel

last: Sherwood

first: Richard

middle: J

last: Bennett


title: Expression analysis of Caulobacter crescentus NA1000 Plac::CCNA_00382 (ccrM) vs Caulobacter crescentus

status: Public on Jan 08 2014

city: Lausanne

first: Diego

last: Gonzalez

address: Quartier UNIL-Sorge, Bâtiment Biophore

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

summary:
Investigation of whole genome gene expression level changes in a  Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM) mutant, compared to the wild-type strain.  The mutations engineered into this strain cause the CcrM DNA methyltransferase to be overexpressed and the chromosome to be constitutively methylated at the adenine at GANTC motifs.
References of strains: CcrMOE: Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716.  WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol, 192, 3678-3688; Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716.

overall_design: A six chip study using total RNA recovered from three separate wild-type cultures of Caulonacter crescentus NA1000 and three separate cultures of a triple mutant strain, Caulonacter crescentus NA1000 Plac::CCNA_00382 (ccrM), in which the ccrM gene coding for a DNA methyltransferase methylating the adenine in GANTC motifs is truncated and its product inactive.  Each chip measures the expression level of 3933 genes from Caulobacter crescentus NA1000 with 3 probes per gene and with three-fold technical redundancy.

first: Justine

last: Collier


title: Sweet orange genes regulated by Xanthomonas citri (Xc) in the presence or absence of cycloheximide (Ch), or Ch alone

status: Public on Jan 10 2014

city: Campinas

first: Celso

middle: Eduardo

last: Benedetti

state: SP

address: R. Giuseppe Maximo Scolfaro 10000

country: Brazil

institute: Laboratorio Nacional de Biociencias

summary:
Microarray analyses of sweet orange leaves infiltrated with Xc in the presence or absence of Ch, or Ch alone
This experiment was used to identify genes up-regulated by Xc independently of protein synthesis

overall_design: Citrus leaves were infiltrated with a suspension of Xc with or without Ch, and mRNA was extrated and processed 8h post inoculation (8hpi)

first: A

last: Pereira

first: C

middle: E


title: Expression analysis of Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) [DccrM] vs Caulobacter crescentus NA1000 wild type [WT]

summary:
Investigation of whole genome gene expression level changes in a  Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM) mutant, compared to the wild-type strain.  The mutations engineered into this strain render it incapable of methylating its genome on the adenine at GANTC motifs.
References for strains : WT: Marks, M.E., Castro-Rojas, C.M., Teiling, C., Du, L., Kapatral, V., Walunas, T.L. and Crosson, S. (2010) The genetic basis of laboratory adaptation in Caulobacter crescentus. J Bacteriol, 192, 3678-3688; Collier, J. and Shapiro, L. (2009) Feedback control of DnaA-mediated replication initiation by replisome-associated HdaA protein in Caulobacter. J Bacteriol, 191, 5706-5716.  DccrM: Gonzalez, D. and Collier, J. (2013) DNA methylation by CcrM activates the transcription of two genes required for the division of Caulobacter crescentus. Mol Microbiol, 88, 203-218.

overall_design: A six chip study using total RNA recovered from three separate wild-type cultures of Caulobacter crescentus NA1000 and three separate cultures of a triple mutant strain, Caulobacter crescentus NA1000 delta-CCNA_00382 (ccrM), in which the ccrM gene coding for a DNA methyltransferase methylating the adenine in GANTC motifs is truncated and its product inactive.  Each chip measures the expression level of 3933 genes from Caulobacter crescentus NA1000 with 3 probes per gene and with three-fold technical redundancy.

first: Gonzalez

last: Diego

first: Collier

last: Justine


title: Candida lusitaniae haploid nutrition

summary: Transcriptional profiling of C. lusitaniae WT a and WT alpha cells on 0.37% PDA (potato dextrose agar) for 30 minutes (m), 2 hours (h), or 24h hybridized against WT a and  WT alpha cells in  YPD (yeast peptone dextrose) for 2h

overall_design: WT a or WT alpha cells were incubated on PDA medium for 30 minutes, 2 hours, or 24 hours and hybridized against WT a or alpha cells (respectively) incubated on YPD for 2 hours, 2 biological replicates


title: Genome-wide cDNA screening of IFIT1 promoter activation factors in human hepato cellarlar carcinoma cell line Huh-7

city: Los Angeles

first: Meng

last: Li

state: CA

address: 2003 Zonal Avenue

institute: University of Southern California

summary: To identify novel ghost factors regulating the expression of Interferon Stimulated Genes (ISGs), we conducted genome-wide cDNA screening in Huh-7 IFIT-1 Luc cells

platform_organism:
Homo sapiens
Mus musculus

overall_design: Huh-7 cells stably expressing IFIT1 luciferase reporter were plated into the wells with pre-spotted cDNA clones from MGS collection (http://mgc.nci.nih.gov/) (reverse transfection).  The inducibility of luciferase activity upon the introduction of each cDNA clone was then measure to determine the regulator of IFIT1 expression.  Two biological replicates were tested and the averages were taken for measurement.

first: Takeshi

last: Saito

first: Timothy

last: Tellinghuisen


title: transcriptional changes in sweet orange in response to infection by citrus canker bacteria and their effector proteins PthAs and PthCs

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

overall_design: Refer to individual Series


title: Sweet orange genes regulated by TAL effectors of Xanthomonas citri (Xc) or Xanthomonas aurantifolii pathotype C

summary:
Microarray analyses of sweet orange epicotyls transiently transfected with the pthA2, pthA4 or pthC1 gene, relative to epicotyls transfected with the uid gene (GUS)
This experiment was used to identify sweet oragne genes regulated by TAL effectors

overall_design: Citrus epicotyls were transformed with the TAL effector genes via Agrobacterium transfection, and mRNA was extrated and processed 72h after bacterial-plant incubation


title: Rat insulin-producing INS-1E exposed to cytokines IL-1β and IFN-γ

status: Public on Dec 19 2013

city: Brussels

first: Miguel

last: Lopes

address: Campus de la Plaine Boulevard du Triomphe

department: Computer Science Department

country: Belgium

institute: Universite Libre de Bruxelles

summary:
In the context of T1 Diabetes, pro-inflammatory cytokines IL-1β and IFN-γ are known to contribute to β-cell apoptosis;
The measurement of mRNA expression following β-cell exposure to these cytokines gives a picture of the changes in gene expression characterizing the path to β-cell dysfunction and death.

overall_design: INS1 cell lines were cultured in medium with or without IL-1β and IFN-γ. The samples were collected at various time points for profiling with Affymetrix Rat ST arrays. These experiments were performed on two separate occasions.

first: Burak

last: Kutlu


title: Exploring the function of the grape regulators VvMYB5a and MYB5b by heterologous expression in anthocyanin petunia mutants

city: Verona

first: Sara

last: Zenoni

address: Le Grazie

department: Biotecnology

country: Italy

institute: University of Verona

summary: To obtain insights about the roles of VvMYB5a and VvMYB5b, here we perform complementation analyses using petunia regulatory mutants impaired in pigment accumulation in flower epidermis, proven to be a valid tool for gene functional studies.

overall_design: We created three transgenic petunia lines overexpressing VvMYB5a, VvMYB5b and VvMYBA1 and we compared petal transcriptomes of each overexpressors with the untransformed one.

first: Cavallini

last: Erika

first: Zamboni

last: Anita

first: Zenoni

last: Sara

first: Finezzo

last: Laura

first: Pezzotti

last: Mario

first: Tornielli

middle: G

last: Battista


title: Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments [GE]

status: Public on Nov 28 2013

city: New York

first: Jungeui

last: Hong

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

summary: One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. The large fitness increases associated with these alleles limits the genetic heterogeneity of adapting populations even in environments with multiple nitrogen sources. Complete identification of acquired point mutations, in individual lineages and entire populations, identified heterogeneity at the level of genetic loci but common themes at the level of functional modules, including genes controlling phosphatidylinositol-3-phosphate metabolism and vacuole biogenesis. Adaptive strategies shared with other nutrient-limited environments point to selection of genetic variation in the TORC1 and Ras/PKA signaling pathways as a general mechanism underlying improved growth in nutrient-limited environments. Within a single population we observed the repeated independent selection of a multi-locus genotype, comprised of the functionally related genes GAT1, MEP2 and LST4. By studying the fitness of individual alleles, and their combination, as well as the evolutionary history of the evolving population, we find that the order in which these mutations are acquired is constrained by epistasis. The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution. Our results provide insight into the mechanistic basis by which cells adapt to nutrient-limited environments and suggest that knowledge of the selective environment and the regulatory mechanisms important for growth and survival in that environment greatly increases the predictability of adaptive evolution.

overall_design: mRNA from each evolved clone or from the ancestral strain growing in the specificied nitrogen-limited condition was co-hybridized with mRNA from the ancestral strain grown in ammonium limited media

first: David

last: Gresham


title: Suppression of prp28-1 splicing defect by prp8-tes allele

status: Public on Jan 01 2014

city: San Francisco

first: Argenta

last: Price

institute: University of California, San Francisco

summary: DEAD-box proteins, a family of RNA-dependent ATPases, promote the numerous conformational rearrangements required for spliceosome assembly, activation, and disassembly. Previous work showed that a cold-sensitive substitution in DEAD-box protein Prp28 prevents the switch from U1 to U6 snRNA pairing with the 5’ splice site. Little is known about how Prp28 is regulated, although U5 snRNP protein Prp8 is a potential coordinator of Prp28 and other spliceosomal ATPases. We conducted a targeted selection in Prp8 for cold-insensitive suppressors of prp28-1, then used splicing specific microarrays to assess suppression of the prp28-1 splicing defect.

overall_design: Splicing specific microarrays were used to assess suppression of the prp28-1 splicing defect by a prp8 allele (prp8-tes) that suppresses prp28-1 cold-sensitivity

middle: M

first: Janina

last: Gornemann

first: Christine

last: Guthrie

last: Brow


title: Chromosomal status of GM00285 and GM05563 fibroblast and iPSCs

status: Public on Nov 26 2013

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

type: Genome variation profiling by genome tiling array

summary: We generated induced pluripotent stem cells (iPSCs) from ring chromosome patients' cells.  To examine chromosomal status in these iPSCs, we performed SNP microarray analysis using Agilent Sureprint G3 Human CGH + SNP 4x180k microarray platform.

overall_design: SNP analysis of fibroblast of GM00285 and GM05563 and iPSCs of GM00285 clone 1, GM00285 clone 3, GM05563 clone 1


title: Expression data from Pseudomonas putida KT2440 Tn5 mutants

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

country: Germany

institute: Medical School Hannover

summary: We used Progenika oligonucleotide arrays to monitor the gene expression after cold shock from 30°C to 10°C. The 10°C samples of the P. putida wild type were compared to those of the respective P. putida KT2440 Tn5 mutants affected in either cbrA (PP4695), cbrB (PP4696), pcnB (PP4697), vacB (PP4880) or bipA (PP5044).

overall_design: Cultures were grown in minimal medium supplemented with succinate at 30°C. In mid-exponential phase, cells were cooled down to 10°C. Two hours after the medium had reached 10°C, cells were harvested for subsequent RNA extraction.


title: microRNA expression associated with emphysematous lung destruction

status: Public on Dec 31 2013

first: Stephanie

last: Christenson

state: California

address: 513 PARNASSUS AVENUE, HSE1305

department: Pulmonary and Critical Care

summary: Background: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by varying degrees of emphysematous lung destruction and small airway disease, each with distinct effects on clinical outcomes. There is little known about how microRNAs contribute specifically to the emphysema phenotype. We examined how microRNA expression is altered with regional emphysema severity within the lung and how these microRNAs regulate disease-associated gene-expression networks.    Results: We profiled microRNAs in different regions in the lung with varying degrees of emphysema from 6 smokers with COPD and 2 controls (8 regions x 8 lungs = 64 samples). 63 microRNAs (p<0.05) were altered with regional emphysema severity as quantified by mean linear intercept (Lm). MicroRNA and gene expression data were then integrated in the same samples. A subset of microRNAs, including miR-638, miR-30c, and miR-181d, correlated with many of their predicted gene targets, suggesting a role in regulating the gene networks that underlie emphysematous lung destruction. Modulating miR-638 expression in primary human lung fibroblasts recapitulated the alterations in its targeted gene-expression network associated with emphysema progression. Pathway analysis revealed that genes involved in oxidative stress and accelerated aging were affected by miR-638 knock-down in fibroblasts. Many miR-638 gene targets in these pathways were amongst those negatively correlated with miR-638 expression in emphysematous lung tissue.     Conclusions: Our findings demonstrate that microRNAs are altered with regional emphysema severity and modulate disease-associated gene expression networks. Furthermore, miR-638 may regulate gene expression associated with the oxidative stress response and aging in emphysematous lung tissue and fibroblasts.

overall_design: Paired samples were obtained from 8 regions at regular intervals between the apex and base of each explanted lung from six patients with severe COPD and two donors. The degree of emphysematous destruction was quantified in one sample from each region by mean linear intercept (Lm), while microRNA expression was profiled in the adjacent sample from the same region using the NCode Version 3 microRNA microarrays (Invitrogen, Carlsbad, CA). After quality control 60 samples were used for the analysis.

first: Corry-Anke

last: Brandsma

first: Joshua

middle: D

last: Campbell

first: Darryl

last: Knight

first: Dmitri

middle: V

last: Pechkovsky

first: James

middle: C

last: Hogg

first: Wim

last: Timens

first: Dirkje

middle: S

last: Postma

first: Marc

last: Lenburg

first: Avrum

last: Spira


title: Identification of microRNA landscape of inflammation-induced colorectal carcinogenesis

city: Liège

first: Claire

last: Josse

state: Liège

address: rue de l'hopital, 1

department: Medical Oncology

institute: CHU Liege

summary: Inflammatory conditions can contribute to tumor formation. However, any clear marker predicting progression to cancer are still lacking. The aim of our study was to analyze microRNA modulations accompanying inflammation-induced tumor development to determine whether these microRNA may jointly affect the expression of genes involved in cancer. For this purpose, we used the well-established azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced mouse model of colitis-associated cancer. We performed a microRNA microarray to establish microRNA expression profiles in mouse whole colon at early and late time points during inflammation and/or tumor growth. Chronic inflammation and carcinogenesis were associated with distinct changes in microRNA expression. Nevertheless, prediction algorithms of microRNA-mRNA interactions and computational analyses based on ranked microRNA lists consistently identified putative target genes that play essential roles in tumor growth or belong to key carcinogenesis-related networks or signaling pathways. Hence, inflammation, through microRNA, may affect unexpected genes or signaling pathways, thereby contributing to carcinogenesis. The present method can lead to the identification of novel genes or signaling pathways involved in cancer development.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: miRNA microarray profiling in whole mouse colon at 4 time points during AOM/DSS treatment. Controls : PBS, DSS alone or AOM alone, at two time points; 10 experimental conditions, 5 replicates per experimental conditions, one replicate per array hybridized in dual color with a commercial reference (Universal Reference, Miltenyi Biotec GmbH)

first: Nassim

last: Bouznad


title: Global gene profiling of rotenone-induced neuronal death

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

summary: Rotenone is a naturally occurring toxic substance from the Leguminosa plant and belongs to the group of compounds known as rotenoids (Bové et al., 2005). It is commercially used as a pesticide and is epidemiologically linked to PD. Being lipophilic, rotenone can diffuse across biological membranes in the body and gain entry to all the organs and cells (Bové et al., 2005). Rotenone can bind to complex I of the electron transport chain (ETC) and inhibit the enzymatic activity of the NADH-ubiquinone reductase (Schuler and Casida, 2001). This interferes with the oxidation phosphorylation process, and eventually causes cell damage via oxidative stress. Rotenone may also cause the depolymerisation of microtubules into tubulin monomers (Marshall and Himes, 1978). Accumulation of tubulin monomers is potentially cytotoxic, and it is believed that parkin reverses cytotoxicity by ubiquitinating these monomers and targeting them for proteasome degradation (Ren et al., 2003.). Unfortunately, in PD patients with parkin mutations, this is not possible and tubulin accumulates to harmful levels in the cells.

overall_design: A total of 13 RNA samples were analyzed. Cultured murine primary cortical neurons were treated with 10nM rotenone over a time-course of 8h, 15h and 24h (n=3) in addition to the vehicle control (n=4).

first: Nam

last: Cheung

first: Minghui

first: Zhao

middle: F

last: Peng

first: Jayapal

last: Manikandan


title: Comparison of phosphorylation status of Wnt proteins in control and Fto deficient cells upon Wnt 3a stimulation

status: Public on Nov 21 2013

city: London

first: Daniel

middle: Peter Sayer

last: Osborn

address: Human Genetics Research Centre

country: United Kingdom

institute: St George's University of London

summary: Wnt Phospho protein profiling comparing control and Fto deficient cell after Wnt3a stimulation

overall_design: Control vs Fto deficient MEFs treated with Wnt 3a condioned medium for 40 minutes. 6 replicates per array

middle: P

first: Sonia

last: Christou-Savina


title: Tiling microarray analysis of gene expression profile of Escherichia coli galT mutant cells under D-galactose-stressed condition

status: Public on Dec 17 2013

city: Bethesda

first: Andrei

middle: Nikolai

last: Trostel

state: Maryland

address: 9000 Rockville Pike, Building 37, Room 5138

department: Laboratory of Molecular Biology

institute: National Institutes of Health

type: Expression profiling by genome tiling array

summary: To understand the altered gene expression by D-galactose in galT cells, the cells were grown in the presence and absence of D-galactose and tiling array analysis was performed for transcriptome profiling. A galT defect causes the disease Galactosemia in human. This work helps us to study the human metabolic disease Galactosemia.

overall_design: Total RNAs were isolated from Escherichia coli galT strain grown in the absence and presence of D-galactose. The transcriptome profile of galT cells was figured out in the galactose-stressed condition.

first: Sang-Jun

last: Lee

first: Sankar

last: Adhya


title: Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

first: Jungeui

last: Hong


title: Gene expression transcriptome of porcine induced pluripotent stem cell

city: Yangling

first: Wang

last: Huayan

state: Shaanxi

address: No.3 Taicheng Road

department: College of Veterinary Medicine

country: China

institute: Northwest A&F University

summary: Pig induced pluripotent stem cells (piPSCs) have significant biomedical and agricultural applications. We analyzed the transcriptional profiles of pig iPSC lines derived from different labs using Affymetrix GeneChip Pig Genome Array and published microarray datasets of mouse and human iPSCs. Our results demonstrated that cell surface proteins of EpCAM (epithelial cells adhesion molecule) were significantly upregulated in complete fully reprogrammed pig iPSCs, but not in partially reprogrammed cells. EpCAM could be markers for evaluating pig cell reprogramming and selecting successful reprogramming. We analyzed gene expression levels of the six key developmental signaling pathways, including JAK-STAT, NOTCH, TGF-βb, WNT, MAPK and VEGF in pig, human and mouse iPSCs, respectively. The result demonstrates that the core transcriptional network to maintain pluripotency and self-renewal in pig are different from mouse and human. Pig iPSCs lacked expression of specific naïve state markers (e.g. Klf family genes Klf2/4/5, Tbx3), but expressed unregulated primed state markers (e.g. Otx2 and Fabp7). Dlk1-Dio3 domain was silenced in piPSCs as previously seen in mouse and human iPSCs, which explains rare success of generation of pig chimeric and cloned offspring. Our analyses decipher pig somatic cells undergoes reprogramming into a primed state and maintains its regulatory network with define feature with human iPSCs and mouse EpiSCs.

overall_design: We compare gene expression profiles of pig iPS cell lines generated by our lab with cell lines derived from other labs with different levels of marker expression and plasticity.

first: Yajun

last: Liu

first: Huayan

last: Wang


title: Protein Array Screening of Myelodysplastic Syndromes I

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

department: Biochemistry and Molecular Biology

institute: Michigan State University

summary:
In a two-stage study we investigated levels of Immunoglobulin G (IgG) reactivity in plasma from Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) post MDS patients (59 and 16 cases respectively) as compared to healthy cohort (34).  In Stage I we utilized high-throughput protein arrays (23 232 total signals, in duplicate) to identify proteins of high-interest.  In Stage II we designed new protein arrays (352 total signals, in duplicate) to further focus on 25 of the proteins from Stage I and expanded to a larger cohort, including both male and female samples (161 MDS and 43 AML patients; 112 healthy controls).   Stage I resulted in 35 proteins displaying increased IgG reactivity in patients as compared to the healthy controls (P< 4.3 x10-07, Bonferroni Corrected P<0.01).   This protein subset included 14 proteins associated with cancer, 12 with apoptosis, and 3 with the NFAT Regulation canonical pathway.  Using the focused arrays we performed a classification of MDS patients and healthy controls.   Stage II subsequently identified a high-interest focused set of 3 proteins, namely AKT3, FCGR3A and ARL8B displaying aberrant increased reactivity in patient subgroups, in concordance with Stage I.   Autoantibody reactivity against specific proteins provides complementary information to other known molecular signatures for MDS and may enhance our capabilities for detecting and classifying MDS.
In the study presented here, MDS patients were classified into Stable, Transforming or AML post MDS (L) classes retrospectively.  The different patients were compared to a healthy cohort to assess increased autoantibody reactivity to specific patients as opposed to healthy groups

sample_organism:
Homo sapiens
unidentified

overall_design: Stage 1 of Study: 111 Files Analyzed, 37 sMDS, 22 tMDS, 16 AML(L), 34 Healthy and 2 Negative Controls (used to eliminate non-plasma signals)

middle: I

first: Rui

first: Michael

last: Snyder

first: Peter

last: Greenberg


title: Bifidobacterium bifidum PRL2010 actively changes the expression profiles of mouse

status: Public on Nov 19 2013

city: Parma

first: Marco

last: Ventura

address: Viale delle Scienze 11/A

department: Dept. Life Sciences

institute: University of Parma

summary: We studied the global transcription profiling of mouse upon colonization with Bifidobacterium bifidum PRL2010 by using DNA microarrays.

overall_design: Two groups of mice consisting each of two animals were orally inoculated with either 109 CFU of PRL2010 cells (test strain) or water (control). Animals were 3 months old female BALB/c mice. Bacterial colonization was established by five consecutive daily administrations using a micropipette tip placed immediately behind the incisors.

first: Francesca

last: Turroni


title: Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments [aCGH]

overall_design: DNA from each evolved clone or population is hybridized vs DNA from the ancestral strain

first: David

last: Gresham


title: Differential expression of miRNAs in Brassica napus root following infection with Plasmodiophora brassicae

city: Cleveland

first: Sanjay

last: Gupta

state: Ohio

address: 10900 Euclid Avenue

department: Department of Urology

institute: Case Western Reserve University

summary: Canola (oilseed rape, Brassica napus L.), is susceptible to infection by the biotrophic protist Plasmodiophora brassicae, the causal agent of clubroot. To understand the roles of microRNAs (miRNAs) during the post-transcriptional regulation of disease initiation and progression, we have characterized the changes in miRNA expression profiles in canola roots during clubroot disease development and have compared these to uninfected roots. Two different stages of clubroot development were targeted in this miRNA profiling study: an early time of 10-dpi for disease initiation and a later 20-dpi, by which time the pathogen had colonized the roots (as evident by visible gall formation and histological observations). P. brassicae responsive miRNAs were identified and validated by qRT-PCR of miRNAs and the subsequent validation of the target mRNAs through starBase degradome analysis, and through 5’ RLM-RACE. This study identifies putative miRNA-regulated genes with roles during clubroot disease initiation and development. Putative target genes identified in this study included: transcription factors (TFs), hormone-related genes, as well as genes associated with plant stress response regulation such as cytokinin, auxin/ethylene response elements. The results of our study may assist in elucidating the role of miRNAs in post-transcriptional regulation of target genes during disease development and may contribute to the development of strategies to engineer durable resistance to this important phytopathogen.

platform_organism:
Physcomitrium patens
Picea glauca
Picea sitchensis
Pinus taeda
Liriodendron tulipifera
Persea americana
Populus tremuloides
Populus trichocarpa
Populus trichocarpa x Populus deltoides
Malus domestica
Prunus persica
Lupinus luteus
Medicago truncatula
Phaseolus vulgaris
Phaseolus coccineus
Manihot esculenta
Ricinus communis
Nicotiana sylvestris
Nicotiana tabacum
Nicotiana benthamiana
Petunia x hybrida
Ipomoea batatas
Lactuca sativa
Hordeum vulgare
Oryza rufipogon
Oryza sativa
Oryza brachyantha
Oryza nivara
Cenchrus americanus
Sorghum bicolor
Lolium arundinaceum
Phleum pratense
Lotus japonicus
Cenchrus ciliaris
Ipomoea nil
Prunus armeniaca
Peridictyon sanctum
Panicum virgatum
Populus tremula x Populus tremuloides
Rorippa indica
Oryza barthii
Nasturtium officinale
Nuphar advena
Prunus salicina
Hordeum vulgare subsp. vulgare
Populus tremula
Oenocarpus bataua
Malcolmia maritima

overall_design: In this miRNA-microarray experiment a total of 4 samples were analyzed with their 3 biological replicates. In which 2 samples C 10 DAY and C 20 DAY was used as referrence contols.

first: Shiv

last: Verma

first: Nat

last: Kav


title: Affymetrix axiom EUR array data for MDS fibroblasts and iPSCs

first: Yohei

last: Hayashi

summary: MDS patients are characterized as the deletion in chromosome 17. We generated induced pluripotent stem cells (iPSCs) from MDS fibroblasts. We performed SNP microarray analysis using Affymetrix axiom EUR array platform.

overall_design: Affymetrix axiom EUR arrays were performed according to the manufacturer's directions on DNA extracted from MDS fibroblasts and iPSCs.


title: Expression analysis of human embryonic stem cell (hESC) lines growing with/ without FGF2 growth factor

status: Public on Nov 16 2013

city: Chicago

first: Sergey

last: Malchenko

state: IL

address: 2300 Children's Plaza

institute: Northwestern University's Feinberg School of Medicine

summary: Investigation of whole genome gene expression level changes in five hESC lines as a result of FGF2 withdrawal.

overall_design: Five hESC lines were grown in parallel with and without FGF2

first: Vasily

last: Galat


title: Candida glabrata response to sorbic acid

status: Public on Nov 15 2013

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

summary: BG14(wt) and BG14hog1∆ cells were exposed to weak acid  (20mM sorbic acid for 20min) to define the role of Hog1 for gene expression during weak acid stress.

overall_design: untreated control and 20 min treatment for both wild type and mutant. 3 biological replicates


title: Expression analysis of C. elegans wild-type N2 and rsks-1, daf-2, daf-2 rsks-1 and daf-16; daf-2 rsks-1 mutants

status: Public on Nov 14 2013

city: Nanjing

first: Di

last: Chen

state: Jiangsu

address: 12 Xuefu Rd, Pukou

department: Model Animal Research Center

institute: Nanjing University

summary:
Investigation of whole genome gene expression level changes in C. elegans rsks-1, daf-2, daf-2 rsks-1 and daf-16; daf-2 rsks-1 mutant compared to the wild-type N2 strain.  The mutants have altered longevity phenotypes.
The mutants analyzed in this study are further described in Di Chen, Patrick Wai-Lun Li, Benjamin A. Goldstein, Waijiao Cai, Emma Lynn Thomas, Fen Chen, Alan E. Hubbard, Simon Melov and Pankaj Kapahi, Germline Signaling Mediates the Synergistically Prolonged Longevity by Double Mutations in daf-2 and rsks-1 in C. elegans, Cell Reports (CELL-REPORTS-D-13-00388).

overall_design: A 47 chip study using total RNAs from C. elegans wild-type N2 (9 replicates), rsks-1 mutant (9 replicates), daf-2 mutant (9 replicates), daf-2 rsks-1 double mutant (10 replicates) and daf-16; daf-2 rsks-1 triple mutant (10 replicates) measured gene expression levels at the whole genome level.

first: Chen

last: Di

first: Kapahi

last: Pankaj

first: Melov

last: Simon


title: Bifidobacterium bifidum PRL2010 actively changes the expression profiles of human cell lines

summary: We studied the global transcription profiling of human cell lines upon colonization with Bifidobacterium bifidum PRL2010 by using DNA microarrays.

overall_design: We decided to use HT29 monolayer as an in vitro model to investigate the molecular impact of B. bifidum PRL2010 on human intestinal transcriptome. HT29 monolayers cultivated at 15 days of post confluence were placed in contact with PRL2010 cells for a range of time spanning from 0 h, 1 h (T1), 2 h (T2) to 4 h (T4).


title: Protein Array Screening of Myelodysplastic Syndromes

first: George

last: Mias

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

overall_design: Refer to individual Series


title: Protein Array Screening of Myelodysplastic Syndromes II

overall_design: Stage 2 of study:  633 Files analyzed for: 316 Patients in duplicate and a negative control.  The proteins on the array were selected following a first stage using ProtoArrays

first: Rui

first: Michael

last: Snyder


status: Public on Nov 12 2013

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

summary: The microarrays experiments was performed with the purpose of identify transcriptional networks activated by copper. This experiment correspond the work tituled Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels (work in preparation).Mauricio Latorrea,b, Jessica Galloway-Peñac,d,e, Jung Hyeo Rhoc,d, Marko Budinichf,  Barbara E. Murrayc,d,e, Alejandro Maassb,f, Mauricio Gonzáleza,b,f*.    a INTA, Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile.  b Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile.    c Division of Infectious Disease, Department of Medicine, University of Texas Medical School, Houston, Texas, United States of America.  d Center for the Study of Emerging and Reemerging Pathogens, University of Texas Medical School, Houston, Texas, United States of America.   e Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America  f Mathomics, Center for Mathematical Modeling (UMI2807CNRS), Santiago, Chile.  * Corresponding author. Address: El Líbano 5524, Santiago 11, Chile. Fax: +56 (2) 2214030.

overall_design: A eight chip study (two technical replicates) using total RNA recovered from four separate cultures of: Enterococcus faecalis OG1RF (N medium growth),  Enterococcus faecalis OG1RF copΔ mutant strain (N medium growth), Enterococcus faecalis OG1RF copΔ mutant low copper treatment (N medium growth + 0.05 mM CuSO4) and Enterococcus faecalis OG1RF copΔ mutant low copper treatment (N medium growth + 0.5 mM CuSO4). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).


title: Dataset #1 for genome-wide analysis of heritable dog osteosarcoma in 3 breeds

city: Cambridge

first: Elinor

last: Karlsson

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: Osteosarcoma in dogs is a spontaneously occurring disease with a global tumor gene expression signature indistinguishable from human pediatric tumors and clinical progression is remarkably similar. Unlike human OS, canine OS is a highly heritable disease with some large and giant dog breeds at >10x increased risk. We did a genome wide association study of osteosarcoma using the Illumina CanineHD genotyping array in three breeds: greyhound (mortality from OS = 26%), rottweiler (17%) and Irish wolfhound (IWH, 21%) and identified 33 inherited risk loci explaining 55 to 85% of phenotype variance in each breed.

overall_design: Data created for a genome-wide association studio of heritable osteosarcoma risk factors in dogs, including 267 racing greyhounds (153 affected (A) + 114 unaffected (U)), 135 rottweilers (80 A + 55 U), 141 IWH (76 A + 65 U) and 19 AKC greyhounds using the Illumina CanineHD array (~170,000 SNPs genomewide)

first: Kerstin

last: Lindblad-Toh


title: Genome-wide analysis of heritable dog osteosarcoma in 3 breeds


title: Expression profile of select inflammation-related genes after miR-466l overexpression or knockdown in human macrophages

status: Public on Nov 08 2013

city: Boston

first: Yongsheng

last: Li

address: 77 Ave Louis Pasteur, HIM836

department: Anethesiology

institute: Brigham and Women's Hospital

summary: Human Peripheral blood mononuclear cells (PBMC) were isolated from healthy human whole blood by density gradient centrifugation using Histopaque®-1077 and cultured in RPMI (containing 10% FBS) with 10 ng/ml human recombinant GM-CSF at 37 °C for 7 days. These cells are confirmed as human macrophages. These macrophages were transfected with vector control, miR-466l,anti-miR-negative or anti-miR-466l (37 °C, 72h). After transfection, total RNA was extracted for reverse transcription. The product cDNA was collected for real-time PCR with respective primers.

overall_design: In the study presented here, lentiviral vector control (VC), miR-466l, anti-miR-negative (anti-miR-neg) or anti-miR-466l transfected human macrophages were used to acquire expression profiles of a total of  60 unique genes related to inflammation

first: Charles

middle: N

last: Serhan


title: A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function (array)

first: Ann

last: Harris

address: 2430 N Halsted Street Box 211

institute: Lurie Children's Hospital of Chicago Research Center

summary: Distal cell-type-specific regulatory elements may be located at very large distances from the genes that they control and are often hidden within intergenic regions or in introns of other genes. The development of methods that enable mapping of regions of open chromatin genome wide has greatly advanced the identification and characterisation of these elements. Here we use DNase I hypersensitivity mapping followed by deep sequencing (DNase-seq) to generate a map of open chromatin in primary human tracheal epithelial (HTE) cells and use bioinformatic approaches to characterise the distribution of these sites within the genome and with respect to gene promoters, intronic and intergenic regions. Genes with THE-selective open chromatin at their promoters were associated with multiple pathways of epithelial function and differentiation. The data predict novel cell-type-specific regulatory elements for genes involved in HTE cell function, such as structural proteins and ion channels, and the transcription factors that may interact with them to control gene expression. Moreover, the map of open chromatin can identify the location of potentially critical regulatory elements in genome-wide association studies (GWAS) in which the strongest association is with single nucleotide polymorphisms in non-coding regions of the genome. We demonstrate its relevance to a recent GWAS that identifies modifiers of cystic fibrosis lung disease severity. Since HTE cells have many functional similarities with bronchial epithelial cells and other differentiated cells in the respiratory epithelium, these data are of direct relevance to elucidating the molecular basis of normal lung function and lung disease.

overall_design: HTE (human tracheal epithelial) cells were isolated from  human trachea postmortem and grown as described previously (Davis P.B. et al.1990). Total RNA was extracted by Trizol and the samples shipped to NimbleGen for gene expression analysis on NimbleGen 4 X 72K HG18 60mer arrays.

first: J

last: Bischof

first: C

last: Ott

first: S

middle: H

last: Leir

first: N

last: Gosalia

first: L

last: Song

first: D

last: London

first: T

last: Furey

middle: U

last: Cotton

first: G

last: Crawford

first: A


title: Dataset #3 for genome-wide analysis of heritable dog osteosarcoma in 3 breeds


title: Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically

status: Public on Nov 01 2013

first: Claire

last: Vieille

state: MI

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

summary: For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures.

overall_design: Hybridizations used NimbleGen expression array chips (Product no. A4385-00-01, platform accession no GPL15883) designed against the 5,657 ORFs encoded in the A. variabilis genome (GenBank accession no. CP000117). Each ORF was represented by seventeen 60-mer oligonucleotides. Each oligonucleotide was present in four internal replicates. The twenty-seven microarray data files were normalized against each other. Expression array data were analyzed using ArrayStar 3.0 (DNASTAR, Madison, WI).

first: Jeong-Jin

last: Park

first: Sigal

last: Lechno-Yossef

last: Wolk


title: Whi3 RIP-Chip

status: Public on Oct 31 2013

city: Stony Brook

first: Ying

last: Cai

state: New York

address: Life Sciences Building Rm 363

department: Molecular Genetics and Microbiology

institute: Stony Brook University

summary: Whi3 associated mRNAs were identified by immunoprecipitation of TAP-tagged Whi3 followed by microarray analysis

overall_design: RNA IP of Whi3-TAP and Whi3-dRRM-TAP with total RNA as reference. Each sample has 2 replicates

first: Hong

last: Wang


title: TE-Array-- A high throughput tool to study transposon transcription

city: Baltimore

first: Kathleen

middle: Helen

last: Burns

state: MD

address: 720 Rutland Ave Ross 524

department: Pathology

institute: Johns Hopkins University School of Medicine

type:
Expression profiling by array
Other

summary: TE-Array is a custom Agilent microarray that probes for transposable elements in both sense and antisense orientations in humans and mice. TE-Array was used to study expression levels of transposable elements (TE) in a panel of normal mouse tissues.

sample_organism:
Homo sapiens
Mus musculus

overall_design: TE-Array comprises of 4 different custom Agilent 4X44K designs. These 4 different designs have probes for human sense orientation, human antisense orientation, mouse sense orientation and mouse antisense orientation transposable elements. These array designs were used to study the transposon abundance profile in 7 different mouse tissue samples, 2 mouse cell lines and 1 transposon transfected versus untransfected human cell line.

first: Veena

last: Gnanakkan

first: Andrew

last: Jaffe

first: Lixin

last: Dai

first: Jie

last: Fu

first: Sarah

middle: J

last: Wheelan

first: Hyam

last: Levitsky

first: Rafael

last: Irizarry

first: Jef

last: Boeke


title: Epigenetically induced paucity of histone H2A.Z stabilizes fission yeast ectopic centromeres

status: Public on Nov 03 2013

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

institute: Kochi University of Technology

type: Genome binding/occupancy profiling by genome tiling array

summary: In most eukaryotes, the centromere is epigenetically defined by nucleosomes that contain the histone H3 variant centromere protein A (CENP-A). Specific targeting of the CENP-A-loading chaperone to the centromere is vital for stable centromere propagation; however, the existence of ectopic centromeres (neocentromeres) indicates that this chaperone can function in different chromatin environments. The mechanism responsible for accommodating the CENP-A chaperone at novel chromatin regions is poorly understood. Here, we report the identification of transient, immature neocentromeres in Schizosaccharomyces pombe, which show reduced association with the CENP-A chaperone Scm3 attributable to persistence of the histone H2A variant H2A.Z. Following acquisition of adjacent heterochromatin or relocation of the immature neocentromeres to subtelomeric regions, H2A.Z was depleted and Scm3 was replenished, leading to subsequent stabilization of the neocentromeres. These findings provide novel insights into histone variant-mediated epigenetic control of neocentromere establishment.

overall_design: Comparison of chromosomal distributions of centromeric proteins and heterochromatin proteins between the NC survivors and their derivatives.

first: Yuki

last: Ogiyama


title: Cancer-induced Muscle Wasting is IKKβ-dependent and NF-kappaB-independent

first: Susan

last: Kandarian

address: 635commonwealth ave, Rm444

department: Health Sciences

institute: Boston University

summary: Existing data suggest that NF-kappaB signaling is a key regulator of cancer-induced skeletal muscle wasting.  However, identification of the components of this signaling pathway and of the NF-κB transcription factors that regulate wasting is far from complete.  In muscles of C26 tumor bearing mice, overexpression of d.n. IKKβ blocked muscle wasting by 69%, the IκBα-super repressor blocked wasting by 41%.  In contrast, overexpression of d.n. IKKα or d.n. NIK did not block C26-induced wasting.  Surprisingly, overexpression of d.n. p65 or d.n. c-Rel did not significantly block muscle wasting.  Genome-wide mRNA expression arrays showed upregulation of many genes previously implicated in muscle atrophy.  To test if these upregulated genes were direct targets of NF-κB transcription factors, we compared genome-wide p65 or p50 binding to DNA in control and cachectic muscle using ChIP-sequencing.  Bioinformatic analysis of ChIP-seq data from control and C26 muscles showed increased p65 and p50 binding to a few regulatory and structural genes but only two of these genes were upregulated with atrophy.  The p65 and p50 ChIP-seq data are consistent with our finding of no significant change in protein binding to an NF-κB oligo in a gel shift assay.  Taken together, these data support the idea that although inhibition of IκBα, and particularly IKKβ, blocks cancer-induced wasting, the alternative NF-κB signaling pathway is not required.  In addition, the downstream NF-κB transcription factors do not regulate the transcriptional changes.  These data are consistent with the growing body of literature showing that there are NF-κB-independent substrates of IKKβ and IκBα that regulate physiological processes.

overall_design: To compare gene expression changes in atrophied muscles from C26 tumor bearing mice, gastrocnemius/plantaris muscles were harvested from 4 C26 tumor-bearing mice, and 3 control non tumor-bearing mice.  Total RNA were isolated and pooled (2-3 muslces in the same group per RNA sample ) to make equal amount of total RNA per sample. Three pooled total RNA samples from healthy control muscles and 3 pooled total RNA from muscles of C26 tumor bearing mice were labelled and hybridized on 6 Mouse Affyemtrix Gene 1.0 ST arrays. Two-side t-tests and multiple test corrections were performed to identify differentially expressed genes due to C26 tumor bearing induced cachexia.

first: Evangeline

middle: W

last: Cornwell

first: Azadeh

last: Mirbod

first: Chia-Ling

last: Wu

first: Robert

last: Jackman


title: Array comparative genomic hybridization data from 313 CLL specimens to study outcome associations

status: Public on Sep 07 2013

city: Rutherford

first: Jane

last: Houldsworth

state: NJ

address: 201 Route 17 North

institute: Cancer Genetics, Inc.

summary: This study investigates genomic imbalance in chronic lymphocytic leukemia (CLL) and aims to identify genomic gains and losses with prognostic significance.

overall_design: Two-condition experiment, Test CLL specimens vs. Reference human genome DNA equimixture of normal male and normal female.

first: Thodima

last: Venkata


title: Real-time quantitative PCR analysis reveals high expression of activin A during NK-DC interactions

status: Public on Nov 13 2013

city: Brescia

first: Pascal

last: Seeger

address: Viale Europa 11

department: Department of Molecular and Translational Medicine

institute: University of Brescia

summary: The interaction of natural killer (NK) cells with dendritic cells (DC) results in reciprocal cell activation through the interaction of membrane proteins and the release of soluble factors. Here we report that in NK-DC cocultures, among a set of 84 cytokines investigated, activin A was the second highest induced gene, with CXCL8 being the most upregulated one. Activin A is a member of the TGF-β superfamily and was previously shown to possess both pro- and antiinflammatory activities. In NK-DC cocultures, the induction of activin A required cell contact and was dependent on the presence of proinflammatory cytokines (i.e. IFN-γ, TNF-α and GM-CSF) as well as on NK cell-mediated DC killing. CD1+ DC were the main activin A producer cells among myeloid blood DC subsets.  In NK-DC cocultures, inhibition of acitivn A by follistatin, a natural inhibitory protein, or by a specific blocking antibody, resulted in the upregulation of proinflammatory cytokine release (i.e. IL-6, IL-8, TNF-α) by DC and in the increase of DC maturation. In conclusion, our study reports that activin A, produced during NK-DC interactions, represents a relevant negative feedback mechanism that might function to prevent excessive immune activation by DC.

overall_design: Human CD14 positive monocytes were differentiated to DC in vitro in the presence of IL-4 (20 ng/ml) and GM-CSF (50 ng/ml) for 6 days. Immature DC were then cocultured with allogeneic IL-15-activated NK cells (at 1:1 NK:DC ratio) for 0, 2 and 6 hrs. RNA was obtained from three independent coculture experiments. Equal amount of total RNA from each experiment was pooled prior to gene expression analysis. The gene expression of common cytokines was quantified using an RT2 Profiler PCR Array (Qiagen).

first: Daniela

last: Bosisio

first: Silvia

last: Parolini

first: Raffaele

last: Badolato

first: Angela

last: Gismondi

last: Santoni

first: Silvano

last: Sozzani


title: Chip-chip for H4K16ac in HEK293 cells

status: Public on Jul 01 2013

city: New Delhi

first: Pankaj

last: Kumar

state: Delhi

address: Mall Road,

department: G N R Knowledge Center for Genome Informatics

country: India

institute: Institiue of Genomics and Integrative Biology

summary: Genome-wide distribution of H4K16 acetylation modification was analyzed in human cells

overall_design: Compare immunoprecipitated (IP) and Input DNA samples using NimbleGen Human ChIP-chip 2.1M Whole-Genome Tiling -10 Array Set

first: Nobuo

last: Horikoshi

first: Girdhar

middle: G

last: Sharma

first: Min

last: Chen

first: Clayton

last: Hunt

first: Kenneth

last: Westover

first: Shantanu

last: Chowdhury

first: Tej

middle: K

last: Pandita


title: Lachancea kluyveri (formerly Saccharomyces kluyveri); Growth on different nitrogen sources.

status: Public on Jun 21 2013

city: Lund

first: Anna

middle: Andersson

last: Rasmussen

address: Sölvegatan 23

department: Molecular Cellbiology

country: Sweden

institute: Lund University

summary: Transcriptional profiling of the yeast Lachancea kluyveri when grown on minimal media with different compounds added as the sole nitrogen source. Cells grown on uracil, uridine, dihydrouracil and ammonia were profiled using cells grown on proline as the reference.

overall_design:
Five conditions, of one was used as reference. Each grown in 4 parallell biological replicates, which were extracted, labeled and hybridized individually, except for the reference where the replicates were pooled. 1 technical replicate.

Please note that raw data files for the following samples are not available;
Skluy_uracil_rep2, Skluy_dihydrouracil_rep3, Skluy_uridine_rep4


title: Distinct effects of  topoisomerase II inhibitors on tumor cell lines (part 1)

status: Public on Jun 04 2013

city: Palo Alto

first: Baoxu

last: Pang

state: CALIFORNIA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

summary: One major class of anti-cancer drugs targets topoisomerase II to induce DNA double-strand breaks and cell death of fast growing cells.  Here, we compare three members of this class - the antracyclines doxorubicin and aclarubicin, and a chemically unrelated compound, etoposide. Aclarubicin does not induce DNA breaks. We define a new activity for the antracyclines: unsupported histone eviction from ´open´ or loosely packed chromosomal areas reflecting exon and promoter regions. As a result, the epigenome and the transcriptome are strongly affected.

overall_design: Tissue culture cells were treated with doxorubicin, aclarubicin or etoposide for 2 hours. Then drugs were removed by extensive washing. cells were further cultured for indicated days before total RNA were extracted and compared to un-treated control.

first: Arno

last: Velds

first: Ron

last: Kerkhoven

first: Jacques

last: Neefjes


title: Expression data from porcine monocytes sorted on expression of CD14 and CD163

status: Public on Feb 14 2013

city: München

first: Lynsey

last: Fairbairn

address: Troger str. 1

institute: Technical University Munich

summary: Human and mouse monocytes can be divided into 2 different sub-populations, using CD14-CD16 and Ly6C-CX3CR1 respectively. We investigated the pig monocytes sub-populations and found that all porcine monocyte express CD16 and CD172α but can be divided into 2 subpopulation using CD14 and the scavenger receptor CD163. The CD14hi-CD163low population resemble to the inflammatory monocytes whereas the CD14low-CD163hi display more a resident monocyte type. Pig monocyte can be differentiated into macrophages when cultured with rhCSF-1 and show an increase in size, granularity and autofluorescence, and express the common macrophage markers CD14, CD16 and CD172α. Gene expression in these 2 sub-populations was profiled using the newly-developed and annotated pig whole genome snowball microarray, showing a distinct pattern between inflammatory and resident monocytes but this difference would be more a maturation process instead of two separate subsets. Furthermore, the expression of certain genes such as CD36, CLEC4E or TREM-1 proved to share the same pattern as human monocytes, quite different from mouse monocytes. These results emphasize the potential role of the pigs as a model for human inflammatory disease and will improved our knowledge on the mononuclear phagocyte system development.

overall_design: Porcine PBMCs were isolated from the blood of three seperate pigs, FACS sorted on expression of CD14 and CD163 and RNA isolated from each sample, a total of 6 microarrays were hybridised

first: L

first: R

last: Kapetanovic

first: D

last: Beraldi

last: Sester

first: C

last: Tuggle

first: A

middle: L

last: Archibald

middle: A

last: Hume


title: A transcriptomic analysis of a Caucasian family cohort of high risks for the metabolic syndrome [HumanWG-6 v2.0]

status: Public on Apr 05 2013

city: Milwaukee

first: Yi

last: Zhang

state: WI

address: 8701 W Watertown Plank Rd

department: Medicine

institute: Medical College of Wisconsin

summary: Metabolic Syndrome (MetS) is a strong predictor for diabetes and cardiovascular disease and is defined by a constellation of phenotypes including increased and adverse body fat distribution, insulin resistance, abnormalities in lipids and lipoproteins, malfunctional cardiovascular performance, and abnormal levels of adipokines and cytokines. We assayed in a subset of our family cohort phentoyped for MetS phentoypes, the genome-wde transcript levels using the Illumina Human WG-6 v2 expression arrays.

overall_design: Genome-wide gene expression was assayed in members of families that originally contribute to linkage signals in a previous genome-wide linkage scans for multiple MetS phenotypes.

first: Jack

last: Kent

first: Michael

last: Olivier

first: Diana

last: Cerjak

first: Joanne

middle: E

last: Curran

first: Melanie

last: Carless

first: Harald

last: Göring

first: John

last: Blangero

first: Ahmed

last: Kissebah


title: Tissue specific expression of non-coding RNAs

status: Public on Jun 01 2013

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

type: Non-coding RNA profiling by genome tiling array

summary: Thousands of novel non-coding RNAs (ncRNA) has been identified in recent years. Only few have been functionally characterized and it is thus unclear which and how many are functional. Here, we characterize expression of ncRNAs in twelve human tissues using a costum designed microarray. The study serve as a first analysis to gain further insight into expression behavior of a broad and comprehensive collection of ncRNAs and pinpoint a set of ncRNAs we believe are functional.

overall_design: Expression was measured in triplicates of twelve human tissues using a custom-designed array containing 26,910 non-coding RNA features and a set of 6,856 protein-coding genes.

middle: M

first: Disa

last: Tehler

first: Torben

middle: F

last: Orntoft

first: Anders

last: Lund

first: Jakob

middle: S

last: Pedersen


title: Intrinsic glioma subtypes in EORTC 26951 (part 2)

status: Public on Feb 01 2013

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

summary: Background: Intrinsic glioma subtypes (IGS) are molecularly similar tumors that can be identified based on unsupervised gene-expression analysis. Here, we have evaluated the clinical relevance of these subtypes within EORTC26951, a randomized phase III clinical trial investigating adjuvant procarbazine, CCNU (lomustine) and vincristine (PCV) chemotherapy in anaplastic oligodendroglial tumors. Our study is the first to include gene-expression profiles of formalin-fixed and paraffin-embedded (FFPE) clinical trial samples. Methods: Gene-expression profiling was performed in 140 samples: 47 fresh frozen and 93 FFPE, on HU133_Plus_2.0 and HuEx_1.0_st arrays (Affymetrix), respectively.  Results: All previously identified six intrinsic glioma subtypes are present in EORTC26951. This confirms that different molecular subtypes are present within a well-defined histological subtype. Intrinsic subtypes are highly prognostic for overall- (OS) and progression-free survival (PFS). They are prognostic for PFS independent of clinical (age, performance, tumor location), molecular (1p19qLOH, IDH1 mutation, MGMT methylation) and histological parameters. Combining known molecular (1p19LOH, IDH1) prognostic parameters with intrinsic subtypes improves outcome prediction (Proportion of Explained Variation 30% v 23%). Specific genetic changes (IDH1, 1p19qLOH and EGFR amplification) segregate into different subtypes. We identified one subtype, IGS-9 (characterized by a high percentage of 1p19qLOH and IDH1 mutations), that especially benefits from PCV chemotherapy. Median OS in this subtype was 5.5 years after radiotherapy (RT) alone v 12.8 years after RT/PCV; P=0.0349; HR 2.18, 95% CI [1.06, 4.50]. Conclusion: Intrinsic subtypes are highly prognostic in EORTC26951 and improve outcome prediction when combined with other prognostic factors. Tumors assigned to IGS-9 benefit from adjuvant PCV

overall_design: A total of 140 samples were included in this study, profiles of 95 were FFPE derived samples run on exon arrays. 12 samples (part 2) can also be found in GSE16011 (PMID 19920198 and 16357140), and 6 from Oncomine (part 3).

first: Lale

last: Erdem

first: Lonneke

last: Gravendeel

first: Johan

last: de Rooi

first: Paul

last: Eilers

last: Idbaih

first: Wim

last: Spliet

first: Wilfred

last: den Dunnen

first: Johannes

last: Teepen

first: Pieter

last: Wesseling

first: Peter

last: Sillevis Smitt

last: Kros

first: Thierry

last: Gorlia

first: Martin

last: van den Bent


title: Comparative transcriptomic profiling of liver tissue from lean (fa/+) female Zucker rats (~15 weeks old) fed a standard diet supplemented (0.5% w/w) with a rosemary extract enriched in carnosic acid (40% CA)

status: Public on Sep 15 2013

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

summary: We used Affymetrix microarrays to investigate gene expression changes in the liver of lean female Zucker rats exposed to a normal diet supplemented with a rosemary extract rich in the diterpenic compound, carnosic acid (CA).

overall_design:
The aim of this work was to determine whether the daily intake (with the standard diet) of the rosemary extract (RE) enriched in CA (40%) for 64 days exerted any modulatory effects, at the level of gene expression, in the liver of lean Zucker female rats. Female lean Zucker rats were randomly assigned to two experimental groups (n= 7 animals per group) as follows: (1) control group, fed a standard diet (CT); (2) treated group, fed a standard diet supplemented (0.05% w/w) with the RE rich in CA (RE). At the end of the experimental procedure (64 days), total RNA was extracted from the liver to compare differential gene expression between the two groups.
Liver differential gene expression after 64 days of supplementation between the CT group and the RE group (effects of the extract supplementation).

first: María

middle: T

last: Romo-Vaquero

first: Nicolas

last: Issaly


title: eQTL Analysis Identifies Novel Associations Between Genotype and Gene Expression in the Human Intestine (Illumina SNP)

status: Public on Dec 01 2012

city: Toronto

first: Boyko

last: Kabakchiev

state: Ontario

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

country: Canada

institute: Mount Sinai Hospital

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

summary: Genome-wide association studies (GWAS) have been pivotal to increasing our understanding of intestinal disease. However, the mode by which genetic variation results in phenotypic change remains largely unknown, with many associated polymorphisms likely to modulate gene expression. Analyses of expression quantitative trait loci (eQTL) to date indicate that as many as 50% of these are tissue specific. Here we report a comprehensive eQTL scan of intestinal tissue.

overall_design: Subjects who had undergone ileal pouch anal anastomosis and closure of ileostomy at least one year prior to recruitment were prospectively enrolled at Mount Sinai Hospital in Toronto. Endoscopically and histologically normal tissue biopsies from the afferent limb of these individuals were obtained and preserved in RNAlater. Total RNA was extracted with the QIAGEN miRNeasy Kit and mRNA analysis was performed on Affymetrix Human Gene 1.0 ST arrays. DNA was obtained from whole-blood samples from the same individuals and genotyped using the Illumina beadchips. Cis- and trans-eQTL analyses were carried out on 173 subjects encompassing the expression levels of 19,047 unique autosomal genes listed in the NCBI database and over 580K dbSNPs (Call Rate  ≥ 95%; MAF  ≥ 5%; Hardy–Weinberg equilibrium (HWE) χ2 p-values  ≥ 10-6). This work was done in a custom software pipeline and the Kruskal-Wallis test was used to compare expression values across different genotypes. False discovery rate correction for multiple testing was applied at an alpha level of 5%.

first: B

first: M

last: Silverberg


title: Oncorhynchus mykiss muscle cells: Small vs. Large fish

status: Public on Nov 29 2012

city: Guelph

first: Andrea

middle: Lynne

last: Kocmarek

address: Science Complex, University of Guelph

department: Intergrative Biology

institute: University of Guelph

summary: Transcriptional profiling of rainbow trout muscle cells comparing muscle cells from small fish with muscle cells from large fish at two time periods.

overall_design: Two-condition experiment, small vs. large-fish muscle cells. Sept. and Dec. spawning fish.  Biological replicates: 4 small replicates, 4 large replicates for each time period.

first: Moira

last: Ferguson

first: Roy

last: Danzmann


title: Gene expression profile of L428 cells conditional expressing PU.1

status: Public on Nov 22 2012

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

institute: Kumamoto university of Medicine

summary: PU.1 is an Ets family transcription factor that is essential for the differentiation of both myeloid and lymphoid cells. PU.1 is down-regulated in classical Hodgkin lymphoma cells via methylation of the PU.1 promoter. To evaluate whether down-regulation of PU.1 is essential for the growth of cHL cells, we generated L428 derived  cell lines conditionally express PU.1 by tet-off system (designated L428tetPU.1). Conditonally expressed PU.1 by tetracycline removal induced complete growth arrest and apoptosis in L428 cells. To elucidate the mechanisms underlying cell cycle arrest and apoptosis induced by PU.1, we compared gene expression profiles of L428tetPU.1 cells 0, 1 and 3 days after PU.1 induction, by DNA microarray.

overall_design: We extracted total RNA from L428tetPU.1 cells 0, 1 and 3 days after PU.1 induction by tetracycline removal. We compared gene expression profiles of KL428tetPU.1 cells 0, 1 and 3 days after PU.1 induction using DNA microarray analysis. 4 independent experiments were performed with each RNA samples.

first: Hiromichi

last: Yuki

first: Shikiko

last: Ueno

first: Hiro

last: Tatetsu

first: Hiroaki

last: Niiro

first: Tadafumi

last: Iino

first: Shinya

last: Endo

first: Yawara

last: Kawano

first: Yoshihiro

last: Komohara

first: Motohiro

last: Takeya

first: Hiroyuki

last: Hata

first: Seiji

last: Okada

first: Toshiki

last: Watanabe

first: Koichi

last: Akashi

last: Mitsuya


title: Expression analysis with Phospholipase C over expression

status: Public on Sep 01 2012

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

summary: The regulation of phospholipid biosynthesis in Saccharomyces cerevisiae through cis-acting upstream activating sequence inositol (UASino) and trans-acting elements, such as the INO2-INO4 complex and OPI1 by inositol supplementation in growth is thoroughly studied. In this study, we provide evidence for the regulation of lipid biosynthesis by phosphatidylinositol-specific phospholipase C (PLC) through UASino and two trans-acting elements. Gene expression analysis and radiolabelling experiments demonstrated that the overexpression of rice PLC in yeast cells altered phospholipid biosynthesis at the levels of transcriptional and enzyme activity.

overall_design: There are two biological replicates two hour and five hour induction with galactose. The genome wide expression of Saccharomyces cerevisiae strain BY4741 harbouring (rice) rPLC-pYES2  and a vectro control (pYES2) were compare with each other. (Agilent Gene Expression Saccharomyces cerevisiae 8x15k array AMADID: 016333)

first: Sunny

middle: D

last: Rupwate

first: Preeti

first: Ram

last: Rajasekharan


title: A genomic signature of gene-environment interactions in C. elegans

status: Public on Jun 30 2012

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

summary:
The phenotype is an interplay between genetic and environmental components, however the relationship between these two is difficult to predict. For any particular environment only a handful of genes show gene environment interaction [refs]. This may imply that certain constrains prevent genes to participate in gene environment interaction that possibly could be used to predict potential targets for such interaction under different sets of environmental conditions.
Our approach was to culture 6 C. elegans strains (5 geographical isolates + 1 mutant straint) at 20°C, then split the culture into 5 conditions. We measured mRNA abundances in 4-cell stage embryos using microarray with three separately collected 50-embryo replicates collected for each combination of strain and environment.

overall_design: 90 microarrays of C. elegans for 6 strains * 5 conditions in triplicates.

first: Vladislav

last: Grishkevich

first: Tamar

last: Hashimshony

first: Shay

last: Ben-Elazar

first: Daniel

last: Schott

first: Craig

last: Hunter


status: Public on Jun 15 2012

city: Ithaca

first: John

middle: D.

last: Helmann

state: NY

address: 372 Wing Hall

department: Microbiology

country: USA

institute: Cornell University

summary: Transcriptional profile of the rpoC G1122D mutant during log growth phase in LB medium.

overall_design: Bacillus subtilis W168, WT vs. rpoC (G1122D). The experiment was conducted two times using three independent total RNA preparations (biological triplicates). Each comparison was performed in dye-swap with the same RNA preparation. For each paried comparison, one sample was labeled with Alexa Fluor 555 and the other was with Alexa Fluor 647.

first: Yong

middle: H

last: Lee


title: ATP2A2 and miRNA in human myocardial infarction

status: Public on Apr 30 2012

city: Ljubljana

first: Emanuela

last: Boštjančič

address: Korytkova 2

department: Institute of Pathology

country: Slovenia

institute: Faculty of Medicine

summary:
Cardiac sarco(endo)plasmic reticulum calcium ATPase-2 (SERCA2) plays one of the central roles in myocardial contractility. Both, SERCA2 mRNA and protein are reduced in myocardial infarction (MI), but the correlation has not been always observed. MicroRNAs (miRNAs) act by targeting 3'-UTR mRNA, causing translational repression in physiological and pathological conditions, including cardiovascular diseases. The aim of our study was to identify miRNAs that could influence SERCA2 expression in human MI.
The protein SERCA2 was decreased and 43 miRNAs were deregulated in infarcted myocardium compared to remote myocardium.
miRNAs binding prediction to SERCA2 identified 213 putative miRNAs. TAM and miRNApath identified 18 functional and 21 diseased states related to heart diseases. Combing all results, we identified certain miRNAs as potential regulators of SERCA2.

overall_design: All the samples were stored as FFPE tissue and in RNAlater. Expression of SERCA2 was analyzed by western blot and miRNA expression was analyzed by microarrays and qPCR in samples of remote and infarcted myocardium from 6 patients who died of MI. Bioinformatic analysis including six prediction programmes (TargetScan, PicTar, miRBase, miRDB, Human MicroRNA Targets, and microrna.org), TAM and miRNApath annotation, and free-energy of binding (RNA22, RNAfold), was performed. Nine up-regulated miRNAs were analyzed for free-energy of binding and flanking regions, and nine miRNAs were used for validation with qPCR. Based on qPCR the comparison between FFPE and RNAlater as well as different reference genes was also performed.


status: Public on Apr 24 2012

address: Sir CV Raman Avenue

department: Biochemistry

institute: Indian Institute of Science

overall_design: There are two biological replicates two hour and five hour induction with galactose. The genome wide expression of Saccharomyces cerevisiae strain BY4741 harbouring rPLC-pYES2  and a vectro control (pYES2) were compare with each other. (Agilent Gene Expression Saccharomyces cerevisiae 8x15k array AMADID: 016333)


title: A major genome region underlying artemisinin resistance in malaria

status: Public on May 01 2012

city: Notre Dame

first: Michael

last: Ferdig

state: IN

address: 280 Galvin Life Science

department: Biological Sciences

institute: University of Notre Dame

summary: Evolving resistance to artemisinin-based compounds in SE Asia threatens to derail attempts to control and eliminate malaria. Resistance has been confirmed in western Cambodia, has recently emerged in western Thailand, but is absent from neighboring Laos. Artemisinin resistance results in reduced parasite clearance rates (CR) from the blood following treatment. We used a two-phase approach to identify the genes underlying this ongoing selective event. Comparison of geographical differentiation and haplotype structure at 6,969 polymorphic SNPs in 91 parasites from western Cambodia, western Thailand and Laos identified 33 strongly selected genome regions. We screened SNPs and microsatellites within these genome regions in 718 parasites from western Thailand, and identified a 35kb region of chr 13 showing strong association (P=10-6 to 10-11) with slow CR. This region contains several compelling candidate loci, such as HSP70, for assessment by transfection. These results illustrate the efficacy of targeted association for identifying the genetic basis of adaptive traits.

overall_design: 91 malaria parasite isolates assayed for single nucleotide polymorphisms across 45K loci

first: Ian

last: Cheeseman

first: Tim

middle: J

last: Anderson


status: Public on Mar 01 2012

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

address: Av. Libertador Bernardo OHiggins 611

department: ICI

institute: Universidad de OHiggins

summary: To further investigate the homeostatic response of E. faecalis to Fe exposure, we examine the whole-genome transcriptional response of wild-type (WT) exposed to non toxic Fe excess. This experiment correspond the work titled Transcriptomic response of Enterococcus faecalis to iron excess (work in preparation)

overall_design: A four chip study using total RNA recovered from four separate wild-type cultures of Enterococcus faecalis OG1RF, two controls samples  (N medium growth) and two iron samples (N medium gowth with 0.5 mM Fe-NTA).  Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).

first: Guadalupe

last: López

first: Angélica

last: Reyes-Jara

first: Gabriel

last: Betanzos

first: Verónica

last: Cambiazo

last: González


title: Transcriptomic response of immune signaling pathways in intestinal epithelial cells exposed to commensals, pathogens and probiotics

status: Public on Dec 31 2011

city: Montreal

first: Thomas

middle: Allan

last: Tompkins

state: Qc

address: 6100 Royalmount Avenue

department: R&D

institute: Lallemand Health Solutions Inc.

summary: In order to understand the appropriate use of potentially beneficial Gram positive microbes through their introduction in the gut microbiome, it is necessary to understand the influence of individual bacteria on the host response system at a cellular level. In the present study we showed that lipopolysaccharide (LPS), flagellated Gram negative bacteria, potentially beneficial Gram positive bacteria and yeast interact differently with human intestinal enterocytes (IEC) with a custom-designed expression microarray evaluating 17 specific host-response pathways. Only, LPS and flagellated Gram negative bacteria induced inflammatory response, while a subset of Gram positive microbes had anti-inflammatory potential. The main outcome from the study was the differential regulation of the central MAPK signaling pathway by these Gram positive microbes versus commensal/pathogenic Gram negative bacteria. The microarray was efficient to highlight the impact of individual bacteria on IEC response, but q-RT-PCR validation demonstrated some underestimation for down regulated genes by the microarray. This Immune Array will allow us to better understand the mechanisms underlying pathogen-induced host immune responses, aid in the selection potentially probiotic microbes and perhaps select biomarkers for future clinical studies.

overall_design: In this study, human immune response was assessed by stimulating HT-29 intestinal epithelial cells (IEC) with different microorganisms (or LPS) individually. For each of the 12 different treatments, between 4 and 8 biological replicates were performed, analyzed with dye-swaps and hybridized against control or untreated cells. Genes that were showing a 1.3 mRNA transcript abundance fold change and a P-value below 0.05 were considered to be differentially expressed.

first: Julie

last: Audy

first: Olivier

last: Mathieu

first: Jocelyn

last: Belvis

first: Vanessa

last: de Carvalho


title: Ribosomal Protein Gene Deletions in Diamond Blackfan Anemia

status: Public on Jan 15 2012

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

institute: University of Arkansas for Medical Sciences

summary:
Diamond Blackfan anemia is a congenital bone marrow failure syndrome characterized by hypoproliferative anemia, often with associated physical abnormalities.  Perturbations of the ribosome appear critically important to the development of DBA, as alterations in 9 different ribosomal protein genes have been identified in multiple unrelated families, along with rarer abnormalities of additional ribosomal proteins.  However, presently only 50-60% of patients have an identifiable genetic lesion by ribosomal protein gene sequencing.
Using genome-wide SNP array to evaluate for regions of recurrent copy variation, we identified deletions at known DBA-related ribosomal protein gene loci in 17% (9/51) of patients without an identifiable mutation, including RPS19, RPS17, RPS26, and RPL35A

overall_design:
[Illumina platforms] A total of 68 samples were analyzed on Illumina Omni1_Quad or Illumina OmniExpress Genotyping bead arrays; 51 affected probands, 1 affected sibling, 1 unaffected sibling, and 15 parents.

[NimbleGen platform] 5 samples where a deletion was identified by SNP array and one sample where no deletion was identified were run on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused arrays for confirmation.

first: Adrianna

last: Vlachos

first: Eva

last: Atsidaftos

first: Hannah

last: Carlson-Donohoe

middle: C

last: Markello

first: Robert

last: Arceci

first: Steven

middle: R

last: Ellis

first: Jeffrey

last: Lipton

first: David

last: Bodine


status: Public on Dec 13 2011

first: John

last: Helmann

summary: Transcriptional profile of the rocG gudB double null mutant during log growth phase in LB medium.

overall_design: Bacillus subtilis W168, WT vs. delta-rocG delta-gudB. The experiment was conducted two times using three independent total RNA preparations (biological triplicates). For each paried comparison, WT was labeled with Alexa Fluor 555 and the rocG gudB double mutant was with Alexa Fluor 647.

first: Yong

last: Lee


title: MCF-7 and ZR-75-1 cell lines hypoxia

status: Public on Nov 04 2011

city: Oslo

first: Elisabet

last: Gjernes

address: Department of Medical Genetics | University of Oslo P.O. Box 1036 Blindern,

department: Department of Medical Genetics

country: Norway

institute: University of Oslo/Oslo University Hospital

summary: N-myc downstream-regulated gene 1 (*NDRG1*) is induced by cellular stress such as hypoxia and DNA damage, and in humans, germ line mutations cause Charcot-Marie-Tooth disease. However, the roles of NDRG1 in the cell are not fully understood. Previously, NDRG1 was shown to mediate doxorubicin resistance under hypoxia, suggesting a role for NDRG1 in cell survival under these conditions. We found decreased apoptosis in doxorubicin-treated cells expressing NDRG1 shRNAs under normoxia, demonstrating a requirement for NDRG1 in apoptosis in breast epithelial cells under normal oxygen pressure. We further compared expression profiles in human breast epithelial cells ectopically over-expressing NDRG1 with cells expressing NDRG1 shRNAs in order to identify biological pathways where NDRG1 is involved. The results suggest that NDRG1 may have roles connected to vesicle transport.  The previously reported roles of NDRG1 in apoptosis,  myelin sheet maintenance, enhanced exocytosis in mast cells and in cellular responses to hypoxia, heavy metals, and androgen may all converge by NDRG1 having a role linked to vesicle transport.

overall_design: Two condition design,  MCF-7 and ZR-75-1 cell lines grown in hypoxia compared to cells grown at normoxia.

first: Hanne

middle: A

last: Askautrud

first: G

last: Gunnes

first: M

last: Sletten

first: D

last: Ross

first: A

middle: L

last: Børresen-Dale

first: N

last: Iversen

last: Tranulis

first: E

last: Frengen


title: Global gene expression analysis reveals a link between NDRG1 and vesicle transport.

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

overall_design: Refer to individual Series


title: NDRG1 siRNA and overexpression in breast cell lines

overall_design:
SUM102 and ME16C2 stably transduced with siRNA against NDRG1 compared with empty vector control
ZR-75-1 stably transduced with NDRG1 overexpression construct compared with empty vector control
Two condition design


title: A role for Snf2 related nucleosome spacing enzymes in genome-wide nucleosome organization

status: Public on Sep 02 2011

first: Genotypic

last: technology

summary: The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleosome spacing enzymes is required to maintain this organization. In the absence of these enzymes regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicated that ATP-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome.

overall_design:
Agilent two-color experiment,Organism: Saccharomyces cerevisiae  ,Slides: Agilent Gene Expression S. cerevisiae 8x15k array AMADID: 016333, Labeling kit: Agilent’s Quick-Amp labeling Kit (p/n5190-0444)Method: T7 promoter based-linear amplification to generate labeled complementary RNA.
Other data used in this study are provided in GEO Series GSE31301 and GSE31015.

first: Triantaffyllos

last: Gkikopoulos

first: Vijender

last: Singh

first: Pieta

last: Schofield

first: Jane

last: Mellor

first: Michaela

last: Smolle

first: Geoffrey

last: Barton

first: Jerry

last: Workman

first: Marina

last: Pinskaya

first: Tom

last: Owen-Hughes


title: Bacillus subtilis 168 moenomycin stimulon

status: Public on Jun 17 2011

first: John

last: Helmann

summary: Transcriptional response of Bacillus subtilis to moenomycin in wild-type 168.

overall_design: Bacillus subtilis 168, WT (-MOE) vs. WT (+MOE). The experiment was conducted in triplicate using three independent total RNA preparations. Untreated samples were labeled with Alexa Fluor 555 and moenomycin treated samples were labeled with Alexa Fluor 647.

first: Anna-Barbara

last: Hachmann


title: Dataset #2 for genome-wide analysis of heritable dog osteosarcoma in 3 breeds

status: Public on Nov 12 2013

city: Cambridge

first: Elinor

last: Karlsson

state: MA

address: 7 Cambridge Center

institute: Broad Institute

summary: Osteosarcoma in dogs is a spontaneously occurring disease with a global tumor gene expression signature indistinguishable from human pediatric tumors and clinical progression is remarkably similar. Unlike human OS, canine OS is a highly heritable disease with some large and giant dog breeds at >10x increased risk. We did a genome wide association study of osteosarcoma using the Illumina CanineHD genotyping array in three breeds: greyhound (mortality from OS = 26%), rottweiler (17%) and Irish wolfhound (IWH, 21%) and identified 33 inherited risk loci explaining 55 to 85% of phenotype variance in each breed.

overall_design: Data created for a genome-wide association studio of heritable osteosarcoma risk factors in dogs, including 267 racing greyhounds (153 affected (A) + 114 unaffected (U)), 135 rottweilers (80 A + 55 U), 141 IWH (76 A + 65 U) and 19 AKC greyhounds using the Illumina CanineHD array (~170,000 SNPs genomewide)

first: Kerstin

last: Lindblad-Toh


title: Prognostic Gene Expression Signature of Carcinoma Associated Fibroblasts in Non-Small Cell Lung Cancer [genome variation profiling]

status: Public on Apr 08 2011

first: Ming-Sound

last: Tsao

institute: Ontario Cancer Institute/ Princess Margaret Hospital

summary:
The tumor microenvironment strongly influences cancer development, progression and metastasis. The role of carcinoma-associated fibroblasts (CAFs) in these processes and their clinical impact has not been studied systematically in non-small cell lung carcinoma (NSCLC). We established primary cultures of CAFs and matched normal fibroblasts (NFs) from 15 resected NSCLC. We demonstrate that CAFs have greater ability than NFs to enhance the tumorigenicity of lung cancer cell lines. Microarray gene expression analysis of the 15 matched CAF and NF cell lines identified 46 differentially expressed genes, encoding for proteins that are significantly enriched for extracellular proteins regulated by the TGF-beta signaling pathway. We have identified a subset of 11 genes that formed a prognostic gene expression signature, which was validated in multiple independent NSCLC microarray datasets. Functional annotation using protein-protein interaction analyses of these and published cancer stroma-associated gene expression changes revealed prominent involvement of the focal adhesion and MAPK signalling pathways. Fourteen (30%) of the 46 genes also were differentially expressed in laser-capture micro-dissected corresponding primary tumor stroma compared to the matched normal lung. Six of these 14 genes could be induced by TGF-beta1 in NF. The results establish the prognostic impact of CAF-associated gene expression changes in NSCLC patients.
Genotyping profiles of 4 pairs of  were included in a molecular characterization of NSCLC fibroblast cell lines (CAFs) vs. normal lung fibroblasts (NFs).

overall_design: Genotyping profiles of 4 paired primary NSCLC fibroblast cell lines (CAFs) and normal lung fibroblasts (NFs) were generated. CNV was assessed using paired analysis.

first: Roya

last: Navab

first: Dan

last: Strumpf


title: Regulon prediction of the sporulation factors Spo0A, SigF, SigE, and SigG in Clostridium acetobutylicum ATCC 824

status: Public on Feb 28 2011

city: Newark

first: Eleftherios

middle: Terry

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical Engineering

institute: University of Delaware

summary: Clostridium acetobutylicum, the endospore-forming anaerobe best known for its ABE (acetone-butanol-ethanol) fermentation, has received renewed attention recently for the biological production of butanol, both for bulk chemical production and as a potential biofuel. With butanol production in mind, most of the recent research on C. acetobutylicum has focused on increasing butanol production, tolerance to butanol, and optimizing it for various substrates. However, an equally important trait, though less understood, is its sporulation program, which it coupled to solvent formation. The model organism for endospore formation is Bacillus subtilis, but significant physiological, metabolic, and genomic differences exist between the two organisms. Despite these differences, the major sporulation-related transcription/sigma factors are conserved between the two species. These transcription/sigma factors are activated in a cascade manner such that Spo0A becomes active first, followed by σF, then σE, then σG, and finally σK. The goal of this study is to determine the regulons of 4 of these transcription/sigma factors (Spo0A, σF, σE, and σG) and compare them to those in B. subtilis. To accomplish this goal, individual mutant strains were created for Spo0A, σF, σE, and σG, in which the transcription/sigma factor is silenced. These mutants were then compared transcriptionally using microarrays to determine the regulon of each transcription/sigma factor. To help avoid false positives, comparisons were made between strains in which the downstream transcription/sigma factor is silenced (e.g., for the Spo0A regulon, the Spo0A mutant was compared against the σF mutant and the σE mutant, since they are both upregulated by Spo0A) rather than just the WT. For each regulon, 4 timepoints were taken, since it is very difficult to synchronize sporulation in C. acetobutylicum cultures, and dye-swaps were prepared for each timepoint.

overall_design: Four transcription/sigma factor regulons were investigated: Spo0A, σF, σE, and σG. For Spo0A, two comparison were made: Spo0A mutant vs σF mutant and Spo0A mutant vs σE mutant. For σF, two comparison were also made: σF mutant vs σE mutant and σF mutant vs σG mutant. Finally for σE and σG, only one comparison for each was made: σE mutant vs σG mutant and σG mutant vs wild-type, respectively. For each comparison, 4 timepoints were analyzed, and dye-swaps were prepared for each timepoint comparison. Timepoints were chosen based on when each transcription/sigma factor was expected to be active, based on a previous study [Jones, SW, et al. Genome Biol. 2008;9(7):R114.].

first: Shawn

middle: W

last: Jones

first: Bryan

middle: P

last: Tracy

first: Yili

last: Chen


title: Bacillithiol as Part of the Response of Staphylococcus aureus to Oxidative Stress

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

summary: Overnight cultures of wild type COL or the bshA mutant were back-diluted to an O.D.650 of 0.1 in 30 mL of TSB. The cells were grown at 37C with shaking in a 300mL flask until they reached an O.D.650 of 1.1. The cells were then equally separated into 50mL Falcon tubes, so that each tube had 10mL of culture. One tube for each strain was induced with 1 mM diamide and one with 10 mM H2O2, which we did not send for analysis. All cultures were allowed to continue growing at 37C with shaking for another 20 minutes. RNA extractions were carried out as previously described in Tamber et al., Infect Imunn, 2010.

overall_design: Microarray was used to evaluate alteration in the transcriptome of COL and its bshA mutant strain in the presence/absence of bacillithiol

first: Ana

last: Posada

first: Patrice

last: Francois

first: Ambrose

last: Cheung